Starting phenix.real_space_refine
on Tue Feb 11 18:43:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yzb_39688/02_2025/8yzb_39688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yzb_39688/02_2025/8yzb_39688.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yzb_39688/02_2025/8yzb_39688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yzb_39688/02_2025/8yzb_39688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yzb_39688/02_2025/8yzb_39688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yzb_39688/02_2025/8yzb_39688.cif"
  }
  resolution = 3.29
  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=  -0.011 sd=   0.288
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      37      5.16       5
     C    4137      2.51       5
     N    1072      2.21       5
     O    1202      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6448
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1568
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 4880
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4995
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS B  34 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B  34 " occ=0.50
  Time building chain proxies: 6.38, per 1000 atoms: 0.99
  Number of scatterers: 6448
  At special positions: 0
  Unit cell: (84.49, 96.39, 117.81, 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      37     16.00
     O    1202      8.00
     N    1072      7.00
     C    4137      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 344 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 530 " - pdb=" SG  CYS B 542 " 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: 1.47
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      60.2% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 4.198A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    Processing helix  chain 'A' and resid 367 through 372
      removed outlier: 3.862A  pdb=" N   PHE A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 3.589A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.811A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'B' and resid 20 through 53
      removed outlier: 3.886A  pdb=" N   GLN B  24 " --> pdb=" O   THR B  20 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N  AHIS B  34 " --> pdb=" O   ASP B  30 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ASP B  38 " --> pdb=" O  AHIS B  34 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU B  39 " --> pdb=" O   GLU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 77
      removed outlier: 3.534A  pdb=" N   VAL B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.521A  pdb=" N   MET B  82 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 88
      removed outlier: 3.570A  pdb=" N   GLU B  87 " --> pdb=" O   PRO B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 101
      removed outlier: 3.754A  pdb=" N   GLN B  96 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU B 100 " --> pdb=" O   GLN B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.513A  pdb=" N   SER B 106 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 130
    Processing helix  chain 'B' and resid 147 through 155
    Processing helix  chain 'B' and resid 157 through 194
      removed outlier: 3.581A  pdb=" N   ARG B 161 " --> pdb=" O   ASP B 157 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   TRP B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ARG B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   LYS B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   GLN B 175 " --> pdb=" O   GLU B 171 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B 176 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
      removed outlier: 3.711A  pdb=" N   GLU B 181 " --> pdb=" O   ARG B 177 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU B 182 " --> pdb=" O   PRO B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 204
    Processing helix  chain 'B' and resid 205 through 208
    Processing helix  chain 'B' and resid 220 through 231
      removed outlier: 3.588A  pdb=" N   GLU B 224 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLU B 231 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 252
      removed outlier: 3.645A  pdb=" N   ASN B 250 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 267
      No H-bonds generated for 'chain 'B' and resid 265 through 267'
    Processing helix  chain 'B' and resid 275 through 277
      No H-bonds generated for 'chain 'B' and resid 275 through 277'
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 293 through 301
    Processing helix  chain 'B' and resid 303 through 317
    Processing helix  chain 'B' and resid 324 through 331
      removed outlier: 4.181A  pdb=" N   TRP B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLU B 329 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 385
      removed outlier: 3.650A  pdb=" N   TYR B 385 " --> pdb=" O   TYR B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 388
      No H-bonds generated for 'chain 'B' and resid 386 through 388'
    Processing helix  chain 'B' and resid 389 through 393
    Processing helix  chain 'B' and resid 399 through 413
