Starting phenix.real_space_refine
on Wed Sep 17 03:43:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jdr_61397/09_2025/9jdr_61397.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jdr_61397/09_2025/9jdr_61397.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jdr_61397/09_2025/9jdr_61397.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jdr_61397/09_2025/9jdr_61397.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jdr_61397/09_2025/9jdr_61397.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jdr_61397/09_2025/9jdr_61397.map"
  }
  resolution = 3.5
  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=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2264      2.51       5
     N     532      2.21       5
     O     555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3371
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3371
          Classifications: {'peptide': 422}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 405}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 0.94, per 1000 atoms: 0.28
  Number of scatterers: 3371
  At special positions: 0
  Unit cell: (75.9, 64.9, 83.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     555      8.00
     N     532      7.00
     C    2264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 126.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 0 sheets defined
      70.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 52
    Processing helix  chain 'A' and resid 53 through 58
      removed outlier: 3.638A  pdb=" N   ASN A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 75
      removed outlier: 3.937A  pdb=" N   THR A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
      removed outlier: 3.850A  pdb=" N   GLN A  73 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 93
      removed outlier: 3.598A  pdb=" N   TYR A  86 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY A  87 " --> pdb=" O   GLN A  83 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A  89 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLY A  90 " --> pdb=" O   TYR A  86 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   SER A  91 " --> pdb=" O   GLY A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 109
      removed outlier: 3.623A  pdb=" N   LEU A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLU A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.741A  pdb=" N   VAL A 125 " --> pdb=" O   GLN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 3.649A  pdb=" N   GLY A 138 " --> pdb=" O   TRP A 134 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA A 140 " --> pdb=" O   ALA A 136 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   PHE A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 3.653A  pdb=" N   PHE A 148 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 157
    Processing helix  chain 'A' and resid 170 through 178
      removed outlier: 3.668A  pdb=" N   TYR A 175 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ILE A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   PHE A 177 " --> pdb=" O   TRP A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 3.609A  pdb=" N   THR A 183 " --> pdb=" O   CYS A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 203
      removed outlier: 3.513A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU A 201 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 218
      removed outlier: 4.810A  pdb=" N   ALA A 212 " --> pdb=" O   ALA A 208 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA A 214 " --> pdb=" O   TYR A 210 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   HIS A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
    Processing helix  chain 'A' and resid 240 through 246
      removed outlier: 3.619A  pdb=" N   PHE A 246 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 257
      removed outlier: 3.767A  pdb=" N   GLU A 254 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   HIS A 257 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 269
      removed outlier: 4.307A  pdb=" N   TYR A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 275 through 285
      removed outlier: 4.113A  pdb=" N   ILE A 281 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      Proline residue:  A 282  - end of helix
      removed outlier: 3.576A  pdb=" N   ALA A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 292
      removed outlier: 3.700A  pdb=" N   ALA A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 3.712A  pdb=" N   LEU A 296 " --> pdb=" O   ASP A 293 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASP A 297 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 293 through 297'
    Processing helix  chain 'A' and resid 308 through 329
      removed outlier: 3.740A  pdb=" N   ASP A 312 " --> pdb=" O   ASN A 308 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ALA A 314 " --> pdb=" O   TRP A 310 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   MET A 318 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   HIS A 321 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A 325 " --> pdb=" O   HIS A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 341
      removed outlier: 3.564A  pdb=" N   VAL A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 341 " --> pdb=" O   TRP A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 355
    Processing helix  chain 'A' and resid 356 through 365
      removed outlier: 3.951A  pdb=" N   VAL A 360 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.589A  pdb=" N   ILE A 369 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 384
      removed outlier: 3.793A  pdb=" N   VAL A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLY A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 389
    Processing helix  chain 'A' and resid 391 through 400
      removed outlier: 3.521A  pdb=" N   ALA A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   HIS A 397 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   MET A 398 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 427
      removed outlier: 3.984A  pdb=" N   LEU A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 436
      removed outlier: 3.909A  pdb=" N   VAL A 432 " --> pdb=" O   ASN A 428 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   VAL A 433 " --> pdb=" O   ALA A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 459
      removed outlier: 3.579A  pdb=" N   SER A 447 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   PHE A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLN A 454 " --> pdb=" O   ASN A 450 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A 455 " --> pdb=" O   PHE A 451 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY A 459 " --> pdb=" O   VAL A 455 " (cutoff:3.500A)

    98 hydrogen bonds defined for protein.
