Starting phenix.real_space_refine
on Tue Mar  3 15:34:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xf2_33168/03_2026/7xf2_33168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xf2_33168/03_2026/7xf2_33168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xf2_33168/03_2026/7xf2_33168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xf2_33168/03_2026/7xf2_33168.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xf2_33168/03_2026/7xf2_33168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xf2_33168/03_2026/7xf2_33168.map"
  }
  resolution = 3.73
  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=   0.016 sd=   0.082
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      46      5.16       5
     C    4165      2.51       5
     N    1109      2.21       5
     O    1271      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6591
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3450
          Classifications: {'peptide': 440}
          Link IDs: {'PTRANS': 19, 'TRANS': 420}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3141
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 15, 'TRANS': 384}
          Chain breaks: 4
  Time building chain proxies: 1.36, per 1000 atoms: 0.21
  Number of scatterers: 6591
  At special positions: 0
  Unit cell: (96.48, 109.88, 88.44, 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      46     16.00
     O    1271      8.00
     N    1109      7.00
     C    4165      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: 0.47
  Conformation dependent library (CDL) restraints added in 171.0 milliseconds
  

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 4 sheets defined
      65.8% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 25
    Processing helix  chain 'A' and resid 76 through 85
    Processing helix  chain 'A' and resid 92 through 110
      removed outlier: 3.570A  pdb=" N   ASP A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   THR A 104 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU A 107 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 4.158A  pdb=" N   ASN A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 123 through 128'
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 164 through 179
      removed outlier: 3.868A  pdb=" N   ILE A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ALA A 169 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   THR A 172 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER A 177 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 200
    Processing helix  chain 'A' and resid 202 through 219
      removed outlier: 3.518A  pdb=" N   SER A 206 " --> pdb=" O   ASP A 202 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN A 215 " --> pdb=" O   ASN A 211 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL A 216 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 248
      removed outlier: 3.562A  pdb=" N   ALA A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 299
      removed outlier: 3.591A  pdb=" N   LEU A 282 " --> pdb=" O   CYS A 278 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 322
      removed outlier: 3.626A  pdb=" N   GLN A 314 " --> pdb=" O   LYS A 310 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   MET A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 349
      removed outlier: 3.682A  pdb=" N   MET A 349 " --> pdb=" O   MET A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 357
      removed outlier: 3.595A  pdb=" N   CYS A 356 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 382
      removed outlier: 4.161A  pdb=" N   LEU A 380 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 409
      removed outlier: 4.178A  pdb=" N   ALA A 393 " --> pdb=" O   GLU A 389 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 398 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 424
      removed outlier: 4.268A  pdb=" N   ALA A 421 " --> pdb=" O   ASP A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 466
      removed outlier: 4.189A  pdb=" N   LEU A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A 436 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL A 437 " --> pdb=" O   ILE A 433 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA A 442 " --> pdb=" O   ARG A 438 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   LYS A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE A 464 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 24
      removed outlier: 3.671A  pdb=" N   LEU B   7 " --> pdb=" O   ALA B   3 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TYR B  10 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL B  18 " --> pdb=" O   THR B  14 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA B  22 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 110
      removed outlier: 3.781A  pdb=" N   GLY B  87 " --> pdb=" O   VAL B  83 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLN B  88 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN B  91 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS B  93 " --> pdb=" O   GLU B  89 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE B 105 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 127
      removed outlier: 4.122A  pdb=" N   ASN B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 123 through 127'
    Processing helix  chain 'B' and resid 158 through 164
      removed outlier: 3.569A  pdb=" N   PHE B 162 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 180
      removed outlier: 4.221A  pdb=" N   VAL B 171 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS B 173 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLU B 176 " --> pdb=" O   THR B 172 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 188
    Processing helix  chain 'B' and resid 189 through 200
      removed outlier: 4.510A  pdb=" N   PHE B 193 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 219
      removed outlier: 4.469A  pdb=" N   SER B 205 " --> pdb=" O   MET B 201 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL B 216 " --> pdb=" O   MET B 212 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ILE B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LYS B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 254
      removed outlier: 3.547A  pdb=" N   VAL B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN B 245 " --> pdb=" O   LYS B 241 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP B 246 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 299
      removed outlier: 3.722A  pdb=" N   GLU B 269 " --> pdb=" O   MET B 265 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ALA B 274 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   PHE B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 322
    Processing helix  chain 'B' and resid 334 through 349
      removed outlier: 3.652A  pdb=" N   MET B 349 " --> pdb=" O   MET B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 357
      removed outlier: 4.243A  pdb=" N   ASN B 355 " --> pdb=" O   PRO B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 383
      removed outlier: 4.373A  pdb=" N   LYS B 383 " --> pdb=" O   PRO B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 409
      removed outlier: 3.837A  pdb=" N   HIS B 394 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   PHE B 395 " --> pdb=" O   SER B 391 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 466
      removed outlier: 3.712A  pdb=" N   VAL B 431 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ARG B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B 442 " --> pdb=" O   ARG B 438 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS B 449 " --> pdb=" O   SER B 445 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ARG B 463 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL B 465 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148
      removed outlier: 6.601A  pdb=" N   THR A 147 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   ARG A 332 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148
      removed outlier: 6.753A  pdb=" N   THR B 147 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)

    354 hydrogen bonds defined for protein.
