Starting phenix.real_space_refine
on Sat Aug 23 12:01:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xjt_38405/08_2025/8xjt_38405.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xjt_38405/08_2025/8xjt_38405.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xjt_38405/08_2025/8xjt_38405.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xjt_38405/08_2025/8xjt_38405.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xjt_38405/08_2025/8xjt_38405.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xjt_38405/08_2025/8xjt_38405.map"
  }
  resolution = 3.9
  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=   0.001 sd=   0.059
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      61      5.16       5
     C    7577      2.51       5
     N    2085      2.21       5
     O    2243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 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: 11966
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 5740
          Classifications: {'peptide': 747}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 703}
    Chain: "B"
      Number of atoms: 5740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 5740
          Classifications: {'peptide': 747}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 703}
    Chain: "C"
      Number of atoms: 486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 486
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 3, 'TRANS': 57}
          Chain breaks: 1
  Time building chain proxies: 3.01, per 1000 atoms: 0.25
  Number of scatterers: 11966
  At special positions: 0
  Unit cell: (124.283, 99.2082, 158.079, 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      61     16.00
     O    2243      8.00
     N    2085      7.00
     C    7577      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: 0.82
  Conformation dependent library (CDL) restraints added in 549.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2864

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 12 sheets defined
      37.9% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 37
      removed outlier: 3.666A  pdb=" N   GLY A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 53
      removed outlier: 3.724A  pdb=" N   GLY A  53 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 60
      removed outlier: 4.000A  pdb=" N   LEU A  59 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASP A  60 " --> pdb=" O   GLN A  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 55 through 60'
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 4.807A  pdb=" N   GLU A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 4.208A  pdb=" N   SER A 139 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 154
    Processing helix  chain 'A' and resid 160 through 168
      removed outlier: 3.632A  pdb=" N   LEU A 168 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 196
    Processing helix  chain 'A' and resid 256 through 261
    Processing helix  chain 'A' and resid 290 through 303
    Processing helix  chain 'A' and resid 323 through 336
      removed outlier: 3.729A  pdb=" N   ILE A 327 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 352
      removed outlier: 3.992A  pdb=" N   ALA A 351 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 375
    Processing helix  chain 'A' and resid 457 through 466
    Processing helix  chain 'A' and resid 467 through 475
      removed outlier: 3.772A  pdb=" N   THR A 474 " --> pdb=" O   PRO A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 486
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.678A  pdb=" N   ALA A 540 " --> pdb=" O   GLN A 537 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   HIS A 541 " --> pdb=" O   TRP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 558
      removed outlier: 3.503A  pdb=" N   GLU A 548 " --> pdb=" O   HIS A 544 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY A 558 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 578
      removed outlier: 3.535A  pdb=" N   ALA A 573 " --> pdb=" O   THR A 570 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   ALA A 575 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   ASN A 576 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A 577 " --> pdb=" O   GLN A 574 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER A 578 " --> pdb=" O   ALA A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 596
      removed outlier: 3.660A  pdb=" N   ALA A 588 " --> pdb=" O   CYS A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 608
      No H-bonds generated for 'chain 'A' and resid 606 through 608'
    Processing helix  chain 'A' and resid 609 through 618
    Processing helix  chain 'A' and resid 622 through 635
    Processing helix  chain 'A' and resid 667 through 676
      removed outlier: 3.704A  pdb=" N   TRP A 671 " --> pdb=" O   ASP A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 713
      removed outlier: 4.359A  pdb=" N   LEU A 705 " --> pdb=" O   ASP A 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 36
      removed outlier: 3.632A  pdb=" N   PHE B  30 " --> pdb=" O   THR B  26 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLN B  36 " --> pdb=" O   HIS B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 51
      removed outlier: 3.568A  pdb=" N   ALA B  51 " --> pdb=" O   GLU B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 60
