Starting phenix.real_space_refine
on Thu Jul 24 21:10:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xf2_33168/07_2025/7xf2_33168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xf2_33168/07_2025/7xf2_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xf2_33168/07_2025/7xf2_33168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xf2_33168/07_2025/7xf2_33168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xf2_33168/07_2025/7xf2_33168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xf2_33168/07_2025/7xf2_33168.cif"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 23.34, per 1000 atoms: 3.54
  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: 1.95
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.45
  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: 3.85

  Time building geometry restraints manager: 2.29 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:             105.050
  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:             0.020
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     47.890
  Find NCS groups from input model:        0.640
  Set up NCS constraints:                  0.060
  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:8.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  162.560
-------------------------------------------------------------------------------
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 : 14.17
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.008   0.001   TRP A 392 
 HIS   0.007   0.002   HIS A 130 
 PHE   0.009   0.001   PHE B 358 
 TYR   0.016   0.002   TYR B 255 
 ARG   0.007   0.001   ARG A 103 

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

*********************** 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  : 1.699 
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: 0.8785 (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: 0.3952
  time to fit residues: 41.8874
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  : 1.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0270
   chunk 42 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    4.8046

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 HIS
B 163 GLN
B 195 ASN
** 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 = 0.3313 r_free = 0.3313 target = 0.044026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.037644 restraints weight = 67535.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.038631 restraints weight = 34843.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.039283 restraints weight = 21623.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6703  Z= 0.188
  Angle     :  0.743  10.802   9052  Z= 0.388
  Chirality :  0.042   0.136   1042
  Planarity :  0.006   0.060   1159
  Dihedral  :  5.262  28.378    900
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.13 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.27), residues: 824
  helix: -1.10 (0.21), residues: 489
  sheet: -3.72 (1.75), residues: 6
  loop : -2.48 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 392 
 HIS   0.008   0.002   HIS A 130 
 PHE   0.016   0.001   PHE B 179 
 TYR   0.030   0.002   TYR B 297 
 ARG   0.005   0.001   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06321 (  354)
  hydrogen bonds       : angle       5.25782 ( 1050)
  covalent geometry    : bond        0.00397 ( 6703)
  covalent geometry    : angle       0.74322 ( 9052)

*********************** 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
  64 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7869 (tmm) cc_final: 0.7643 (tmm)
REVERT: A   93 LYS cc_start: 0.9096 (tppt) cc_final: 0.8853 (tppt)
REVERT: A  103 ARG cc_start: 0.8605 (mtp180) cc_final: 0.8085 (mmm-85)
REVERT: A  106 MET cc_start: 0.9340 (mmp) cc_final: 0.9041 (mmm)
REVERT: A  212 MET cc_start: 0.9506 (mmp) cc_final: 0.9294 (tpp)
REVERT: A  265 MET cc_start: 0.8835 (tpp) cc_final: 0.8587 (mpp)
REVERT: A  283 MET cc_start: 0.9669 (tpp) cc_final: 0.9363 (mmm)
REVERT: A  430 TYR cc_start: 0.9064 (p90) cc_final: 0.8838 (p90)
REVERT: A  436 LEU cc_start: 0.9826 (tp) cc_final: 0.9588 (tt)
REVERT: B   88 GLN cc_start: 0.8123 (tt0) cc_final: 0.7884 (tt0)
REVERT: B  283 MET cc_start: 0.9543 (tpp) cc_final: 0.9339 (mmm)
REVERT: B  297 TYR cc_start: 0.8968 (m-80) cc_final: 0.8401 (m-80)
REVERT: B  320 MET cc_start: 0.8848 (mmp) cc_final: 0.8542 (mmm)
REVERT: B  354 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (mmt)
  outliers start: 6
  outliers final: 2
  residues processed: 63
  average time/residue: 0.4731
  time to fit residues: 41.0105
Evaluate side-chains
  53 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 2.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 HIS
Chi-restraints excluded: chain B residue  260 THR
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 26 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 61 optimal weight:    8.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:   30.0000
   chunk 45 optimal weight:    1.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 457 ASN
** 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 = 0.3282 r_free = 0.3282 target = 0.042533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.036164 restraints weight = 68932.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.037127 restraints weight = 35563.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.037769 restraints weight = 22315.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6703  Z= 0.177
  Angle     :  0.657  10.494   9052  Z= 0.341
  Chirality :  0.040   0.129   1042
  Planarity :  0.005   0.056   1159
  Dihedral  :  5.063  27.447    900
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.60 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.29), residues: 824
  helix: -0.16 (0.23), residues: 504
  sheet: -3.73 (1.66), residues: 6
  loop : -2.16 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 461 
 HIS   0.009   0.002   HIS A 130 
 PHE   0.010   0.001   PHE A 360 
 TYR   0.018   0.002   TYR A  72 
 ARG   0.004   0.001   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04527 (  354)
  hydrogen bonds       : angle       4.56234 ( 1050)
  covalent geometry    : bond        0.00377 ( 6703)
  covalent geometry    : angle       0.65686 ( 9052)

