Starting phenix.real_space_refine
on Wed Sep 17 10:55:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ut9_64485/09_2025/9ut9_64485.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ut9_64485/09_2025/9ut9_64485.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ut9_64485/09_2025/9ut9_64485.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ut9_64485/09_2025/9ut9_64485.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ut9_64485/09_2025/9ut9_64485.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ut9_64485/09_2025/9ut9_64485.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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      56      5.16       5
     C    5067      2.51       5
     N    1369      2.21       5
     O    1466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7958
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 490, 3962
          Classifications: {'peptide': 490}
          Link IDs: {'PTRANS': 22, 'TRANS': 467}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 3996
          Classifications: {'peptide': 514}
          Link IDs: {'PTRANS': 26, 'TRANS': 487}
          Chain breaks: 3
  Time building chain proxies: 2.06, per 1000 atoms: 0.26
  Number of scatterers: 7958
  At special positions: 0
  Unit cell: (95.04, 87.36, 118.08, 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      56     16.00
     O    1466      8.00
     N    1369      7.00
     C    5067      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 513 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 495 " - pdb=" SG  CYS A 514 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 499 " - pdb=" SG  CYS A 517 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 535 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B 351 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 517 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 373 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 499 " - pdb=" SG  CYS B 518 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 503 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 524 " - pdb=" SG  CYS B 538 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 541 " - pdb=" SG  CYS B 554 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 416.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1896

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 11 sheets defined
      37.0% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 85
      removed outlier: 3.819A  pdb=" N   TYR A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 115
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 3.633A  pdb=" N   PHE A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.684A  pdb=" N   ASP A 173 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
      removed outlier: 3.940A  pdb=" N   HIS A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 229
      removed outlier: 3.960A  pdb=" N   ARG A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 265
    Processing helix  chain 'A' and resid 280 through 291
      removed outlier: 4.432A  pdb=" N   PHE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 4.686A  pdb=" N   ILE A 306 " --> pdb=" O   GLU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 319
      removed outlier: 3.830A  pdb=" N   HIS A 318 " --> pdb=" O   GLU A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 341
      removed outlier: 3.595A  pdb=" N   TRP A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 373
    Processing helix  chain 'A' and resid 373 through 380
    Processing helix  chain 'A' and resid 384 through 404
      removed outlier: 3.764A  pdb=" N   VAL A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 425
      removed outlier: 3.836A  pdb=" N   LEU A 420 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LEU A 421 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   GLU A 422 " --> pdb=" O   TRP A 418 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU A 423 " --> pdb=" O   GLN A 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
      removed outlier: 3.694A  pdb=" N   GLN B  27 " --> pdb=" O   CYS B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 4.027A  pdb=" N   LEU B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 4.304A  pdb=" N   LYS B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
      removed outlier: 3.690A  pdb=" N   LEU B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 161
      removed outlier: 3.575A  pdb=" N   VAL B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS B 155 " --> pdb=" O   MET B 151 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE B 156 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE B 159 " --> pdb=" O   LYS B 155 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   PHE B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.614A  pdb=" N   LEU B 174 " --> pdb=" O   MET B 171 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER B 175 " --> pdb=" O   GLU B 172 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 176 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 171 through 176'
    Processing helix  chain 'B' and resid 189 through 205
      removed outlier: 4.499A  pdb=" N   GLN B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU B 194 " --> pdb=" O   ASP B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 232
      removed outlier: 3.916A  pdb=" N   ALA B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 265
      removed outlier: 3.725A  pdb=" N   ASP B 258 " --> pdb=" O   GLY B 254 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B 260 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 290
    Processing helix  chain 'B' and resid 306 through 311
