Starting phenix.real_space_refine
on Sat Aug 23 09:54:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cni_16758/08_2025/8cni_16758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cni_16758/08_2025/8cni_16758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cni_16758/08_2025/8cni_16758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cni_16758/08_2025/8cni_16758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cni_16758/08_2025/8cni_16758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cni_16758/08_2025/8cni_16758.cif"
  }
  resolution = 3.35
  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=   0.028
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
     S      31      5.16       5
     C    3750      2.51       5
     N     921      2.21       5
     O    1016      1.98       5
     H    5679      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 11397
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 7677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 7677
          Classifications: {'peptide': 494}
          Link IDs: {'PTRANS': 22, 'TRANS': 471}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1860
          Classifications: {'peptide': 124}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "C"
      Number of atoms: 1860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1860
          Classifications: {'peptide': 124}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
  Time building chain proxies: 2.17, per 1000 atoms: 0.19
  Number of scatterers: 11397
  At special positions: 0
  Unit cell: (94.35, 102, 114.75, 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      31     16.00
     O    1016      8.00
     N     921      7.00
     C    3750      6.00
     H    5679      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 161 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03

  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: 0.99
  Conformation dependent library (CDL) restraints added in 241.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 5 sheets defined
      52.7% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 33 through 39
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 54 through 59
    Processing helix  chain 'B' and resid 66 through 84
      removed outlier: 3.549A  pdb=" N   SER B  71 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU B  74 " --> pdb=" O   ALA B  70 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   MET B  78 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 95
      removed outlier: 3.577A  pdb=" N   LEU B  91 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ALA B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 114
    Processing helix  chain 'B' and resid 114 through 121
      removed outlier: 3.952A  pdb=" N   VAL B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 130
      removed outlier: 4.303A  pdb=" N   GLN B 126 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   GLY B 127 " --> pdb=" O   HIS B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 190
      removed outlier: 3.541A  pdb=" N   LEU B 171 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY B 177 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS B 180 " --> pdb=" O   VAL B 176 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ALA B 181 " --> pdb=" O   GLY B 177 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN B 182 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   THR B 184 " --> pdb=" O   LYS B 180 " (cutoff:3.500A)
      Proline residue:  B 185  - end of helix
      removed outlier: 3.540A  pdb=" N   ALA B 188 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLN B 190 " --> pdb=" O   PHE B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 194
    Processing helix  chain 'B' and resid 195 through 208
      removed outlier: 3.525A  pdb=" N   THR B 199 " --> pdb=" O   GLY B 195 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   TRP B 205 " --> pdb=" O   ARG B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 227
      removed outlier: 3.558A  pdb=" N   ALA B 214 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE B 215 " --> pdb=" O   ASN B 211 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ALA B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR B 223 " --> pdb=" O   GLY B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 251
      removed outlier: 3.945A  pdb=" N   ALA B 238 " --> pdb=" O   TYR B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 254
      No H-bonds generated for 'chain 'B' and resid 252 through 254'
    Processing helix  chain 'B' and resid 262 through 277
      removed outlier: 3.587A  pdb=" N   THR B 266 " --> pdb=" O   GLY B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
      removed outlier: 3.891A  pdb=" N   MET B 306 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 335
      removed outlier: 4.016A  pdb=" N   VAL B 320 " --> pdb=" O   ARG B 316 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS B 328 " --> pdb=" O   LYS B 324 " (cutoff:3.500A)