      removed outlier: 4.051A  pdb=" N   LEU B  59 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASP B  60 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 55 through 60'
    Processing helix  chain 'B' and resid 78 through 83
      removed outlier: 4.115A  pdb=" N   PHE B  82 " --> pdb=" O   ASP B  78 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY B  83 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 78 through 83'
    Processing helix  chain 'B' and resid 85 through 91
    Processing helix  chain 'B' and resid 93 through 109
      removed outlier: 3.542A  pdb=" N   ARG B  97 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU B 101 " --> pdb=" O   ARG B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 138
      removed outlier: 3.605A  pdb=" N   LEU B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 155
    Processing helix  chain 'B' and resid 160 through 168
    Processing helix  chain 'B' and resid 182 through 197
    Processing helix  chain 'B' and resid 255 through 262
    Processing helix  chain 'B' and resid 290 through 303
    Processing helix  chain 'B' and resid 323 through 335
      removed outlier: 3.954A  pdb=" N   ILE B 327 " --> pdb=" O   ILE B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 352
    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
      removed outlier: 4.195A  pdb=" N   LEU B 471 " --> pdb=" O   GLN B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 486
      removed outlier: 3.567A  pdb=" N   LEU B 480 " --> pdb=" O   ASP B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 560
      removed outlier: 3.563A  pdb=" N   GLN B 546 " --> pdb=" O   SER B 542 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU B 555 " --> pdb=" O   ALA B 551 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP B 557 " --> pdb=" O   THR B 553 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   GLY B 558 " --> pdb=" O   ALA B 554 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   MET B 559 " --> pdb=" O   LEU B 555 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ASN B 560 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 596
      removed outlier: 3.553A  pdb=" N   ARG B 582 " --> pdb=" O   SER B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 617
    Processing helix  chain 'B' and resid 621 through 635
      removed outlier: 3.831A  pdb=" N   VAL B 625 " --> pdb=" O   ALA B 621 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   TRP B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU B 631 " --> pdb=" O   HIS B 627 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLU B 633 " --> pdb=" O   LEU B 629 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLN B 634 " --> pdb=" O   TRP B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 674
    Processing helix  chain 'B' and resid 701 through 715
      removed outlier: 3.667A  pdb=" N   LEU B 705 " --> pdb=" O   ASP B 701 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY B 715 " --> pdb=" O   LEU B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 723
    Processing helix  chain 'C' and resid 787 through 797
    Processing helix  chain 'C' and resid 817 through 829
      removed outlier: 4.194A  pdb=" N   LEU C 825 " --> pdb=" O   LEU C 821 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU C 826 " --> pdb=" O   THR C 822 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ARG C 827 " --> pdb=" O   SER C 823 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASP C 828 " --> pdb=" O   ARG C 824 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 834 through 839
    Processing helix  chain 'C' and resid 843 through 854
    Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 255
    Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 277
      removed outlier: 3.551A  pdb=" N   HIS A 428 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASN A 276 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 417 " --> pdb=" O   MET A 429 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377
    Processing sheet with id=AA4, first strand: chain 'A' and resid 449 through 455
      removed outlier: 3.707A  pdb=" N   VAL A 499 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 521
      removed outlier: 3.516A  pdb=" N   GLY A 521 " --> pdb=" O   ASN A 690 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 13
      removed outlier: 3.518A  pdb=" N   ASN B 276 " --> pdb=" O   ASN B 426 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   HIS B 428 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13
      removed outlier: 3.559A  pdb=" N   VAL B 427 " --> pdb=" O   SER B 419 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET B 429 " --> pdb=" O   VAL B 417 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL B 417 " --> pdb=" O   MET B 429 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 122 through 123
      removed outlier: 7.441A  pdb=" N   GLY B 122 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 377
    Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 451
    Processing sheet with id=AB2, first strand: chain 'B' and resid 454 through 455
      removed outlier: 3.500A  pdb=" N   ALA B 455 " --> pdb=" O   CYS B 493 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 520 through 521

    369 hydrogen bonds defined for protein.