    Processing helix  chain 'B' and resid 314 through 318
    Processing helix  chain 'B' and resid 333 through 347
    Processing helix  chain 'B' and resid 347 through 356
      removed outlier: 3.624A  pdb=" N   CYS B 351 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 374
      removed outlier: 3.776A  pdb=" N   CYS B 373 " --> pdb=" O   CYS B 370 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ASP B 374 " --> pdb=" O   PRO B 371 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 370 through 374'
    Processing helix  chain 'B' and resid 378 through 383
      removed outlier: 4.236A  pdb=" N   ALA B 383 " --> pdb=" O   GLN B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 408
    Processing helix  chain 'B' and resid 422 through 429
      removed outlier: 3.774A  pdb=" N   LEU B 426 " --> pdb=" O   PRO B 423 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU B 427 " --> pdb=" O   TRP B 424 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLU B 428 " --> pdb=" O   GLN B 425 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.501A  pdb=" N   LEU A  29 " --> pdb=" O   TYR A  96 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR A  96 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   TYR A  33 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   GLU A  97 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU A  35 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   VAL A  99 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   GLY A  37 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A  38 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL A 138 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLN A 161 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 240
      removed outlier: 7.809A  pdb=" N   ILE A 206 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLN A 237 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL A 208 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   THR A 239 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   VAL A 210 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL A 272 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   TRP A 298 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   ILE A 325 " --> pdb=" O   TRP A 298 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU A 448 " --> pdb=" O   SER A 467 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   SER A 467 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE A 450 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 504 through 507
    Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 525
    Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 31
      removed outlier: 6.613A  pdb=" N   TYR B  35 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   ASP B  98 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 39
      removed outlier: 7.126A  pdb=" N   GLY B  38 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   VAL B 141 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   GLN B 164 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243
      removed outlier: 7.719A  pdb=" N   VAL B 209 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 9.380A  pdb=" N   GLY B 241 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ALA B 211 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   VAL B 243 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   GLY B 213 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   VAL B 270 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 8.641A  pdb=" N   PHE B 324 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   ALA B 299 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
      removed outlier: 10.316A  pdb=" N   GLN B 326 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   VAL B 321 " --> pdb=" O   TRP B 459 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   TYR B 454 " --> pdb=" O   ARG B 473 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   ARG B 473 " --> pdb=" O   TYR B 454 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU B 456 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN B 462 " --> pdb=" O   VAL B 465 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   VAL B 465 " --> pdb=" O   GLN B 462 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 434 through 436
    Processing sheet with id=AB2, first strand: chain 'B' and resid 508 through 512

    264 hydrogen bonds defined for protein.
    744 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: 1.26

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2616
        1.34 -     1.47: 2012
        1.47 -     1.59: 3448
        1.59 -     1.72: 0
        1.72 -     1.84: 78
  Bond restraints: 8154
  Sorted by residual:
  bond pdb=" N   ASP A  26 "
       pdb=" CA  ASP A  26 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   PRO B 246 "
       pdb=" CD  PRO B 246 "
    ideal  model  delta    sigma   weight residual
    1.473  1.497 -0.024 1.40e-02 5.10e+03 2.87e+00
  bond pdb=" N   LEU B  23 "
       pdb=" CA  LEU B  23 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.54e+00
  bond pdb=" CA  ASP B 535 "
       pdb=" C   ASP B 535 "
    ideal  model  delta    sigma   weight residual
    1.532  1.521  0.012 9.60e-03 1.09e+04 1.47e+00
  bond pdb=" CB  CYS B 517 "
       pdb=" SG  CYS B 517 "
    ideal  model  delta    sigma   weight residual
    1.808  1.768  0.040 3.30e-02 9.18e+02 1.43e+00
  ... (remaining 8149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 10587
        1.24 -     2.48: 378
        2.48 -     3.71: 86
        3.71 -     4.95: 30
        4.95 -     6.19: 4
  Bond angle restraints: 11085
  Sorted by residual:
  angle pdb=" C   ASN A 540 "
        pdb=" CA  ASN A 540 "
        pdb=" CB  ASN A 540 "
      ideal   model   delta    sigma   weight residual
     115.89  111.05    4.84 1.32e+00 5.74e-01 1.34e+01
  angle pdb=" CA  TYR B 529 "
        pdb=" CB  TYR B 529 "
        pdb=" CG  TYR B 529 "
      ideal   model   delta    sigma   weight residual
     113.90  119.71   -5.81 1.80e+00 3.09e-01 1.04e+01
  angle pdb=" N   VAL B 381 "
        pdb=" CA  VAL B 381 "
        pdb=" C   VAL B 381 "
      ideal   model   delta    sigma   weight residual
     113.47  110.30    3.17 1.01e+00 9.80e-01 9.84e+00
  angle pdb=" CA  TYR B 394 "
        pdb=" CB  TYR B 394 "
        pdb=" CG  TYR B 394 "
      ideal   model   delta    sigma   weight residual
     113.90  119.26   -5.36 1.80e+00 3.09e-01 8.86e+00
  angle pdb=" C   ASP A 307 "
        pdb=" CA  ASP A 307 "
        pdb=" CB  ASP A 307 "
      ideal   model   delta    sigma   weight residual
     110.16  114.04   -3.88 1.33e+00 5.65e-01 8.53e+00
  ... (remaining 11080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4260
       17.83 -    35.66: 428
       35.66 -    53.48: 139
       53.48 -    71.31: 49
       71.31 -    89.14: 6
  Dihedral angle restraints: 4882
    sinusoidal: 1954
      harmonic: 2928
  Sorted by residual:
  dihedral pdb=" CB  CYS B 370 "
           pdb=" SG  CYS B 370 "
           pdb=" SG  CYS B 373 "
           pdb=" CB  CYS B 373 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.87   85.87     1      1.00e+01 1.00e-02 8.91e+01
  dihedral pdb=" CB  CYS A 538 "
           pdb=" SG  CYS A 538 "
           pdb=" SG  CYS A 551 "
           pdb=" CB  CYS A 551 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.78  -69.78     1      1.00e+01 1.00e-02 6.28e+01
  dihedral pdb=" CB  CYS A 233 "
           pdb=" SG  CYS A 233 "
           pdb=" SG  CYS A 513 "
           pdb=" CB  CYS A 513 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.26   52.26     1      1.00e+01 1.00e-02 3.72e+01
  ... (remaining 4879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 767
       0.032 -    0.064: 328
       0.064 -    0.095: 73
       0.095 -    0.127: 53
       0.127 -    0.159: 5
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CA  ILE B 235 "
            pdb=" N   ILE B 235 "
            pdb=" C   ILE B 235 "
            pdb=" CB  ILE B 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" CG  LEU B 456 "
            pdb=" CB  LEU B 456 "
            pdb=" CD1 LEU B 456 "
            pdb=" CD2 LEU B 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CA  ILE A 207 "
            pdb=" N   ILE A 207 "
            pdb=" C   ILE A 207 "
            pdb=" CB  ILE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 439 "    0.037 5.00e-02 4.00e+02   5.64e-02 5.09e+00
        pdb=" N   PRO A 440 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 440 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 440 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 332 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO A 333 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 333 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 333 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 394 "    0.016 2.00e-02 2.50e+03   1.11e-02 2.47e+00
        pdb=" CG  TYR B 394 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 394 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 394 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 394 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 394 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 394 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 394 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1429 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 630
        2.73 -     3.28: 7462
        3.28 -     3.82: 11860
        3.82 -     4.36: 14210
        4.36 -     4.90: 25084
  Nonbonded interactions: 59246
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  88 "
            pdb=" ND1 HIS A 400 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" OG1 THR B 407 "
            pdb=" OD1 ASN B 429 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   ASP A 307 "
            pdb=" OD1 ASP A 307 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   SER B 267 "
            pdb=" OG  SER B 267 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" N   TRP B 546 "
            pdb=" O   PHE B 555 "
     model   vdw
     2.287 3.120
  ... (remaining 59241 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.900
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.930
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
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   0.040   8170  Z= 0.168
  Angle     :  0.604   6.189  11117  Z= 0.328
  Chirality :  0.041   0.159   1226
  Planarity :  0.004   0.056   1432
  Dihedral  : 16.570  89.141   2938
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.37 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 18.54 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.26), residues: 990
  helix:  0.53 (0.30), residues: 331
  sheet: -1.28 (0.38), residues: 173
  loop : -2.16 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  30 
 TYR   0.026   0.002   TYR B 394 
 PHE   0.018   0.001   PHE A 515 
 TRP   0.009   0.001   TRP A 304 
 HIS   0.006   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8154)
  covalent geometry    : angle       0.59704 (11085)
  SS BOND              : bond        0.00231 (   16)
  SS BOND              : angle       1.77907 (   32)
  hydrogen bonds       : bond        0.19236 (  264)
  hydrogen bonds       : angle       6.16088 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.8342 (t80) cc_final: 0.8083 (t80)