      Proline residue:  B 331  - end of helix
    Processing helix  chain 'B' and resid 336 through 356
      removed outlier: 4.618A  pdb=" N   MET B 346 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLN B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   VAL B 351 " --> pdb=" O   GLN B 347 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 352 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   HIS B 356 " --> pdb=" O   LEU B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 393
      removed outlier: 3.834A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      Proline residue:  B 390  - end of helix
    Processing helix  chain 'B' and resid 396 through 403
      removed outlier: 3.804A  pdb=" N   ASN B 403 " --> pdb=" O   VAL B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 439
      removed outlier: 3.723A  pdb=" N   ALA B 414 " --> pdb=" O   LEU B 410 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE B 419 " --> pdb=" O   VAL B 415 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   MET B 421 " --> pdb=" O   MET B 417 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS B 436 " --> pdb=" O   SER B 432 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 462
    Processing helix  chain 'B' and resid 463 through 471
      removed outlier: 3.676A  pdb=" N   LEU B 468 " --> pdb=" O   PRO B 464 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE B 469 " --> pdb=" O   GLN B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 476
      removed outlier: 3.869A  pdb=" N   PHE B 475 " --> pdb=" O   PHE B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 487
      removed outlier: 3.661A  pdb=" N   LEU B 481 " --> pdb=" O   SER B 477 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU B 482 " --> pdb=" O   ILE B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 501
    Processing helix  chain 'B' and resid 504 through 519
      removed outlier: 3.616A  pdb=" N   ALA B 516 " --> pdb=" O   SER B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 568
      removed outlier: 4.203A  pdb=" N   TYR B 543 " --> pdb=" O   GLN B 539 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE B 545 " --> pdb=" O   ASN B 541 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   THR B 554 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
    Processing helix  chain 'A' and resid 108 through 112
    Processing helix  chain 'C' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'B' and resid 443 through 447
      removed outlier: 3.521A  pdb=" N   VAL B 450 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 7
      removed outlier: 3.943A  pdb=" N   GLN A   3 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A  79 " --> pdb=" O   CYS A  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12
      removed outlier: 3.769A  pdb=" N   LEU A  93 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   ALA A  50 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A  50 " --> pdb=" O   TYR A  59 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.540A  pdb=" N   VAL C  79 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.804A  pdb=" N   TYR C  33 " --> pdb=" O   ALA C  99 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    765 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: 2.62

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5672
        1.03 -     1.23: 17
        1.23 -     1.42: 2512
        1.42 -     1.61: 3295
        1.61 -     1.81: 49
  Bond restraints: 11545
  Sorted by residual:
  bond pdb=" CB  ILE B 210 "
       pdb=" CG2 ILE B 210 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.20e-01
  bond pdb=" CB  ARG B  44 "
       pdb=" CG  ARG B  44 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 3.00e-02 1.11e+03 7.68e-01
  bond pdb=" CB  ASN B 204 "
       pdb=" CG  ASN B 204 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.64e-01
  bond pdb=" CG  TYR B 109 "
       pdb=" CD1 TYR B 109 "
    ideal  model  delta    sigma   weight residual
    1.389  1.372  0.017 2.10e-02 2.27e+03 6.55e-01
  bond pdb=" CB  THR B 101 "
       pdb=" CG2 THR B 101 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.35e-01
  ... (remaining 11540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 19164
        0.97 -     1.94: 1559
        1.94 -     2.92: 58
        2.92 -     3.89: 21
        3.89 -     4.86: 8
  Bond angle restraints: 20810
  Sorted by residual:
  angle pdb=" N   ILE A  28 "
        pdb=" CA  ILE A  28 "
        pdb=" C   ILE A  28 "
      ideal   model   delta    sigma   weight residual
     111.91  109.73    2.18 8.90e-01 1.26e+00 5.97e+00
  angle pdb=" N   ILE A  28 "
        pdb=" CA  ILE A  28 "
        pdb=" CB  ILE A  28 "
      ideal   model   delta    sigma   weight residual
     112.39  110.24    2.15 1.17e+00 7.31e-01 3.38e+00
  angle pdb=" N   MET B 497 "
        pdb=" CA  MET B 497 "
        pdb=" C   MET B 497 "
      ideal   model   delta    sigma   weight residual