    1041 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: 1.46

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3224
        1.33 -     1.45: 2473
        1.45 -     1.57: 6488
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 12275
  Sorted by residual:
  bond pdb=" CA  GLY B 206 "
       pdb=" C   GLY B 206 "
    ideal  model  delta    sigma   weight residual
    1.515  1.475  0.040 1.00e-02 1.00e+04 1.58e+01
  bond pdb=" CB  THR A 368 "
       pdb=" CG2 THR A 368 "
    ideal  model  delta    sigma   weight residual
    1.521  1.412  0.109 3.30e-02 9.18e+02 1.10e+01
  bond pdb=" CB  VAL A 269 "
       pdb=" CG2 VAL A 269 "
    ideal  model  delta    sigma   weight residual
    1.521  1.419  0.102 3.30e-02 9.18e+02 9.48e+00
  bond pdb=" CB  VAL A 102 "
       pdb=" CG1 VAL A 102 "
    ideal  model  delta    sigma   weight residual
    1.521  1.420  0.101 3.30e-02 9.18e+02 9.28e+00
  bond pdb=" CB  MET A 429 "
       pdb=" CG  MET A 429 "
    ideal  model  delta    sigma   weight residual
    1.520  1.433  0.087 3.00e-02 1.11e+03 8.46e+00
  ... (remaining 12270 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 15674
        2.36 -     4.72: 884
        4.72 -     7.08: 151
        7.08 -     9.43: 37
        9.43 -    11.79: 6
  Bond angle restraints: 16752
  Sorted by residual:
  angle pdb=" N   SER A 180 "
        pdb=" CA  SER A 180 "
        pdb=" C   SER A 180 "
      ideal   model   delta    sigma   weight residual
     110.80  122.59  -11.79 2.13e+00 2.20e-01 3.07e+01
  angle pdb=" C   SER C 815 "
        pdb=" N   LEU C 816 "
        pdb=" CA  LEU C 816 "
      ideal   model   delta    sigma   weight residual
     121.19  129.31   -8.12 1.59e+00 3.96e-01 2.61e+01
  angle pdb=" N   GLU A 631 "
        pdb=" CA  GLU A 631 "
        pdb=" CB  GLU A 631 "
      ideal   model   delta    sigma   weight residual
     110.39  118.43   -8.04 1.66e+00 3.63e-01 2.34e+01
  angle pdb=" N   VAL A 722 "
        pdb=" CA  VAL A 722 "
        pdb=" C   VAL A 722 "
      ideal   model   delta    sigma   weight residual
     112.29  107.75    4.54 9.40e-01 1.13e+00 2.34e+01
  angle pdb=" C   SER B 180 "
        pdb=" N   CYS B 181 "
        pdb=" CA  CYS B 181 "
      ideal   model   delta    sigma   weight residual
     121.54  130.76   -9.22 1.91e+00 2.74e-01 2.33e+01
  ... (remaining 16747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.51: 6436
       18.51 -    37.01: 666
       37.01 -    55.52: 84
       55.52 -    74.03: 25
       74.03 -    92.54: 16
  Dihedral angle restraints: 7227
    sinusoidal: 2760
      harmonic: 4467
  Sorted by residual:
  dihedral pdb=" CA  ASP B 158 "
           pdb=" C   ASP B 158 "
           pdb=" N   LEU B 159 "
           pdb=" CA  LEU B 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.71   27.29     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  ASP B 130 "
           pdb=" C   ASP B 130 "
           pdb=" N   VAL B 131 "
           pdb=" CA  VAL B 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.66  -26.34     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  THR A 179 "
           pdb=" C   THR A 179 "
           pdb=" N   SER A 180 "
           pdb=" CA  SER A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.84   26.16     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 7224 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1543
       0.094 -    0.188: 274
       0.188 -    0.282: 33
       0.282 -    0.376: 8
       0.376 -    0.469: 1
  Chirality restraints: 1859
  Sorted by residual:
  chirality pdb=" CB  ILE A 422 "
            pdb=" CA  ILE A 422 "
            pdb=" CG1 ILE A 422 "
            pdb=" CG2 ILE A 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.47 2.00e-01 2.50e+01 5.51e+00
  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   -2.26   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CA  THR A 726 "
            pdb=" N   THR A 726 "
            pdb=" C   THR A 726 "
            pdb=" CB  THR A 726 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.19    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 1856 not shown)

  Planarity restraints: 2197
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 451 "    0.053 5.00e-02 4.00e+02   7.76e-02 9.64e+00
        pdb=" N   PRO A 452 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 452 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 452 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 395 "    0.050 5.00e-02 4.00e+02   7.48e-02 8.94e+00
        pdb=" N   PRO A 396 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 396 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 396 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 445 "    0.015 2.00e-02 2.50e+03   2.97e-02 8.84e+00
        pdb=" C   VAL A 445 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL A 445 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 446 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2194 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2154
        2.76 -     3.30: 10385
        3.30 -     3.83: 18091
        3.83 -     4.37: 19358
        4.37 -     4.90: 35348
  Nonbonded interactions: 85336
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 483 "
            pdb=" O   ARG A 731 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" CD2 LEU B 204 "
            pdb=" CG2 VAL B 252 "
     model   vdw
     2.248 3.880
  nonbonded pdb=" OE2 GLU A 309 "
            pdb=" OG1 THR A 338 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   SER B 419 "
            pdb=" OG  SER B 419 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   SER A 419 "
            pdb=" OG  SER A 419 "
     model   vdw
     2.304 3.040
  ... (remaining 85331 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'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  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:                    0.040