REVERT: A  525 PHE cc_start: 0.8097 (p90) cc_final: 0.7827 (p90)
  outliers start: 2
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1120
  time to fit residues: 17.5711
Evaluate side-chains
  59 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  529 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 GLN
A 460 ASN
B  27 GLN
B 265 GLN
B 469 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.106841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.069629 restraints weight = 16432.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 3.90
r_work: 0.2897 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8170  Z= 0.172
  Angle     :  0.604   6.833  11117  Z= 0.319
  Chirality :  0.043   0.136   1226
  Planarity :  0.004   0.038   1432
  Dihedral  :  4.605  38.793   1086
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.35 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.75 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.27), residues: 990
  helix:  1.17 (0.31), residues: 323
  sheet: -1.14 (0.38), residues: 180
  loop : -1.86 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 317 
 TYR   0.028   0.002   TYR B 529 
 PHE   0.016   0.002   PHE B 350 
 TRP   0.035   0.002   TRP A 455 
 HIS   0.007   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 8154)
  covalent geometry    : angle       0.60137 (11085)
  SS BOND              : bond        0.00227 (   16)
  SS BOND              : angle       1.28112 (   32)
  hydrogen bonds       : bond        0.05429 (  264)
  hydrogen bonds       : angle       4.55595 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.8460 (t80) cc_final: 0.8186 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 76
  average time/residue: 0.0811
  time to fit residues: 8.9897
Evaluate side-chains
  63 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  529 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.106381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.069707 restraints weight = 16384.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 3.89
r_work: 0.2906 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8170  Z= 0.136
  Angle     :  0.536   6.143  11117  Z= 0.283
  Chirality :  0.042   0.136   1226
  Planarity :  0.004   0.039   1432
  Dihedral  :  4.279  33.548   1086
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.15 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.41 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.27), residues: 990
  helix:  1.54 (0.31), residues: 318
  sheet: -0.94 (0.38), residues: 178
  loop : -1.63 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.025   0.001   TYR B 529 
 PHE   0.010   0.001   PHE A 525 
 TRP   0.047   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8154)
  covalent geometry    : angle       0.53399 (11085)
  SS BOND              : bond        0.00129 (   16)
  SS BOND              : angle       1.06707 (   32)
  hydrogen bonds       : bond        0.04536 (  264)
  hydrogen bonds       : angle       4.09751 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  338 PHE cc_start: 0.8475 (t80) cc_final: 0.8256 (t80)
  outliers start: 21
  outliers final: 9
  residues processed: 81
  average time/residue: 0.0735
  time to fit residues: 8.9703
Evaluate side-chains
  59 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  538 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0570
   chunk 46 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
B 207 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.106521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.070085 restraints weight = 16650.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 3.93
r_work: 0.2911 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8170  Z= 0.119
  Angle     :  0.524   6.831  11117  Z= 0.274
  Chirality :  0.041   0.134   1226
  Planarity :  0.004   0.038   1432
  Dihedral  :  4.022  23.543   1084
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.85 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 17.63 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.27), residues: 990
  helix:  1.66 (0.31), residues: 324
  sheet: -0.81 (0.39), residues: 178
  loop : -1.51 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 290 
 TYR   0.021   0.001   TYR B 394 
 PHE   0.009   0.001   PHE B 435 
 TRP   0.060   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8154)
  covalent geometry    : angle       0.52208 (11085)
  SS BOND              : bond        0.00153 (   16)
  SS BOND              : angle       1.06029 (   32)
  hydrogen bonds       : bond        0.04081 (  264)
  hydrogen bonds       : angle       3.91538 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.9120 (m-30) cc_final: 0.8627 (t0)
REVERT: A  338 PHE cc_start: 0.8491 (t80) cc_final: 0.8255 (t80)
  outliers start: 12
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0739
  time to fit residues: 7.3667
Evaluate side-chains
  64 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  465 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 434 HIS
B  27 GLN
B 265 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.106470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.069773 restraints weight = 16611.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 3.91
r_work: 0.2907 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8170  Z= 0.127
  Angle     :  0.518   7.642  11117  Z= 0.271
  Chirality :  0.041   0.135   1226
  Planarity :  0.004   0.038   1432
  Dihedral  :  3.939  22.019   1084
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.15 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.41 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.27), residues: 990