*********************** 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
  69 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.8579 (mtp180) cc_final: 0.8071 (mmm-85)
REVERT: A  134 MET cc_start: 0.9211 (mtm) cc_final: 0.8889 (ptt)
REVERT: A  157 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7941 (mt)
REVERT: A  162 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8848 (m-80)
REVERT: A  221 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7431 (t0)
REVERT: A  283 MET cc_start: 0.9617 (tpp) cc_final: 0.9374 (mmm)
REVERT: A  289 ARG cc_start: 0.9342 (mmt90) cc_final: 0.9079 (mmm-85)
REVERT: B    1 MET cc_start: 0.6890 (ttt) cc_final: 0.6517 (ptt)
REVERT: B  175 MET cc_start: 0.8998 (tpp) cc_final: 0.8725 (tpp)
REVERT: B  283 MET cc_start: 0.9501 (tpp) cc_final: 0.9301 (mmm)
REVERT: B  297 TYR cc_start: 0.9041 (m-80) cc_final: 0.8527 (m-80)
REVERT: B  345 MET cc_start: 0.9439 (mmt) cc_final: 0.8950 (mmm)
REVERT: B  354 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8452 (mmt)
  outliers start: 18
  outliers final: 8
  residues processed: 66
  average time/residue: 0.2920
  time to fit residues: 24.8784
Evaluate side-chains
  57 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  130 HIS
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  162 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  166 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 26 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 64 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 7 optimal weight:    9.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 457 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.042916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.036530 restraints weight = 68780.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.037500 restraints weight = 35774.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.038154 restraints weight = 22422.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3949

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= 0.135
  Angle     :  0.636  10.472   9052  Z= 0.322
  Chirality :  0.039   0.138   1042
  Planarity :  0.005   0.060   1159
  Dihedral  :  4.854  25.755    900
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.68 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.29), residues: 824
  helix:  0.24 (0.23), residues: 509
  sheet: -3.87 (1.46), residues: 6
  loop : -2.04 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 461 
 HIS   0.007   0.002   HIS A 130 
 PHE   0.008   0.001   PHE B 395 
 TYR   0.016   0.001   TYR A  72 
 ARG   0.002   0.000   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04081 (  354)
  hydrogen bonds       : angle       4.31038 ( 1050)
  covalent geometry    : bond        0.00292 ( 6703)
  covalent geometry    : angle       0.63584 ( 9052)

*********************** 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: 13
    poor density    : 46
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.8529 (mtp180) cc_final: 0.8014 (mmm-85)
REVERT: A  106 MET cc_start: 0.9198 (mmm) cc_final: 0.8942 (mmm)
REVERT: A  157 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7927 (mt)
REVERT: A  162 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8870 (m-80)
REVERT: A  283 MET cc_start: 0.9656 (tpp) cc_final: 0.9440 (mmm)
REVERT: A  289 ARG cc_start: 0.9324 (mmt90) cc_final: 0.9119 (mmm-85)
REVERT: A  345 MET cc_start: 0.9454 (tpp) cc_final: 0.9036 (mmt)
REVERT: A  349 MET cc_start: 0.9272 (mmp) cc_final: 0.9055 (mmp)
REVERT: B   85 ARG cc_start: 0.8689 (tpt170) cc_final: 0.8451 (tpt170)
REVERT: B  175 MET cc_start: 0.9153 (tpp) cc_final: 0.8690 (tpp)
REVERT: B  297 TYR cc_start: 0.9155 (m-80) cc_final: 0.8533 (m-80)
REVERT: B  345 MET cc_start: 0.9295 (mmt) cc_final: 0.8964 (mmm)
REVERT: B  354 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8459 (mmt)
  outliers start: 13
  outliers final: 6
  residues processed: 56
  average time/residue: 0.2892
  time to fit residues: 21.4374
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  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
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   81 MET
Chi-restraints excluded: chain B residue  134 MET
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 16 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 58 optimal weight:    8.9990
   chunk 54 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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**
B 323 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.042293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.035908 restraints weight = 69494.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.036876 restraints weight = 36368.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.037513 restraints weight = 22894.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   6703  Z= 0.149
  Angle     :  0.614   9.373   9052  Z= 0.314
  Chirality :  0.039   0.135   1042
  Planarity :  0.005   0.056   1159
  Dihedral  :  4.772  25.221    900
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.89 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.29), residues: 824
  helix:  0.51 (0.23), residues: 508
  sheet: -3.70 (1.39), residues: 6
  loop : -2.03 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 461 
 HIS   0.008   0.002   HIS A 130 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.023   0.002   TYR A  46 
 ARG   0.007   0.000   ARG A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  354)
  hydrogen bonds       : angle       4.22507 ( 1050)
  covalent geometry    : bond        0.00328 ( 6703)
  covalent geometry    : angle       0.61413 ( 9052)