    288 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: 0.35

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 527
        1.32 -     1.44: 1086
        1.44 -     1.57: 1841
        1.57 -     1.69: 1
        1.69 -     1.82: 31
  Bond restraints: 3486
  Sorted by residual:
  bond pdb=" CA  GLN A 220 "
       pdb=" CB  GLN A 220 "
    ideal  model  delta    sigma   weight residual
    1.530  1.460  0.069 1.55e-02 4.16e+03 2.00e+01
  bond pdb=" CA  HIS A 257 "
       pdb=" C   HIS A 257 "
    ideal  model  delta    sigma   weight residual
    1.522  1.585 -0.063 1.43e-02 4.89e+03 1.94e+01
  bond pdb=" CA  GLN A  62 "
       pdb=" C   GLN A  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.459  0.061 1.40e-02 5.10e+03 1.88e+01
  bond pdb=" C   GLN A  62 "
       pdb=" N   VAL A  63 "
    ideal  model  delta    sigma   weight residual
    1.334  1.291  0.043 1.09e-02 8.42e+03 1.59e+01
  bond pdb=" CA  LYS A 116 "
       pdb=" C   LYS A 116 "
    ideal  model  delta    sigma   weight residual
    1.523  1.472  0.051 1.34e-02 5.57e+03 1.44e+01
  ... (remaining 3481 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.35: 4699
        4.35 -     8.70: 51
        8.70 -    13.05: 3
       13.05 -    17.40: 3
       17.40 -    21.75: 2
  Bond angle restraints: 4758
  Sorted by residual:
  angle pdb=" N   GLN A 220 "
        pdb=" CA  GLN A 220 "
        pdb=" C   GLN A 220 "
      ideal   model   delta    sigma   weight residual
     110.32   88.57   21.75 1.59e+00 3.96e-01 1.87e+02
  angle pdb=" C   PHE A 115 "
        pdb=" CA  PHE A 115 "
        pdb=" CB  PHE A 115 "
      ideal   model   delta    sigma   weight residual
     109.35   92.11   17.24 1.98e+00 2.55e-01 7.58e+01
  angle pdb=" N   ALA A 221 "
        pdb=" CA  ALA A 221 "
        pdb=" C   ALA A 221 "
      ideal   model   delta    sigma   weight residual
     111.34   98.94   12.40 1.49e+00 4.50e-01 6.93e+01
  angle pdb=" N   LYS A 116 "
        pdb=" CA  LYS A 116 "
        pdb=" C   LYS A 116 "
      ideal   model   delta    sigma   weight residual
     110.80   93.20   17.60 2.13e+00 2.20e-01 6.83e+01
  angle pdb=" N   PHE A 115 "
        pdb=" CA  PHE A 115 "
        pdb=" C   PHE A 115 "
      ideal   model   delta    sigma   weight residual
     109.24  122.13  -12.89 1.67e+00 3.59e-01 5.96e+01
  ... (remaining 4753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.82: 1776
       13.82 -    27.64: 142
       27.64 -    41.46: 26
       41.46 -    55.28: 3
       55.28 -    69.09: 2
  Dihedral angle restraints: 1949
    sinusoidal: 718
      harmonic: 1231
  Sorted by residual:
  dihedral pdb=" N   GLN A 220 "
           pdb=" C   GLN A 220 "
           pdb=" CA  GLN A 220 "
           pdb=" CB  GLN A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  105.69   17.11     0      2.50e+00 1.60e-01 4.68e+01
  dihedral pdb=" C   PHE A 115 "
           pdb=" N   PHE A 115 "
           pdb=" CA  PHE A 115 "
           pdb=" CB  PHE A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.23  -16.37     0      2.50e+00 1.60e-01 4.29e+01
  dihedral pdb=" N   LYS A 116 "
           pdb=" C   LYS A 116 "
           pdb=" CA  LYS A 116 "
           pdb=" CB  LYS A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.35   15.45     0      2.50e+00 1.60e-01 3.82e+01
  ... (remaining 1946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 368
       0.057 -    0.114: 137
       0.114 -    0.171: 17
       0.171 -    0.228: 4
       0.228 -    0.285: 3
  Chirality restraints: 529
  Sorted by residual:
  chirality pdb=" CA  ASN A 117 "
            pdb=" N   ASN A 117 "
            pdb=" C   ASN A 117 "
            pdb=" CB  ASN A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  LYS A 116 "
            pdb=" N   LYS A 116 "
            pdb=" C   LYS A 116 "
            pdb=" CB  LYS A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  GLN A 220 "
            pdb=" N   GLN A 220 "
            pdb=" C   GLN A 220 "
            pdb=" CB  GLN A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 526 not shown)

  Planarity restraints: 573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 117 "   -0.021 2.00e-02 2.50e+03   4.15e-02 1.72e+01
        pdb=" C   ASN A 117 "    0.072 2.00e-02 2.50e+03
        pdb=" O   ASN A 117 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   HIS A 118 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 374 "    0.067 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO A 375 "   -0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 248 "    0.019 2.00e-02 2.50e+03   3.79e-02 1.43e+01
        pdb=" C   GLY A 248 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   GLY A 248 "    0.025 2.00e-02 2.50e+03
        pdb=" N   HIS A 249 "    0.022 2.00e-02 2.50e+03
  ... (remaining 570 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 845
        2.78 -     3.31: 2866
        3.31 -     3.84: 5249
        3.84 -     4.37: 6123
        4.37 -     4.90: 10226
  Nonbonded interactions: 25309
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 401 "
            pdb=" OH  TYR A 425 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG  SER A 227 "
