Starting phenix.real_space_refine
on Fri Aug 22 14:58:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8el8_28224/08_2025/8el8_28224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8el8_28224/08_2025/8el8_28224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8el8_28224/08_2025/8el8_28224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8el8_28224/08_2025/8el8_28224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8el8_28224/08_2025/8el8_28224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8el8_28224/08_2025/8el8_28224.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.108
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    2868      2.51       5
     N     778      2.21       5
     O     792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4467
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1046
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 4, 'TRANS': 135}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 97
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 82
    Chain: "B"
      Number of atoms: 3421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3421
          Classifications: {'peptide': 457}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 15, 'TRANS': 441}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 221
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 14, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 154
  Time building chain proxies: 1.49, per 1000 atoms: 0.33
  Number of scatterers: 4467
  At special positions: 0
  Unit cell: (53.6823, 80.9495, 110.773, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O     792      8.00
     N     778      7.00
     C    2868      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 191.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1148

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      67.2% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 252 through 265
    Processing helix  chain 'A' and resid 280 through 291
      removed outlier: 3.680A  pdb=" N   LEU A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 291 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 298
    Processing helix  chain 'A' and resid 299 through 303
      removed outlier: 3.507A  pdb=" N   ALA A 303 " --> pdb=" O   PRO A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 338
      removed outlier: 3.962A  pdb=" N   THR A 322 " --> pdb=" O   ASP A 318 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ARG A 323 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ALA A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ILE A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 338 " --> pdb=" O   ARG A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 378
      removed outlier: 3.674A  pdb=" N   TYR A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 13
      removed outlier: 3.622A  pdb=" N   GLY B  13 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 29
      removed outlier: 3.615A  pdb=" N   GLU B  19 " --> pdb=" O   ALA B  15 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG B  20 " --> pdb=" O   GLY B  16 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG B  23 " --> pdb=" O   GLU B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 38
      No H-bonds generated for 'chain 'B' and resid 36 through 38'
    Processing helix  chain 'B' and resid 39 through 54
      removed outlier: 3.519A  pdb=" N   LEU B  54 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 74
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 3.923A  pdb=" N   THR B  84 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 97
      removed outlier: 3.577A  pdb=" N   ILE B  91 " --> pdb=" O   GLU B  87 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU B  92 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 128
    Processing helix  chain 'B' and resid 129 through 139
      removed outlier: 3.674A  pdb=" N   GLN B 133 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU B 136 " --> pdb=" O   GLN B 132 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU B 137 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 150
      removed outlier: 3.909A  pdb=" N   LYS B 143 " --> pdb=" O   ASN B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 175
    Processing helix  chain 'B' and resid 176 through 185
    Processing helix  chain 'B' and resid 187 through 201
      removed outlier: 3.754A  pdb=" N   LEU B 191 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   SER B 201 " --> pdb=" O   GLU B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 238
    Processing helix  chain 'B' and resid 249 through 264
      removed outlier: 3.675A  pdb=" N   VAL B 255 " --> pdb=" O   HIS B 251 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET B 256 " --> pdb=" O   GLN B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 286
      removed outlier: 4.137A  pdb=" N   GLU B 275 " --> pdb=" O   GLU B 271 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B 286 " --> pdb=" O   VAL B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 298
      removed outlier: 4.722A  pdb=" N   ASP B 294 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   VAL B 295 " --> pdb=" O   CYS B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 355
      removed outlier: 3.574A  pdb=" N   HIS B 343 " --> pdb=" O   MET B 339 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASP B 354 " --> pdb=" O   GLU B 350 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LYS B 355 " --> pdb=" O   LYS B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 377
      removed outlier: 4.072A  pdb=" N   THR B 364 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      Proline residue:  B 365  - end of helix
      removed outlier: 3.729A  pdb=" N   ALA B 376 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 389
    Processing helix  chain 'B' and resid 404 through 412
    Processing helix  chain 'B' and resid 417 through 432
      removed outlier: 3.708A  pdb=" N   LYS B 421 " --> pdb=" O   ASP B 417 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ALA B 425 " --> pdb=" O   LYS B 421 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU B 428 " --> pdb=" O   ALA B 424 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 431 " --> pdb=" O   PHE B 427 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 443
      removed outlier: 3.596A  pdb=" N   LYS B 441 " --> pdb=" O   ASP B 437 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 455
      removed outlier: 5.193A  pdb=" N   GLY B 450 " --> pdb=" O   GLY B 446 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   LEU B 451 " --> pdb=" O   ASN B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 482
      removed outlier: 3.500A  pdb=" N   LYS B 479 " --> pdb=" O   THR B 475 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210
      removed outlier: 6.295A  pdb=" N   LEU A  46 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ILE A 231 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   PHE A 277 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   TYR A 233 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ILE A 274 " --> pdb=" O   TYR A 347 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   HIS A 349 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   LEU A 276 " --> pdb=" O   HIS A 349 " (cutoff:3.500A)

    234 hydrogen bonds defined for protein.
