Starting phenix.real_space_refine
on Thu Sep 10 22:13:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n9y_0383/09_2026/6n9y_0383.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n9y_0383/09_2026/6n9y_0383.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n9y_0383/09_2026/6n9y_0383.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n9y_0383/09_2026/6n9y_0383.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6n9y_0383/09_2026/6n9y_0383.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n9y_0383/09_2026/6n9y_0383.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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      39      5.16       5
     C    2874      2.51       5
     N     798      2.21       5
     O     816      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4527
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 4527
          Classifications: {'peptide': 552}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 531}
  Time building chain proxies: 1.06, per 1000 atoms: 0.23
  Number of scatterers: 4527
  At special positions: 0
  Unit cell: (104.86, 72.76, 112.35, 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      39     16.00
     O     816      8.00
     N     798      7.00
     C    2874      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 103.0 milliseconds
  

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      56.3% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 9
      removed outlier: 3.990A  pdb=" N   TYR A   8 " --> pdb=" O   PHE A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 25
      removed outlier: 4.098A  pdb=" N   ALA A  17 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR A  20 " --> pdb=" O   ASN A  16 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ALA A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 38
      removed outlier: 4.239A  pdb=" N   CYS A  37 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU A  38 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 34 through 38'
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 60 through 73
      removed outlier: 4.204A  pdb=" N   TYR A  65 " --> pdb=" O   PRO A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 91
      removed outlier: 4.235A  pdb=" N   GLN A  91 " --> pdb=" O   LYS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 115
      removed outlier: 3.638A  pdb=" N   LYS A 100 " --> pdb=" O   ASP A  96 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A 109 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLU A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 123
      removed outlier: 3.613A  pdb=" N   VAL A 122 " --> pdb=" O   MET A 118 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LYS A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 146
      removed outlier: 3.812A  pdb=" N   ILE A 145 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR A 146 " --> pdb=" O   PRO A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 202
      removed outlier: 4.325A  pdb=" N   GLY A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   GLN A 190 " --> pdb=" O   GLY A 186 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN A 192 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN A 193 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE A 194 " --> pdb=" O   GLN A 190 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS A 195 " --> pdb=" O   HIS A 191 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 199 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ARG A 200 " --> pdb=" O   ARG A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 230 through 249
      removed outlier: 3.545A  pdb=" N   ALA A 234 " --> pdb=" O   MET A 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LYS A 235 " --> pdb=" O   ASP A 231 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   HIS A 236 " --> pdb=" O   ASP A 232 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 237 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ARG A 239 " --> pdb=" O   LYS A 235 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ILE A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLN A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 265
    Processing helix  chain 'A' and resid 274 through 279
    Processing helix  chain 'A' and resid 290 through 297
    Processing helix  chain 'A' and resid 303 through 307
      removed outlier: 3.619A  pdb=" N   TRP A 307 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 318
      removed outlier: 3.533A  pdb=" N   GLU A 316 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 334
      removed outlier: 3.776A  pdb=" N   ILE A 328 " --> pdb=" O   TRP A 324 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   MET A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASP A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 344
      removed outlier: 3.982A  pdb=" N   LEU A 342 " --> pdb=" O   GLN A 338 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS A 343 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 362
      removed outlier: 3.927A  pdb=" N   LEU A 361 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 422
      removed outlier: 3.760A  pdb=" N   ILE A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR A 413 " --> pdb=" O   GLU A 409 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   THR A 414 " --> pdb=" O   ALA A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 3.626A  pdb=" N   PHE A 438 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 443 " --> pdb=" O   MET A 439 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TRP A 447 " --> pdb=" O   VAL A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 465
      removed outlier: 3.553A  pdb=" N   ARG A 454 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A 455 " --> pdb=" O   LYS A 451 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 458 " --> pdb=" O   ARG A 454 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG A 459 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 491
      removed outlier: 4.115A  pdb=" N   ASP A 487 " --> pdb=" O   GLY A 483 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS A 491 " --> pdb=" O   ASP A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 519
      removed outlier: 3.757A  pdb=" N   GLU A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 550
      removed outlier: 4.065A  pdb=" N   LEU A 541 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149
    Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 162
      removed outlier: 3.699A  pdb=" N   PHE A 159 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER A 161 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ALA A 167 " --> pdb=" O   MET A 218 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU A 220 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   TYR A 169 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 354
      removed outlier: 3.638A  pdb=" N   CYS A 351 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 353 " --> pdb=" O   LYS A 368 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LYS A 368 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   THR A 369 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   ASN A 403 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   TYR A 399 " --> pdb=" O   GLU A 373 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   HIS A 398 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)

    166 hydrogen bonds defined for protein.