      removed outlier: 3.744A  pdb=" N   MET B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER B 409 " --> pdb=" O   GLY B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 421
    Processing helix  chain 'B' and resid 431 through 447
      removed outlier: 3.552A  pdb=" N   THR B 445 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 466
      removed outlier: 4.326A  pdb=" N   PHE B 452 " --> pdb=" O   GLY B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 471
      No H-bonds generated for 'chain 'B' and resid 469 through 471'
    Processing helix  chain 'B' and resid 472 through 485
    Processing helix  chain 'B' and resid 499 through 502
    Processing helix  chain 'B' and resid 503 through 508
    Processing helix  chain 'B' and resid 512 through 533
      removed outlier: 4.011A  pdb=" N   TYR B 516 " --> pdb=" O   PHE B 512 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   PHE B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN B 524 " --> pdb=" O   LEU B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
      removed outlier: 3.718A  pdb=" N   LYS B 541 " --> pdb=" O   PRO B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 559
      removed outlier: 3.852A  pdb=" N   GLY B 551 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   MET B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 564
      removed outlier: 3.984A  pdb=" N   GLU B 564 " --> pdb=" O   GLY B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 575
    Processing helix  chain 'B' and resid 581 through 600
      Proline residue:  B 590  - end of helix
      removed outlier: 3.876A  pdb=" N   LYS B 596 " --> pdb=" O   PHE B 592 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ASP B 597 " --> pdb=" O   THR B 593 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLN B 598 " --> pdb=" O   TRP B 594 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.934A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   CYS A 432 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.734A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 134
      removed outlier: 5.736A  pdb=" N   GLU B 140 " --> pdb=" O   ASN B 134 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263
      removed outlier: 5.902A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 352
      removed outlier: 5.944A  pdb=" N   ASP B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    844 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: 1.70

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1071
        1.30 -     1.43: 1872
        1.43 -     1.55: 3638
        1.55 -     1.68: 0
        1.68 -     1.81: 58
  Bond restraints: 6639
  Sorted by residual:
  bond pdb=" CA  ASP B  38 "
       pdb=" C   ASP B  38 "
    ideal  model  delta    sigma   weight residual
    1.523  1.441  0.083 1.30e-02 5.92e+03 4.05e+01
  bond pdb=" C   PHE B  40 "
       pdb=" O   PHE B  40 "
    ideal  model  delta    sigma   weight residual
    1.236  1.173  0.064 1.15e-02 7.56e+03 3.05e+01
  bond pdb=" C   LEU B  39 "
       pdb=" O   LEU B  39 "
    ideal  model  delta    sigma   weight residual
    1.236  1.170  0.067 1.29e-02 6.01e+03 2.66e+01
  bond pdb=" CA  PHE B  40 "
       pdb=" CB  PHE B  40 "
    ideal  model  delta    sigma   weight residual
    1.530  1.452  0.078 1.57e-02 4.06e+03 2.46e+01
  bond pdb=" N   LEU B  39 "
       pdb=" CA  LEU B  39 "
    ideal  model  delta    sigma   weight residual
    1.458  1.394  0.064 1.30e-02 5.92e+03 2.39e+01
  ... (remaining 6634 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 8916
        2.05 -     4.09: 95
        4.09 -     6.14: 10
        6.14 -     8.18: 1
        8.18 -    10.23: 3
  Bond angle restraints: 9025
  Sorted by residual:
  angle pdb=" N   ASP B  38 "
        pdb=" CA  ASP B  38 "
        pdb=" C   ASP B  38 "
      ideal   model   delta    sigma   weight residual
     111.28  121.51  -10.23 1.09e+00 8.42e-01 8.80e+01
  angle pdb=" C   LEU B  39 "
        pdb=" CA  LEU B  39 "
        pdb=" CB  LEU B  39 "
      ideal   model   delta    sigma   weight residual
     110.38  119.20   -8.82 2.04e+00 2.40e-01 1.87e+01
  angle pdb=" N   LEU B  39 "
        pdb=" CA  LEU B  39 "
        pdb=" C   LEU B  39 "
      ideal   model   delta    sigma   weight residual
     112.23  106.82    5.41 1.26e+00 6.30e-01 1.85e+01
  angle pdb=" C   ASP B  38 "
        pdb=" CA  ASP B  38 "
        pdb=" CB  ASP B  38 "
      ideal   model   delta    sigma   weight residual
     110.79  104.00    6.79 1.66e+00 3.63e-01 1.67e+01
  angle pdb=" N   ASN A 370 "
        pdb=" CA  ASN A 370 "
        pdb=" C   ASN A 370 "
      ideal   model   delta    sigma   weight residual
     111.69  106.77    4.92 1.23e+00 6.61e-01 1.60e+01
  ... (remaining 9020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.50: 3750
       12.50 -    25.00: 128
       25.00 -    37.51: 21
       37.51 -    50.01: 10
       50.01 -    62.51: 4
  Dihedral angle restraints: 3913
    sinusoidal: 1582
      harmonic: 2331
  Sorted by residual:
  dihedral pdb=" C   LEU B  39 "
           pdb=" N   LEU B  39 "
           pdb=" CA  LEU B  39 "
           pdb=" CB  LEU B  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.48    9.88     0      2.50e+00 1.60e-01 1.56e+01
  dihedral pdb=" CA  PHE A 347 "
           pdb=" C   PHE A 347 "
           pdb=" N   ALA A 348 "