  Process input model:                     11.180
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
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      :  0.014   0.119  12275  Z= 0.545
  Angle     :  1.261  11.793  16752  Z= 0.690
  Chirality :  0.075   0.469   1859
  Planarity :  0.008   0.078   2197
  Dihedral  : 15.568  92.536   4363
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 11.70 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  1.84 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -4.42 (0.17), residues: 1547
  helix: -2.76 (0.16), residues: 543
  sheet: -2.93 (0.34), residues: 186
  loop : -3.10 (0.18), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG B 265 
 TYR   0.040   0.004   TYR A 398 
 PHE   0.039   0.003   PHE B 124 
 TRP   0.023   0.003   TRP B 133 
 HIS   0.016   0.002   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.01355 (12275)
  covalent geometry    : angle       1.26144 (16752)
  hydrogen bonds       : bond        0.17619 (  365)
  hydrogen bonds       : angle       6.77620 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  594 MET cc_start: 0.7362 (ttm) cc_final: 0.7106 (mtt)
REVERT: A  692 VAL cc_start: 0.9609 (t) cc_final: 0.9283 (m)
REVERT: B  315 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8081 (tt0)
REVERT: B  432 GLU cc_start: 0.8420 (tt0) cc_final: 0.8097 (tt0)
REVERT: B  691 TRP cc_start: 0.7054 (m100) cc_final: 0.6793 (m100)
  outliers start: 9
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0777
  time to fit residues: 15.4303
Evaluate side-chains
  101 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  315 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0870
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:   40.0000
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 342 GLN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 HIS
B 302 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.179740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.160607 restraints weight = 13103.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.132376 restraints weight = 32082.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.126695 restraints weight = 29320.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.123782 restraints weight = 24102.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.123189 restraints weight = 18933.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12275  Z= 0.122
  Angle     :  0.628   9.484  16752  Z= 0.322
  Chirality :  0.044   0.163   1859
  Planarity :  0.005   0.059   2197
  Dihedral  :  5.999  79.743   1679
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.50 %
    Favored  : 91.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -3.21 (0.19), residues: 1547
  helix: -1.22 (0.20), residues: 545
  sheet: -2.36 (0.38), residues: 167
  loop : -2.78 (0.19), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 271 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.010   0.001   PHE B 124 
 TRP   0.012   0.001   TRP A  31 
 HIS   0.008   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12275)
  covalent geometry    : angle       0.62760 (16752)
  hydrogen bonds       : bond        0.04337 (  365)
  hydrogen bonds       : angle       4.61843 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: B  432 GLU cc_start: 0.8119 (tt0) cc_final: 0.7912 (tt0)
REVERT: B  701 ASP cc_start: 0.8066 (p0) cc_final: 0.7580 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 122
  average time/residue: 0.0809
  time to fit residues: 15.6527
Evaluate side-chains
  105 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  559 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 133 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 149 optimal weight:   40.0000
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 342 GLN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 645 HIS
A 710 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.174125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.158850 restraints weight = 13340.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.119509 restraints weight = 33043.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.117417 restraints weight = 35387.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.115610 restraints weight = 30582.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.115449 restraints weight = 21020.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  12275  Z= 0.238
  Angle     :  0.699   8.507  16752  Z= 0.361
  Chirality :  0.047   0.173   1859
  Planarity :  0.005   0.067   2197
  Dihedral  :  5.509  23.217   1676
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.05 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -2.83 (0.20), residues: 1547
  helix: -0.50 (0.22), residues: 533
  sheet: -2.65 (0.35), residues: 181
  loop : -2.71 (0.19), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 699 
 TYR   0.018   0.002   TYR A 398 
 PHE   0.027   0.002   PHE B 124 
 TRP   0.012   0.001   TRP B 133 
 HIS   0.010   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 (12275)
  covalent geometry    : angle       0.69916 (16752)
  hydrogen bonds       : bond        0.05382 (  365)
  hydrogen bonds       : angle       4.56628 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7314 (mm-30)
REVERT: A  631 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8022 (mm-30)
REVERT: A  697 GLU cc_start: 0.7625 (pm20) cc_final: 0.6724 (tm-30)
REVERT: B  432 GLU cc_start: 0.8192 (tt0) cc_final: 0.7959 (tt0)
REVERT: B  701 ASP cc_start: 0.8140 (p0) cc_final: 0.7795 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 114
  average time/residue: 0.0795
  time to fit residues: 14.2380
Evaluate side-chains
  109 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  315 GLU