    483 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.52

  Time building geometry restraints manager: 0.32 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: 1485
        1.34 -     1.46: 1065
        1.46 -     1.58: 2025
        1.58 -     1.70: 0
        1.70 -     1.82: 61
  Bond restraints: 4636
  Sorted by residual:
  bond pdb=" N   ARG A 164 "
       pdb=" CA  ARG A 164 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.17e-02 7.31e+03 7.73e+00
  bond pdb=" C   SER A 365 "
       pdb=" N   PRO A 366 "
    ideal  model  delta    sigma   weight residual
    1.336  1.314  0.022 1.25e-02 6.40e+03 3.17e+00
  bond pdb=" CA  ALA A 126 "
       pdb=" C   ALA A 126 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.013 9.60e-03 1.09e+04 1.94e+00
  bond pdb=" C   GLU A  60 "
       pdb=" O   GLU A  60 "
    ideal  model  delta    sigma   weight residual
    1.249  1.237  0.011 8.50e-03 1.38e+04 1.80e+00
  bond pdb=" N   ASN A  40 "
       pdb=" CA  ASN A  40 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.66e+00
  ... (remaining 4631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 5743
        1.86 -     3.72: 444
        3.72 -     5.59: 54
        5.59 -     7.45: 16
        7.45 -     9.31: 5
  Bond angle restraints: 6262
  Sorted by residual:
  angle pdb=" N   GLY A 363 "
        pdb=" CA  GLY A 363 "
        pdb=" C   GLY A 363 "
      ideal   model   delta    sigma   weight residual
     112.33  118.30   -5.97 1.10e+00 8.26e-01 2.95e+01
  angle pdb=" C   THR A 204 "
        pdb=" N   CYS A 205 "
        pdb=" CA  CYS A 205 "
      ideal   model   delta    sigma   weight residual
     120.51  128.35   -7.84 1.45e+00 4.76e-01 2.92e+01
  angle pdb=" C   TYR A 163 "
        pdb=" N   ARG A 164 "
        pdb=" CA  ARG A 164 "
      ideal   model   delta    sigma   weight residual
     121.19  128.46   -7.27 1.59e+00 3.96e-01 2.09e+01
  angle pdb=" C   THR A 362 "
        pdb=" N   GLY A 363 "
        pdb=" CA  GLY A 363 "
      ideal   model   delta    sigma   weight residual
     120.44  124.68   -4.24 1.09e+00 8.42e-01 1.51e+01
  angle pdb=" N   ALA A 126 "
        pdb=" CA  ALA A 126 "
        pdb=" C   ALA A 126 "
      ideal   model   delta    sigma   weight residual
     110.91  106.37    4.54 1.17e+00 7.31e-01 1.51e+01
  ... (remaining 6257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.03: 2355
       10.03 -    20.06: 321
       20.06 -    30.09: 68
       30.09 -    40.12: 23
       40.12 -    50.16: 13
  Dihedral angle restraints: 2780
    sinusoidal: 1161
      harmonic: 1619
  Sorted by residual:
  dihedral pdb=" CA  ASN A 129 "
           pdb=" C   ASN A 129 "
           pdb=" N   SER A 130 "
           pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.60  -41.40     0      5.00e+00 4.00e-02 6.86e+01
  dihedral pdb=" CA  GLU A 255 "
           pdb=" C   GLU A 255 "
           pdb=" N   GLU A 256 "
           pdb=" CA  GLU A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.08  -33.92     0      5.00e+00 4.00e-02 4.60e+01
  dihedral pdb=" CA  THR A 406 "
           pdb=" C   THR A 406 "
           pdb=" N   GLY A 407 "
           pdb=" CA  GLY A 407 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.03  -32.97     0      5.00e+00 4.00e-02 4.35e+01
  ... (remaining 2777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 383
       0.043 -    0.086: 203
       0.086 -    0.129: 49
       0.129 -    0.171: 16
       0.171 -    0.214: 2
  Chirality restraints: 653
  Sorted by residual:
  chirality pdb=" CB  ILE A 313 "
            pdb=" CA  ILE A 313 "
            pdb=" CG1 ILE A 313 "
            pdb=" CG2 ILE A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  ILE A 166 "
            pdb=" CA  ILE A 166 "
            pdb=" CG1 ILE A 166 "
            pdb=" CG2 ILE A 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.00e-01
  chirality pdb=" CG  LEU A 135 "
            pdb=" CB  LEU A 135 "
            pdb=" CD1 LEU A 135 "
            pdb=" CD2 LEU A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.33e-01
  ... (remaining 650 not shown)

  Planarity restraints: 812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 530 "   -0.042 5.00e-02 4.00e+02   6.36e-02 6.46e+00
        pdb=" N   PRO A 531 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 531 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 531 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  25 "    0.042 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO A  26 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A  26 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  26 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 142 "   -0.040 5.00e-02 4.00e+02   5.94e-02 5.65e+00