     112.89  110.92    1.97 1.24e+00 6.50e-01 2.51e+00
  angle pdb=" N   PHE B 502 "
        pdb=" CA  PHE B 502 "
        pdb=" C   PHE B 502 "
      ideal   model   delta    sigma   weight residual
     113.41  111.54    1.87 1.22e+00 6.72e-01 2.34e+00
  angle pdb=" N   THR B  51 "
        pdb=" CA  THR B  51 "
        pdb=" C   THR B  51 "
      ideal   model   delta    sigma   weight residual
     111.82  113.59   -1.77 1.16e+00 7.43e-01 2.32e+00
  ... (remaining 20805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 5038
       16.24 -    32.49: 275
       32.49 -    48.73: 98
       48.73 -    64.98: 53
       64.98 -    81.22: 4
  Dihedral angle restraints: 5468
    sinusoidal: 2854
      harmonic: 2614
  Sorted by residual:
  dihedral pdb=" CA  ILE B 496 "
           pdb=" C   ILE B 496 "
           pdb=" N   MET B 497 "
           pdb=" CA  MET B 497 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  ARG B  29 "
           pdb=" C   ARG B  29 "
           pdb=" N   ARG B  30 "
           pdb=" CA  ARG B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  LEU B  95 "
           pdb=" C   LEU B  95 "
           pdb=" N   LEU B  96 "
           pdb=" CA  LEU B  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.69  -16.31     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 5465 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 502
       0.027 -    0.053: 270
       0.053 -    0.080: 79
       0.080 -    0.106: 23
       0.106 -    0.133: 20
  Chirality restraints: 894
  Sorted by residual:
  chirality pdb=" CA  ILE B 132 "
            pdb=" N   ILE B 132 "
            pdb=" C   ILE B 132 "
            pdb=" CB  ILE B 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  ILE B 447 "
            pdb=" N   ILE B 447 "
            pdb=" C   ILE B 447 "
            pdb=" CB  ILE B 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  chirality pdb=" CA  ILE B 359 "
            pdb=" N   ILE B 359 "
            pdb=" C   ILE B 359 "
            pdb=" CB  ILE B 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 891 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  61 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO B  62 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  62 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  62 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 337 "   -0.022 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO B 338 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 338 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 338 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 330 "   -0.021 5.00e-02 4.00e+02   3.10e-02 1.53e+00
        pdb=" N   PRO B 331 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 331 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 331 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 863
        2.22 -     2.81: 24290
        2.81 -     3.41: 28917
        3.41 -     4.00: 39375
        4.00 -     4.60: 60807
  Nonbonded interactions: 154252
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 534 "
            pdb=" H   ASN B 536 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" OE1 GLU A  89 "
            pdb=" H   GLU A  89 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" HZ3 LYS B 308 "
            pdb=" OE2 GLU B 321 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" OG1 THR C  91 "
            pdb=" H   VAL C 123 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" OE1 GLN A 117 "
            pdb=" H   GLN A 117 "
     model   vdw
     1.665 2.450
  ... (remaining 154247 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

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:             1.320
  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:             0.070
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.160
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
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      :  0.005   0.035   5869  Z= 0.210
  Angle     :  0.481   4.860   7980  Z= 0.258
  Chirality :  0.038   0.133    894
  Planarity :  0.003   0.034    989
  Dihedral  :  9.349  54.018   2018
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  5.05 %
    Favored  : 94.61 %
  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: -1.46 (0.33), residues: 728
  helix: -1.66 (0.26), residues: 358
  sheet: -0.25 (0.51), residues: 120
  loop :  0.19 (0.44), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 125 
 TYR   0.011   0.001   TYR B 109 
 PHE   0.009   0.001   PHE B 372 
 TRP   0.010   0.001   TRP B 208 
 HIS   0.001   0.001   HIS B 529 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 5866)
  covalent geometry    : angle       0.48099 ( 7974)
  SS BOND              : bond        0.00213 (    3)
  SS BOND              : angle       0.16481 (    6)
  hydrogen bonds       : bond        0.30459 (  275)
  hydrogen bonds       : angle      10.35326 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8319 (tpt170)