  helix:  1.59 (0.31), residues: 330
  sheet: -0.67 (0.39), residues: 180
  loop : -1.45 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.019   0.001   TYR B 394 
 PHE   0.010   0.001   PHE B 435 
 TRP   0.062   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8154)
  covalent geometry    : angle       0.51526 (11085)
  SS BOND              : bond        0.00173 (   16)
  SS BOND              : angle       1.04166 (   32)
  hydrogen bonds       : bond        0.04193 (  264)
  hydrogen bonds       : angle       3.83879 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.9114 (m-30) cc_final: 0.8646 (t0)
REVERT: B  171 MET cc_start: 0.8396 (mtp) cc_final: 0.8090 (mtp)
REVERT: B  525 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8872 (pp20)
  outliers start: 17
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0553
  time to fit residues: 5.9995
Evaluate side-chains
  63 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  465 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0870
   chunk 15 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    1.0762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.105400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.068761 restraints weight = 16607.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 3.91
r_work: 0.2886 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8170  Z= 0.162
  Angle     :  0.533   7.859  11117  Z= 0.279
  Chirality :  0.042   0.143   1226
  Planarity :  0.004   0.036   1432
  Dihedral  :  4.000  24.383   1084
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.85 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.09 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.27), residues: 990
  helix:  1.61 (0.31), residues: 329
  sheet: -0.67 (0.39), residues: 180
  loop : -1.44 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 553 
 TYR   0.018   0.001   TYR B 394 
 PHE   0.013   0.001   PHE B 435 
 TRP   0.073   0.002   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8154)
  covalent geometry    : angle       0.53061 (11085)
  SS BOND              : bond        0.00201 (   16)
  SS BOND              : angle       1.03305 (   32)
  hydrogen bonds       : bond        0.04629 (  264)
  hydrogen bonds       : angle       3.86181 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 51
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.9137 (m-30) cc_final: 0.8722 (t0)
REVERT: A  249 MET cc_start: 0.7852 (ptm) cc_final: 0.7135 (ppp)
REVERT: B  525 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8949 (pp20)
  outliers start: 20
  outliers final: 15
  residues processed: 66
  average time/residue: 0.0719
  time to fit residues: 7.3639
Evaluate side-chains
  64 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  465 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.106032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.069390 restraints weight = 16713.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 3.91
r_work: 0.2898 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8170  Z= 0.132
  Angle     :  0.506   7.687  11117  Z= 0.263
  Chirality :  0.041   0.135   1226
  Planarity :  0.003   0.036   1432
  Dihedral  :  3.877  21.169   1084
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.65 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.66 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.28), residues: 990
  helix:  1.65 (0.31), residues: 330
  sheet: -0.60 (0.40), residues: 180
  loop : -1.30 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 378 
 TYR   0.017   0.001   TYR B 394 
 PHE   0.010   0.001   PHE B 435 
 TRP   0.054   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8154)
  covalent geometry    : angle       0.50368 (11085)
  SS BOND              : bond        0.00156 (   16)
  SS BOND              : angle       0.94699 (   32)
  hydrogen bonds       : bond        0.04131 (  264)
  hydrogen bonds       : angle       3.74666 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.9134 (m-30) cc_final: 0.8654 (t0)
REVERT: A  249 MET cc_start: 0.7954 (ptm) cc_final: 0.7318 (ppp)
REVERT: A  378 ARG cc_start: 0.9002 (tpp80) cc_final: 0.8633 (ttp-110)
REVERT: B  525 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8902 (pp20)
  outliers start: 16
  outliers final: 14
  residues processed: 64
  average time/residue: 0.0711
  time to fit residues: 7.0578
Evaluate side-chains
  64 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  465 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 265 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.106575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.069361 restraints weight = 16589.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 3.88
r_work: 0.2889 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8170  Z= 0.134
  Angle     :  0.510   7.920  11117  Z= 0.265
  Chirality :  0.041   0.138   1226
  Planarity :  0.003   0.037   1432
  Dihedral  :  3.832  19.739   1084
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.65 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.89 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.28), residues: 990
  helix:  1.71 (0.31), residues: 329
  sheet: -0.62 (0.40), residues: 178
  loop : -1.29 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 378 
 TYR   0.016   0.001   TYR B 394 
 PHE   0.011   0.001   PHE B 435 
 TRP   0.049   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8154)
  covalent geometry    : angle       0.50878 (11085)
  SS BOND              : bond        0.00152 (   16)
  SS BOND              : angle       0.86401 (   32)