        pdb=" N   PRO A 143 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 143 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 143 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 809 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 892
        2.76 -     3.30: 4207
        3.30 -     3.83: 7008
        3.83 -     4.37: 8154
        4.37 -     4.90: 13831
  Nonbonded interactions: 34092
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 155 "
            pdb=" OH  TYR A 169 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   ALA A 452 "
            pdb=" OG  SER A 455 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OD2 ASP A  77 "
            pdb=" OG1 THR A  80 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR A 168 "
            pdb=" OD1 ASN A 238 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" O   MET A  52 "
            pdb=" OG1 THR A  56 "
     model   vdw
     2.363 3.040
  ... (remaining 34087 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.580
  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:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.930
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
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      :  0.008   0.063   4636  Z= 0.355
  Angle     :  1.101   9.311   6262  Z= 0.644
  Chirality :  0.054   0.214    653
  Planarity :  0.007   0.064    812
  Dihedral  : 10.299  50.156   1740
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  1.04 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.98 (0.27), residues: 550
  helix: -4.16 (0.15), residues: 249
  sheet: -2.11 (0.73), residues: 51
  loop : -2.47 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 423 
 TYR   0.026   0.003   TYR A 253 
 PHE   0.023   0.003   PHE A 485 
 TRP   0.015   0.003   TRP A 433 
 HIS   0.015   0.003   HIS A 398 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00766 /  0.36 ( 4636)
  covalent geometry    : angle       1.10123 /  0.64 ( 6262)
  hydrogen bonds       : bond        0.31800 / 20.99 (  166)
  hydrogen bonds       : angle      10.51166 /  7.44 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 ILE cc_start: 0.8735 (tp) cc_final: 0.8527 (mt)
REVERT: A  449 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7410 (pp)
REVERT: A  510 MET cc_start: 0.7131 (mmm) cc_final: 0.6854 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0966
  time to fit residues: 12.2834
Evaluate side-chains
  60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    4.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  47 ASN
A 124 GLN
A 236 HIS
A 276 HIS
A 338 GLN
A 347 GLN
A 391 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.070651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.063103 restraints weight = 18008.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.064810 restraints weight = 9345.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.065991 restraints weight = 5811.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.066857 restraints weight = 4006.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.067445 restraints weight = 2943.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4636  Z= 0.153
  Angle     :  0.674   7.764   6262  Z= 0.360
  Chirality :  0.043   0.179    653
  Planarity :  0.006   0.055    812
  Dihedral  :  6.259  34.408    628
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  8.96 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.24 (0.31), residues: 550
  helix: -2.33 (0.25), residues: 267
  sheet: -1.15 (0.99), residues: 29
  loop : -1.94 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  66 
 TYR   0.015   0.002   TYR A 169 
 PHE   0.016   0.002   PHE A 272 
 TRP   0.010   0.001   TRP A 326 
 HIS   0.005   0.001   HIS A 276 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.15 ( 4636)
  covalent geometry    : angle       0.67421 /  0.36 ( 6262)
  hydrogen bonds       : bond        0.05038 /  3.40 (  166)
  hydrogen bonds       : angle       5.62268 /  3.92 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A   39 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7233 (m-80)
REVERT: A   70 LEU cc_start: 0.9298 (tp) cc_final: 0.8830 (tp)
REVERT: A  246 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8258 (mp10)
REVERT: A  534 GLU cc_start: 0.7769 (tp30) cc_final: 0.7481 (pm20)
REVERT: A  535 SER cc_start: 0.8776 (t) cc_final: 0.8120 (p)
REVERT: A  549 ARG cc_start: 0.6583 (ttm110) cc_final: 0.5994 (ttt180)
  outliers start: 10
  outliers final: 4