            pdb=" OD2 ASP A 293 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG  SER A 215 "
            pdb=" O   ALA A 286 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" N   GLN A 220 "
            pdb=" O   GLN A 220 "
     model   vdw
     2.337 2.496
  nonbonded pdb=" O   TYR A 193 "
            pdb=" OG  SER A 197 "
     model   vdw
     2.355 3.040
  ... (remaining 25304 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.500
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
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   0.069   3486  Z= 0.412
  Angle     :  1.249  21.752   4758  Z= 0.722
  Chirality :  0.060   0.285    529
  Planarity :  0.010   0.101    573
  Dihedral  : 11.080  69.094   1161
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.00 %
    Favored  : 95.71 %
  Cbeta Deviations :  1.27 %
  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: -6.89 (0.23), residues: 418
  helix: -4.63 (0.12), residues: 275
  sheet:  None (None), residues: 0
  loop : -4.02 (0.41), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 171 
 TYR   0.026   0.003   TYR A 175 
 PHE   0.021   0.003   PHE A 335 
 TRP   0.032   0.003   TRP A 196 
 HIS   0.007   0.002   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00815 ( 3486)
  covalent geometry    : angle       1.24870 ( 4758)
  hydrogen bonds       : bond        0.35368 (   98)
  hydrogen bonds       : angle      10.85307 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   85 PHE cc_start: 0.8316 (t80) cc_final: 0.8035 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.0719
  time to fit residues: 6.7958
Evaluate side-chains
  46 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
A 153 GLN
A 377 ASN
A 428 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.203123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.175946 restraints weight = 4724.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.180590 restraints weight = 2621.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.183604 restraints weight = 1776.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.185514 restraints weight = 1369.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.186876 restraints weight = 1157.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3486  Z= 0.125
  Angle     :  0.610   5.410   4758  Z= 0.327
  Chirality :  0.043   0.268    529
  Planarity :  0.007   0.076    573
  Dihedral  :  6.399  22.266    454
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.86 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -5.60 (0.30), residues: 418
  helix: -3.73 (0.19), residues: 273
  sheet:  None (None), residues: 0
  loop : -3.29 (0.49), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 105 
 TYR   0.010   0.001   TYR A 465 
 PHE   0.020   0.001   PHE A 177 
 TRP   0.024   0.002   TRP A 445 
 HIS   0.002   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3486)
  covalent geometry    : angle       0.61023 ( 4758)
  hydrogen bonds       : bond        0.04136 (   98)
  hydrogen bonds       : angle       5.94023 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  271 MET cc_start: 0.5495 (ttt) cc_final: 0.4893 (mtt)
  outliers start: 5
  outliers final: 1
  residues processed: 49
  average time/residue: 0.0756
  time to fit residues: 4.4894
Evaluate side-chains
  45 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  437 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0980
   overall best weight:    0.4338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.205226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.177458 restraints weight = 4662.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.182201 restraints weight = 2577.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.185406 restraints weight = 1747.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.187413 restraints weight = 1345.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.188930 restraints weight = 1131.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3486  Z= 0.110
  Angle     :  0.554   6.426   4758  Z= 0.288
  Chirality :  0.041   0.145    529
  Planarity :  0.006   0.070    573
  Dihedral  :  5.679  22.971    453
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.00 %
    Favored  : 88.00 %
  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: -4.85 (0.33), residues: 418
  helix: -3.06 (0.23), residues: 282
  sheet:  None (None), residues: 0
  loop : -3.14 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 352 
 TYR   0.010   0.001   TYR A 465 
 PHE   0.013   0.001   PHE A 177 
 TRP   0.015   0.001   TRP A 445 
 HIS   0.001   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3486)
  covalent geometry    : angle       0.55417 ( 4758)
  hydrogen bonds       : bond        0.03214 (   98)
  hydrogen bonds       : angle       5.24198 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  148 PHE cc_start: 0.8005 (m-80) cc_final: 0.7578 (m-80)
REVERT: A  271 MET cc_start: 0.5253 (ttt) cc_final: 0.4653 (mtt)
  outliers start: 7
  outliers final: 2
  residues processed: 47
  average time/residue: 0.0623
  time to fit residues: 3.6725