    1050 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: 0.98

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2150
        1.34 -     1.46: 1428
        1.46 -     1.58: 3051
        1.58 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6703
  Sorted by residual:
  bond pdb=" CA  TYR A  46 "
       pdb=" CB  TYR A  46 "
    ideal  model  delta    sigma   weight residual
    1.526  1.490  0.036 1.76e-02 3.23e+03 4.26e+00
  bond pdb=" CG  ARG B 103 "
       pdb=" CD  ARG B 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.63e+00
  bond pdb=" CA  ASN B 424 "
       pdb=" CB  ASN B 424 "
    ideal  model  delta    sigma   weight residual
    1.539  1.483  0.056 4.88e-02 4.20e+02 1.33e+00
  bond pdb=" NE  ARG B 103 "
       pdb=" CZ  ARG B 103 "
    ideal  model  delta    sigma   weight residual
    1.326  1.338 -0.012 1.10e-02 8.26e+03 1.12e+00
  bond pdb=" CB  ARG B 103 "
       pdb=" CG  ARG B 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.58e-01
  ... (remaining 6698 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 8867
        1.91 -     3.81: 164
        3.81 -     5.72: 14
        5.72 -     7.62: 3
        7.62 -     9.53: 4
  Bond angle restraints: 9052
  Sorted by residual:
  angle pdb=" CA  LEU A  45 "
        pdb=" CB  LEU A  45 "
        pdb=" CG  LEU A  45 "
      ideal   model   delta    sigma   weight residual
     116.30  125.83   -9.53 3.50e+00 8.16e-02 7.41e+00
  angle pdb=" C   CYS B 418 "
        pdb=" N   LEU B 419 "
        pdb=" CA  LEU B 419 "
      ideal   model   delta    sigma   weight residual
     121.54  126.51   -4.97 1.91e+00 2.74e-01 6.76e+00
  angle pdb=" N   GLY A 252 "
        pdb=" CA  GLY A 252 "
        pdb=" C   GLY A 252 "
      ideal   model   delta    sigma   weight residual
     113.37  116.74   -3.37 1.34e+00 5.57e-01 6.31e+00
  angle pdb=" N   LEU B 425 "
        pdb=" CA  LEU B 425 "
        pdb=" C   LEU B 425 "
      ideal   model   delta    sigma   weight residual
     112.72  109.71    3.01 1.28e+00 6.10e-01 5.54e+00
  angle pdb=" CA  LEU B 434 "
        pdb=" CB  LEU B 434 "
        pdb=" CG  LEU B 434 "
      ideal   model   delta    sigma   weight residual
     116.30  124.47   -8.17 3.50e+00 8.16e-02 5.45e+00
  ... (remaining 9047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.02: 3638
       16.02 -    32.04: 388
       32.04 -    48.06: 83
       48.06 -    64.09: 15
       64.09 -    80.11: 7
  Dihedral angle restraints: 4131
    sinusoidal: 1651
      harmonic: 2480
  Sorted by residual:
  dihedral pdb=" CA  VAL A 251 "
           pdb=" C   VAL A 251 "
           pdb=" N   GLY A 252 "
           pdb=" CA  GLY A 252 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.05  -27.95     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  CYS B 256 "
           pdb=" C   CYS B 256 "
           pdb=" N   ARG B 257 "
           pdb=" CA  ARG B 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.13   23.87     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  GLN B 261 "
           pdb=" C   GLN B 261 "
           pdb=" N   LEU B 262 "
           pdb=" CA  LEU B 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.54   23.46     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 4128 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 547
       0.028 -    0.055: 331
       0.055 -    0.083: 113
       0.083 -    0.111: 41
       0.111 -    0.138: 10
  Chirality restraints: 1042
  Sorted by residual:
  chirality pdb=" CA  THR A 378 "
            pdb=" N   THR A 378 "
            pdb=" C   THR A 378 "
            pdb=" CB  THR A 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE A 131 "
            pdb=" N   ILE A 131 "
            pdb=" C   ILE A 131 "
            pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  ILE A 363 "
            pdb=" N   ILE A 363 "
            pdb=" C   ILE A 363 "
            pdb=" CB  ILE A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1039 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 257 "    0.053 5.00e-02 4.00e+02   8.04e-02 1.03e+01
        pdb=" N   PRO B 258 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO B 258 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 258 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 219 "    0.037 5.00e-02 4.00e+02   5.60e-02 5.02e+00
        pdb=" N   PRO A 220 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  49 "   -0.035 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO A  50 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A  50 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  50 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 202
        2.69 -     3.24: 7912
        3.24 -     3.79: 10301
        3.79 -     4.35: 13389
        4.35 -     4.90: 19871
