Starting phenix.real_space_refine
on Sat Aug 23 10:30:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xbl_38222/08_2025/8xbl_38222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xbl_38222/08_2025/8xbl_38222.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xbl_38222/08_2025/8xbl_38222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xbl_38222/08_2025/8xbl_38222.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xbl_38222/08_2025/8xbl_38222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xbl_38222/08_2025/8xbl_38222.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      58      5.16       5
     C    7285      2.51       5
     N    2011      2.21       5
     O    2155      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11509
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 749, 5758
          Classifications: {'peptide': 749}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 705}
    Chain: "B"
      Number of atoms: 5751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 748, 5751
          Classifications: {'peptide': 748}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 704}
  Time building chain proxies: 3.06, per 1000 atoms: 0.27
  Number of scatterers: 11509
  At special positions: 0
  Unit cell: (99.825, 96.525, 152.625, 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      58     16.00
     O    2155      8.00
     N    2011      7.00
     C    7285      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 562.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 14 sheets defined
      38.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 37
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 55 through 60
    Processing helix  chain 'A' and resid 85 through 92
    Processing helix  chain 'A' and resid 93 through 111
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 3.741A  pdb=" N   LEU A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 155
    Processing helix  chain 'A' and resid 156 through 158
      No H-bonds generated for 'chain 'A' and resid 156 through 158'
    Processing helix  chain 'A' and resid 159 through 169
    Processing helix  chain 'A' and resid 182 through 197
    Processing helix  chain 'A' and resid 256 through 262
    Processing helix  chain 'A' and resid 289 through 304
    Processing helix  chain 'A' and resid 307 through 309
      No H-bonds generated for 'chain 'A' and resid 307 through 309'
    Processing helix  chain 'A' and resid 323 through 336
      removed outlier: 3.659A  pdb=" N   ILE A 327 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 359 through 375
    Processing helix  chain 'A' and resid 407 through 411
      removed outlier: 3.509A  pdb=" N   ARG A 410 " --> pdb=" O   PRO A 407 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET A 411 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 407 through 411'
    Processing helix  chain 'A' and resid 457 through 475
      removed outlier: 4.162A  pdb=" N   THR A 469 " --> pdb=" O   THR A 465 " (cutoff:3.500A)
      Proline residue:  A 470  - end of helix
    Processing helix  chain 'A' and resid 476 through 487
    Processing helix  chain 'A' and resid 544 through 558
      removed outlier: 4.355A  pdb=" N   GLY A 558 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 596
    Processing helix  chain 'A' and resid 609 through 618
    Processing helix  chain 'A' and resid 621 through 635
      removed outlier: 3.609A  pdb=" N   VAL A 625 " --> pdb=" O   ALA A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 678
      removed outlier: 4.297A  pdb=" N   TRP A 671 " --> pdb=" O   ASP A 667 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A 672 " --> pdb=" O   ARG A 668 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 677 " --> pdb=" O   GLU A 673 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ASP A 678 " --> pdb=" O   ALA A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 713
    Processing helix  chain 'A' and resid 719 through 723
    Processing helix  chain 'B' and resid 26 through 36
    Processing helix  chain 'B' and resid 45 through 53
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 78 through 82
    Processing helix  chain 'B' and resid 85 through 91
    Processing helix  chain 'B' and resid 95 through 110
    Processing helix  chain 'B' and resid 130 through 139
    Processing helix  chain 'B' and resid 144 through 155
    Processing helix  chain 'B' and resid 156 through 158
      No H-bonds generated for 'chain 'B' and resid 156 through 158'
    Processing helix  chain 'B' and resid 159 through 169
    Processing helix  chain 'B' and resid 182 through 197
    Processing helix  chain 'B' and resid 256 through 262
    Processing helix  chain 'B' and resid 289 through 304
    Processing helix  chain 'B' and resid 323 through 336
      removed outlier: 3.559A  pdb=" N   ILE B 327 " --> pdb=" O   ILE B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 354