           pdb=" CA  ALA A 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.16   15.84     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  ARG A 498 "
           pdb=" CB  ARG A 498 "
           pdb=" CG  ARG A 498 "
           pdb=" CD  ARG A 498 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.94   57.06     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 3910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 907
       0.099 -    0.199: 25
       0.199 -    0.298: 2
       0.298 -    0.397: 1
       0.397 -    0.497: 1
  Chirality restraints: 936
  Sorted by residual:
  chirality pdb=" CA  LEU B  39 "
            pdb=" N   LEU B  39 "
            pdb=" C   LEU B  39 "
            pdb=" CB  LEU B  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.17e+00
  chirality pdb=" CA  ASP B  38 "
            pdb=" N   ASP B  38 "
            pdb=" C   ASP B  38 "
            pdb=" CB  ASP B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.12e+00
  chirality pdb=" CA  PHE A 377 "
            pdb=" N   PHE A 377 "
            pdb=" C   PHE A 377 "
            pdb=" CB  PHE A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 933 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  39 "    0.009 2.00e-02 2.50e+03   1.70e-02 2.90e+00
        pdb=" C   LEU B  39 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LEU B  39 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE B  40 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  37 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.83e+00
        pdb=" C   GLU B  37 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   GLU B  37 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASP B  38 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  38 "    0.007 2.00e-02 2.50e+03   1.32e-02 1.75e+00
        pdb=" C   ASP B  38 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ASP B  38 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU B  39 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1323
        2.77 -     3.31: 6066
        3.31 -     3.84: 9857
        3.84 -     4.37: 11463
        4.37 -     4.90: 20361
  Nonbonded interactions: 49070
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 177 "
            pdb=" O   GLU B 495 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   VAL B 364 "
            pdb=" OG1 THR B 365 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   ILE B 151 "
            pdb=" OG  SER B 155 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OD1 ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OD1 ASN B 394 "
            pdb=" N   GLY B 395 "
     model   vdw
     2.323 3.120
  ... (remaining 49065 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  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:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.930
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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      :  0.003   0.083   6639  Z= 0.246
  Angle     :  0.545  10.226   9025  Z= 0.344
  Chirality :  0.042   0.497    936
  Planarity :  0.002   0.029   1170
  Dihedral  :  7.277  62.511   2399
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  2.87 %
    Favored  : 95.70 %
  Cbeta Deviations :  0.13 %
  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: -0.85 (0.28), residues: 791
  helix:  0.11 (0.26), residues: 382
  sheet:  1.47 (0.71), residues: 45
  loop : -1.55 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 302 
 HIS   0.002   0.000   HIS B 374 
 PHE   0.009   0.001   PHE B  40 
 TYR   0.012   0.001   TYR B  41 
 ARG   0.002   0.000   ARG B 169 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 HIS cc_start: 0.7840 (t70) cc_final: 0.7465 (t-170)
REVERT: B  462 MET cc_start: 0.8401 (mtp) cc_final: 0.8195 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 165
  average time/residue: 0.2419
  time to fit residues: 50.1947
Evaluate side-chains
  85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  34 HIS    B
B  42 GLN
B 265 HIS
B 340 GLN
B 401 HIS
B 472 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.052502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.044449 restraints weight = 53312.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.2697 rms_B_bonded: 3.76
r_work: 0.2580 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   6639  Z= 0.260
  Angle     :  0.676   9.535   9025  Z= 0.362
  Chirality :  0.047   0.299    936
  Planarity :  0.004   0.030   1170
  Dihedral  :  4.893  45.393    864
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.19 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.16 (0.29), residues: 791
  helix:  0.98 (0.26), residues: 382
  sheet:  1.36 (0.68), residues: 50
  loop : -1.04 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 473 
 HIS   0.005   0.002   HIS B 228 
 PHE   0.019   0.003   PHE B 369 
 TYR   0.018   0.002   TYR B 385 
 ARG   0.007   0.001   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8611 (tp30) cc_final: 0.8312 (tp30)
REVERT: A  493 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8792 (mp10)
  outliers start: 16
  outliers final: 7
  residues processed: 108
  average time/residue: 0.2011
  time to fit residues: 28.8555
Evaluate side-chains