  Nonbonded interactions: 51675
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 168 "
            pdb=" OG1 THR B 172 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" O   ALA A 169 "
            pdb=" OG1 THR A 172 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   ILE B 203 "
            pdb=" OG  SER B 206 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ALA B 304 "
            pdb=" OG1 THR B 307 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ARG A 174 "
            pdb=" OG  SER A 177 "
     model   vdw
     2.226 3.040
  ... (remaining 51670 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 38 or resid 80 through 116 or resid 122 through  \ 
360 or resid 373 through 409 or resid 418 through 466))
  selection = chain 'B'
}

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:             19.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.880
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
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      :  0.004   0.056   6703  Z= 0.187
  Angle     :  0.653   9.529   9052  Z= 0.357
  Chirality :  0.041   0.138   1042
  Planarity :  0.005   0.080   1159
  Dihedral  : 14.121  80.108   2507
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.36 %
    Favored  : 94.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.97 (0.22), residues: 824
  helix: -3.30 (0.16), residues: 486
  sheet: -4.06 (1.92), residues: 6
  loop : -3.06 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 103 
 TYR   0.016   0.002   TYR B 255 
 PHE   0.009   0.001   PHE B 358 
 TRP   0.008   0.001   TRP A 392 
 HIS   0.007   0.002   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6703)
  covalent geometry    : angle       0.65322 ( 9052)
  hydrogen bonds       : bond        0.30412 (  354)
  hydrogen bonds       : angle      10.00255 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 TYR cc_start: 0.8488 (m-10) cc_final: 0.8062 (m-80)
REVERT: A  345 MET cc_start: 0.8786 (tpp) cc_final: 0.8403 (tpp)
REVERT: A  436 LEU cc_start: 0.9350 (tp) cc_final: 0.9143 (tt)
REVERT: B   88 GLN cc_start: 0.7579 (tt0) cc_final: 0.7336 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1393
  time to fit residues: 15.0235
Evaluate side-chains
  57 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   30.0000
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
A 457 ASN
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 GLN
B 195 ASN
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.037331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.029365 restraints weight = 62517.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.030200 restraints weight = 38561.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.030780 restraints weight = 27385.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.031196 restraints weight = 21273.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.031469 restraints weight = 17618.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   6703  Z= 0.216
  Angle     :  0.745  10.238   9052  Z= 0.389
  Chirality :  0.042   0.144   1042
  Planarity :  0.006   0.057   1159
  Dihedral  :  5.345  28.366    900
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.99 %
    Favored  : 87.80 %
  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: -2.47 (0.27), residues: 824
  helix: -1.06 (0.21), residues: 492
  sheet: -3.70 (1.84), residues: 6
  loop : -2.42 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 103 
 TYR   0.027   0.002   TYR A 120 
 PHE   0.017   0.002   PHE B 179 
 TRP   0.009   0.002   TRP B 392 
 HIS   0.008   0.003   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 6703)
  covalent geometry    : angle       0.74508 ( 9052)
  hydrogen bonds       : bond        0.05588 (  354)
  hydrogen bonds       : angle       5.11906 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 MET cc_start: 0.9524 (mmp) cc_final: 0.9156 (mmm)
REVERT: A  212 MET cc_start: 0.9577 (mmp) cc_final: 0.9314 (tpp)
REVERT: A  265 MET cc_start: 0.8834 (tpp) cc_final: 0.8588 (mpp)
REVERT: A  283 MET cc_start: 0.9737 (tpp) cc_final: 0.9491 (mmm)
REVERT: A  345 MET cc_start: 0.9550 (tpp) cc_final: 0.9000 (tpp)
REVERT: A  430 TYR cc_start: 0.9265 (p90) cc_final: 0.9044 (p90)
REVERT: A  436 LEU cc_start: 0.9862 (tp) cc_final: 0.9635 (tt)
REVERT: A  457 ASN cc_start: 0.9783 (OUTLIER) cc_final: 0.9385 (t0)
REVERT: B   88 GLN cc_start: 0.8430 (tt0) cc_final: 0.8198 (tt0)
REVERT: B  175 MET cc_start: 0.9119 (tpp) cc_final: 0.8866 (tpp)
REVERT: B  283 MET cc_start: 0.9646 (tpp) cc_final: 0.9336 (mmm)
REVERT: B  297 TYR cc_start: 0.9102 (m-80) cc_final: 0.8490 (m-80)
REVERT: B  349 MET cc_start: 0.8844 (mmt) cc_final: 0.8623 (mmm)
REVERT: B  354 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (mmt)