    Processing helix  chain 'B' and resid 359 through 375
    Processing helix  chain 'B' and resid 457 through 467
    Processing helix  chain 'B' and resid 467 through 475
    Processing helix  chain 'B' and resid 476 through 487
    Processing helix  chain 'B' and resid 542 through 557
    Processing helix  chain 'B' and resid 578 through 597
    Processing helix  chain 'B' and resid 609 through 618
    Processing helix  chain 'B' and resid 621 through 635
    Processing helix  chain 'B' and resid 668 through 676
      removed outlier: 3.520A  pdb=" N   SER B 672 " --> pdb=" O   ARG B 668 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 714
      removed outlier: 4.202A  pdb=" N   LEU B 705 " --> pdb=" O   ASP B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 723
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177
      removed outlier: 8.357A  pdb=" N   TYR A 175 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   VAL A 123 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL A 125 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177
      removed outlier: 8.357A  pdb=" N   TYR A 175 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   VAL A 123 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL A 125 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ALA A 248 " --> pdb=" O   VAL A  19 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   VAL A  19 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL A 250 " --> pdb=" O   MET A  17 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   MET A  17 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   VAL A 252 " --> pdb=" O   ILE A  15 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA A 268 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ILE A 430 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   SER A 273 " --> pdb=" O   HIS A 428 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   HIS A 428 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   VAL A 275 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ASN A 426 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ARG A 414 " --> pdb=" O   ILE A 311 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR A 313 " --> pdb=" O   ARG A 414 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   GLY A 312 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   GLY A 347 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL A 314 " --> pdb=" O   GLY A 347 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   CYS A 344 " --> pdb=" O   TYR A 398 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43
      removed outlier: 3.624A  pdb=" N   LYS A  68 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77
    Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377
    Processing sheet with id=AA6, first strand: chain 'A' and resid 449 through 455
    Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 654
      removed outlier: 6.336A  pdb=" N   TRP A 520 " --> pdb=" O   LEU A 602 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   SER A 604 " --> pdb=" O   TRP A 520 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   LEU A 522 " --> pdb=" O   SER A 604 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 174 through 176
      removed outlier: 8.415A  pdb=" N   TYR B 175 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 175 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA B 248 " --> pdb=" O   VAL B  19 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   VAL B  19 " --> pdb=" O   ALA B 248 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL B 250 " --> pdb=" O   MET B  17 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   MET B  17 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL B 252 " --> pdb=" O   ILE B  15 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ALA B 268 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   ILE B 270 " --> pdb=" O   GLU B 432 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   GLU B 432 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY B 272 " --> pdb=" O   ILE B 430 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG B 414 " --> pdb=" O   ILE B 311 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   TYR B 313 " --> pdb=" O   ARG B 414 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 43
      removed outlier: 3.841A  pdb=" N   THR B  42 " --> pdb=" O   LYS B  68 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 65
    Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 77
    Processing sheet with id=AB3, first strand: chain 'B' and resid 376 through 377
    Processing sheet with id=AB4, first strand: chain 'B' and resid 449 through 455
    Processing sheet with id=AB5, first strand: chain 'B' and resid 600 through 602
      removed outlier: 7.278A  pdb=" N   TRP B 520 " --> pdb=" O   THR B 601 " (cutoff:3.500A)

    473 hydrogen bonds defined for protein.
