Starting phenix.real_space_refine
on Thu Jul  2 06:13:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sne_40624/07_2026/8sne_40624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sne_40624/07_2026/8sne_40624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sne_40624/07_2026/8sne_40624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sne_40624/07_2026/8sne_40624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sne_40624/07_2026/8sne_40624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sne_40624/07_2026/8sne_40624.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.062
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1384 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       3      5.49       5
     S      33      5.16       5
     C    3883      2.51       5
     N     988      2.21       5
     O    1116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6025
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 488, 3979
          Classifications: {'peptide': 488}
          Link IDs: {'PTRANS': 13, 'TRANS': 474}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 950
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "C"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 956
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "D"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 27
          Unusual residues: {'BDP': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 86
          Ad-hoc single atom residues: {' MN': 2}
          Unusual residues: {'3PE': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 2
  Time building chain proxies: 1.08, per 1000 atoms: 0.18
  Number of scatterers: 6025
  At special positions: 0
  Unit cell: (65.88, 75.6, 165.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      33     16.00
     P       3     15.00
     O    1116      8.00
     N     988      7.00
     C    3883      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " 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
  Links applied
    BETA1-3
      " NAG D   1 " - " BDP D   2 "
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 218.5 milliseconds
  

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      45.7% alpha, 23.8% 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 39 through 73
      removed outlier: 3.983A  pdb=" N   PHE A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 107
    Processing helix  chain 'A' and resid 127 through 138
      removed outlier: 3.923A  pdb=" N   ALA A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 160
      removed outlier: 3.835A  pdb=" N   THR A 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 217 through 220
    Processing helix  chain 'A' and resid 238 through 254
    Processing helix  chain 'A' and resid 254 through 262
      removed outlier: 4.148A  pdb=" N   TRP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 289
      removed outlier: 4.874A  pdb=" N   ASP A 285 " --> pdb=" O   ASN A 281 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 303 through 312
    Processing helix  chain 'A' and resid 331 through 354
      removed outlier: 4.821A  pdb=" N   TRP A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   TYR A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 362
      removed outlier: 6.886A  pdb=" N   PHE A 362 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 392
      removed outlier: 4.280A  pdb=" N   LEU A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   PHE A 378 " --> pdb=" O   GLN A 374 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 379 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 420
      removed outlier: 3.694A  pdb=" N   ALA A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 428
      removed outlier: 3.811A  pdb=" N   PHE A 425 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 438
      removed outlier: 3.975A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 450
      removed outlier: 3.568A  pdb=" N   PHE A 450 " --> pdb=" O   MET A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 497
    Processing helix  chain 'A' and resid 504 through 534
    Processing helix  chain 'A' and resid 539 through 552
    Processing helix  chain 'C' and resid 72 through 75
      removed outlier: 3.686A  pdb=" N   ARG C  75 " --> pdb=" O   ASP C  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 72 through 75'
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 4.145A  pdb=" N   THR C  90 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 7.132A  pdb=" N   VAL A  84 " --> pdb=" O   ARG A 115 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   ILE A 117 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   VAL A  86 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   VAL A 119 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ILE A  88 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   ASP A 121 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   GLY A  90 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA A  89 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   LEU A 272 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   VAL A 317 " --> pdb=" O   LYS A 225 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   VAL A 227 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   THR A 319 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   GLY A 229 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   PHE A 321 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 9.606A  pdb=" N   CYS A 231 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   VAL A 323 " --> pdb=" O   CYS A 231 " (cutoff:3.500A)
      removed outlier: 9.670A  pdb=" N   ILE A 233 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   TRP A 325 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501
      removed outlier: 6.183A  pdb=" N   PHE A 500 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 8
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.734A  pdb=" N   SER B 123 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.734A  pdb=" N   SER B 123 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12
      removed outlier: 4.577A  pdb=" N   ASP C  33 " --> pdb=" O   GLU C  98 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ASN C  32 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   ALA C  52 " --> pdb=" O   ASN C  32 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   MET C  34 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   ARG C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12
    Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 23

    332 hydrogen bonds defined for protein.