  outliers start: 9
  outliers final: 2
  residues processed: 62
  average time/residue: 0.0912
  time to fit residues: 7.3331
Evaluate side-chains
  53 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 HIS
Chi-restraints excluded: chain A residue  457 ASN
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  354 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 73 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 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 = 0.3297 r_free = 0.3297 target = 0.043259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.036949 restraints weight = 67972.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.037909 restraints weight = 34747.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.038561 restraints weight = 21787.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.038997 restraints weight = 15361.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.039273 restraints weight = 11863.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6703  Z= 0.147
  Angle     :  0.647   9.626   9052  Z= 0.335
  Chirality :  0.039   0.132   1042
  Planarity :  0.005   0.056   1159
  Dihedral  :  5.034  26.438    900
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.14 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.29), residues: 824
  helix: -0.18 (0.22), residues: 501
  sheet: -3.73 (1.69), residues: 6
  loop : -2.20 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  85 
 TYR   0.010   0.002   TYR B 297 
 PHE   0.009   0.001   PHE A 409 
 TRP   0.007   0.001   TRP B 461 
 HIS   0.008   0.002   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6703)
  covalent geometry    : angle       0.64719 ( 9052)
  hydrogen bonds       : bond        0.04704 (  354)
  hydrogen bonds       : angle       4.51103 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 LYS cc_start: 0.9078 (tppt) cc_final: 0.8672 (tppt)
REVERT: A  103 ARG cc_start: 0.8465 (mtp180) cc_final: 0.7969 (mmm-85)
REVERT: A  162 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8857 (m-80)
REVERT: A  212 MET cc_start: 0.9540 (mmp) cc_final: 0.9328 (tpp)
REVERT: A  283 MET cc_start: 0.9664 (tpp) cc_final: 0.9380 (mmm)
REVERT: A  430 TYR cc_start: 0.8861 (p90) cc_final: 0.8627 (p90)
REVERT: B    1 MET cc_start: 0.6852 (ttt) cc_final: 0.6177 (ptt)
REVERT: B  175 MET cc_start: 0.9062 (tpp) cc_final: 0.8626 (tpp)
REVERT: B  283 MET cc_start: 0.9558 (tpp) cc_final: 0.9085 (mmm)
REVERT: B  297 TYR cc_start: 0.9063 (m-80) cc_final: 0.8519 (m-80)
REVERT: B  320 MET cc_start: 0.8701 (mmm) cc_final: 0.8494 (tpt)
REVERT: B  345 MET cc_start: 0.9414 (mmt) cc_final: 0.9003 (mmm)
REVERT: B  354 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8463 (mmt)
  outliers start: 13
  outliers final: 4
  residues processed: 65
  average time/residue: 0.1088
  time to fit residues: 9.0251
Evaluate side-chains
  52 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  354 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 4 optimal weight:    0.5980
   chunk 19 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 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 = 0.3154 r_free = 0.3154 target = 0.036753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.029097 restraints weight = 63581.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.029871 restraints weight = 40480.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.030408 restraints weight = 29221.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.030799 restraints weight = 22919.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.031069 restraints weight = 19107.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6703  Z= 0.148
  Angle     :  0.635   9.392   9052  Z= 0.322
  Chirality :  0.039   0.134   1042
  Planarity :  0.005   0.057   1159
  Dihedral  :  4.861  24.180    900
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.28 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.29), residues: 824
  helix:  0.14 (0.23), residues: 505
  sheet: -3.73 (1.54), residues: 6
  loop : -2.13 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  85 
 TYR   0.032   0.002   TYR B 255 
 PHE   0.010   0.001   PHE B 395 
 TRP   0.007   0.001   TRP B 461 
 HIS   0.007   0.002   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6703)
  covalent geometry    : angle       0.63502 ( 9052)
  hydrogen bonds       : bond        0.04106 (  354)
  hydrogen bonds       : angle       4.31844 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.8421 (mtp180) cc_final: 0.7876 (mtp180)
REVERT: A  106 MET cc_start: 0.9253 (mmm) cc_final: 0.9004 (mmm)
REVERT: A  212 MET cc_start: 0.9587 (mmp) cc_final: 0.9324 (tpp)
REVERT: A  221 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7584 (t0)
