Starting phenix.real_space_refine
on Tue Mar 11 18:12:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yzb_39688/03_2025/8yzb_39688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yzb_39688/03_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_39688/03_2025/8yzb_39688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yzb_39688/03_2025/8yzb_39688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yzb_39688/03_2025/8yzb_39688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yzb_39688/03_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-5624/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: 6.22, per 1000 atoms: 0.96
  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: 1.43
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.63

  Time building geometry restraints manager: 1.73 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.590
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.120
-------------------------------------------------------------------------------
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  : 0.714 
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: 0.2312
  time to fit residues: 48.0576
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  : 0.778 
-------------------------------------------------------------------------------
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 = 41)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.044459 restraints weight = 53312.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.2697 rms_B_bonded: 3.72
r_work: 0.2580 rms_B_bonded: 4.19 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: 0.8778
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  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8608 (tp30) cc_final: 0.8310 (tp30)
REVERT: A  493 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8791 (mp10)
  outliers start: 16
  outliers final: 7
  residues processed: 108
  average time/residue: 0.2033
  time to fit residues: 29.3625
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  : 0.804 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 228 HIS
B 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.046798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.039047 restraints weight = 54117.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2541 rms_B_bonded: 3.52
r_work: 0.2423 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2424 r_free = 0.2424    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2424 r_free = 0.2424    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2424
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8961
moved from start:          0.6153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   6639  Z= 0.374
  Angle     :  0.738  13.485   9025  Z= 0.401
  Chirality :  0.051   0.338    936
  Planarity :  0.005   0.030   1170
  Dihedral  :  5.253  46.352    863
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.48 %
    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: -0.04 (0.29), residues: 791
  helix:  0.71 (0.26), residues: 394
  sheet:  1.75 (0.72), residues: 48
  loop : -1.13 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 473 
 HIS   0.008   0.002   HIS B 374 
 PHE   0.028   0.003   PHE B 369 
 TYR   0.026   0.002   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
  97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8847 (tp30) cc_final: 0.8540 (tp30)
REVERT: A  347 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8397 (m-80)
REVERT: B  203 TRP cc_start: 0.9200 (OUTLIER) cc_final: 0.8594 (m-10)
REVERT: B  383 MET cc_start: 0.9055 (ttm) cc_final: 0.8332 (mtp)
REVERT: B  512 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7913 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1955
  time to fit residues: 23.5379
Evaluate side-chains
  80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 59 optimal weight:    0.2980
   chunk 58 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.2820 r_free = 0.2820 target = 0.048443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2576 r_free = 0.2576 target = 0.040275 restraints weight = 62892.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.2572 rms_B_bonded: 4.16
r_work: 0.2445 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2445 r_free = 0.2445    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2445 r_free = 0.2445    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.6241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6639  Z= 0.226
  Angle     :  0.631  16.287   9025  Z= 0.337
  Chirality :  0.046   0.304    936
  Planarity :  0.004   0.034   1170
  Dihedral  :  5.055  45.794    863
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 10.90 %
    Favored  : 86.08 %
  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:  0.29 (0.29), residues: 791
  helix:  1.04 (0.26), residues: 393
  sheet:  1.69 (0.72), residues: 52
  loop : -1.03 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 473 
 HIS   0.004   0.001   HIS B 228 
 PHE   0.019   0.002   PHE B 369 
 TYR   0.015   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  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8965 (tp30) cc_final: 0.8679 (tp30)
REVERT: A  347 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8137 (m-80)
REVERT: A  364 ASP cc_start: 0.8768 (t0) cc_final: 0.8022 (p0)
REVERT: A  471 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8822 (mm-30)
REVERT: B  203 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.8416 (m-10)
REVERT: B  512 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7432 (t80)
REVERT: B  610 TRP cc_start: 0.9202 (t60) cc_final: 0.8950 (t60)
  outliers start: 21
  outliers final: 8
  residues processed: 84
  average time/residue: 0.2119
  time to fit residues: 23.7566
Evaluate side-chains
  78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
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  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  175 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 59 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.2824 r_free = 0.2824 target = 0.048483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.040521 restraints weight = 58395.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2584 rms_B_bonded: 3.93
r_work: 0.2460 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2463 r_free = 0.2463    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2463 r_free = 0.2463    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.6293