    675 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: 0.54

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 853
        1.33 -     1.45: 998
        1.45 -     1.57: 2647
        1.57 -     1.68: 2
        1.68 -     1.80: 38
  Bond restraints: 4538
  Sorted by residual:
  bond pdb=" O3P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.476  0.134 2.00e-02 2.50e+03 4.48e+01
  bond pdb=" O2P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.480  0.130 2.00e-02 2.50e+03 4.21e+01
  bond pdb=" O1P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.481  0.129 2.00e-02 2.50e+03 4.17e+01
  bond pdb=" OG1 TPO B 473 "
       pdb=" P   TPO B 473 "
    ideal  model  delta    sigma   weight residual
    1.717  1.598  0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" CA  LYS B 479 "
       pdb=" C   LYS B 479 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.35e-02 5.49e+03 1.67e+01
  ... (remaining 4533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 6000
        1.87 -     3.74: 131
        3.74 -     5.61: 26
        5.61 -     7.48: 7
        7.48 -     9.35: 3
  Bond angle restraints: 6167
  Sorted by residual:
  angle pdb=" N   ARG B 183 "
        pdb=" CA  ARG B 183 "
        pdb=" C   ARG B 183 "
      ideal   model   delta    sigma   weight residual
     111.07  118.31   -7.24 1.07e+00 8.73e-01 4.58e+01
  angle pdb=" N   TYR B 442 "
        pdb=" CA  TYR B 442 "
        pdb=" C   TYR B 442 "
      ideal   model   delta    sigma   weight residual
     111.36  117.49   -6.13 1.09e+00 8.42e-01 3.16e+01
  angle pdb=" N   THR B 443 "
        pdb=" CA  THR B 443 "
        pdb=" C   THR B 443 "
      ideal   model   delta    sigma   weight residual
     112.68  119.02   -6.34 1.33e+00 5.65e-01 2.27e+01
  angle pdb=" N   GLY B 188 "
        pdb=" CA  GLY B 188 "
        pdb=" C   GLY B 188 "
      ideal   model   delta    sigma   weight residual
     112.73  118.17   -5.44 1.20e+00 6.94e-01 2.06e+01
  angle pdb=" C   LYS B 482 "
        pdb=" N   PRO B 483 "
        pdb=" CA  PRO B 483 "
      ideal   model   delta    sigma   weight residual
     119.05  114.40    4.65 1.11e+00 8.12e-01 1.75e+01
  ... (remaining 6162 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 2477
       16.84 -    33.67: 216
       33.67 -    50.51: 38
       50.51 -    67.34: 5
       67.34 -    84.18: 3
  Dihedral angle restraints: 2739
    sinusoidal: 986
      harmonic: 1753
  Sorted by residual:
  dihedral pdb=" C   TPO B 473 "
           pdb=" N   TPO B 473 "
           pdb=" CA  TPO B 473 "
           pdb=" CB  TPO B 473 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.34   -9.26     0      2.50e+00 1.60e-01 1.37e+01
  dihedral pdb=" CB  GLU B 223 "
           pdb=" CG  GLU B 223 "
           pdb=" CD  GLU B 223 "
           pdb=" OE1 GLU B 223 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.18  -84.18     1      3.00e+01 1.11e-03 9.59e+00
  dihedral pdb=" CB  LYS B 273 "
           pdb=" CG  LYS B 273 "
           pdb=" CD  LYS B 273 "
           pdb=" CE  LYS B 273 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.69   54.69     3      1.50e+01 4.44e-03 9.30e+00
  ... (remaining 2736 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 511
       0.040 -    0.079: 197
       0.079 -    0.119: 33
       0.119 -    0.158: 11
       0.158 -    0.198: 4
  Chirality restraints: 756
  Sorted by residual:
  chirality pdb=" CA  TYR B 442 "
            pdb=" N   TYR B 442 "
            pdb=" C   TYR B 442 "
            pdb=" CB  TYR B 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.76e-01
  chirality pdb=" CB  VAL B  83 "
            pdb=" CA  VAL B  83 "
            pdb=" CG1 VAL B  83 "
            pdb=" CG2 VAL B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.27e-01