  residues processed: 80
  average time/residue: 0.0734
  time to fit residues: 7.3827
Evaluate side-chains
  63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  498 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:   30.0000
   chunk 21 optimal weight:    9.9990
   chunk 12 optimal weight:    0.0770
   chunk 2 optimal weight:    0.0670
   chunk 1 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   overall best weight:    4.6282

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.069918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.062121 restraints weight = 18211.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.063853 restraints weight = 9553.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.065030 restraints weight = 5993.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.065877 restraints weight = 4184.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.066482 restraints weight = 3128.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4636  Z= 0.133
  Angle     :  0.614   6.811   6262  Z= 0.321
  Chirality :  0.042   0.165    653
  Planarity :  0.004   0.039    812
  Dihedral  :  5.654  31.903    626
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.08 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.35), residues: 550
  helix: -1.17 (0.30), residues: 262
  sheet: -1.03 (0.97), residues: 29
  loop : -1.53 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 315 
 TYR   0.015   0.002   TYR A 253 
 PHE   0.015   0.002   PHE A 272 
 TRP   0.007   0.001   TRP A 326 
 HIS   0.007   0.001   HIS A 320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 4636)
  covalent geometry    : angle       0.61370 /  0.32 ( 6262)
  hydrogen bonds       : bond        0.03983 /  2.70 (  166)
  hydrogen bonds       : angle       5.19574 /  3.66 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   39 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7150 (m-80)
REVERT: A  101 MET cc_start: 0.8499 (mtp) cc_final: 0.8175 (mtt)
REVERT: A  510 MET cc_start: 0.7907 (mmm) cc_final: 0.7606 (mmt)
REVERT: A  534 GLU cc_start: 0.7666 (tp30) cc_final: 0.7203 (pm20)
REVERT: A  535 SER cc_start: 0.8705 (t) cc_final: 0.7968 (p)
  outliers start: 7
  outliers final: 4
  residues processed: 69
  average time/residue: 0.0700
  time to fit residues: 6.3244
Evaluate side-chains
  61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  548 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 17 optimal weight:   20.0000
   chunk 11 optimal weight:   30.0000
   chunk 37 optimal weight:   40.0000
   chunk 42 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0070
   chunk 25 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   overall best weight:    5.0006

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.070058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.062015 restraints weight = 18166.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.063754 restraints weight = 9695.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.064980 restraints weight = 6127.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.065818 restraints weight = 4285.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.066456 restraints weight = 3219.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4636  Z= 0.137
  Angle     :  0.597   6.913   6262  Z= 0.311
  Chirality :  0.041   0.157    653
  Planarity :  0.004   0.035    812
  Dihedral  :  5.466  29.148    626
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.33 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.36), residues: 550
  helix: -0.74 (0.31), residues: 267
  sheet: -0.77 (1.02), residues: 29
  loop : -1.45 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 297 
 TYR   0.012   0.001   TYR A 169 
 PHE   0.015   0.001   PHE A 272 
 TRP   0.009   0.001   TRP A 326 
 HIS   0.002   0.001   HIS A 276 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 4636)
  covalent geometry    : angle       0.59723 /  0.31 ( 6262)
  hydrogen bonds       : bond        0.03597 /  2.42 (  166)
  hydrogen bonds       : angle       5.01813 /  3.55 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7069 (m-80)
REVERT: A   66 ARG cc_start: 0.8401 (tpm170) cc_final: 0.8109 (tpm170)
REVERT: A   70 LEU cc_start: 0.9201 (tp) cc_final: 0.8694 (mt)
REVERT: A  510 MET cc_start: 0.7915 (mmm) cc_final: 0.7708 (mmt)
  outliers start: 10
  outliers final: 5
  residues processed: 67
  average time/residue: 0.0615
  time to fit residues: 5.4093
Evaluate side-chains