Evaluate side-chains
  40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  437 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0670
   chunk 33 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.202742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.175574 restraints weight = 4606.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.180128 restraints weight = 2556.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.183185 restraints weight = 1738.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.185051 restraints weight = 1345.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.186490 restraints weight = 1142.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3486  Z= 0.126
  Angle     :  0.551   6.126   4758  Z= 0.286
  Chirality :  0.042   0.149    529
  Planarity :  0.005   0.066    573
  Dihedral  :  5.523  23.261    453
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 11.71 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.36 (0.35), residues: 418
  helix: -2.68 (0.25), residues: 283
  sheet:  None (None), residues: 0
  loop : -2.97 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 105 
 TYR   0.010   0.001   TYR A 465 
 PHE   0.014   0.001   PHE A 177 
 TRP   0.016   0.001   TRP A 421 
 HIS   0.002   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3486)
  covalent geometry    : angle       0.55125 ( 4758)
  hydrogen bonds       : bond        0.03113 (   98)
  hydrogen bonds       : angle       5.07123 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   62 GLN cc_start: 0.7286 (pm20) cc_final: 0.7059 (pm20)
REVERT: A  271 MET cc_start: 0.5320 (ttt) cc_final: 0.4671 (mtt)
REVERT: A  335 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6212 (p90)
REVERT: A  352 ARG cc_start: 0.5953 (ttm110) cc_final: 0.5458 (mtp85)
  outliers start: 9
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0609
  time to fit residues: 4.0600
Evaluate side-chains
  50 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0970
   chunk 24 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.1980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.204632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.176864 restraints weight = 4665.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.181613 restraints weight = 2602.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.184720 restraints weight = 1776.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.186828 restraints weight = 1378.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.188046 restraints weight = 1159.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3486  Z= 0.103
  Angle     :  0.519   5.631   4758  Z= 0.268
  Chirality :  0.041   0.131    529
  Planarity :  0.005   0.060    573
  Dihedral  :  5.254  23.971    453
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.00 %
    Favored  : 85.43 %
  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: -3.88 (0.37), residues: 418
  helix: -2.35 (0.27), residues: 281
  sheet:  None (None), residues: 0
  loop : -2.67 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 105 
 TYR   0.014   0.001   TYR A 401 
 PHE   0.011   0.001   PHE A 177 
 TRP   0.012   0.001   TRP A 445 
 HIS   0.002   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3486)
  covalent geometry    : angle       0.51876 ( 4758)
  hydrogen bonds       : bond        0.02703 (   98)
  hydrogen bonds       : angle       4.82158 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   62 GLN cc_start: 0.7300 (pm20) cc_final: 0.7060 (pm20)
REVERT: A  148 PHE cc_start: 0.8043 (m-80) cc_final: 0.7573 (m-80)
REVERT: A  237 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6916 (m)
REVERT: A  335 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.6204 (p90)
REVERT: A  352 ARG cc_start: 0.5633 (ttm110) cc_final: 0.5219 (mtp180)
  outliers start: 9
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0584
  time to fit residues: 3.8904
Evaluate side-chains
  53 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0170
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0040
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.4230

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** 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 = 0.4343 r_free = 0.4343 target = 0.205057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.177495 restraints weight = 4624.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.182164 restraints weight = 2586.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.185318 restraints weight = 1773.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.187201 restraints weight = 1375.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.188739 restraints weight = 1169.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3486  Z= 0.102
  Angle     :  0.514   6.022   4758  Z= 0.264
  Chirality :  0.041   0.148    529
  Planarity :  0.005   0.063    573
  Dihedral  :  5.137  23.625    453
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.14 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.67 (0.37), residues: 418
  helix: -2.15 (0.27), residues: 284