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  631 GLU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 144 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 119 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   chunk 138 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 342 GLN
A 357 HIS
A 595 ASN
A 645 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.178608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.161801 restraints weight = 13133.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.159545 restraints weight = 35085.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.130518 restraints weight = 36814.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.123030 restraints weight = 31414.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.122423 restraints weight = 25172.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12275  Z= 0.121
  Angle     :  0.572   7.413  16752  Z= 0.292
  Chirality :  0.043   0.201   1859
  Planarity :  0.004   0.050   2197
  Dihedral  :  4.914  19.860   1676
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.09 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -2.37 (0.20), residues: 1547
  helix:  0.09 (0.23), residues: 528
  sheet: -2.45 (0.36), residues: 174
  loop : -2.58 (0.19), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  97 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.011   0.001   PHE B 124 
 TRP   0.009   0.001   TRP A  31 
 HIS   0.010   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12275)
  covalent geometry    : angle       0.57247 (16752)
  hydrogen bonds       : bond        0.03778 (  365)
  hydrogen bonds       : angle       4.05917 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  631 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7836 (mm-30)
REVERT: A  697 GLU cc_start: 0.7761 (pm20) cc_final: 0.6664 (tm-30)
REVERT: B  701 ASP cc_start: 0.8102 (p0) cc_final: 0.7772 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 123
  average time/residue: 0.0829
  time to fit residues: 16.3579
Evaluate side-chains
  114 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  631 GLU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  209 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 152 optimal weight:   40.0000
   chunk 145 optimal weight:    0.7980
   chunk 140 optimal weight:   30.0000
   chunk 93 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0870
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A 645 HIS
C 846 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.179566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.163465 restraints weight = 13034.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.161327 restraints weight = 33341.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.133793 restraints weight = 36277.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.125305 restraints weight = 30092.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.124711 restraints weight = 24929.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12275  Z= 0.110
  Angle     :  0.553   9.564  16752  Z= 0.279
  Chirality :  0.042   0.170   1859
  Planarity :  0.004   0.052   2197
  Dihedral  :  4.518  19.090   1676
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 14.05 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -2.07 (0.21), residues: 1547
  helix:  0.46 (0.23), residues: 531
  sheet: -2.25 (0.36), residues: 173
  loop : -2.51 (0.19), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 699 
 TYR   0.009   0.001   TYR B 104 
 PHE   0.010   0.001   PHE B 124 
 TRP   0.007   0.001   TRP A  31 
 HIS   0.011   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (12275)
  covalent geometry    : angle       0.55338 (16752)
  hydrogen bonds       : bond        0.03388 (  365)
  hydrogen bonds       : angle       3.85307 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  631 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7530 (mm-30)
REVERT: A  697 GLU cc_start: 0.7639 (pm20) cc_final: 0.6563 (tm-30)
REVERT: B  691 TRP cc_start: 0.6911 (m100) cc_final: 0.6330 (m100)
REVERT: B  701 ASP cc_start: 0.7977 (p0) cc_final: 0.7764 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0737
  time to fit residues: 14.7145
Evaluate side-chains
  116 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  631 GLU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 152 optimal weight:   40.0000
   chunk 77 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 131 optimal weight:    7.9990
   chunk 127 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
B 467 GLN
C 846 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.175147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.159170 restraints weight = 13197.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.124238 restraints weight = 33980.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.120017 restraints weight = 35624.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.118679 restraints weight = 29987.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.117754 restraints weight = 24313.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  12275  Z= 0.191
  Angle     :  0.632   8.671  16752  Z= 0.322
  Chirality :  0.046   0.214   1859
  Planarity :  0.005   0.052   2197
  Dihedral  :  4.800  20.807   1676
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.56 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -2.11 (0.21), residues: 1547
  helix:  0.45 (0.23), residues: 531
  sheet: -2.32 (0.36), residues: 175
  loop : -2.53 (0.20), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 265 
 TYR   0.015   0.002   TYR A 398 
 PHE   0.022   0.001   PHE B 124 
 TRP   0.009   0.001   TRP B 133 
 HIS   0.009   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (12275)
  covalent geometry    : angle       0.63154 (16752)
  hydrogen bonds       : bond        0.04552 (  365)