*********************** 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
  64 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.8443 (mtp180) cc_final: 0.8001 (mmm-85)
REVERT: A  190 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8077 (p90)
REVERT: A  221 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7503 (t0)
REVERT: A  345 MET cc_start: 0.9377 (tpp) cc_final: 0.8706 (tpp)
REVERT: A  349 MET cc_start: 0.9181 (mmp) cc_final: 0.8485 (mmp)
REVERT: B   85 ARG cc_start: 0.8609 (tpt170) cc_final: 0.8356 (tpt170)
REVERT: B  134 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.8953 (mtp)
REVERT: B  175 MET cc_start: 0.9128 (tpp) cc_final: 0.8662 (tpp)
REVERT: B  297 TYR cc_start: 0.9190 (m-10) cc_final: 0.8591 (m-80)
REVERT: B  345 MET cc_start: 0.9246 (mmt) cc_final: 0.9020 (mmm)
  outliers start: 18
  outliers final: 7
  residues processed: 61
  average time/residue: 0.2373
  time to fit residues: 18.9739
Evaluate side-chains
  52 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  260 THR
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 29 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 20 optimal weight:   30.0000
   chunk 71 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 34 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   chunk 13 optimal weight:   20.0000
   overall best weight:    5.3188

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 GLN ** 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 = 0.3268 r_free = 0.3268 target = 0.041564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.035238 restraints weight = 69604.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.036192 restraints weight = 36623.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.036830 restraints weight = 23124.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6703  Z= 0.171
  Angle     :  0.652  11.151   9052  Z= 0.327
  Chirality :  0.040   0.135   1042
  Planarity :  0.005   0.057   1159
  Dihedral  :  4.757  25.176    900
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.50 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.29), residues: 824
  helix:  0.54 (0.23), residues: 508
  sheet: -3.68 (1.25), residues: 6
  loop : -1.99 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 461 
 HIS   0.008   0.002   HIS A 130 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.013   0.001   TYR B 255 
 ARG   0.005   0.000   ARG A 289 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  354)
  hydrogen bonds       : angle       4.27086 ( 1050)
  covalent geometry    : bond        0.00364 ( 6703)
  covalent geometry    : angle       0.65167 ( 9052)

*********************** 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
  59 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 MET cc_start: 0.9172 (mtm) cc_final: 0.8874 (ptt)
REVERT: A  162 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8693 (m-10)
REVERT: A  190 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8278 (p90)
REVERT: A  265 MET cc_start: 0.8987 (tpp) cc_final: 0.8757 (mmt)
REVERT: A  345 MET cc_start: 0.9395 (tpp) cc_final: 0.8553 (tpp)
REVERT: B   85 ARG cc_start: 0.8626 (tpt170) cc_final: 0.8373 (tpt170)
REVERT: B  134 MET cc_start: 0.9481 (ttp) cc_final: 0.8920 (mtp)
REVERT: B  175 MET cc_start: 0.9226 (tpp) cc_final: 0.8698 (tpp)
REVERT: B  297 TYR cc_start: 0.9222 (m-10) cc_final: 0.8575 (m-80)
REVERT: B  345 MET cc_start: 0.9320 (mmt) cc_final: 0.9038 (mmm)
  outliers start: 17
  outliers final: 7
  residues processed: 57
  average time/residue: 0.2089
  time to fit residues: 16.3247
Evaluate side-chains
  51 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
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  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  166 THR
Chi-restraints excluded: chain B residue  260 THR
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 69 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0970
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    4.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 GLN ** 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 = 0.3145 r_free = 0.3145 target = 0.036158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.028594 restraints weight = 64358.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.029359 restraints weight = 40751.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.029904 restraints weight = 29325.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.4691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6703  Z= 0.153
  Angle     :  0.644   9.802   9052  Z= 0.320
  Chirality :  0.039   0.137   1042
  Planarity :  0.005   0.057   1159
  Dihedral  :  4.712  25.000    900
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.29), residues: 824
  helix:  0.58 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.91 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 461 
 HIS   0.007   0.002   HIS A 130 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.014   0.001   TYR B 255 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  354)
  hydrogen bonds       : angle       4.23496 ( 1050)
  covalent geometry    : bond        0.00332 ( 6703)
  covalent geometry    : angle       0.64407 ( 9052)