    1356 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: 2.16

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2395
        1.32 -     1.45: 2946
        1.45 -     1.57: 6386
        1.57 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 11811
  Sorted by residual:
  bond pdb=" CA  ILE B 561 "
       pdb=" C   ILE B 561 "
    ideal  model  delta    sigma   weight residual
    1.524  1.495  0.030 1.05e-02 9.07e+03 7.95e+00
  bond pdb=" C   PRO B  94 "
       pdb=" O   PRO B  94 "
    ideal  model  delta    sigma   weight residual
    1.235  1.199  0.036 1.30e-02 5.92e+03 7.69e+00
  bond pdb=" CG  LEU B 480 "
       pdb=" CD1 LEU B 480 "
    ideal  model  delta    sigma   weight residual
    1.521  1.430  0.091 3.30e-02 9.18e+02 7.54e+00
  bond pdb=" CG1 ILE B 210 "
       pdb=" CD1 ILE B 210 "
    ideal  model  delta    sigma   weight residual
    1.513  1.411  0.102 3.90e-02 6.57e+02 6.80e+00
  bond pdb=" CB  MET B 429 "
       pdb=" CG  MET B 429 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.68e+00
  ... (remaining 11806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 15402
        2.42 -     4.84: 593
        4.84 -     7.25: 91
        7.25 -     9.67: 33
        9.67 -    12.09: 3
  Bond angle restraints: 16122
  Sorted by residual:
  angle pdb=" N   LYS B  95 "
        pdb=" CA  LYS B  95 "
        pdb=" C   LYS B  95 "
      ideal   model   delta    sigma   weight residual
     114.04  105.46    8.58 1.24e+00 6.50e-01 4.79e+01
  angle pdb=" N   ASN A 595 "
        pdb=" CA  ASN A 595 "
        pdb=" C   ASN A 595 "
      ideal   model   delta    sigma   weight residual
     111.14  104.67    6.47 1.08e+00 8.57e-01 3.58e+01
  angle pdb=" C   ILE B 561 "
        pdb=" N   PRO B 562 "
        pdb=" CA  PRO B 562 "
      ideal   model   delta    sigma   weight residual
     120.38  115.35    5.03 1.03e+00 9.43e-01 2.39e+01
  angle pdb=" N   GLU A 631 "
        pdb=" CA  GLU A 631 "
        pdb=" CB  GLU A 631 "
      ideal   model   delta    sigma   weight residual
     110.28  117.81   -7.53 1.55e+00 4.16e-01 2.36e+01
  angle pdb=" C   THR A 179 "
        pdb=" N   SER A 180 "
        pdb=" CA  SER A 180 "
      ideal   model   delta    sigma   weight residual
     121.54  130.54   -9.00 1.91e+00 2.74e-01 2.22e+01
  ... (remaining 16117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 6168
       17.83 -    35.65: 642
       35.65 -    53.48: 94
       53.48 -    71.30: 26
       71.30 -    89.13: 16
  Dihedral angle restraints: 6946
    sinusoidal: 2647
      harmonic: 4299
  Sorted by residual:
  dihedral pdb=" CA  HIS A 541 "
           pdb=" C   HIS A 541 "
           pdb=" N   SER A 542 "
           pdb=" CA  SER A 542 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.43  -29.57     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  ASP B 211 "
           pdb=" C   ASP B 211 "
           pdb=" N   LEU B 212 "
           pdb=" CA  LEU B 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.21  -27.79     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  MET A 224 "
           pdb=" C   MET A 224 "
           pdb=" N   ILE A 225 "
           pdb=" CA  ILE A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.99   26.01     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 6943 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1360
       0.071 -    0.142: 347
       0.142 -    0.214: 53
       0.214 -    0.285: 16
       0.285 -    0.356: 6
  Chirality restraints: 1782
  Sorted by residual:
  chirality pdb=" CB  VAL B 362 "
            pdb=" CA  VAL B 362 "
            pdb=" CG1 VAL B 362 "
            pdb=" CG2 VAL B 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" CB  VAL A 362 "
            pdb=" CA  VAL A 362 "
            pdb=" CG1 VAL A 362 "
            pdb=" CG2 VAL A 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CB  THR B 534 "
            pdb=" CA  THR B 534 "
            pdb=" OG1 THR B 534 "
            pdb=" CG2 THR B 534 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.20    0.35 2.00e-01 2.50e+01 3.10e+00
  ... (remaining 1779 not shown)

  Planarity restraints: 2117
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 630 "    0.025 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP A 630 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 630 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 630 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 630 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 630 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 630 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 630 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 630 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 630 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 357 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   HIS B 357 "    0.053 2.00e-02 2.50e+03
        pdb=" O   HIS B 357 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ALA B 358 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 611 "   -0.050 5.00e-02 4.00e+02   7.44e-02 8.87e+00