  57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  548 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 34 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 48 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    7.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.068835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.060928 restraints weight = 18465.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.062644 restraints weight = 9836.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.063817 restraints weight = 6238.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.064653 restraints weight = 4382.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.065272 restraints weight = 3289.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4636  Z= 0.185
  Angle     :  0.652   6.872   6262  Z= 0.339
  Chirality :  0.043   0.156    653
  Planarity :  0.005   0.035    812
  Dihedral  :  5.565  28.189    626
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.04 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.36), residues: 550
  helix: -0.63 (0.31), residues: 269
  sheet: -1.56 (0.81), residues: 39
  loop : -1.43 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  78 
 TYR   0.013   0.002   TYR A  14 
 PHE   0.013   0.002   PHE A 272 
 TRP   0.007   0.001   TRP A 326 
 HIS   0.003   0.001   HIS A 276 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.19 ( 4636)
  covalent geometry    : angle       0.65185 /  0.34 ( 6262)
  hydrogen bonds       : bond        0.03749 /  2.51 (  166)
  hydrogen bonds       : angle       5.14012 /  3.64 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7353 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0480
  time to fit residues: 3.8921
Evaluate side-chains
  57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  498 ASP
Chi-restraints excluded: chain A residue  548 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0170
   chunk 6 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 40 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   chunk 11 optimal weight:   20.0000
   overall best weight:    3.5624

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.070017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.062054 restraints weight = 18312.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.063796 restraints weight = 9665.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.064977 restraints weight = 6067.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.065805 restraints weight = 4243.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.066347 restraints weight = 3184.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4636  Z= 0.116
  Angle     :  0.582   6.860   6262  Z= 0.301
  Chirality :  0.041   0.155    653
  Planarity :  0.004   0.039    812
  Dihedral  :  5.121  25.442    626
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.46 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.36), residues: 550
  helix: -0.37 (0.31), residues: 268
  sheet: -0.77 (1.02), residues: 29
  loop : -1.45 (0.41), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.012   0.001   TYR A 169 
 PHE   0.009   0.001   PHE A 272 
 TRP   0.006   0.001   TRP A 326 
 HIS   0.002   0.001   HIS A 276 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 4636)
  covalent geometry    : angle       0.58199 /  0.30 ( 6262)
  hydrogen bonds       : bond        0.03189 /  2.16 (  166)
  hydrogen bonds       : angle       4.80211 /  3.43 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7478 (m-80)
REVERT: A   68 VAL cc_start: 0.7882 (t) cc_final: 0.7629 (p)
REVERT: A  331 MET cc_start: 0.8636 (ppp) cc_final: 0.8435 (ppp)
REVERT: A  510 MET cc_start: 0.8248 (mmt) cc_final: 0.7810 (mmt)
  outliers start: 8
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0573
  time to fit residues: 4.8333
Evaluate side-chains
  57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  495 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0000
   chunk 5 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   chunk 53 optimal weight:   40.0000
   chunk 52 optimal weight:    8.9990
   overall best weight:    4.7590

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.069660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.061830 restraints weight = 18180.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.063523 restraints weight = 9587.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.064680 restraints weight = 6028.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.065357 restraints weight = 4231.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.066019 restraints weight = 3293.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4636  Z= 0.137