  hydrogen bonds       : bond        0.04226 (  264)
  hydrogen bonds       : angle       3.72460 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.9110 (m-30) cc_final: 0.8649 (t0)
REVERT: A  249 MET cc_start: 0.7936 (ptm) cc_final: 0.7286 (ppp)
REVERT: A  378 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8642 (ttp-110)
REVERT: B  525 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8953 (pp20)
  outliers start: 17
  outliers final: 15
  residues processed: 66
  average time/residue: 0.0783
  time to fit residues: 7.7406
Evaluate side-chains
  63 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  465 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.0470
   chunk 54 optimal weight:    0.9980
   chunk 71 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0070
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.3296

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.107629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.071261 restraints weight = 16503.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 3.93
r_work: 0.2930 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   8170  Z= 0.091
  Angle     :  0.490   7.220  11117  Z= 0.255
  Chirality :  0.040   0.152   1226
  Planarity :  0.003   0.037   1432
  Dihedral  :  3.796  26.249   1084
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 19.57 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.28), residues: 990
  helix:  1.92 (0.31), residues: 324
  sheet: -0.68 (0.39), residues: 188
  loop : -1.15 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.014   0.001   TYR B 394 
 PHE   0.011   0.001   PHE A 525 
 TRP   0.066   0.001   TRP A 455 
 HIS   0.006   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 8154)
  covalent geometry    : angle       0.48873 (11085)
  SS BOND              : bond        0.00126 (   16)
  SS BOND              : angle       0.91571 (   32)
  hydrogen bonds       : bond        0.03331 (  264)
  hydrogen bonds       : angle       3.65438 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.9129 (m-30) cc_final: 0.8663 (t0)
REVERT: A  249 MET cc_start: 0.7709 (ptm) cc_final: 0.6967 (ppp)
REVERT: A  378 ARG cc_start: 0.9057 (tpp80) cc_final: 0.8742 (ttp-110)
REVERT: B  171 MET cc_start: 0.8328 (mtp) cc_final: 0.8123 (mtp)
REVERT: B  525 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8956 (pp20)
  outliers start: 10
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0723
  time to fit residues: 6.3642
Evaluate side-chains
  58 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0980
   chunk 16 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.107110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.070337 restraints weight = 16516.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 3.92
r_work: 0.2916 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8170  Z= 0.109
  Angle     :  0.491   6.851  11117  Z= 0.255
  Chirality :  0.040   0.155   1226
  Planarity :  0.003   0.037   1432
  Dihedral  :  3.725  23.868   1084
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 19.45 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.28), residues: 990
  helix:  1.91 (0.31), residues: 324
  sheet: -0.63 (0.39), residues: 188
  loop : -1.09 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.015   0.001   TYR B 394 
 PHE   0.010   0.001   PHE A 525 
 TRP   0.065   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8154)
  covalent geometry    : angle       0.48886 (11085)
  SS BOND              : bond        0.00142 (   16)
  SS BOND              : angle       0.92795 (   32)
  hydrogen bonds       : bond        0.03764 (  264)
  hydrogen bonds       : angle       3.66709 (  744)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A  231 ASP cc_start: 0.9087 (m-30) cc_final: 0.8634 (t0)
REVERT: A  249 MET cc_start: 0.7750 (ptm) cc_final: 0.6975 (ppp)
REVERT: A  378 ARG cc_start: 0.9057 (tpp80) cc_final: 0.8739 (ttp-110)
REVERT: B  171 MET cc_start: 0.8458 (mtp) cc_final: 0.8152 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0815
  time to fit residues: 7.2257
Evaluate side-chains
  57 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  373 PHE
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0170
   chunk 71 optimal weight:    0.6980
   chunk 21 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 46 optimal weight:    0.1980
   overall best weight:    0.4218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.072338 restraints weight = 15861.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 3.69
r_work: 0.2866 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053   8170  Z= 0.096
  Angle     :  0.495  10.682  11117  Z= 0.257
  Chirality :  0.040   0.143   1226
  Planarity :  0.003   0.038   1432
  Dihedral  :  3.650  23.385   1084
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.94 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.68 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.28), residues: 990
  helix:  2.10 (0.31), residues: 318
  sheet: -0.59 (0.39), residues: 188
  loop : -0.95 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 247 
 TYR   0.014   0.001   TYR B 529 
 PHE   0.012   0.001   PHE A 525 
 TRP   0.059   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 8154)
  covalent geometry    : angle       0.49354 (11085)
  SS BOND              : bond        0.00118 (   16)
  SS BOND              : angle       0.81906 (   32)
  hydrogen bonds       : bond        0.03354 (  264)
  hydrogen bonds       : angle       3.59626 (  744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1896.53 seconds
wall clock time: 33 minutes 12.51 seconds (1992.51 seconds total)