  chirality pdb=" CA  TPO B 473 "
            pdb=" N   TPO B 473 "
            pdb=" C   TPO B 473 "
            pdb=" CB  TPO B 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.18 2.00e-01 2.50e+01 7.75e-01
  ... (remaining 753 not shown)

  Planarity restraints: 771
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 478 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.15e+00
        pdb=" C   TYR B 478 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   TYR B 478 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS B 479 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  81 "   -0.031 5.00e-02 4.00e+02   4.61e-02 3.39e+00
        pdb=" N   PRO B  82 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B  82 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  82 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 347 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO A 348 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 348 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 348 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 768 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1688
        2.90 -     3.40: 4128
        3.40 -     3.90: 6539
        3.90 -     4.40: 6902
        4.40 -     4.90: 12571
  Nonbonded interactions: 31828
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 206 "
            pdb=" N   GLU B 207 "
     model   vdw
     2.403 3.120
  nonbonded pdb=" O   LEU A 259 "
            pdb=" OG  SER A 262 "
     model   vdw
     2.431 3.040
  nonbonded pdb=" OE1 GLN A 281 "
            pdb=" NZ  LYS A 325 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" O   LEU B 300 "
            pdb=" OG1 THR B 301 "
     model   vdw
     2.459 3.040
  nonbonded pdb=" N   GLU B 185 "
            pdb=" O   GLU B 185 "
     model   vdw
     2.473 2.496
  ... (remaining 31823 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: 0.00
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.570
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
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      :  0.007   0.134   4538  Z= 0.337
  Angle     :  0.704   9.354   6167  Z= 0.416
  Chirality :  0.044   0.198    756
  Planarity :  0.004   0.046    771
  Dihedral  : 13.199  84.180   1591
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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 aren not related in a simple way.
  whole:  0.75 (0.35), residues: 573
  helix:  1.29 (0.28), residues: 348
  sheet:  1.88 (0.99), residues: 28
  loop : -1.14 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 435 
 TYR   0.008   0.001   TYR B 208 
 PHE   0.017   0.002   PHE B 163 
 TRP   0.007   0.001   TRP A 268 
 HIS   0.007   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00681 ( 4538)
  covalent geometry    : angle       0.70448 ( 6167)
  hydrogen bonds       : bond        0.18252 (  234)
  hydrogen bonds       : angle       5.20977 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.130 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0675
  time to fit residues: 5.0556
Evaluate side-chains
  46 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0040
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.131527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.097852 restraints weight = 5599.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 2.41
r_work: 0.2944 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4538  Z= 0.105
  Angle     :  0.453   6.552   6167  Z= 0.238
  Chirality :  0.037   0.125    756
  Planarity :  0.003   0.040    771
  Dihedral  :  3.702  19.604    639
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.55 %
    Favored  : 93.23 %
  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 aren not related in a simple way.