  Angle     :  0.609   8.457   6262  Z= 0.315
  Chirality :  0.041   0.146    653
  Planarity :  0.004   0.040    812
  Dihedral  :  5.092  25.292    626
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.88 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.36), residues: 550
  helix: -0.20 (0.32), residues: 269
  sheet: -0.77 (1.00), residues: 29
  loop : -1.45 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 323 
 TYR   0.012   0.001   TYR A 169 
 PHE   0.009   0.001   PHE A 170 
 TRP   0.038   0.001   TRP A 326 
 HIS   0.003   0.001   HIS A 236 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 4636)
  covalent geometry    : angle       0.60928 /  0.31 ( 6262)
  hydrogen bonds       : bond        0.03317 /  2.23 (  166)
  hydrogen bonds       : angle       4.84265 /  3.47 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7555 (m-80)
REVERT: A   68 VAL cc_start: 0.7834 (t) cc_final: 0.7600 (p)
REVERT: A  510 MET cc_start: 0.8273 (mmt) cc_final: 0.8026 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0525
  time to fit residues: 4.1786
Evaluate side-chains
  61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  256 GLU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  548 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 30 optimal weight:   40.0000
   chunk 1 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    6.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.068840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.061016 restraints weight = 18470.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.062677 restraints weight = 9729.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.063834 restraints weight = 6140.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.064616 restraints weight = 4323.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.065232 restraints weight = 3292.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4636  Z= 0.169
  Angle     :  0.642   7.725   6262  Z= 0.332
  Chirality :  0.043   0.147    653
  Planarity :  0.004   0.038    812
  Dihedral  :  5.296  24.883    626
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.88 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.37), residues: 550
  helix: -0.19 (0.32), residues: 266
  sheet: -1.39 (0.79), residues: 39
  loop : -1.25 (0.44), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.013   0.001   TYR A  14 
 PHE   0.011   0.001   PHE A 170 
 TRP   0.023   0.001   TRP A 326 
 HIS   0.003   0.001   HIS A 236 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.17 ( 4636)
  covalent geometry    : angle       0.64204 /  0.33 ( 6262)
  hydrogen bonds       : bond        0.03487 /  2.33 (  166)
  hydrogen bonds       : angle       4.94808 /  3.53 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7494 (m-80)
REVERT: A  510 MET cc_start: 0.8290 (mmt) cc_final: 0.8027 (mmt)
  outliers start: 12
  outliers final: 10
  residues processed: 57
  average time/residue: 0.0545
  time to fit residues: 4.1602
Evaluate side-chains
  58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  256 GLU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  548 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 11 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 47 optimal weight:    0.0170
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 16 optimal weight:   30.0000
   chunk 42 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.6624

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.070778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.062800 restraints weight = 18162.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.064513 restraints weight = 9590.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.065715 restraints weight = 6072.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.066511 restraints weight = 4260.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.067087 restraints weight = 3211.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.4742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4636  Z= 0.113
  Angle     :  0.601   7.279   6262  Z= 0.309
  Chirality :  0.041   0.154    653
  Planarity :  0.004   0.034    812
  Dihedral  :  4.927  24.501    626
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.50 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.37), residues: 550
  helix: -0.07 (0.33), residues: 266
  sheet: -0.42 (0.98), residues: 29
  loop : -1.17 (0.43), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 281 
 TYR   0.013   0.001   TYR A 169 
 PHE   0.008   0.001   PHE A 272 
 TRP   0.020   0.001   TRP A 326 
 HIS   0.002   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.11 ( 4636)