REVERT: A  283 MET cc_start: 0.9614 (tpp) cc_final: 0.9406 (mmm)
REVERT: A  289 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8734 (mmm-85)
REVERT: A  345 MET cc_start: 0.9472 (tpp) cc_final: 0.9051 (mmt)
REVERT: A  349 MET cc_start: 0.8986 (mmt) cc_final: 0.8622 (mmm)
REVERT: B    1 MET cc_start: 0.7060 (ttt) cc_final: 0.6508 (ptt)
REVERT: B   85 ARG cc_start: 0.8644 (tpt170) cc_final: 0.8396 (tpt170)
REVERT: B  175 MET cc_start: 0.9302 (tpp) cc_final: 0.8889 (tpp)
REVERT: B  283 MET cc_start: 0.9589 (tpp) cc_final: 0.9384 (mmm)
REVERT: B  297 TYR cc_start: 0.9230 (m-80) cc_final: 0.8604 (m-80)
REVERT: B  345 MET cc_start: 0.9306 (mmt) cc_final: 0.8975 (mmm)
REVERT: B  354 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8505 (mmt)
  outliers start: 14
  outliers final: 6
  residues processed: 57
  average time/residue: 0.1024
  time to fit residues: 7.5674
Evaluate side-chains
  52 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  354 MET
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0980
   chunk 80 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 69 optimal weight:   20.0000
   chunk 65 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 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 = 0.3301 r_free = 0.3301 target = 0.042938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.036608 restraints weight = 69698.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.037568 restraints weight = 35922.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.038201 restraints weight = 22336.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.038623 restraints weight = 15778.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.038919 restraints weight = 12272.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6703  Z= 0.121
  Angle     :  0.589   9.532   9052  Z= 0.298
  Chirality :  0.038   0.138   1042
  Planarity :  0.005   0.066   1159
  Dihedral  :  4.689  23.229    900
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.82 %
    Favored  : 81.64 %
  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: -0.80 (0.29), residues: 824
  helix:  0.37 (0.23), residues: 509
  sheet: -3.40 (1.45), residues: 6
  loop : -1.99 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 289 
 TYR   0.009   0.001   TYR B 255 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.007   0.001   TRP B 461 
 HIS   0.008   0.002   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6703)
  covalent geometry    : angle       0.58939 ( 9052)
  hydrogen bonds       : bond        0.03771 (  354)
  hydrogen bonds       : angle       4.15022 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.8328 (mtp180) cc_final: 0.7839 (mmm-85)
REVERT: A  162 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8866 (m-80)
REVERT: A  190 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8121 (p90)
REVERT: A  212 MET cc_start: 0.9557 (mmp) cc_final: 0.9312 (tpp)
REVERT: A  221 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7253 (t0)
REVERT: A  283 MET cc_start: 0.9629 (tpp) cc_final: 0.9401 (mmm)
REVERT: A  345 MET cc_start: 0.9445 (tpp) cc_final: 0.8743 (tpp)
REVERT: A  349 MET cc_start: 0.8956 (mmt) cc_final: 0.8001 (mmm)
REVERT: B    1 MET cc_start: 0.6429 (ttt) cc_final: 0.6058 (ptt)
REVERT: B   85 ARG cc_start: 0.8686 (tpt170) cc_final: 0.8354 (tpt170)
REVERT: B  134 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.8921 (mtp)
REVERT: B  175 MET cc_start: 0.9238 (tpp) cc_final: 0.8834 (tpp)
REVERT: B  283 MET cc_start: 0.9552 (tpp) cc_final: 0.9332 (mmm)
REVERT: B  297 TYR cc_start: 0.9234 (m-10) cc_final: 0.8610 (m-80)
REVERT: B  345 MET cc_start: 0.9285 (mmt) cc_final: 0.8999 (mmm)
REVERT: B  354 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8417 (mmt)
  outliers start: 19
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0841
  time to fit residues: 7.0247
Evaluate side-chains
  54 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  354 MET
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 64 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0980
   chunk 18 optimal weight:    0.1980
   overall best weight:    3.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 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 = 0.3162 r_free = 0.3162 target = 0.036671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.029066 restraints weight = 64589.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.029826 restraints weight = 40840.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.030379 restraints weight = 29342.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.030768 restraints weight = 22929.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.031036 restraints weight = 19045.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.4435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6703  Z= 0.129