        pdb=" N   PRO A 612 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 612 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 612 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 2114 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2194
        2.76 -     3.30: 10837
        3.30 -     3.83: 20673
        3.83 -     4.37: 25014
        4.37 -     4.90: 41502
  Nonbonded interactions: 100220
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 309 "
            pdb=" OG1 THR A 338 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG1 THR A 483 "
            pdb=" O   ARG A 731 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   PRO B 308 "
            pdb=" OH  TYR B 343 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   SER B  96 "
            pdb=" ND1 HIS B 100 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   ARG B 582 "
            pdb=" OG1 THR B 586 "
     model   vdw
     2.274 3.040
  ... (remaining 100215 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 2 through 749)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.110
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.450
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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      :  0.011   0.102  11811  Z= 0.468
  Angle     :  1.111  12.091  16122  Z= 0.593
  Chirality :  0.068   0.356   1782
  Planarity :  0.008   0.074   2117
  Dihedral  : 15.273  89.127   4192
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.97 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.50 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.60 (0.19), residues: 1493
  helix: -1.80 (0.18), residues: 539
  sheet: -1.05 (0.36), residues: 212
  loop : -1.80 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 693 
 TYR   0.024   0.003   TYR B 535 
 PHE   0.022   0.003   PHE B 197 
 TRP   0.057   0.003   TRP A 630 
 HIS   0.016   0.002   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.01109 (11811)
  covalent geometry    : angle       1.11126 (16122)
  hydrogen bonds       : bond        0.13991 (  466)
  hydrogen bonds       : angle       7.91058 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.456 
Fit side-chains
REVERT: B  582 ARG cc_start: 0.6491 (mtm110) cc_final: 0.5857 (mtm110)
  outliers start: 7
  outliers final: 1
  residues processed: 121
  average time/residue: 0.1140
  time to fit residues: 20.1952
Evaluate side-chains
  94 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    0.0670
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A  28 HIS
A  56 GLN
A 460 GLN
A 658 ASN
B  56 GLN
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 HIS
B 501 ASN
B 560 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.147168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.104287 restraints weight = 15263.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.39
r_work: 0.2999 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11811  Z= 0.139
  Angle     :  0.620   7.237  16122  Z= 0.319
  Chirality :  0.044   0.225   1782
  Planarity :  0.005   0.061   2117
  Dihedral  :  5.920  58.764   1619
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.29 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  5.58 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.20), residues: 1493
  helix: -0.43 (0.21), residues: 544
  sheet: -1.12 (0.37), residues: 205
  loop : -1.59 (0.21), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 115 
 TYR   0.015   0.001   TYR B 112 
 PHE   0.010   0.001   PHE B 197 
 TRP   0.017   0.001   TRP A 630 
 HIS   0.008   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11811)
  covalent geometry    : angle       0.62006 (16122)
  hydrogen bonds       : bond        0.04243 (  466)
  hydrogen bonds       : angle       5.76079 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 ILE cc_start: 0.7752 (tp) cc_final: 0.7450 (tp)
REVERT: A  703 ASP cc_start: 0.8380 (t0) cc_final: 0.8036 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 116
  average time/residue: 0.1123
  time to fit residues: 19.1145
Evaluate side-chains
  98 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  658 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 145 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 127 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 47 optimal weight:    0.2980
   chunk 17 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.146617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.104206 restraints weight = 15381.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.31
r_work: 0.2993 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11811  Z= 0.148
  Angle     :  0.597   7.244  16122  Z= 0.303
  Chirality :  0.043   0.161   1782
  Planarity :  0.005   0.056   2117
  Dihedral  :  5.565  59.522   1619
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.89 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  9.08 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.21), residues: 1493
  helix:  0.26 (0.22), residues: 539
  sheet: -1.16 (0.37), residues: 199
  loop : -1.41 (0.22), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 115 
 TYR   0.014   0.001   TYR B 535 
 PHE   0.010   0.001   PHE A  21 
 TRP   0.016   0.001   TRP B 133 