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= 0.201
  Angle     :  0.644  16.274   9025  Z= 0.340
  Chirality :  0.047   0.370    936
  Planarity :  0.004   0.033   1170
  Dihedral  :  4.786  44.775    863
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.34 %
    Favored  : 85.51 %
  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:  0.49 (0.30), residues: 791
  helix:  1.19 (0.27), residues: 394
  sheet:  1.62 (0.72), residues: 52
  loop : -0.88 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 473 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.017   0.002   PHE B 369 
 TYR   0.013   0.001   TYR B  50 
 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
  83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.802 
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: 0.8909 (OUTLIER) cc_final: 0.8169 (m-80)
REVERT: A  364 ASP cc_start: 0.8675 (t0) cc_final: 0.8081 (p0)
REVERT: B  203 TRP cc_start: 0.9195 (OUTLIER) cc_final: 0.8479 (m-10)
REVERT: B  512 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7454 (t80)
REVERT: B  610 TRP cc_start: 0.9122 (t60) cc_final: 0.8871 (t60)
  outliers start: 15
  outliers final: 8
  residues processed: 79
  average time/residue: 0.2131
  time to fit residues: 22.2690
Evaluate side-chains
  74 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
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  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  175 GLN
Chi-restraints excluded: chain B residue  203 TRP
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:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   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 = 0.2831 r_free = 0.2831 target = 0.048708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.040809 restraints weight = 58227.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.2594 rms_B_bonded: 3.87
r_work: 0.2470 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2472 r_free = 0.2472    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 = 0.2472 r_free = 0.2472    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.6386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6639  Z= 0.194
  Angle     :  0.657  18.330   9025  Z= 0.346
  Chirality :  0.047   0.361    936
  Planarity :  0.004   0.031   1170
  Dihedral  :  4.733  43.695    863
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  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:  0.50 (0.30), residues: 791
  helix:  1.25 (0.27), residues: 394
  sheet:  1.58 (0.72), residues: 52
  loop : -0.95 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 473 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.016   0.001   PHE B 369 
 TYR   0.017   0.001   TYR B  50 
 ARG   0.003   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
  83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8060 (m-80)
REVERT: A  364 ASP cc_start: 0.8669 (t0) cc_final: 0.8094 (p0)
REVERT: B  203 TRP cc_start: 0.9232 (OUTLIER) cc_final: 0.8505 (m-10)
REVERT: B  512 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7457 (t80)
REVERT: B  601 ASN cc_start: 0.9075 (p0) cc_final: 0.8872 (p0)
REVERT: B  610 TRP cc_start: 0.9072 (t60) cc_final: 0.8837 (t60)
  outliers start: 14
  outliers final: 9
  residues processed: 78
  average time/residue: 0.2289
  time to fit residues: 23.9377
Evaluate side-chains
  79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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  512 PHE
Chi-restraints excluded: chain B residue  579 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    0.0980
   chunk 2 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.2810 r_free = 0.2810 target = 0.047955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.040732 restraints weight = 33342.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.2592 rms_B_bonded: 2.87
r_work: 0.2490 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2491
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2491 r_free = 0.2491    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 = 0.2491 r_free = 0.2491    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2491
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8892
moved from start:          0.6499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6639  Z= 0.232
  Angle     :  0.685  15.232   9025  Z= 0.364
  Chirality :  0.047   0.289    936
  Planarity :  0.004   0.032   1170
  Dihedral  :  4.834  44.017    863
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.77 %
    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:  0.40 (0.29), residues: 791
  helix:  1.20 (0.27), residues: 394
  sheet:  1.57 (0.74), residues: 48
  loop : -1.02 (0.30), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 473 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.019   0.002   PHE B 369 
 TYR   0.016   0.001   TYR B  50 
 ARG   0.005   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
  86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8110 (m-80)
REVERT: A  364 ASP cc_start: 0.8634 (t0) cc_final: 0.8038 (p0)
REVERT: B  115 ARG cc_start: 0.8183 (tpm170) cc_final: 0.7872 (tpp-160)
REVERT: B  203 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.8440 (m-10)
REVERT: B  512 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7614 (t80)
REVERT: B  601 ASN cc_start: 0.9035 (p0) cc_final: 0.8834 (p0)
REVERT: B  610 TRP cc_start: 0.9038 (t60) cc_final: 0.8790 (t60)
  outliers start: 17
  outliers final: 10
  residues processed: 81
  average time/residue: 0.2156
  time to fit residues: 23.5310
Evaluate side-chains
  80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
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  203 TRP
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0770
   chunk 67 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.2844 r_free = 0.2844 target = 0.049094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.041593 restraints weight = 39652.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.2617 rms_B_bonded: 3.22
r_work: 0.2508 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2510
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2510 r_free = 0.2510    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 = 0.2510 r_free = 0.2510    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.6530

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= 0.193
  Angle     :  0.701  21.172   9025  Z= 0.367
  Chirality :  0.047   0.405    936
  Planarity :  0.004   0.031   1170
  Dihedral  :  4.693  42.856    863
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  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 : 0.00 %