    915 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: 0.68

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 936
        1.31 -     1.43: 1779
        1.43 -     1.56: 3395
        1.56 -     1.68: 8
        1.68 -     1.81: 51
  Bond restraints: 6169
  Sorted by residual:
  bond pdb=" C2' UDP A 601 "
       pdb=" C1' UDP A 601 "
    ideal  model  delta    sigma   weight residual
    1.530  1.327  0.203 1.40e-02 5.10e+03 2.11e+02
  bond pdb=" O4' UDP A 601 "
       pdb=" C1' UDP A 601 "
    ideal  model  delta    sigma   weight residual
    1.415  1.600 -0.185 1.40e-02 5.10e+03 1.75e+02
  bond pdb=" C4' UDP A 601 "
       pdb=" C3' UDP A 601 "
    ideal  model  delta    sigma   weight residual
    1.526  1.365  0.161 1.30e-02 5.92e+03 1.54e+02
  bond pdb=" C5  UDP A 601 "
       pdb=" C6  UDP A 601 "
    ideal  model  delta    sigma   weight residual
    1.343  1.490 -0.147 1.60e-02 3.91e+03 8.49e+01
  bond pdb=" C3' UDP A 601 "
       pdb=" C2' UDP A 601 "
    ideal  model  delta    sigma   weight residual
    1.530  1.627 -0.097 1.30e-02 5.92e+03 5.62e+01
  ... (remaining 6164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 8241
        2.88 -     5.76: 116
        5.76 -     8.65: 14
        8.65 -    11.53: 1
       11.53 -    14.41: 1
  Bond angle restraints: 8373
  Sorted by residual:
  angle pdb=" C2  UDP A 601 "
        pdb=" N3  UDP A 601 "
        pdb=" C4  UDP A 601 "
      ideal   model   delta    sigma   weight residual
     126.93  120.16    6.77 1.00e+00 1.00e+00 4.59e+01
  angle pdb=" O2B UDP A 601 "
        pdb=" PB  UDP A 601 "
        pdb=" O3A UDP A 601 "
      ideal   model   delta    sigma   weight residual
     102.95  109.34   -6.39 1.00e+00 1.00e+00 4.09e+01
  angle pdb=" O1B UDP A 601 "
        pdb=" PB  UDP A 601 "
        pdb=" O3A UDP A 601 "
      ideal   model   delta    sigma   weight residual
     102.95  109.32   -6.37 1.00e+00 1.00e+00 4.05e+01
  angle pdb=" O5' UDP A 601 "
        pdb=" PA  UDP A 601 "
        pdb=" O3A UDP A 601 "
      ideal   model   delta    sigma   weight residual
     104.35  110.17   -5.82 1.00e+00 1.00e+00 3.39e+01
  angle pdb=" N1  UDP A 601 "
        pdb=" C2  UDP A 601 "
        pdb=" N3  UDP A 601 "
      ideal   model   delta    sigma   weight residual
     114.79  120.08   -5.29 1.00e+00 1.00e+00 2.80e+01
  ... (remaining 8368 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 3153
       17.64 -    35.28: 395
       35.28 -    52.92: 113
       52.92 -    70.55: 38
       70.55 -    88.19: 6
  Dihedral angle restraints: 3705
    sinusoidal: 1564
      harmonic: 2141
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -20.16  -65.84     1      1.00e+01 1.00e-02 5.67e+01
  dihedral pdb=" CA  GLN A 172 "
           pdb=" C   GLN A 172 "
           pdb=" N   PRO A 173 "
           pdb=" CA  PRO A 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.96   20.04     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CG  ARG A 508 "
           pdb=" CD  ARG A 508 "
           pdb=" NE  ARG A 508 "
           pdb=" CZ  ARG A 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.61   42.61     2      1.50e+01 4.44e-03 9.78e+00
  ... (remaining 3702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 868
       0.093 -    0.186: 48
       0.186 -    0.278: 4
       0.278 -    0.371: 1
       0.371 -    0.464: 1
  Chirality restraints: 922
  Sorted by residual:
  chirality pdb=" CBG Y01 A 602 "
            pdb=" CAQ Y01 A 602 "
            pdb=" CBD Y01 A 602 "
            pdb=" CBI Y01 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.80    0.46 2.00e-01 2.50e+01 5.38e+00
  chirality pdb=" CBH Y01 A 602 "
            pdb=" CAT Y01 A 602 "
            pdb=" CAZ Y01 A 602 "
            pdb=" CBF Y01 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.55   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CBE Y01 A 602 "
            pdb=" CAP Y01 A 602 "
            pdb=" CBB Y01 A 602 "
            pdb=" CBI Y01 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.82   -0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 919 not shown)

  Planarity restraints: 1027
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  86 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.84e+00
        pdb=" N   PRO B  87 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B  87 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  87 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 270 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.04e+00
        pdb=" N   PRO A 271 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  13 "    0.019 5.00e-02 4.00e+02   2.96e-02 1.40e+00