*********************** 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
  58 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.8730 (m-10)
REVERT: A  190 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8390 (p90)
REVERT: A  345 MET cc_start: 0.9375 (tpp) cc_final: 0.8598 (tpp)
REVERT: B   85 ARG cc_start: 0.8578 (tpt170) cc_final: 0.8353 (tpt170)
REVERT: B  134 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.8910 (mtp)
REVERT: B  148 MET cc_start: 0.8488 (mmm) cc_final: 0.8282 (tpt)
REVERT: B  175 MET cc_start: 0.9328 (tpp) cc_final: 0.8867 (tpp)
REVERT: B  297 TYR cc_start: 0.9294 (m-10) cc_final: 0.8634 (m-80)
REVERT: B  345 MET cc_start: 0.9320 (mmt) cc_final: 0.9098 (mmm)
  outliers start: 14
  outliers final: 6
  residues processed: 56
  average time/residue: 0.2137
  time to fit residues: 16.0510
Evaluate side-chains
  51 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  134 MET
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 55 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0010
   chunk 44 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 24 optimal weight:    0.4980
   chunk 51 optimal weight:   30.0000
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:   20.0000
   overall best weight:    1.4390

-------------------------------------------------------------------------------
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 = 0.3171 r_free = 0.3171 target = 0.036798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.029147 restraints weight = 62603.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.029928 restraints weight = 39795.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.030477 restraints weight = 28671.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6703  Z= 0.111
  Angle     :  0.655  10.595   9052  Z= 0.317
  Chirality :  0.039   0.142   1042
  Planarity :  0.005   0.057   1159
  Dihedral  :  4.553  23.422    900
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 19.97 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.30), residues: 824
  helix:  0.71 (0.23), residues: 511
  sheet:  None (None), residues: 0
  loop : -1.86 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 461 
 HIS   0.006   0.001   HIS A 130 
 PHE   0.010   0.001   PHE B 395 
 TYR   0.015   0.001   TYR B 255 
 ARG   0.004   0.000   ARG A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  354)
  hydrogen bonds       : angle       4.00443 ( 1050)
  covalent geometry    : bond        0.00244 ( 6703)
  covalent geometry    : angle       0.65523 ( 9052)

*********************** 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
  55 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8826 (m-80)
REVERT: A  190 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8272 (p90)
REVERT: A  345 MET cc_start: 0.9342 (tpp) cc_final: 0.8567 (tpp)
REVERT: B  134 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8897 (mtp)
REVERT: B  175 MET cc_start: 0.9280 (tpp) cc_final: 0.8746 (tpp)
REVERT: B  178 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.9030 (mm)
REVERT: B  297 TYR cc_start: 0.9307 (m-10) cc_final: 0.8613 (m-80)
REVERT: B  345 MET cc_start: 0.9323 (mmt) cc_final: 0.9111 (mmm)
REVERT: B  354 MET cc_start: 0.8745 (mmt) cc_final: 0.8403 (mmt)
  outliers start: 10
  outliers final: 3
  residues processed: 54
  average time/residue: 0.2169
  time to fit residues: 15.8776
Evaluate side-chains
  48 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
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  378 THR
Chi-restraints excluded: chain B residue  134 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.3980
   chunk 65 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    4.0788

-------------------------------------------------------------------------------
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 = 0.3158 r_free = 0.3158 target = 0.036319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.028778 restraints weight = 64753.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.029530 restraints weight = 41060.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.030083 restraints weight = 29620.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6703  Z= 0.143
  Angle     :  0.659  11.198   9052  Z= 0.324
  Chirality :  0.039   0.145   1042
  Planarity :  0.005   0.056   1159
  Dihedral  :  4.560  22.574    900
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.30), residues: 824
  helix:  0.69 (0.23), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.81 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 461 
 HIS   0.006   0.001   HIS A 130 
 PHE   0.008   0.001   PHE B 395 
 TYR   0.015   0.001   TYR B 255 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03466 (  354)
  hydrogen bonds       : angle       4.12774 ( 1050)
  covalent geometry    : bond        0.00312 ( 6703)
  covalent geometry    : angle       0.65857 ( 9052)