REVERT: B  125 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.6093 (ttt180)
REVERT: B  232 ILE cc_start: 0.8889 (mm) cc_final: 0.8607 (mp)
REVERT: B  263 SER cc_start: 0.8099 (t) cc_final: 0.7884 (t)
REVERT: B  318 ASP cc_start: 0.7796 (p0) cc_final: 0.7537 (t0)
REVERT: B  542 TYR cc_start: 0.7948 (m-80) cc_final: 0.7622 (m-80)
REVERT: A    4 LEU cc_start: 0.9084 (mt) cc_final: 0.8579 (mt)
REVERT: A   84 ASN cc_start: 0.7749 (m-40) cc_final: 0.7480 (m-40)
REVERT: A   93 LEU cc_start: 0.9091 (tp) cc_final: 0.8877 (tp)
REVERT: C   37 PHE cc_start: 0.8393 (m-80) cc_final: 0.8169 (m-80)
REVERT: C  109 GLN cc_start: 0.8387 (pt0) cc_final: 0.7714 (mt0)
REVERT: C  119 THR cc_start: 0.8226 (t) cc_final: 0.8015 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 141
  average time/residue: 0.1471
  time to fit residues: 27.9252
Evaluate side-chains
  125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  178 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0020
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
B 252 GLN
B 403 ASN
B 444 ASN
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 ASN
C 117 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.192806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.109497 restraints weight = 18310.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 2.49
r_work: 0.2840 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5869  Z= 0.172
  Angle     :  0.570   5.892   7980  Z= 0.310
  Chirality :  0.039   0.135    894
  Planarity :  0.004   0.035    989
  Dihedral  :  4.056  18.011    792
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 12.46 %
    Favored  : 87.21 %
  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: -0.56 (0.32), residues: 728
  helix: -0.57 (0.27), residues: 357
  sheet:  0.12 (0.52), residues: 120
  loop :  0.04 (0.43), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  29 
 TYR   0.022   0.001   TYR B 109 
 PHE   0.019   0.002   PHE B 425 
 TRP   0.010   0.001   TRP A 110 
 HIS   0.002   0.001   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5866)
  covalent geometry    : angle       0.56934 ( 7974)
  SS BOND              : bond        0.00443 (    3)
  SS BOND              : angle       1.00298 (    6)
  hydrogen bonds       : bond        0.07457 (  275)
  hydrogen bonds       : angle       6.01979 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8440 (tpt170)
REVERT: B  125 ARG cc_start: 0.8178 (ttp-170) cc_final: 0.5626 (ttt180)
REVERT: B  232 ILE cc_start: 0.8752 (mm) cc_final: 0.8495 (mp)
REVERT: B  542 TYR cc_start: 0.8066 (m-80) cc_final: 0.7570 (m-80)
REVERT: B  567 HIS cc_start: 0.7967 (t70) cc_final: 0.7551 (t-90)
REVERT: A   82 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: A   84 ASN cc_start: 0.7944 (m-40) cc_final: 0.7743 (m-40)
REVERT: C  109 GLN cc_start: 0.8443 (pt0) cc_final: 0.7686 (mt0)
  outliers start: 2
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1338
  time to fit residues: 24.2036
Evaluate side-chains
  120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   77 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 227 ASN
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.194249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110505 restraints weight = 18472.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 2.49
r_work: 0.2825 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   5869  Z= 0.140
  Angle     :  0.505   4.598   7980  Z= 0.269
  Chirality :  0.037   0.136    894
  Planarity :  0.004   0.033    989
  Dihedral  :  3.936  16.120    791
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 13.30 %
    Favored  : 86.20 %
  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: -0.26 (0.33), residues: 728
  helix: -0.16 (0.28), residues: 355
  sheet:  0.24 (0.53), residues: 120
  loop : -0.10 (0.43), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  67 
 TYR   0.014   0.001   TYR B 109 
 PHE   0.013   0.001   PHE B 425 
 TRP   0.010   0.001   TRP A 110 
 HIS   0.002   0.000   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5866)
  covalent geometry    : angle       0.50479 ( 7974)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       0.66730 (    6)
  hydrogen bonds       : bond        0.05903 (  275)
  hydrogen bonds       : angle       5.34075 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8363 (tpt170)
REVERT: B  125 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.5581 (ttt180)
REVERT: B  232 ILE cc_start: 0.8736 (mm) cc_final: 0.8481 (mp)
REVERT: B  267 ASP cc_start: 0.8187 (m-30) cc_final: 0.7796 (m-30)
REVERT: B  393 ASP cc_start: 0.9167 (t70) cc_final: 0.8930 (t0)
REVERT: B  567 HIS cc_start: 0.7864 (t70) cc_final: 0.7463 (t-90)
REVERT: A   27 ASP cc_start: 0.7489 (p0) cc_final: 0.7096 (p0)
REVERT: A   82 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7510 (tm-30)
REVERT: A   84 ASN cc_start: 0.7975 (m-40) cc_final: 0.7733 (m-40)
REVERT: C  109 GLN cc_start: 0.8433 (pt0) cc_final: 0.7666 (mt0)