  79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.046360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2531 r_free = 0.2531 target = 0.038653 restraints weight = 53412.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2529 rms_B_bonded: 3.49
r_work: 0.2410 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2413 r_free = 0.2413    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2413 r_free = 0.2413    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.6182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   6639  Z= 0.413
  Angle     :  0.761  13.415   9025  Z= 0.414
  Chirality :  0.052   0.336    936
  Planarity :  0.005   0.030   1170
  Dihedral  :  5.353  47.183    863
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 11.33 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.12 (0.29), residues: 791
  helix:  0.63 (0.26), residues: 394
  sheet:  1.66 (0.72), residues: 50
  loop : -1.16 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 473 
 HIS   0.007   0.002   HIS B 374 
 PHE   0.030   0.003   PHE B 369 
 TYR   0.028   0.003   TYR B 385 
 ARG   0.008   0.001   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8854 (tp30) cc_final: 0.8546 (tp30)
REVERT: A  347 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8405 (m-80)
REVERT: B   56 GLU cc_start: 0.6872 (pm20) cc_final: 0.6566 (pm20)
REVERT: B  203 TRP cc_start: 0.9208 (OUTLIER) cc_final: 0.8601 (m-10)
REVERT: B  383 MET cc_start: 0.9070 (ttm) cc_final: 0.8323 (mtp)
REVERT: B  512 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7991 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 91
  average time/residue: 0.2037
  time to fit residues: 24.3799
Evaluate side-chains
  78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   62 MET
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  607 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0470
   chunk 58 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
B 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.048671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.040477 restraints weight = 63325.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.2576 rms_B_bonded: 4.21
r_work: 0.2451 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2452 r_free = 0.2452    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2452 r_free = 0.2452    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8894
moved from start:          0.6222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6639  Z= 0.195
  Angle     :  0.635  15.685   9025  Z= 0.340
  Chirality :  0.047   0.323    936
  Planarity :  0.004   0.035   1170
  Dihedral  :  5.059  46.068    863
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.33 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  0.31 (0.30), residues: 791
  helix:  1.04 (0.26), residues: 393
  sheet:  1.72 (0.72), residues: 52
  loop : -1.01 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 473 
 HIS   0.004   0.001   HIS B 228 
 PHE   0.018   0.002   PHE B 369 
 TYR   0.013   0.001   TYR B 385 
 ARG   0.003   0.000   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8956 (tp30) cc_final: 0.8664 (tp30)
REVERT: A  347 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8133 (m-80)
REVERT: A  364 ASP cc_start: 0.8759 (t0) cc_final: 0.8004 (p0)
REVERT: B  203 TRP cc_start: 0.9119 (OUTLIER) cc_final: 0.8406 (m-10)
REVERT: B  512 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7455 (t80)
REVERT: B  610 TRP cc_start: 0.9176 (t60) cc_final: 0.8939 (t60)
  outliers start: 21
  outliers final: 8
  residues processed: 87
  average time/residue: 0.1982
  time to fit residues: 23.0894
Evaluate side-chains
  77 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   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 = 0.2799 r_free = 0.2799 target = 0.047564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.039705 restraints weight = 57446.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.2559 rms_B_bonded: 3.86
r_work: 0.2436 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2439 r_free = 0.2439    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2439 r_free = 0.2439    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.6332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6639  Z= 0.237
  Angle     :  0.667  15.417   9025  Z= 0.354
  Chirality :  0.048   0.341    936
  Planarity :  0.004   0.032   1170
  Dihedral  :  4.894  45.782    863
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.20 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: 791
  helix:  1.10 (0.27), residues: 393
  sheet:  1.68 (0.73), residues: 48
  loop : -0.96 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 473 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.020   0.002   PHE B 369 
 TYR   0.016   0.002   TYR B 385 
 ARG   0.004   0.000   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.9015 (tp30) cc_final: 0.8801 (tp30)
REVERT: A  347 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8155 (m-80)
REVERT: A  364 ASP cc_start: 0.8711 (t0) cc_final: 0.8057 (p0)
REVERT: B  203 TRP cc_start: 0.9205 (OUTLIER) cc_final: 0.8523 (m-10)
REVERT: B  512 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7629 (t80)
REVERT: B  610 TRP cc_start: 0.9126 (t60) cc_final: 0.8898 (t60)
  outliers start: 18