        pdb=" N   PRO C  14 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  14 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  14 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1024 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 101
        2.67 -     3.22: 5397
        3.22 -     3.78: 9296
        3.78 -     4.34: 12678
        4.34 -     4.90: 21775
  Nonbonded interactions: 49247
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 172 "
            pdb=" OG1 THR A 183 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" O2B UDP A 601 "
            pdb="MN    MN A 605 "
     model   vdw
     2.174 3.060
  nonbonded pdb=" OE2 GLU A  93 "
            pdb="MN    MN A 604 "
     model   vdw
     2.215 3.060
  nonbonded pdb=" O4  BDP D   2 "
            pdb=" O3B UDP A 601 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A  46 "
            pdb=" OAG Y01 A 602 "
     model   vdw
     2.299 3.040
  ... (remaining 49242 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.170
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.203   6172  Z= 0.484
  Angle     :  0.741  14.409   8380  Z= 0.380
  Chirality :  0.049   0.464    922
  Planarity :  0.004   0.055   1027
  Dihedral  : 17.690  88.192   2335
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.69 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 24.09 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.32), residues: 725
  helix:  1.32 (0.30), residues: 312
  sheet:  0.22 (0.44), residues: 146
  loop : -1.50 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 334 
 TYR   0.016   0.001   TYR A 414 
 PHE   0.014   0.001   PHE A 450 
 TRP   0.012   0.001   TRP A 246 
 HIS   0.001   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00794 /  0.48 ( 6169)
  covalent geometry    : angle       0.74056 /  0.38 ( 8373)
  SS BOND              : bond        0.00379 /  0.20 (    2)
  SS BOND              : angle       1.53782 /  0.84 (    4)
  hydrogen bonds       : bond        0.12315 /  8.10 (  320)
  hydrogen bonds       : angle       5.62656 /  3.96 (  915)
  link_BETA1-3         : bond        0.00349 /  0.18 (    1)
  link_BETA1-3         : angle       0.91520 /  0.47 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 MET cc_start: 0.8746 (ppp) cc_final: 0.8200 (ppp)
REVERT: C   38 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7798 (ttm170)
  outliers start: 4
  outliers final: 1
  residues processed: 86
  average time/residue: 0.4247
  time to fit residues: 38.4893
Evaluate side-chains
  80 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:   30.0000
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.178985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.138085 restraints weight = 6674.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.86
r_work: 0.3158 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.0623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6172  Z= 0.140
  Angle     :  0.513   7.754   8380  Z= 0.269
  Chirality :  0.042   0.166    922
  Planarity :  0.004   0.053   1027
  Dihedral  :  9.429  82.508   1017
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.86 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 23.45 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.32), residues: 725
  helix:  1.58 (0.30), residues: 315
  sheet:  0.36 (0.44), residues: 142
  loop : -1.49 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 334 
 TYR   0.016   0.001   TYR A 414 
 PHE   0.013   0.001   PHE A 450 
 TRP   0.012   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 6169)
  covalent geometry    : angle       0.51128 /  0.27 ( 8373)
  SS BOND              : bond        0.00161 /  0.08 (    2)
  SS BOND              : angle       1.69526 /  0.94 (    4)
  hydrogen bonds       : bond        0.04141 /  2.72 (  320)
  hydrogen bonds       : angle       4.44214 /  3.11 (  915)
  link_BETA1-3         : bond        0.00162 /  0.09 (    1)
  link_BETA1-3         : angle       0.80177 /  0.46 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7390 (mpt180)
REVERT: C   38 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7629 (ttm170)
  outliers start: 24
  outliers final: 10
  residues processed: 95
  average time/residue: 0.3900
  time to fit residues: 39.0959
Evaluate side-chains
  87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   79 SER
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain C residue   58 HIS
Chi-restraints excluded: chain C residue   82 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0060
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0010
   chunk 25 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 154 ASN