  outliers start: 3
  outliers final: 3
  residues processed: 124
  average time/residue: 0.1398
  time to fit residues: 23.6736
Evaluate side-chains
  123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain A residue  101 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0050
   chunk 32 optimal weight:    0.3980
   chunk 70 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 69 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 59 optimal weight:    0.1980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.196826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112797 restraints weight = 18273.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.51
r_work: 0.2892 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5869  Z= 0.100
  Angle     :  0.470   4.624   7980  Z= 0.246
  Chirality :  0.037   0.135    894
  Planarity :  0.003   0.031    989
  Dihedral  :  3.721  15.638    791
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.13 %
    Favored  : 85.69 %
  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: -0.03 (0.32), residues: 728
  helix:  0.14 (0.28), residues: 360
  sheet:  0.20 (0.51), residues: 120
  loop : -0.08 (0.43), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  30 
 TYR   0.010   0.001   TYR B 109 
 PHE   0.011   0.001   PHE B 425 
 TRP   0.010   0.001   TRP A 110 
 HIS   0.002   0.001   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 5866)
  covalent geometry    : angle       0.46931 ( 7974)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       0.78370 (    6)
  hydrogen bonds       : bond        0.04582 (  275)
  hydrogen bonds       : angle       4.81460 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8289 (tpt170)
REVERT: B  232 ILE cc_start: 0.8681 (mm) cc_final: 0.8439 (mp)
REVERT: B  567 HIS cc_start: 0.7759 (t70) cc_final: 0.7369 (t-90)
REVERT: A   27 ASP cc_start: 0.7453 (p0) cc_final: 0.7238 (p0)
REVERT: A   82 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: A   84 ASN cc_start: 0.8003 (m-40) cc_final: 0.7653 (m-40)
REVERT: C  109 GLN cc_start: 0.8421 (pt0) cc_final: 0.7655 (mt0)
  outliers start: 7
  outliers final: 6
  residues processed: 123
  average time/residue: 0.1087
  time to fit residues: 18.8588
Evaluate side-chains
  125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  438 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain C residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 53 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.196303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.112455 restraints weight = 18380.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.50
r_work: 0.3024 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5869  Z= 0.126
  Angle     :  0.472   4.562   7980  Z= 0.246
  Chirality :  0.037   0.134    894
  Planarity :  0.003   0.031    989
  Dihedral  :  3.717  14.985    791
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.13 %
    Favored  : 84.85 %
  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:  0.06 (0.33), residues: 728
  helix:  0.26 (0.28), residues: 358
  sheet:  0.26 (0.50), residues: 120
  loop : -0.14 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 434 
 TYR   0.011   0.001   TYR B 109 
 PHE   0.008   0.001   PHE B 425 
 TRP   0.009   0.001   TRP A 110 
 HIS   0.001   0.000   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5866)
  covalent geometry    : angle       0.47203 ( 7974)
  SS BOND              : bond        0.00133 (    3)
  SS BOND              : angle       0.67150 (    6)
  hydrogen bonds       : bond        0.04595 (  275)
  hydrogen bonds       : angle       4.67455 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8643 (tpp-160) cc_final: 0.8356 (tpt170)
REVERT: B  232 ILE cc_start: 0.8772 (mm) cc_final: 0.8532 (mp)
REVERT: B  567 HIS cc_start: 0.7771 (t70) cc_final: 0.7386 (t-90)
  outliers start: 12
  outliers final: 9
  residues processed: 124
  average time/residue: 0.1172
  time to fit residues: 20.6744
Evaluate side-chains
  128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  438 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain C residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.197303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.113028 restraints weight = 18350.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.50
r_work: 0.3040 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5869  Z= 0.106
  Angle     :  0.462   4.491   7980  Z= 0.240
  Chirality :  0.037   0.134    894
  Planarity :  0.003   0.030    989
  Dihedral  :  3.632  15.013    791
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.64 %
    Favored  : 84.34 %
  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:  0.16 (0.32), residues: 728
  helix:  0.36 (0.28), residues: 360
  sheet:  0.32 (0.50), residues: 120
  loop : -0.12 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 434 
 TYR   0.010   0.001   TYR B 109 
 PHE   0.008   0.001   PHE B 425 
 TRP   0.009   0.001   TRP A 110 