 HIS   0.008   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11811)
  covalent geometry    : angle       0.59724 (16122)
  hydrogen bonds       : bond        0.03877 (  466)
  hydrogen bonds       : angle       5.31499 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 ILE cc_start: 0.7830 (tp) cc_final: 0.7584 (tp)
REVERT: A  630 TRP cc_start: 0.7373 (t60) cc_final: 0.7013 (t60)
REVERT: A  703 ASP cc_start: 0.8406 (t0) cc_final: 0.8061 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1123
  time to fit residues: 18.6303
Evaluate side-chains
  103 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  515 MET
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  658 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0770
   chunk 129 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0030
   chunk 98 optimal weight:    3.9990
   chunk 146 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.5348

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

Flipped N/Q/H residues before XYZ refinement:
A 658 ASN
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.148103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.107790 restraints weight = 15381.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.44
r_work: 0.3014 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11811  Z= 0.117
  Angle     :  0.567   7.106  16122  Z= 0.285
  Chirality :  0.043   0.231   1782
  Planarity :  0.004   0.052   2117
  Dihedral  :  5.261  58.644   1619
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.57 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.21), residues: 1493
  helix:  0.57 (0.22), residues: 547
  sheet: -1.14 (0.36), residues: 212
  loop : -1.40 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 693 
 TYR   0.012   0.001   TYR B 104 
 PHE   0.007   0.001   PHE A 124 
 TRP   0.017   0.001   TRP B 133 
 HIS   0.007   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11811)
  covalent geometry    : angle       0.56729 (16122)
  hydrogen bonds       : bond        0.03516 (  466)
  hydrogen bonds       : angle       5.02196 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  630 TRP cc_start: 0.7450 (t60) cc_final: 0.6976 (t60)
REVERT: A  703 ASP cc_start: 0.8354 (t0) cc_final: 0.8062 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 121
  average time/residue: 0.1184
  time to fit residues: 20.6503
Evaluate side-chains
  108 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  515 MET
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  658 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 142 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 107 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 ASN
B 585 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.143531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.097009 restraints weight = 15337.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.16
r_work: 0.2960 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  11811  Z= 0.270
  Angle     :  0.667   8.591  16122  Z= 0.336
  Chirality :  0.046   0.191   1782
  Planarity :  0.005   0.051   2117
  Dihedral  :  5.527  59.729   1619
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.07 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.21), residues: 1493
  helix:  0.54 (0.22), residues: 541
  sheet: -1.08 (0.36), residues: 213
  loop : -1.38 (0.22), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 265 
 TYR   0.021   0.002   TYR B 112 
 PHE   0.014   0.002   PHE B  21 
 TRP   0.014   0.002   TRP B 133 
 HIS   0.007   0.001   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (11811)
  covalent geometry    : angle       0.66678 (16122)
  hydrogen bonds       : bond        0.04048 (  466)
  hydrogen bonds       : angle       5.18284 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
REVERT: A  630 TRP cc_start: 0.7400 (t60) cc_final: 0.7145 (t60)
REVERT: B  459 GLU cc_start: 0.7761 (tp30) cc_final: 0.7452 (tp30)
  outliers start: 25
  outliers final: 22
  residues processed: 118
  average time/residue: 0.1074
  time to fit residues: 18.7257
Evaluate side-chains
  117 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  726 THR
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  501 ASN
Chi-restraints excluded: chain B residue  515 MET
Chi-restraints excluded: chain B residue  585 GLN
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  686 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0870
   chunk 132 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 47 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 85 optimal weight:    0.2980
   chunk 95 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.146209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.103439 restraints weight = 15347.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.39
r_work: 0.2977 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11811  Z= 0.135
  Angle     :  0.585   7.959  16122  Z= 0.295
  Chirality :  0.043   0.179   1782
  Planarity :  0.004   0.050   2117
  Dihedral  :  5.294  59.838   1619
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.32 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.21), residues: 1493