** A 290 GLN ** 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 = 0.4045 r_free = 0.4045 target = 0.181222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.140508 restraints weight = 6563.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.85
r_work: 0.3214 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6172  Z= 0.107
  Angle     :  0.479   8.587   8380  Z= 0.252
  Chirality :  0.041   0.154    922
  Planarity :  0.004   0.053   1027
  Dihedral  :  8.713  88.450   1017
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.14 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 23.61 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.32), residues: 725
  helix:  1.80 (0.30), residues: 315
  sheet:  0.37 (0.44), residues: 142
  loop : -1.45 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 334 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A 450 
 TRP   0.009   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.11 ( 6169)
  covalent geometry    : angle       0.47846 /  0.25 ( 8373)
  SS BOND              : bond        0.00157 /  0.07 (    2)
  SS BOND              : angle       1.32034 /  0.75 (    4)
  hydrogen bonds       : bond        0.03634 /  2.40 (  320)
  hydrogen bonds       : angle       4.14202 /  2.89 (  915)
  link_BETA1-3         : bond        0.00443 /  0.23 (    1)
  link_BETA1-3         : angle       0.67370 /  0.39 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7218 (mp)
REVERT: A  175 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7409 (mpt180)
REVERT: C   23 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6975 (tp-100)
REVERT: C   38 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7471 (ttm170)
  outliers start: 25
  outliers final: 5
  residues processed: 95
  average time/residue: 0.4175
  time to fit residues: 41.6821
Evaluate side-chains
  83 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   58 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 61 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 3 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   1 GLN
B  13 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.174264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.131933 restraints weight = 6645.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.93
r_work: 0.3130 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6172  Z= 0.128
  Angle     :  0.501   9.829   8380  Z= 0.262
  Chirality :  0.042   0.148    922
  Planarity :  0.004   0.053   1027
  Dihedral  :  8.508  88.749   1016
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.00 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 22.50 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.32), residues: 725
  helix:  1.77 (0.30), residues: 314
  sheet:  0.19 (0.43), residues: 154
  loop : -1.34 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 334 
 TYR   0.016   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A 450 
 TRP   0.011   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 6169)
  covalent geometry    : angle       0.50074 /  0.26 ( 8373)
  SS BOND              : bond        0.00168 /  0.08 (    2)
  SS BOND              : angle       0.94968 /  0.53 (    4)
  hydrogen bonds       : bond        0.03805 /  2.51 (  320)
  hydrogen bonds       : angle       4.09564 /  2.87 (  915)
  link_BETA1-3         : bond        0.00375 /  0.20 (    1)
  link_BETA1-3         : angle       0.66880 /  0.39 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 74
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7266 (mp)
REVERT: A  139 ASN cc_start: 0.7637 (t0) cc_final: 0.7396 (m-40)
REVERT: A  175 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7439 (mpt180)
REVERT: C   23 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7015 (tp40)
REVERT: C   38 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7564 (ttm170)
REVERT: C   75 ARG cc_start: 0.6502 (ttp80) cc_final: 0.6265 (pmm150)
REVERT: C  104 ARG cc_start: 0.7582 (mtm110) cc_final: 0.6843 (mmm160)
  outliers start: 34
  outliers final: 9
  residues processed: 98
  average time/residue: 0.3816
  time to fit residues: 39.5036
Evaluate side-chains
  84 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   58 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0170
   chunk 37 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.180143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.139087 restraints weight = 6702.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.88
r_work: 0.3158 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6172  Z= 0.122
  Angle     :  0.505  12.987   8380  Z= 0.260