 HIS   0.001   0.000   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5866)
  covalent geometry    : angle       0.46237 ( 7974)
  SS BOND              : bond        0.00096 (    3)
  SS BOND              : angle       0.56119 (    6)
  hydrogen bonds       : bond        0.04217 (  275)
  hydrogen bonds       : angle       4.51908 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8625 (tpp-160) cc_final: 0.8327 (tpt170)
REVERT: B  232 ILE cc_start: 0.8729 (mm) cc_final: 0.8495 (mp)
REVERT: B  567 HIS cc_start: 0.7751 (t70) cc_final: 0.7380 (t-90)
REVERT: A   27 ASP cc_start: 0.7449 (p0) cc_final: 0.7120 (p0)
REVERT: A   82 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7336 (tm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1270
  time to fit residues: 22.3315
Evaluate side-chains
  126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  438 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  101 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 63 optimal weight:    0.0270
   chunk 4 optimal weight:    1.9990
   chunk 70 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.197466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.115443 restraints weight = 18128.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 2.96
r_work: 0.2728 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5869  Z= 0.104
  Angle     :  0.456   4.528   7980  Z= 0.237
  Chirality :  0.037   0.135    894
  Planarity :  0.003   0.029    989
  Dihedral  :  3.601  14.677    791
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.97 %
    Favored  : 84.34 %
  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:  0.20 (0.32), residues: 728
  helix:  0.43 (0.29), residues: 358
  sheet:  0.30 (0.49), residues: 120
  loop : -0.17 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  29 
 TYR   0.010   0.001   TYR B 109 
 PHE   0.007   0.001   PHE B  77 
 TRP   0.016   0.001   TRP A 110 
 HIS   0.001   0.000   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5866)
  covalent geometry    : angle       0.45583 ( 7974)
  SS BOND              : bond        0.00099 (    3)
  SS BOND              : angle       0.44139 (    6)
  hydrogen bonds       : bond        0.04041 (  275)
  hydrogen bonds       : angle       4.37896 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8338 (tpt170)
REVERT: B  232 ILE cc_start: 0.8591 (mm) cc_final: 0.8362 (mp)
REVERT: B  567 HIS cc_start: 0.7698 (t70) cc_final: 0.7339 (t-90)
REVERT: A   27 ASP cc_start: 0.7294 (p0) cc_final: 0.6962 (p0)
REVERT: A   82 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7313 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1182
  time to fit residues: 19.8943
Evaluate side-chains
  124 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  438 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  101 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.196996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.113020 restraints weight = 18217.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.49
r_work: 0.2890 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5869  Z= 0.108
  Angle     :  0.456   4.546   7980  Z= 0.236
  Chirality :  0.037   0.135    894
  Planarity :  0.003   0.029    989
  Dihedral  :  3.556  14.311    791
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.15 %
    Favored  : 83.50 %
  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:  0.27 (0.33), residues: 728
  helix:  0.48 (0.29), residues: 358
  sheet:  0.39 (0.50), residues: 120
  loop : -0.15 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  29 
 TYR   0.011   0.001   TYR B 109 
 PHE   0.007   0.001   PHE B  77 
 TRP   0.012   0.001   TRP A 110 
 HIS   0.001   0.000   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5866)
  covalent geometry    : angle       0.45596 ( 7974)
  SS BOND              : bond        0.00116 (    3)
  SS BOND              : angle       0.45689 (    6)
  hydrogen bonds       : bond        0.03928 (  275)
  hydrogen bonds       : angle       4.28753 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8335 (tpt170)
REVERT: B  232 ILE cc_start: 0.8664 (mm) cc_final: 0.8436 (mp)
REVERT: B  567 HIS cc_start: 0.7699 (t70) cc_final: 0.7346 (t-90)
REVERT: A   27 ASP cc_start: 0.7352 (p0) cc_final: 0.7014 (p0)
REVERT: A   82 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7366 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 117
  average time/residue: 0.1075
  time to fit residues: 18.1355
Evaluate side-chains
  121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  438 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain A residue  101 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 72 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0030
   chunk 66 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.196284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.114471 restraints weight = 18162.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.84