  whole:  1.45 (0.37), residues: 573
  helix:  1.96 (0.29), residues: 357
  sheet:  1.07 (0.95), residues: 32
  loop : -1.11 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 154 
 TYR   0.006   0.001   TYR B 184 
 PHE   0.009   0.001   PHE B 163 
 TRP   0.005   0.001   TRP B 466 
 HIS   0.004   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 4538)
  covalent geometry    : angle       0.45280 ( 6167)
  hydrogen bonds       : bond        0.04152 (  234)
  hydrogen bonds       : angle       3.43708 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B  339 MET cc_start: 0.8558 (mmt) cc_final: 0.8247 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 50
  average time/residue: 0.0590
  time to fit residues: 3.8661
Evaluate side-chains
  43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.130734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.097098 restraints weight = 5597.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.39
r_work: 0.2934 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4538  Z= 0.107
  Angle     :  0.428   5.386   6167  Z= 0.224
  Chirality :  0.037   0.126    756
  Planarity :  0.003   0.041    771
  Dihedral  :  3.422  14.516    639
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  9.48 %
    Favored  : 90.07 %
  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 aren not related in a simple way.
  whole:  1.62 (0.37), residues: 573
  helix:  2.10 (0.29), residues: 357
  sheet:  1.26 (0.95), residues: 32
  loop : -1.07 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 435 
 TYR   0.004   0.001   TYR B 184 
 PHE   0.012   0.001   PHE B 163 
 TRP   0.004   0.001   TRP A 264 
 HIS   0.004   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4538)
  covalent geometry    : angle       0.42824 ( 6167)
  hydrogen bonds       : bond        0.04217 (  234)
  hydrogen bonds       : angle       3.21827 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.182 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.8501 (tp40) cc_final: 0.8077 (tp40)
  outliers start: 2
  outliers final: 1
  residues processed: 45
  average time/residue: 0.0541
  time to fit residues: 3.3221
Evaluate side-chains
  43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 58 optimal weight:    0.0030
   chunk 53 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.7796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.094917 restraints weight = 5689.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.54
r_work: 0.2878 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4538  Z= 0.158
  Angle     :  0.477   5.402   6167  Z= 0.249
  Chirality :  0.039   0.124    756
  Planarity :  0.004   0.043    771
  Dihedral  :  3.592  17.189    639
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.61 %
    Favored  : 88.94 %
  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 aren not related in a simple way.
  whole:  1.41 (0.37), residues: 573
  helix:  1.91 (0.29), residues: 357
  sheet:  1.26 (0.97), residues: 32
  loop : -1.13 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 375 
 TYR   0.006   0.001   TYR B 208 
 PHE   0.015   0.002   PHE B 163 
 TRP   0.005   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4538)
  covalent geometry    : angle       0.47746 ( 6167)
  hydrogen bonds       : bond        0.05615 (  234)
  hydrogen bonds       : angle       3.41602 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.134 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.8563 (tp40) cc_final: 0.8158 (tt0)
REVERT: B  154 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7901 (ttm110)
  outliers start: 2
  outliers final: 1
  residues processed: 42
  average time/residue: 0.0576
  time to fit residues: 3.2613
Evaluate side-chains
  40 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.9380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.130014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.095693 restraints weight = 5697.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.44
r_work: 0.2910 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4538  Z= 0.103
  Angle     :  0.411   5.262   6167  Z= 0.215
  Chirality :  0.037   0.125    756
  Planarity :  0.003   0.040    771
  Dihedral  :  3.405  15.741    639
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.51 %
    Favored  : 87.13 %
  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 aren not related in a simple way.