  helix:  0.79 (0.22), residues: 541
  sheet: -1.05 (0.37), residues: 202
  loop : -1.38 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 582 
 TYR   0.012   0.001   TYR B 104 
 PHE   0.007   0.001   PHE A 450 
 TRP   0.018   0.001   TRP B 133 
 HIS   0.007   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11811)
  covalent geometry    : angle       0.58533 (16122)
  hydrogen bonds       : bond        0.03584 (  466)
  hydrogen bonds       : angle       4.99900 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A  630 TRP cc_start: 0.7507 (t60) cc_final: 0.7240 (t60)
REVERT: A  703 ASP cc_start: 0.8428 (t0) cc_final: 0.8096 (t0)
REVERT: B  660 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5809 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 114
  average time/residue: 0.1056
  time to fit residues: 18.2398
Evaluate side-chains
  113 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  726 THR
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  515 MET
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  686 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 135 optimal weight:    9.9990
   chunk 143 optimal weight:    0.9980
   chunk 114 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 120 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 ASN
B 585 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.143710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.100940 restraints weight = 15284.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.34
r_work: 0.2939 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11811  Z= 0.222
  Angle     :  0.633   8.464  16122  Z= 0.318
  Chirality :  0.045   0.183   1782
  Planarity :  0.005   0.050   2117
  Dihedral  :  5.389  59.712   1619
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 12.74 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.21), residues: 1493
  helix:  0.64 (0.22), residues: 554
  sheet: -1.07 (0.36), residues: 213
  loop : -1.40 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  20 
 TYR   0.017   0.002   TYR B 112 
 PHE   0.011   0.001   PHE B  21 
 TRP   0.016   0.001   TRP B 133 
 HIS   0.006   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (11811)
  covalent geometry    : angle       0.63291 (16122)
  hydrogen bonds       : bond        0.03813 (  466)
  hydrogen bonds       : angle       5.05777 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  630 TRP cc_start: 0.7538 (t60) cc_final: 0.7249 (t60)
REVERT: A  703 ASP cc_start: 0.8491 (t0) cc_final: 0.8155 (t0)
REVERT: B  660 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5828 (tp)
  outliers start: 33
  outliers final: 25
  residues processed: 122
  average time/residue: 0.1073
  time to fit residues: 19.8170
Evaluate side-chains
  120 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  726 THR
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  515 MET
Chi-restraints excluded: chain B residue  585 GLN
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  686 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 70 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 139 optimal weight:    3.9990
   chunk 117 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.145748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.102975 restraints weight = 15288.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.34
r_work: 0.2976 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11811  Z= 0.152
  Angle     :  0.603   8.048  16122  Z= 0.300
  Chirality :  0.043   0.174   1782
  Planarity :  0.004   0.050   2117
  Dihedral  :  5.249  59.103   1619
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.99 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.21), residues: 1493
  helix:  0.78 (0.22), residues: 553
  sheet: -0.99 (0.37), residues: 208
  loop : -1.42 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 582 
 TYR   0.013   0.001   TYR B 112 
 PHE   0.008   0.001   PHE A 450 
 TRP   0.018   0.001   TRP B 133 
 HIS   0.007   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (11811)
  covalent geometry    : angle       0.60328 (16122)
  hydrogen bonds       : bond        0.03574 (  466)
  hydrogen bonds       : angle       4.97725 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A  630 TRP cc_start: 0.7551 (t60) cc_final: 0.7310 (t60)
REVERT: A  703 ASP cc_start: 0.8446 (t0) cc_final: 0.8141 (t0)
REVERT: B  468 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8462 (mt)
REVERT: B  660 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5787 (tp)
  outliers start: 29
  outliers final: 25
  residues processed: 122
  average time/residue: 0.1007
  time to fit residues: 18.4927
Evaluate side-chains
  121 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  726 THR
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  515 MET
Chi-restraints excluded: chain B residue  556 LEU
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  686 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 142 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 138 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 585 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.144046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.101359 restraints weight = 15215.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.36