  Chirality :  0.041   0.143    922
  Planarity :  0.004   0.052   1027
  Dihedral  :  8.302  86.891   1016
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 23.45 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.32), residues: 725
  helix:  1.78 (0.30), residues: 315
  sheet:  0.39 (0.44), residues: 142
  loop : -1.40 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 334 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.010   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 6169)
  covalent geometry    : angle       0.50467 /  0.26 ( 8373)
  SS BOND              : bond        0.00157 /  0.08 (    2)
  SS BOND              : angle       0.83436 /  0.47 (    4)
  hydrogen bonds       : bond        0.03717 /  2.45 (  320)
  hydrogen bonds       : angle       4.04399 /  2.83 (  915)
  link_BETA1-3         : bond        0.00285 /  0.15 (    1)
  link_BETA1-3         : angle       0.68035 /  0.40 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7304 (mp)
REVERT: A  139 ASN cc_start: 0.7659 (t0) cc_final: 0.7357 (m-40)
REVERT: A  175 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7392 (mpt180)
REVERT: A  284 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6449 (ttpt)
REVERT: C   23 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7006 (tp40)
REVERT: C   38 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7393 (ttm170)
REVERT: C  104 ARG cc_start: 0.7579 (mtm110) cc_final: 0.6857 (mmm160)
  outliers start: 28
  outliers final: 10
  residues processed: 94
  average time/residue: 0.3684
  time to fit residues: 36.6610
Evaluate side-chains
  86 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   58 HIS
Chi-restraints excluded: chain C residue   86 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 49 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.177988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135778 restraints weight = 6637.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.93
r_work: 0.3152 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6172  Z= 0.122
  Angle     :  0.513  13.091   8380  Z= 0.262
  Chirality :  0.042   0.146    922
  Planarity :  0.004   0.052   1027
  Dihedral  :  8.153  85.805   1016
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.28 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 25.04 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.32), residues: 725
  helix:  1.81 (0.30), residues: 314
  sheet:  0.37 (0.43), residues: 144
  loop : -1.41 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 334 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.013   0.001   PHE C  67 
 TRP   0.010   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 6169)
  covalent geometry    : angle       0.51262 /  0.26 ( 8373)
  SS BOND              : bond        0.00169 /  0.08 (    2)
  SS BOND              : angle       0.83206 /  0.47 (    4)
  hydrogen bonds       : bond        0.03713 /  2.45 (  320)
  hydrogen bonds       : angle       4.04232 /  2.83 (  915)
  link_BETA1-3         : bond        0.00310 /  0.16 (    1)
  link_BETA1-3         : angle       0.75926 /  0.44 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7093 (mp)
REVERT: A   49 PHE cc_start: 0.7891 (t80) cc_final: 0.7445 (t80)
REVERT: A  139 ASN cc_start: 0.7715 (t0) cc_final: 0.7374 (m-40)
REVERT: A  175 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7387 (mpt180)
REVERT: A  284 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6385 (ttpt)
REVERT: C   23 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6995 (tp40)
REVERT: C   38 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.7381 (ttm170)
REVERT: C  104 ARG cc_start: 0.7543 (mtm110) cc_final: 0.6814 (mmm160)
  outliers start: 24
  outliers final: 11
  residues processed: 91
  average time/residue: 0.3807
  time to fit residues: 36.6566
Evaluate side-chains
  88 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain C residue   86 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0010
   chunk 22 optimal weight:    0.0270
   chunk 7 optimal weight:    0.0020
   chunk 3 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0050
   chunk 69 optimal weight:    7.9990
   chunk 17 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.0866

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 290 GLN
A 542 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.184821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.142966 restraints weight = 6698.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.96
r_work: 0.3297 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6172  Z= 0.087
  Angle     :  0.475  12.571   8380  Z= 0.240