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:  0.55 (0.30), residues: 791
  helix:  1.34 (0.27), residues: 394
  sheet:  1.53 (0.73), residues: 51
  loop : -0.98 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 436 
 HIS   0.003   0.001   HIS B 374 
 PHE   0.014   0.001   PHE B 369 
 TYR   0.026   0.001   TYR B  50 
 ARG   0.003   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
  83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8011 (m-80)
REVERT: A  364 ASP cc_start: 0.8638 (t0) cc_final: 0.8119 (p0)
REVERT: B   82 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8662 (ptp)
REVERT: B  115 ARG cc_start: 0.8128 (tpm170) cc_final: 0.7772 (tpp-160)
REVERT: B  203 TRP cc_start: 0.9208 (OUTLIER) cc_final: 0.8371 (m-10)
REVERT: B  470 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8266 (tppp)
REVERT: B  512 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7450 (t80)
REVERT: B  601 ASN cc_start: 0.9042 (p0) cc_final: 0.8834 (p0)
REVERT: B  610 TRP cc_start: 0.9007 (t60) cc_final: 0.8757 (t60)
  outliers start: 14
  outliers final: 6
  residues processed: 78
  average time/residue: 0.2219
  time to fit residues: 22.9367
Evaluate side-chains
  79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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  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  470 LYS
Chi-restraints excluded: chain B residue  512 PHE
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:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.2814 r_free = 0.2814 target = 0.048036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.040410 restraints weight = 46445.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2583 rms_B_bonded: 3.47
r_work: 0.2467 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2469 r_free = 0.2469    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 = 0.2469 r_free = 0.2469    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8906
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      :  0.004   0.044   6639  Z= 0.226
  Angle     :  0.721  19.822   9025  Z= 0.379
  Chirality :  0.048   0.369    936
  Planarity :  0.004   0.037   1170
  Dihedral  :  4.794  42.681    863
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.49 %
    Favored  : 84.51 %
  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:  0.46 (0.29), residues: 791
  helix:  1.26 (0.27), residues: 394
  sheet:  1.71 (0.74), residues: 47
  loop : -1.00 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.018   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: 14
    poor density    : 70
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8139 (m-80)
REVERT: A  364 ASP cc_start: 0.8624 (t0) cc_final: 0.8137 (p0)
REVERT: B   82 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8683 (ptp)
REVERT: B  203 TRP cc_start: 0.9259 (OUTLIER) cc_final: 0.8492 (m-10)
REVERT: B  383 MET cc_start: 0.8853 (ttm) cc_final: 0.8116 (mtp)
REVERT: B  512 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7616 (t80)
REVERT: B  601 ASN cc_start: 0.9062 (p0) cc_final: 0.8854 (p0)
REVERT: B  610 TRP cc_start: 0.9042 (t60) cc_final: 0.8780 (t60)
  outliers start: 14
  outliers final: 9
  residues processed: 81
  average time/residue: 0.2111
  time to fit residues: 22.8273
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  : 0.797 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0570
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.2821 r_free = 0.2821 target = 0.048328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.040584 restraints weight = 52301.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.2586 rms_B_bonded: 3.67
r_work: 0.2467 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2468
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2468 r_free = 0.2468    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 = 0.2468 r_free = 0.2468    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2468
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.6637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6639  Z= 0.222
  Angle     :  0.730  19.195   9025  Z= 0.381
  Chirality :  0.047   0.355    936
  Planarity :  0.004   0.043   1170
  Dihedral  :  4.783  42.591    863
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.77 %
    Favored  : 84.36 %
  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:  0.47 (0.29), residues: 791
  helix:  1.27 (0.27), residues: 394
  sheet:  1.50 (0.73), residues: 51
  loop : -1.01 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 473 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.017   0.001   PHE B 369 
 TYR   0.025   0.001   TYR B  50 
 ARG   0.004   0.000   ARG B 115 

********************** 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
  85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8119 (m-80)
REVERT: A  364 ASP cc_start: 0.8637 (t0) cc_final: 0.8142 (p0)
REVERT: B   82 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8674 (ptp)
REVERT: B  203 TRP cc_start: 0.9255 (OUTLIER) cc_final: 0.8450 (m-10)
REVERT: B  512 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7492 (t80)
REVERT: B  601 ASN cc_start: 0.9068 (p0) cc_final: 0.8863 (p0)
REVERT: B  610 TRP cc_start: 0.9028 (t60) cc_final: 0.8760 (t60)
  outliers start: 13
  outliers final: 8
  residues processed: 81
  average time/residue: 0.2232
  time to fit residues: 24.1247
Evaluate side-chains
  82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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  512 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 58 optimal weight:    0.0030
   chunk 36 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0040
   chunk 50 optimal weight:    0.0970
   chunk 64 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.1600

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

Flipped N/Q/H residues before XYZ refinement:
A 339 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.051616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.043833 restraints weight = 48659.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2684 rms_B_bonded: 3.59
r_work: 0.2568 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2569
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.6605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6639  Z= 0.176
  Angle     :  0.683  18.177   9025  Z= 0.355
  Chirality :  0.045   0.320    936
  Planarity :  0.004   0.049   1170
  Dihedral  :  4.453  39.156    863
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.49 %
    Favored  : 84.36 %
  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:  0.72 (0.30), residues: 791
  helix:  1.54 (0.27), residues: 389
  sheet:  1.46 (0.72), residues: 51
  loop : -0.91 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 436 
 HIS   0.003   0.000   HIS A 339 
 PHE   0.007   0.001   PHE B 315 
 TYR   0.028   0.001   TYR B  50 
 ARG   0.005   0.000   ARG B 115 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3498.65 seconds
wall clock time: 60 minutes 40.86 seconds (3640.86 seconds total)