  sheet:  None (None), residues: 0
  loop : -2.70 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 105 
 TYR   0.016   0.001   TYR A  86 
 PHE   0.010   0.001   PHE A 177 
 TRP   0.011   0.001   TRP A 445 
 HIS   0.002   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3486)
  covalent geometry    : angle       0.51437 ( 4758)
  hydrogen bonds       : bond        0.02625 (   98)
  hydrogen bonds       : angle       4.70677 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  148 PHE cc_start: 0.8049 (m-80) cc_final: 0.7553 (m-80)
REVERT: A  237 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6984 (m)
REVERT: A  335 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.6208 (p90)
REVERT: A  352 ARG cc_start: 0.5626 (ttm110) cc_final: 0.5183 (mtt-85)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 0.0640
  time to fit residues: 3.9960
Evaluate side-chains
  49 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.0030
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.2980
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 ASN ** 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 = 0.4325 r_free = 0.4325 target = 0.203377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.175531 restraints weight = 4756.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.180292 restraints weight = 2622.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.183440 restraints weight = 1780.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.185578 restraints weight = 1372.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.186932 restraints weight = 1152.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3486  Z= 0.112
  Angle     :  0.517   5.718   4758  Z= 0.266
  Chirality :  0.041   0.150    529
  Planarity :  0.005   0.063    573
  Dihedral  :  5.114  23.710    453
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.14 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.46 (0.37), residues: 418
  helix: -2.00 (0.28), residues: 284
  sheet:  None (None), residues: 0
  loop : -2.62 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 105 
 TYR   0.009   0.001   TYR A 465 
 PHE   0.011   0.001   PHE A 177 
 TRP   0.011   0.001   TRP A 445 
 HIS   0.002   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3486)
  covalent geometry    : angle       0.51710 ( 4758)
  hydrogen bonds       : bond        0.02682 (   98)
  hydrogen bonds       : angle       4.63762 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  148 PHE cc_start: 0.8058 (m-80) cc_final: 0.7563 (m-80)
REVERT: A  271 MET cc_start: 0.5164 (ttt) cc_final: 0.4642 (tpp)
REVERT: A  335 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6218 (p90)
  outliers start: 8
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0662
  time to fit residues: 4.0186
Evaluate side-chains
  47 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0770
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.4938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.203532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.175578 restraints weight = 4735.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.180344 restraints weight = 2614.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.183483 restraints weight = 1774.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.185624 restraints weight = 1370.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.187151 restraints weight = 1149.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3486  Z= 0.110
  Angle     :  0.515   5.732   4758  Z= 0.265
  Chirality :  0.041   0.142    529
  Planarity :  0.005   0.062    573
  Dihedral  :  5.105  23.947    453
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.43 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.28 (0.37), residues: 418
  helix: -1.87 (0.28), residues: 283
  sheet:  None (None), residues: 0
  loop : -2.51 (0.50), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 105 
 TYR   0.010   0.001   TYR A 401 
 PHE   0.010   0.001   PHE A 177 
 TRP   0.010   0.001   TRP A 421 
 HIS   0.002   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3486)
  covalent geometry    : angle       0.51455 ( 4758)
  hydrogen bonds       : bond        0.02678 (   98)
  hydrogen bonds       : angle       4.60383 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  148 PHE cc_start: 0.8044 (m-80) cc_final: 0.7561 (m-80)
REVERT: A  271 MET cc_start: 0.5209 (ttt) cc_final: 0.4713 (tpp)
REVERT: A  335 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6212 (p90)
  outliers start: 10
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0672
  time to fit residues: 3.9680
Evaluate side-chains
  46 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.5980
   chunk 18 optimal weight:    0.4980
   chunk 41 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.203315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.175381 restraints weight = 4684.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.180108 restraints weight = 2625.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.183238 restraints weight = 1792.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.185172 restraints weight = 1388.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.186735 restraints weight = 1182.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3486  Z= 0.117