r_work: 0.2944 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11811  Z= 0.221
  Angle     :  0.644   9.921  16122  Z= 0.320
  Chirality :  0.045   0.182   1782
  Planarity :  0.005   0.049   2117
  Dihedral  :  5.337  59.102   1619
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 12.66 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.21), residues: 1493
  helix:  0.71 (0.22), residues: 553
  sheet: -0.91 (0.37), residues: 206
  loop : -1.41 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 582 
 TYR   0.017   0.002   TYR B 112 
 PHE   0.011   0.001   PHE A 450 
 TRP   0.016   0.001   TRP B 133 
 HIS   0.006   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 (11811)
  covalent geometry    : angle       0.64433 (16122)
  hydrogen bonds       : bond        0.03762 (  466)
  hydrogen bonds       : angle       5.04434 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  703 ASP cc_start: 0.8505 (t0) cc_final: 0.8202 (t0)
REVERT: B  468 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: B  660 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5881 (tp)
  outliers start: 32
  outliers final: 25
  residues processed: 122
  average time/residue: 0.1044
  time to fit residues: 19.6081
Evaluate side-chains
  122 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  726 THR
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  515 MET
Chi-restraints excluded: chain B residue  556 LEU
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  686 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 139 optimal weight:    8.9990
   chunk 21 optimal weight:    0.5980
   chunk 43 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0170
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 585 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.146938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.103808 restraints weight = 15233.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.39
r_work: 0.2994 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11811  Z= 0.122
  Angle     :  0.590  10.186  16122  Z= 0.293
  Chirality :  0.043   0.177   1782
  Planarity :  0.004   0.050   2117
  Dihedral  :  5.091  58.169   1619
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.07 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.22), residues: 1493
  helix:  0.89 (0.22), residues: 559
  sheet: -0.92 (0.37), residues: 202
  loop : -1.41 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 582 
 TYR   0.011   0.001   TYR B 482 
 PHE   0.007   0.001   PHE A 124 
 TRP   0.033   0.001   TRP A 630 
 HIS   0.006   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (11811)
  covalent geometry    : angle       0.59016 (16122)
  hydrogen bonds       : bond        0.03371 (  466)
  hydrogen bonds       : angle       4.87367 ( 1356)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  703 ASP cc_start: 0.8392 (t0) cc_final: 0.8093 (t0)
REVERT: B  468 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8339 (mt)
REVERT: B  660 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5771 (tp)
  outliers start: 28
  outliers final: 22
  residues processed: 119
  average time/residue: 0.1042
  time to fit residues: 18.5563
Evaluate side-chains
  119 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  391 ASP
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  658 ASN
Chi-restraints excluded: chain A residue  726 THR
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  556 LEU
Chi-restraints excluded: chain B residue  585 GLN
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  686 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 92 optimal weight:    1.9990
   chunk 139 optimal weight:   20.0000
   chunk 129 optimal weight:    6.9990
   chunk 140 optimal weight:    7.9990
   chunk 142 optimal weight:    9.9990
   chunk 102 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.142168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.099821 restraints weight = 15321.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.37
r_work: 0.2911 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  11811  Z= 0.314
  Angle     :  0.715  10.573  16122  Z= 0.355
  Chirality :  0.048   0.197   1782
  Planarity :  0.005   0.048   2117
  Dihedral  :  5.460  59.318   1619
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.66 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.21), residues: 1493
  helix:  0.65 (0.22), residues: 554
  sheet: -0.99 (0.36), residues: 213
  loop : -1.38 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 582 
 TYR   0.021   0.002   TYR B 112 
 PHE   0.014   0.002   PHE B  21 
 TRP   0.039   0.002   TRP A 630 
 HIS   0.008   0.002   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 (11811)
  covalent geometry    : angle       0.71472 (16122)
  hydrogen bonds       : bond        0.03978 (  466)
  hydrogen bonds       : angle       5.11346 ( 1356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3838.20 seconds
wall clock time: 66 minutes 36.49 seconds (3996.49 seconds total)