  whole:  1.58 (0.37), residues: 573
  helix:  2.08 (0.29), residues: 357
  sheet:  1.30 (0.95), residues: 32
  loop : -1.13 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  94 
 TYR   0.005   0.001   TYR B 442 
 PHE   0.010   0.001   PHE B 163 
 TRP   0.003   0.000   TRP B 466 
 HIS   0.003   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4538)
  covalent geometry    : angle       0.41128 ( 6167)
  hydrogen bonds       : bond        0.03968 (  234)
  hydrogen bonds       : angle       3.17995 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.181 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.8495 (tp40) cc_final: 0.8063 (tt0)
REVERT: B  154 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7903 (ttm110)
  outliers start: 6
  outliers final: 2
  residues processed: 47
  average time/residue: 0.0554
  time to fit residues: 3.4698
Evaluate side-chains
  41 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 SER
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 19 optimal weight:    0.0000
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0970
   chunk 31 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.3382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.134215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.099976 restraints weight = 5767.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.47
r_work: 0.2974 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4538  Z= 0.076
  Angle     :  0.382   5.239   6167  Z= 0.197
  Chirality :  0.035   0.125    756
  Planarity :  0.003   0.037    771
  Dihedral  :  3.118  11.925    639
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 13.09 %
    Favored  : 86.23 %
  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 aren not related in a simple way.
  whole:  1.77 (0.37), residues: 573
  helix:  2.29 (0.29), residues: 356
  sheet:  1.08 (1.06), residues: 28
  loop : -1.07 (0.44), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  94 
 TYR   0.004   0.000   TYR B 478 
 PHE   0.009   0.001   PHE B 163 
 TRP   0.002   0.000   TRP A 268 
 HIS   0.002   0.000   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00156 ( 4538)
  covalent geometry    : angle       0.38214 ( 6167)
  hydrogen bonds       : bond        0.02490 (  234)
  hydrogen bonds       : angle       2.93777 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.172 
Fit side-chains
REVERT: B  154 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7764 (ttm110)
  outliers start: 3
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0641
  time to fit residues: 4.0235
Evaluate side-chains
  42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0470
   chunk 47 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.4682

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.128687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.094212 restraints weight = 5729.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.44
r_work: 0.2887 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4538  Z= 0.137
  Angle     :  0.450   6.623   6167  Z= 0.231
  Chirality :  0.038   0.124    756
  Planarity :  0.004   0.041    771
  Dihedral  :  3.303  14.030    639
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 14.00 %
    Favored  : 85.55 %
  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 aren not related in a simple way.
  whole:  1.53 (0.37), residues: 573
  helix:  2.04 (0.29), residues: 359
  sheet:  1.16 (1.09), residues: 28
  loop : -1.11 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 406 
 TYR   0.006   0.001   TYR B 442 
 PHE   0.014   0.001   PHE B 163 
 TRP   0.005   0.001   TRP A 264 
 HIS   0.004   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4538)
  covalent geometry    : angle       0.44984 ( 6167)
  hydrogen bonds       : bond        0.04910 (  234)
  hydrogen bonds       : angle       3.21427 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.107 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.8547 (tp40) cc_final: 0.8082 (tt0)
  outliers start: 2
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0504
  time to fit residues: 2.8892
Evaluate side-chains
  43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 SER
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0370
   chunk 42 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 8 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.6858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.131812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.097404 restraints weight = 5649.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.44
r_work: 0.2964 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4538  Z= 0.088
  Angle     :  0.407   7.366   6167  Z= 0.207
  Chirality :  0.036   0.125    756
  Planarity :  0.003   0.041    771
  Dihedral  :  3.183  12.518    639
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 14.67 %
    Favored  : 85.10 %
  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 aren not related in a simple way.