  Chirality :  0.040   0.140    922
  Planarity :  0.004   0.052   1027
  Dihedral  :  7.506  80.838   1016
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.83 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.32), residues: 725
  helix:  2.06 (0.30), residues: 315
  sheet:  0.20 (0.41), residues: 158
  loop : -1.18 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 334 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.009   0.001   PHE A  49 
 TRP   0.006   0.001   TRP A 234 
 HIS   0.001   0.000   HIS C  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00178 /  0.09 ( 6169)
  covalent geometry    : angle       0.47418 /  0.24 ( 8373)
  SS BOND              : bond        0.00271 /  0.13 (    2)
  SS BOND              : angle       0.58604 /  0.33 (    4)
  hydrogen bonds       : bond        0.02997 /  1.99 (  320)
  hydrogen bonds       : angle       3.83409 /  2.68 (  915)
  link_BETA1-3         : bond        0.00274 /  0.14 (    1)
  link_BETA1-3         : angle       1.00161 /  0.57 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7008 (mp)
REVERT: A   49 PHE cc_start: 0.7827 (t80) cc_final: 0.7317 (t80)
REVERT: A  135 LYS cc_start: 0.8318 (mttt) cc_final: 0.8108 (mtmm)
REVERT: A  284 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6163 (ttpt)
REVERT: B   32 TYR cc_start: 0.9108 (m-80) cc_final: 0.8706 (m-80)
REVERT: C   38 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7331 (ttm170)
  outliers start: 18
  outliers final: 5
  residues processed: 92
  average time/residue: 0.3441
  time to fit residues: 33.5634
Evaluate side-chains
  85 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 64 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 223 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.178372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137241 restraints weight = 6602.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.84
r_work: 0.3159 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6172  Z= 0.137
  Angle     :  0.524  12.527   8380  Z= 0.267
  Chirality :  0.042   0.146    922
  Planarity :  0.004   0.051   1027
  Dihedral  :  7.602  82.921   1016
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 26.15 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.32), residues: 725
  helix:  1.93 (0.30), residues: 314
  sheet:  0.31 (0.42), residues: 153
  loop : -1.21 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 334 
 TYR   0.016   0.001   TYR A 414 
 PHE   0.009   0.001   PHE A 450 
 TRP   0.012   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 6169)
  covalent geometry    : angle       0.52409 /  0.27 ( 8373)
  SS BOND              : bond        0.00186 /  0.09 (    2)
  SS BOND              : angle       0.89385 /  0.51 (    4)
  hydrogen bonds       : bond        0.03707 /  2.43 (  320)
  hydrogen bonds       : angle       3.98776 /  2.80 (  915)
  link_BETA1-3         : bond        0.00383 /  0.20 (    1)
  link_BETA1-3         : angle       0.81435 /  0.47 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7103 (mp)
REVERT: A   49 PHE cc_start: 0.7812 (t80) cc_final: 0.7310 (t80)
REVERT: A  139 ASN cc_start: 0.7785 (t0) cc_final: 0.7476 (m-40)
REVERT: A  175 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7433 (mpt180)
REVERT: A  284 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6388 (ttpt)
REVERT: A  349 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8150 (mm-30)
REVERT: C   38 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7398 (ttm170)
REVERT: C  104 ARG cc_start: 0.7487 (mtm110) cc_final: 0.6791 (mmm160)
  outliers start: 20
  outliers final: 8
  residues processed: 87
  average time/residue: 0.3658
  time to fit residues: 33.5385
Evaluate side-chains
  85 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0070
   chunk 14 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.5798

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.179727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.137094 restraints weight = 6694.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.94
r_work: 0.3210 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6172  Z= 0.112
  Angle     :  0.511  12.506   8380  Z= 0.260
  Chirality :  0.041   0.144    922
  Planarity :  0.004   0.051   1027
  Dihedral  :  7.469  81.861   1016
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.10 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.32), residues: 725
  helix:  1.90 (0.30), residues: 315
  sheet:  0.37 (0.42), residues: 152
  loop : -1.18 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 334 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.009   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 6169)