r_work: 0.2904 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5869  Z= 0.126
  Angle     :  0.464   4.571   7980  Z= 0.240
  Chirality :  0.037   0.134    894
  Planarity :  0.003   0.041    989
  Dihedral  :  3.604  14.646    791
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.32 %
    Favored  : 83.33 %
  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:  0.26 (0.33), residues: 728
  helix:  0.46 (0.29), residues: 358
  sheet:  0.46 (0.50), residues: 120
  loop : -0.16 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  67 
 TYR   0.012   0.001   TYR B 109 
 PHE   0.009   0.001   PHE B  77 
 TRP   0.013   0.001   TRP A 110 
 HIS   0.001   0.000   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 5866)
  covalent geometry    : angle       0.46371 ( 7974)
  SS BOND              : bond        0.00121 (    3)
  SS BOND              : angle       0.40838 (    6)
  hydrogen bonds       : bond        0.04032 (  275)
  hydrogen bonds       : angle       4.28370 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8377 (tpt170)
REVERT: B  232 ILE cc_start: 0.8712 (mm) cc_final: 0.8490 (mp)
REVERT: B  567 HIS cc_start: 0.7677 (t70) cc_final: 0.7330 (t-90)
REVERT: A   82 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7329 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 121
  average time/residue: 0.1147
  time to fit residues: 19.8692
Evaluate side-chains
  123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  438 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain A residue  101 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0470
   chunk 61 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0470
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
B 465 GLN
A  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.195272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.112764 restraints weight = 18186.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.44
r_work: 0.2911 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5869  Z= 0.090
  Angle     :  0.455   4.806   7980  Z= 0.235
  Chirality :  0.037   0.136    894
  Planarity :  0.004   0.083    989
  Dihedral  :  3.515  14.522    791
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 15.66 %
    Favored  : 83.67 %
  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:  0.47 (0.33), residues: 728
  helix:  0.66 (0.29), residues: 358
  sheet:  0.53 (0.50), residues: 120
  loop : -0.10 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  67 
 TYR   0.010   0.001   TYR A 100 
 PHE   0.009   0.001   PHE C  37 
 TRP   0.013   0.001   TRP A 110 
 HIS   0.001   0.000   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 5866)
  covalent geometry    : angle       0.45545 ( 7974)
  SS BOND              : bond        0.00101 (    3)
  SS BOND              : angle       0.45117 (    6)
  hydrogen bonds       : bond        0.03580 (  275)
  hydrogen bonds       : angle       4.15519 (  765)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8305 (tpt170)
REVERT: B  243 ILE cc_start: 0.8200 (mm) cc_final: 0.7957 (mt)
REVERT: B  567 HIS cc_start: 0.7629 (t70) cc_final: 0.7280 (t-90)
REVERT: A   27 ASP cc_start: 0.7346 (p0) cc_final: 0.7096 (p0)
REVERT: A   82 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7296 (tm-30)
  outliers start: 4
  outliers final: 4
  residues processed: 122
  average time/residue: 0.1121
  time to fit residues: 19.0879
Evaluate side-chains
  117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  438 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  472 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0970
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:   20.0000
   overall best weight:    0.8178

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.194001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.111402 restraints weight = 18103.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 2.41
r_work: 0.2921 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5869  Z= 0.113
  Angle     :  0.462   4.541   7980  Z= 0.240
  Chirality :  0.037   0.134    894
  Planarity :  0.004   0.061    989
  Dihedral  :  3.520  14.589    791
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.99 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.47 (0.33), residues: 728
  helix:  0.67 (0.29), residues: 358
  sheet:  0.56 (0.50), residues: 120
  loop : -0.13 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  67 
 TYR   0.011   0.001   TYR B 109 
 PHE   0.007   0.001   PHE B  77 
 TRP   0.012   0.001   TRP A 110 
 HIS   0.001   0.001   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5866)
  covalent geometry    : angle       0.46221 ( 7974)
  SS BOND              : bond        0.00124 (    3)
  SS BOND              : angle       0.37934 (    6)
  hydrogen bonds       : bond        0.03772 (  275)
  hydrogen bonds       : angle       4.16399 (  765)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3141.42 seconds
wall clock time: 53 minutes 48.19 seconds (3228.19 seconds total)