  covalent geometry    : angle       0.60135 /  0.31 ( 6262)
  hydrogen bonds       : bond        0.03050 /  2.05 (  166)
  hydrogen bonds       : angle       4.69877 /  3.38 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7475 (m-80)
REVERT: A  175 LEU cc_start: 0.7799 (tt) cc_final: 0.7508 (tp)
REVERT: A  281 ARG cc_start: 0.7929 (ptm-80) cc_final: 0.7297 (ptm-80)
REVERT: A  510 MET cc_start: 0.8219 (mmt) cc_final: 0.7988 (mmt)
  outliers start: 10
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0780
  time to fit residues: 6.5368
Evaluate side-chains
  61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  256 GLU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  548 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 4 optimal weight:   30.0000
   chunk 40 optimal weight:   30.0000
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 47 optimal weight:    8.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.069442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.061691 restraints weight = 18209.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.063346 restraints weight = 9595.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.064522 restraints weight = 6048.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.065322 restraints weight = 4239.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.065912 restraints weight = 3177.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4636  Z= 0.168
  Angle     :  0.672   7.344   6262  Z= 0.344
  Chirality :  0.044   0.155    653
  Planarity :  0.004   0.037    812
  Dihedral  :  5.216  24.846    626
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.96 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.37), residues: 550
  helix: -0.15 (0.32), residues: 268
  sheet: -1.17 (0.81), residues: 39
  loop : -1.30 (0.44), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  66 
 TYR   0.016   0.001   TYR A 248 
 PHE   0.018   0.002   PHE A 272 
 TRP   0.050   0.002   TRP A 326 
 HIS   0.003   0.001   HIS A 236 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.17 ( 4636)
  covalent geometry    : angle       0.67250 /  0.34 ( 6262)
  hydrogen bonds       : bond        0.03405 /  2.28 (  166)
  hydrogen bonds       : angle       4.86997 /  3.49 (  483)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7548 (m-80)
REVERT: A  175 LEU cc_start: 0.8122 (tt) cc_final: 0.7891 (tp)
REVERT: A  281 ARG cc_start: 0.7977 (ptm-80) cc_final: 0.7114 (ptm-80)
REVERT: A  510 MET cc_start: 0.8293 (mmt) cc_final: 0.8027 (mmt)
  outliers start: 9
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0683
  time to fit residues: 5.4048
Evaluate side-chains
  61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  256 GLU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  548 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 14 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 49 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.2651 > 50:)
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.9188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.070150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.062191 restraints weight = 18214.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.063870 restraints weight = 9596.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.065009 restraints weight = 6075.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.065823 restraints weight = 4298.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.066425 restraints weight = 3262.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4636  Z= 0.128
  Angle     :  0.648   7.125   6262  Z= 0.326
  Chirality :  0.042   0.151    653
  Planarity :  0.004   0.036    812
  Dihedral  :  5.032  26.504    626
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.38 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.37), residues: 550
  helix: -0.01 (0.32), residues: 268
  sheet: -0.28 (0.99), residues: 29
  loop : -1.33 (0.43), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 289 
 TYR   0.025   0.001   TYR A 248 
 PHE   0.019   0.001   PHE A 272 
 TRP   0.037   0.001   TRP A 326 
 HIS   0.003   0.001   HIS A 236 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 ( 4636)
  covalent geometry    : angle       0.64843 /  0.33 ( 6262)
  hydrogen bonds       : bond        0.03156 /  2.14 (  166)
  hydrogen bonds       : angle       4.70156 /  3.37 (  483)

===============================================================================
Job complete
usr+sys time: 716.24 seconds
wall clock time: 13 minutes 10.55 seconds (790.55 seconds total)