  Angle     :  0.529   5.313   4758  Z= 0.272
  Chirality :  0.042   0.149    529
  Planarity :  0.005   0.063    573
  Dihedral  :  5.139  23.999    453
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.71 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.18 (0.38), residues: 418
  helix: -1.78 (0.29), residues: 286
  sheet:  None (None), residues: 0
  loop : -2.51 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 105 
 TYR   0.010   0.001   TYR A 465 
 PHE   0.011   0.001   PHE A 177 
 TRP   0.011   0.001   TRP A 421 
 HIS   0.002   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3486)
  covalent geometry    : angle       0.52918 ( 4758)
  hydrogen bonds       : bond        0.02742 (   98)
  hydrogen bonds       : angle       4.66125 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  148 PHE cc_start: 0.8046 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  271 MET cc_start: 0.5180 (ttt) cc_final: 0.4686 (tpp)
REVERT: A  335 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.6290 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0739
  time to fit residues: 4.0800
Evaluate side-chains
  45 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0770
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0000
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.3942

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

Flipped N/Q/H residues before XYZ refinement:
A 192 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.205037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.176744 restraints weight = 4663.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.181559 restraints weight = 2603.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.184764 restraints weight = 1763.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.186889 restraints weight = 1368.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.188196 restraints weight = 1149.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3486  Z= 0.101
  Angle     :  0.521   5.573   4758  Z= 0.266
  Chirality :  0.041   0.146    529
  Planarity :  0.005   0.061    573
  Dihedral  :  4.976  23.854    453
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.00 %
    Favored  : 84.00 %
  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: -2.99 (0.38), residues: 418
  helix: -1.64 (0.29), residues: 281
  sheet:  None (None), residues: 0
  loop : -2.41 (0.49), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 105 
 TYR   0.012   0.001   TYR A 401 
 PHE   0.010   0.001   PHE A 177 
 TRP   0.017   0.001   TRP A 421 
 HIS   0.001   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3486)
  covalent geometry    : angle       0.52073 ( 4758)
  hydrogen bonds       : bond        0.02554 (   98)
  hydrogen bonds       : angle       4.50138 (  288)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   62 GLN cc_start: 0.7227 (pm20) cc_final: 0.6949 (pm20)
REVERT: A  148 PHE cc_start: 0.8037 (m-80) cc_final: 0.7559 (m-80)
REVERT: A  271 MET cc_start: 0.5141 (ttt) cc_final: 0.4679 (tpp)
REVERT: A  335 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.6293 (p90)
  outliers start: 7
  outliers final: 5
  residues processed: 46
  average time/residue: 0.0765
  time to fit residues: 4.3503
Evaluate side-chains
  48 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0270
   chunk 4 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0010
   chunk 32 optimal weight:    0.3980
   chunk 15 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.3644

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.211566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.182440 restraints weight = 4421.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.187037 restraints weight = 2553.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.189974 restraints weight = 1755.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.192277 restraints weight = 1370.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.193669 restraints weight = 1148.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3486  Z= 0.098
  Angle     :  0.510   5.381   4758  Z= 0.262
  Chirality :  0.041   0.150    529
  Planarity :  0.005   0.062    573
  Dihedral  :  4.868  23.524    453
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.00 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.81 (0.38), residues: 418
  helix: -1.56 (0.29), residues: 283
  sheet:  None (None), residues: 0
  loop : -2.21 (0.50), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 352 
 TYR   0.012   0.001   TYR A 401 
 PHE   0.010   0.001   PHE A 177 
 TRP   0.014   0.001   TRP A 421 
 HIS   0.001   0.000   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3486)
  covalent geometry    : angle       0.51032 ( 4758)
  hydrogen bonds       : bond        0.02459 (   98)
  hydrogen bonds       : angle       4.43586 (  288)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 783.23 seconds
wall clock time: 14 minutes 7.77 seconds (847.77 seconds total)