  Angle     :  0.610  10.244   9052  Z= 0.304
  Chirality :  0.039   0.148   1042
  Planarity :  0.005   0.063   1159
  Dihedral  :  4.633  21.863    900
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.10 %
    Favored  : 80.03 %
  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: -0.69 (0.29), residues: 824
  helix:  0.46 (0.23), residues: 510
  sheet: -3.44 (1.34), residues: 6
  loop : -1.94 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 438 
 TYR   0.011   0.001   TYR A  72 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.008   0.001   TRP B 461 
 HIS   0.007   0.002   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6703)
  covalent geometry    : angle       0.61036 ( 9052)
  hydrogen bonds       : bond        0.03708 (  354)
  hydrogen bonds       : angle       4.13447 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8935 (m-80)
REVERT: A  190 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8221 (p90)
REVERT: A  212 MET cc_start: 0.9566 (mmp) cc_final: 0.9288 (tpp)
REVERT: A  221 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7619 (t0)
REVERT: A  345 MET cc_start: 0.9490 (tpp) cc_final: 0.8506 (tpp)
REVERT: B    1 MET cc_start: 0.6824 (ttt) cc_final: 0.6395 (ptt)
REVERT: B   85 ARG cc_start: 0.8697 (tpt170) cc_final: 0.8399 (tpt170)
REVERT: B  134 MET cc_start: 0.9511 (ttp) cc_final: 0.8768 (mtp)
REVERT: B  138 THR cc_start: 0.9614 (OUTLIER) cc_final: 0.9052 (p)
REVERT: B  175 MET cc_start: 0.9361 (tpp) cc_final: 0.8885 (tpp)
REVERT: B  178 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9073 (mm)
REVERT: B  283 MET cc_start: 0.9596 (tpp) cc_final: 0.9392 (mmm)
REVERT: B  345 MET cc_start: 0.9304 (mmt) cc_final: 0.9062 (mmm)
  outliers start: 14
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0928
  time to fit residues: 6.9143
Evaluate side-chains
  54 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0870
   chunk 56 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   chunk 54 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.036818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.029164 restraints weight = 65506.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.029949 restraints weight = 41157.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.030510 restraints weight = 29569.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.030910 restraints weight = 23063.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.031170 restraints weight = 19186.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.4629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6703  Z= 0.127
  Angle     :  0.611   9.822   9052  Z= 0.304
  Chirality :  0.039   0.138   1042
  Planarity :  0.005   0.070   1159
  Dihedral  :  4.577  22.225    900
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.44 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.29), residues: 824
  helix:  0.63 (0.23), residues: 508
  sheet: -3.21 (1.40), residues: 6
  loop : -1.92 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 438 
 TYR   0.008   0.001   TYR B 255 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.008   0.001   TRP B 461 
 HIS   0.006   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6703)
  covalent geometry    : angle       0.61094 ( 9052)
  hydrogen bonds       : bond        0.03681 (  354)
  hydrogen bonds       : angle       4.10872 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8754 (m-10)
REVERT: A  190 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8287 (p90)
REVERT: A  212 MET cc_start: 0.9565 (mmp) cc_final: 0.9287 (tpp)
REVERT: A  221 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7688 (t0)
REVERT: A  345 MET cc_start: 0.9458 (tpp) cc_final: 0.8528 (tpp)
REVERT: B    1 MET cc_start: 0.6833 (ttt) cc_final: 0.6427 (ptt)
REVERT: B   85 ARG cc_start: 0.8682 (tpt170) cc_final: 0.8421 (tpt170)
REVERT: B  106 MET cc_start: 0.9333 (mmm) cc_final: 0.9049 (mmm)
REVERT: B  134 MET cc_start: 0.9522 (OUTLIER) cc_final: 0.8962 (mtp)
REVERT: B  138 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9165 (m)
REVERT: B  175 MET cc_start: 0.9384 (tpp) cc_final: 0.8893 (tpp)
REVERT: B  178 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9075 (mm)
REVERT: B  283 MET cc_start: 0.9590 (tpp) cc_final: 0.9381 (mmm)
REVERT: B  297 TYR cc_start: 0.9351 (m-10) cc_final: 0.8694 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 57
  average time/residue: 0.0943
  time to fit residues: 7.1931
Evaluate side-chains