  whole:  1.67 (0.37), residues: 573
  helix:  2.16 (0.29), residues: 358
  sheet:  1.19 (1.07), residues: 28
  loop : -1.04 (0.45), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  94 
 TYR   0.005   0.001   TYR B 442 
 PHE   0.010   0.001   PHE B 163 
 TRP   0.002   0.000   TRP B 466 
 HIS   0.003   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 4538)
  covalent geometry    : angle       0.40726 ( 6167)
  hydrogen bonds       : bond        0.03374 (  234)
  hydrogen bonds       : angle       3.05095 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.106 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.8460 (tp40) cc_final: 0.7997 (tt0)
REVERT: B  154 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7810 (ttm110)
  outliers start: 1
  outliers final: 1
  residues processed: 44
  average time/residue: 0.0560
  time to fit residues: 3.2952
Evaluate side-chains
  43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0970
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    2.4186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.129393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.093376 restraints weight = 5687.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 2.50
r_work: 0.2851 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4538  Z= 0.204
  Angle     :  0.519   6.277   6167  Z= 0.267
  Chirality :  0.041   0.124    756
  Planarity :  0.004   0.047    771
  Dihedral  :  3.620  17.352    639
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 14.45 %
    Favored  : 85.10 %
  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 aren not related in a simple way.
  whole:  1.28 (0.37), residues: 573
  helix:  1.79 (0.28), residues: 360
  sheet:  1.41 (0.98), residues: 32
  loop : -1.23 (0.45), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 435 
 TYR   0.009   0.001   TYR B 442 
 PHE   0.018   0.002   PHE B 163 
 TRP   0.006   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 4538)
  covalent geometry    : angle       0.51880 ( 6167)
  hydrogen bonds       : bond        0.06371 (  234)
  hydrogen bonds       : angle       3.49734 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.187 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.8649 (tp40) cc_final: 0.8210 (tt0)
REVERT: B  154 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7963 (ttm110)
  outliers start: 2
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0743
  time to fit residues: 4.2688
Evaluate side-chains
  42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0770
   chunk 56 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.134606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.098166 restraints weight = 5667.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 2.55
r_work: 0.2926 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4538  Z= 0.090
  Angle     :  0.417   7.286   6167  Z= 0.213
  Chirality :  0.036   0.125    756
  Planarity :  0.003   0.043    771
  Dihedral  :  3.327  14.277    639
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 13.77 %
    Favored  : 85.55 %
  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 aren not related in a simple way.
  whole:  1.53 (0.37), residues: 573
  helix:  2.00 (0.29), residues: 360
  sheet:  1.27 (1.07), residues: 28
  loop : -1.06 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 406 
 TYR   0.005   0.001   TYR B 442 
 PHE   0.009   0.001   PHE B 163 
 TRP   0.002   0.000   TRP B 466 
 HIS   0.003   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 4538)
  covalent geometry    : angle       0.41661 ( 6167)
  hydrogen bonds       : bond        0.03579 (  234)
  hydrogen bonds       : angle       3.14808 (  675)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.185 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.8465 (tp40) cc_final: 0.8009 (tt0)
REVERT: B  154 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7808 (ttm110)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0717
  time to fit residues: 4.1327
Evaluate side-chains
  42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 SER
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0050
   chunk 7 optimal weight:    0.0050
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.4014

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.132587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.096393 restraints weight = 5631.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.52
r_work: 0.2900 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4538  Z= 0.130
  Angle     :  0.444   6.419   6167  Z= 0.227
  Chirality :  0.038   0.125    756
  Planarity :  0.004   0.044    771
  Dihedral  :  3.357  14.595    639
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 14.00 %
    Favored  : 85.55 %
  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 aren not related in a simple way.
  whole:  1.45 (0.37), residues: 573
  helix:  1.98 (0.29), residues: 358
  sheet:  1.34 (1.09), residues: 28
  loop : -1.16 (0.45), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 435 
 TYR   0.006   0.001   TYR B 442 
 PHE   0.013   0.001   PHE B 163 
 TRP   0.004   0.001   TRP A 264 
 HIS   0.004   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4538)
  covalent geometry    : angle       0.44444 ( 6167)
  hydrogen bonds       : bond        0.04659 (  234)
  hydrogen bonds       : angle       3.22477 (  675)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 968.08 seconds
wall clock time: 17 minutes 13.91 seconds (1033.91 seconds total)