*********************** 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
  55 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8704 (m-10)
REVERT: A  190 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8341 (p90)
REVERT: A  345 MET cc_start: 0.9344 (tpp) cc_final: 0.8589 (tpp)
REVERT: B  134 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.8997 (mtp)
REVERT: B  138 THR cc_start: 0.9629 (OUTLIER) cc_final: 0.9128 (p)
REVERT: B  175 MET cc_start: 0.9316 (tpp) cc_final: 0.8824 (tpp)
REVERT: B  178 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9074 (mm)
REVERT: B  297 TYR cc_start: 0.9328 (m-10) cc_final: 0.8618 (m-80)
REVERT: B  320 MET cc_start: 0.9098 (tpt) cc_final: 0.8757 (mmm)
REVERT: B  345 MET cc_start: 0.9335 (mmt) cc_final: 0.9096 (mmm)
  outliers start: 13
  outliers final: 5
  residues processed: 54
  average time/residue: 0.2125
  time to fit residues: 15.6101
Evaluate side-chains
  50 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  229 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  378 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 24 optimal weight:   20.0000
   chunk 64 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 78 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 17 optimal weight:   30.0000
   chunk 76 optimal weight:    3.9990
   chunk 61 optimal weight:   20.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 355 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.036434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.028866 restraints weight = 66453.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.029641 restraints weight = 42101.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.030192 restraints weight = 30351.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6703  Z= 0.146
  Angle     :  0.687  12.761   9052  Z= 0.333
  Chirality :  0.040   0.171   1042
  Planarity :  0.005   0.053   1159
  Dihedral  :  4.637  23.235    900
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 20.11 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.30), residues: 824
  helix:  0.71 (0.23), residues: 512
  sheet: -2.56 (1.88), residues: 6
  loop : -1.82 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 461 
 HIS   0.006   0.002   HIS A 130 
 PHE   0.010   0.001   PHE B 358 
 TYR   0.010   0.001   TYR B 255 
 ARG   0.005   0.000   ARG A  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  354)
  hydrogen bonds       : angle       4.16039 ( 1050)
  covalent geometry    : bond        0.00321 ( 6703)
  covalent geometry    : angle       0.68661 ( 9052)

********************** 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
  51 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.9505 (OUTLIER) cc_final: 0.8777 (m-10)
REVERT: A  190 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8492 (p90)
REVERT: A  345 MET cc_start: 0.9423 (tpp) cc_final: 0.8686 (tpp)
REVERT: B    1 MET cc_start: 0.8137 (tmm) cc_final: 0.7933 (tmm)
REVERT: B  134 MET cc_start: 0.9505 (ttp) cc_final: 0.9235 (mmm)
REVERT: B  138 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9260 (p)
REVERT: B  175 MET cc_start: 0.9395 (tpp) cc_final: 0.8903 (tpp)
REVERT: B  178 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9107 (mm)
REVERT: B  297 TYR cc_start: 0.9432 (m-10) cc_final: 0.8691 (m-80)
REVERT: B  320 MET cc_start: 0.9081 (tpt) cc_final: 0.8749 (mmm)
REVERT: B  354 MET cc_start: 0.9269 (mtt) cc_final: 0.8960 (mtt)
  outliers start: 11
  outliers final: 6
  residues processed: 51
  average time/residue: 0.1975
  time to fit residues: 13.8458
Evaluate side-chains
  49 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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  229 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   88 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 25 optimal weight:    0.4980
   chunk 81 optimal weight:    6.9990
   chunk 70 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   overall best weight:    3.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 GLN ** 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 = 0.3156 r_free = 0.3156 target = 0.036145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.028562 restraints weight = 65754.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.029310 restraints weight = 42093.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.029850 restraints weight = 30462.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6703  Z= 0.143
  Angle     :  0.673  11.691   9052  Z= 0.328
  Chirality :  0.040   0.143   1042
  Planarity :  0.005   0.052   1159
  Dihedral  :  4.612  23.052    900
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 20.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.30), residues: 824
  helix:  0.70 (0.23), residues: 512
  sheet: -2.63 (1.82), residues: 6
  loop : -1.83 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 461 
 HIS   0.005   0.001   HIS A 130 
 PHE   0.012   0.001   PHE B 395 
 TYR   0.008   0.001   TYR A  72 
 ARG   0.005   0.000   ARG B  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  354)
  hydrogen bonds       : angle       4.14643 ( 1050)
  covalent geometry    : bond        0.00314 ( 6703)
  covalent geometry    : angle       0.67348 ( 9052)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3993.19 seconds
wall clock time: 72 minutes 25.90 seconds (4345.90 seconds total)