  53 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 77 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 17 optimal weight:   30.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.036713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.029219 restraints weight = 66988.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.030002 restraints weight = 41869.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.030562 restraints weight = 29899.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.030961 restraints weight = 23274.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.031236 restraints weight = 19299.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.4803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6703  Z= 0.133
  Angle     :  0.637  10.506   9052  Z= 0.313
  Chirality :  0.039   0.137   1042
  Planarity :  0.005   0.065   1159
  Dihedral  :  4.562  21.865    900
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.11 %
    Favored  : 78.15 %
  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: -0.44 (0.30), residues: 824
  helix:  0.65 (0.23), residues: 509
  sheet:  None (None), residues: 0
  loop : -1.87 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.007   0.001   TYR A 145 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.008   0.001   TRP B 461 
 HIS   0.006   0.002   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6703)
  covalent geometry    : angle       0.63679 ( 9052)
  hydrogen bonds       : bond        0.03573 (  354)
  hydrogen bonds       : angle       4.12075 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8707 (m-10)
REVERT: A  190 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8238 (p90)
REVERT: A  221 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7728 (t0)
REVERT: A  265 MET cc_start: 0.8858 (tpp) cc_final: 0.8644 (mmt)
REVERT: A  345 MET cc_start: 0.9406 (tpp) cc_final: 0.8493 (tpp)
REVERT: B    1 MET cc_start: 0.6786 (ttt) cc_final: 0.6385 (ptt)
REVERT: B   81 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6757 (ptt)
REVERT: B  134 MET cc_start: 0.9459 (ttp) cc_final: 0.9115 (mtp)
REVERT: B  175 MET cc_start: 0.9330 (tpp) cc_final: 0.8816 (tpp)
REVERT: B  178 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9069 (mm)
REVERT: B  260 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9192 (p)
REVERT: B  297 TYR cc_start: 0.9299 (m-10) cc_final: 0.8622 (m-80)
REVERT: B  345 MET cc_start: 0.9056 (mmm) cc_final: 0.8818 (mmm)
REVERT: B  354 MET cc_start: 0.8833 (mmt) cc_final: 0.8571 (mmt)
  outliers start: 13
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0954
  time to fit residues: 7.0664
Evaluate side-chains
  53 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 51 optimal weight:   30.0000
   chunk 55 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 10 optimal weight:    0.2980
   chunk 46 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0040
   chunk 11 optimal weight:   10.0000
   overall best weight:    2.2598

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 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 = 0.3179 r_free = 0.3179 target = 0.037035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.029463 restraints weight = 66576.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.030262 restraints weight = 41596.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.030836 restraints weight = 29681.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.031234 restraints weight = 23057.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.031524 restraints weight = 19175.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.4966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6703  Z= 0.116
  Angle     :  0.647  12.158   9052  Z= 0.312
  Chirality :  0.039   0.145   1042
  Planarity :  0.005   0.071   1159
  Dihedral  :  4.537  22.012    900
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.24 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.30), residues: 824
  helix:  0.67 (0.23), residues: 511
  sheet:  None (None), residues: 0
  loop : -1.87 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 103 
 TYR   0.006   0.001   TYR B 248 
 PHE   0.008   0.001   PHE B 395 
 TRP   0.007   0.001   TRP B 461 
 HIS   0.005   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6703)
  covalent geometry    : angle       0.64709 ( 9052)
  hydrogen bonds       : bond        0.03466 (  354)
  hydrogen bonds       : angle       4.05310 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8885 (m-80)
REVERT: A  190 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8253 (p90)
REVERT: A  221 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7801 (t0)
REVERT: A  345 MET cc_start: 0.9451 (tpp) cc_final: 0.8560 (tpp)
REVERT: B    1 MET cc_start: 0.6878 (ttt) cc_final: 0.6524 (ptt)
REVERT: B   81 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6860 (ptt)
REVERT: B   85 ARG cc_start: 0.8425 (tpt170) cc_final: 0.8021 (tpt170)