  outliers final: 11
  residues processed: 79
  average time/residue: 0.2165
  time to fit residues: 22.6196
Evaluate side-chains
  78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.2807 r_free = 0.2807 target = 0.047826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.040023 restraints weight = 51767.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.2570 rms_B_bonded: 3.67
r_work: 0.2450 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2452 r_free = 0.2452    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2452 r_free = 0.2452    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8914
moved from start:          0.6454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6639  Z= 0.225
  Angle     :  0.681  18.602   9025  Z= 0.361
  Chirality :  0.048   0.366    936
  Planarity :  0.004   0.031   1170
  Dihedral  :  4.925  45.692    863
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.34 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.34 (0.29), residues: 791
  helix:  1.12 (0.27), residues: 394
  sheet:  1.67 (0.74), residues: 48
  loop : -1.02 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 473 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.019   0.002   PHE B 369 
 TYR   0.019   0.001   TYR B  50 
 ARG   0.004   0.000   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8134 (m-80)
REVERT: A  364 ASP cc_start: 0.8711 (t0) cc_final: 0.8082 (p0)
REVERT: B  119 ILE cc_start: 0.8380 (mt) cc_final: 0.8080 (mt)
REVERT: B  203 TRP cc_start: 0.9235 (OUTLIER) cc_final: 0.8442 (m-10)
REVERT: B  431 ASP cc_start: 0.7437 (t0) cc_final: 0.7051 (p0)
REVERT: B  512 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7657 (t80)
REVERT: B  610 TRP cc_start: 0.9106 (t60) cc_final: 0.8856 (t60)
  outliers start: 17
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1985
  time to fit residues: 21.5267
Evaluate side-chains
  79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  607 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.2787 r_free = 0.2787 target = 0.047098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.039871 restraints weight = 33335.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.2566 rms_B_bonded: 2.83
r_work: 0.2466 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.6577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6639  Z= 0.262
  Angle     :  0.719  20.247   9025  Z= 0.384
  Chirality :  0.049   0.368    936
  Planarity :  0.004   0.032   1170
  Dihedral  :  5.056  45.999    863
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.62 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.24 (0.29), residues: 791
  helix:  1.10 (0.27), residues: 393
  sheet:  1.63 (0.74), residues: 48
  loop : -1.17 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 473 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.022   0.002   PHE B 369 
 TYR   0.024   0.002   TYR B  50 
 ARG   0.003   0.000   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8177 (m-80)
REVERT: A  364 ASP cc_start: 0.8648 (t0) cc_final: 0.8043 (p0)
REVERT: B  203 TRP cc_start: 0.9270 (OUTLIER) cc_final: 0.8537 (m-10)
REVERT: B  431 ASP cc_start: 0.7367 (t0) cc_final: 0.7164 (t0)
REVERT: B  512 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7818 (t80)
REVERT: B  610 TRP cc_start: 0.9037 (t60) cc_final: 0.8798 (t60)
  outliers start: 19
  outliers final: 12
  residues processed: 79
  average time/residue: 0.1899
  time to fit residues: 20.2326
Evaluate side-chains
  82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  607 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.0670
   chunk 58 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.047790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.040389 restraints weight = 38844.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2581 rms_B_bonded: 3.08
r_work: 0.2477 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2478 r_free = 0.2478    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2478 r_free = 0.2478    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
moved from start:          0.6602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6639  Z= 0.223
  Angle     :  0.723  23.424   9025  Z= 0.381
  Chirality :  0.048   0.404    936
  Planarity :  0.004   0.031   1170
  Dihedral  :  4.949  45.494    863
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.63 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.32 (0.29), residues: 791
  helix:  1.18 (0.27), residues: 394
  sheet:  1.48 (0.74), residues: 51
  loop : -1.14 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.018   0.002   PHE B 369 
 TYR   0.025   0.001   TYR B  50 
 ARG   0.004   0.000   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8127 (m-80)
REVERT: A  364 ASP cc_start: 0.8622 (t0) cc_final: 0.8093 (p0)
REVERT: B   82 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8660 (ptp)
REVERT: B  203 TRP cc_start: 0.9267 (OUTLIER) cc_final: 0.8479 (m-10)
REVERT: B  431 ASP cc_start: 0.7411 (t0) cc_final: 0.7171 (t0)
REVERT: B  512 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7708 (t80)
REVERT: B  610 TRP cc_start: 0.8999 (t60) cc_final: 0.8760 (t60)
  outliers start: 14
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1963
  time to fit residues: 20.9542