  covalent geometry    : angle       0.51082 /  0.26 ( 8373)
  SS BOND              : bond        0.00191 /  0.09 (    2)
  SS BOND              : angle       0.81500 /  0.47 (    4)
  hydrogen bonds       : bond        0.03509 /  2.30 (  320)
  hydrogen bonds       : angle       3.97388 /  2.79 (  915)
  link_BETA1-3         : bond        0.00347 /  0.18 (    1)
  link_BETA1-3         : angle       0.80440 /  0.47 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7034 (mp)
REVERT: A   49 PHE cc_start: 0.7785 (t80) cc_final: 0.7312 (t80)
REVERT: A  139 ASN cc_start: 0.7636 (t0) cc_final: 0.7335 (m-40)
REVERT: A  175 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7381 (mpt180)
REVERT: A  284 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6454 (ttpt)
REVERT: A  349 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8055 (mm-30)
REVERT: C   71 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7020 (tpp80)
REVERT: C  104 ARG cc_start: 0.7472 (mtm110) cc_final: 0.6778 (mmm160)
  outliers start: 15
  outliers final: 6
  residues processed: 83
  average time/residue: 0.4512
  time to fit residues: 39.2843
Evaluate side-chains
  81 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0470
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.5678

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.179789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.137259 restraints weight = 6635.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.94
r_work: 0.3207 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6172  Z= 0.111
  Angle     :  0.512  12.451   8380  Z= 0.259
  Chirality :  0.041   0.144    922
  Planarity :  0.004   0.050   1027
  Dihedral  :  7.355  81.275   1016
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 28.21 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.32), residues: 725
  helix:  1.90 (0.30), residues: 315
  sheet:  0.39 (0.41), residues: 152
  loop : -1.16 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 334 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.009   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 ( 6169)
  covalent geometry    : angle       0.51170 /  0.26 ( 8373)
  SS BOND              : bond        0.00204 /  0.10 (    2)
  SS BOND              : angle       0.81303 /  0.46 (    4)
  hydrogen bonds       : bond        0.03474 /  2.28 (  320)
  hydrogen bonds       : angle       3.95275 /  2.77 (  915)
  link_BETA1-3         : bond        0.00341 /  0.18 (    1)
  link_BETA1-3         : angle       0.81411 /  0.48 (    3)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7056 (mp)
REVERT: A   49 PHE cc_start: 0.7698 (t80) cc_final: 0.7200 (t80)
REVERT: A  139 ASN cc_start: 0.7688 (t0) cc_final: 0.7373 (m-40)
REVERT: A  284 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6482 (ttpt)
REVERT: C   71 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7029 (tpp80)
  outliers start: 9
  outliers final: 6
  residues processed: 80
  average time/residue: 0.4180
  time to fit residues: 35.1929
Evaluate side-chains
  83 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   82 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 22 optimal weight:    0.6980
   chunk 52 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.179260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.136653 restraints weight = 6625.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.93
r_work: 0.3177 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6172  Z= 0.119
  Angle     :  0.513  12.478   8380  Z= 0.260
  Chirality :  0.041   0.144    922
  Planarity :  0.004   0.050   1027
  Dihedral  :  7.348  81.203   1016
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 26.78 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.32), residues: 725
  helix:  1.86 (0.30), residues: 315
  sheet:  0.36 (0.41), residues: 152
  loop : -1.17 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 334 
 TYR   0.016   0.001   TYR A 414 
 PHE   0.010   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 6169)
  covalent geometry    : angle       0.51281 /  0.26 ( 8373)
  SS BOND              : bond        0.00187 /  0.09 (    2)
  SS BOND              : angle       0.87811 /  0.50 (    4)
  hydrogen bonds       : bond        0.03555 /  2.33 (  320)
  hydrogen bonds       : angle       3.98371 /  2.80 (  915)
  link_BETA1-3         : bond        0.00343 /  0.18 (    1)
  link_BETA1-3         : angle       0.82052 /  0.48 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1708.01 seconds
wall clock time: 29 minutes 51.05 seconds (1791.05 seconds total)