REVERT: B  102 ILE cc_start: 0.9406 (mm) cc_final: 0.9197 (mt)
REVERT: B  134 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9115 (mtp)
REVERT: B  175 MET cc_start: 0.9386 (tpp) cc_final: 0.8761 (tpp)
REVERT: B  260 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9246 (p)
REVERT: B  297 TYR cc_start: 0.9381 (m-10) cc_final: 0.8646 (m-80)
REVERT: B  345 MET cc_start: 0.9045 (mmm) cc_final: 0.8729 (mmm)
REVERT: B  354 MET cc_start: 0.8871 (mmt) cc_final: 0.8609 (mmt)
  outliers start: 14
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0936
  time to fit residues: 6.9474
Evaluate side-chains
  55 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 355 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.036642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.029148 restraints weight = 66453.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.029934 restraints weight = 41709.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.030494 restraints weight = 29844.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.030886 restraints weight = 23289.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.031172 restraints weight = 19377.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.5094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6703  Z= 0.143
  Angle     :  0.676  11.868   9052  Z= 0.326
  Chirality :  0.040   0.155   1042
  Planarity :  0.005   0.065   1159
  Dihedral  :  4.496  21.528    900
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.38 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.30), residues: 824
  helix:  0.68 (0.23), residues: 513
  sheet: -2.55 (1.91), residues: 6
  loop : -1.87 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  92 
 TYR   0.014   0.001   TYR B 248 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.008   0.001   TRP B 461 
 HIS   0.005   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6703)
  covalent geometry    : angle       0.67569 ( 9052)
  hydrogen bonds       : bond        0.03514 (  354)
  hydrogen bonds       : angle       4.10276 ( 1050)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8830 (m-80)
REVERT: A  190 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8220 (p90)
REVERT: A  221 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7610 (t0)
REVERT: A  345 MET cc_start: 0.9377 (tpp) cc_final: 0.8510 (tpp)
REVERT: B   81 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6920 (ptt)
REVERT: B   85 ARG cc_start: 0.8251 (tpt170) cc_final: 0.8002 (tpt170)
REVERT: B  134 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.9156 (mtp)
REVERT: B  175 MET cc_start: 0.9300 (tpp) cc_final: 0.8611 (tpp)
REVERT: B  297 TYR cc_start: 0.9346 (m-10) cc_final: 0.8602 (m-80)
REVERT: B  320 MET cc_start: 0.8782 (tpt) cc_final: 0.8433 (mmm)
REVERT: B  345 MET cc_start: 0.9051 (mmm) cc_final: 0.8543 (mmm)
REVERT: B  354 MET cc_start: 0.8817 (mmt) cc_final: 0.8542 (mmt)
  outliers start: 13
  outliers final: 7
  residues processed: 52
  average time/residue: 0.1021
  time to fit residues: 6.9398
Evaluate side-chains
  53 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 62 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 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 = 0.3184 r_free = 0.3184 target = 0.037037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.029524 restraints weight = 66133.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.030316 restraints weight = 41463.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.030883 restraints weight = 29705.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.031299 restraints weight = 23086.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.031581 restraints weight = 19125.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.5220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6703  Z= 0.125
  Angle     :  0.677  16.165   9052  Z= 0.325
  Chirality :  0.040   0.185   1042
  Planarity :  0.005   0.072   1159
  Dihedral  :  4.501  21.773    900
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.97 %
    Favored  : 78.28 %
  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: -0.38 (0.30), residues: 824
  helix:  0.70 (0.23), residues: 513
  sheet: -2.54 (1.89), residues: 6
  loop : -1.85 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.010   0.001   TYR B 248 
 PHE   0.008   0.001   PHE A 409 
 TRP   0.007   0.001   TRP A 209 
 HIS   0.005   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6703)
  covalent geometry    : angle       0.67690 ( 9052)
  hydrogen bonds       : bond        0.03535 (  354)
  hydrogen bonds       : angle       4.12070 ( 1050)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1376.41 seconds
wall clock time: 24 minutes 37.98 seconds (1477.98 seconds total)