Evaluate side-chains
  82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  607 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 64 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.2798 r_free = 0.2798 target = 0.047466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.039880 restraints weight = 45267.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2564 rms_B_bonded: 3.37
r_work: 0.2453 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2454 r_free = 0.2454    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2454 r_free = 0.2454    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.6654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6639  Z= 0.237
  Angle     :  0.730  21.883   9025  Z= 0.386
  Chirality :  0.048   0.373    936
  Planarity :  0.004   0.032   1170
  Dihedral  :  4.942  45.108    863
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.91 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.30 (0.29), residues: 791
  helix:  1.16 (0.27), residues: 394
  sheet:  1.60 (0.75), residues: 47
  loop : -1.13 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 436 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.019   0.002   PHE B 369 
 TYR   0.024   0.001   TYR B  50 
 ARG   0.003   0.000   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8148 (m-80)
REVERT: A  364 ASP cc_start: 0.8511 (t0) cc_final: 0.8136 (p0)
REVERT: B  203 TRP cc_start: 0.9276 (OUTLIER) cc_final: 0.8531 (m-10)
REVERT: B  431 ASP cc_start: 0.7476 (t0) cc_final: 0.7219 (t0)
REVERT: B  512 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7702 (t80)
REVERT: B  610 TRP cc_start: 0.9040 (t60) cc_final: 0.8786 (t60)
  outliers start: 15
  outliers final: 10
  residues processed: 80
  average time/residue: 0.2088
  time to fit residues: 22.4785
Evaluate side-chains
  83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  607 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.2791 r_free = 0.2791 target = 0.047251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.039480 restraints weight = 52128.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.2552 rms_B_bonded: 3.72
r_work: 0.2432 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2434
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2434 r_free = 0.2434    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2434 r_free = 0.2434    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2434
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8925
moved from start:          0.6696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6639  Z= 0.256
  Angle     :  0.750  21.467   9025  Z= 0.395
  Chirality :  0.048   0.370    936
  Planarity :  0.004   0.032   1170
  Dihedral  :  4.987  45.314    863
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.20 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.30 (0.29), residues: 791
  helix:  1.15 (0.27), residues: 394
  sheet:  1.57 (0.74), residues: 47
  loop : -1.11 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 473 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.020   0.002   PHE B 369 
 TYR   0.024   0.002   TYR B  50 
 ARG   0.003   0.000   ARG B 177 

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8150 (m-80)
REVERT: A  364 ASP cc_start: 0.8526 (t0) cc_final: 0.8146 (p0)
REVERT: B  203 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8527 (m-10)
REVERT: B  431 ASP cc_start: 0.7555 (t0) cc_final: 0.7279 (t0)
REVERT: B  512 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7777 (t80)
REVERT: B  610 TRP cc_start: 0.9068 (t60) cc_final: 0.8802 (t60)
  outliers start: 14
  outliers final: 11
  residues processed: 80
  average time/residue: 0.1990
  time to fit residues: 21.2250
Evaluate side-chains
  84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  607 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    0.2980
   chunk 66 optimal weight:    0.0970
   chunk 19 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0170
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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 = 0.2846 r_free = 0.2846 target = 0.049198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.041522 restraints weight = 46064.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2616 rms_B_bonded: 3.39
r_work: 0.2506 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2509 r_free = 0.2509    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2509 r_free = 0.2509    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.6660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6639  Z= 0.189
  Angle     :  0.693  20.558   9025  Z= 0.363
  Chirality :  0.046   0.347    936
  Planarity :  0.004   0.036   1170
  Dihedral  :  4.729  43.708    863
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.49 %
    Favored  : 84.94 %
  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:  0.49 (0.30), residues: 791
  helix:  1.34 (0.27), residues: 394
  sheet:  1.41 (0.73), residues: 51
  loop : -1.05 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 339 
 PHE   0.012   0.001   PHE B 369 
 TYR   0.027   0.001   TYR B  50 
 ARG   0.004   0.000   ARG B 115 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3225.92 seconds
wall clock time: 57 minutes 54.61 seconds (3474.61 seconds total)