  hydrogen bonds       : angle       4.10187 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7258 (mm-30)
REVERT: A  362 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7438 (p)
REVERT: A  697 GLU cc_start: 0.7637 (pm20) cc_final: 0.6449 (tm-30)
REVERT: B  691 TRP cc_start: 0.6616 (m100) cc_final: 0.6123 (m100)
REVERT: B  701 ASP cc_start: 0.8262 (p0) cc_final: 0.7928 (t0)
  outliers start: 27
  outliers final: 21
  residues processed: 120
  average time/residue: 0.0802
  time to fit residues: 15.6944
Evaluate side-chains
  121 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLU
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  703 ASP
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 132 optimal weight:   30.0000
   chunk 110 optimal weight:    0.5980
   chunk 144 optimal weight:    0.9990
   chunk 59 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   chunk 126 optimal weight:   20.0000
   chunk 135 optimal weight:   20.0000
   chunk 51 optimal weight:    0.1980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN
C 846 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.180710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.165900 restraints weight = 12965.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.129302 restraints weight = 29900.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.126121 restraints weight = 29972.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.126158 restraints weight = 25975.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.125665 restraints weight = 21544.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12275  Z= 0.101
  Angle     :  0.545   8.853  16752  Z= 0.273
  Chirality :  0.042   0.198   1859
  Planarity :  0.004   0.047   2197
  Dihedral  :  4.336  18.003   1676
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.76 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -1.81 (0.21), residues: 1547
  helix:  0.78 (0.23), residues: 531
  sheet: -2.13 (0.36), residues: 173
  loop : -2.42 (0.20), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  20 
 TYR   0.009   0.001   TYR A 104 
 PHE   0.007   0.001   PHE B 124 
 TRP   0.008   0.001   TRP A  31 
 HIS   0.009   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (12275)
  covalent geometry    : angle       0.54453 (16752)
  hydrogen bonds       : bond        0.03075 (  365)
  hydrogen bonds       : angle       3.75883 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A  601 THR cc_start: 0.9251 (m) cc_final: 0.8787 (p)
REVERT: A  697 GLU cc_start: 0.7610 (pm20) cc_final: 0.6571 (tm-30)
REVERT: B  691 TRP cc_start: 0.6979 (m100) cc_final: 0.6420 (m100)
  outliers start: 21
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0793
  time to fit residues: 14.4201
Evaluate side-chains
  116 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 129 optimal weight:   30.0000
   chunk 24 optimal weight:    2.9990
   chunk 143 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 63 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   chunk 133 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0870
   chunk 139 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.9760

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.178602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.160319 restraints weight = 12948.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.127915 restraints weight = 34493.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.124058 restraints weight = 30244.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.122336 restraints weight = 24834.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.122332 restraints weight = 20115.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12275  Z= 0.128
  Angle     :  0.569   9.553  16752  Z= 0.286
  Chirality :  0.043   0.183   1859
  Planarity :  0.004   0.050   2197
  Dihedral  :  4.341  18.275   1676
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.00 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -1.75 (0.21), residues: 1547
  helix:  0.85 (0.23), residues: 532
  sheet: -2.04 (0.36), residues: 175
  loop : -2.43 (0.20), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  97 
 TYR   0.016   0.001   TYR B 383 
 PHE   0.013   0.001   PHE B 124 
 TRP   0.006   0.001   TRP A  31 
 HIS   0.008   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12275)
  covalent geometry    : angle       0.56924 (16752)
  hydrogen bonds       : bond        0.03522 (  365)
  hydrogen bonds       : angle       3.78922 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7473 (p)
REVERT: A  601 THR cc_start: 0.9184 (m) cc_final: 0.8749 (p)
REVERT: A  697 GLU cc_start: 0.7642 (pm20) cc_final: 0.6575 (tm-30)
REVERT: B  691 TRP cc_start: 0.6804 (m100) cc_final: 0.6318 (m100)
  outliers start: 25
  outliers final: 21
  residues processed: 117
  average time/residue: 0.0760
  time to fit residues: 14.6716
Evaluate side-chains
  119 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 89 optimal weight:    8.9990
   chunk 128 optimal weight:    9.9990
   chunk 131 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 142 optimal weight:   20.0000
   chunk 132 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 147 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 645 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.176966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.166929 restraints weight = 13023.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.125943 restraints weight = 36262.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.122835 restraints weight = 37313.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.120330 restraints weight = 29018.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.120688 restraints weight = 22098.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12275  Z= 0.155
  Angle     :  0.593   9.160  16752  Z= 0.298
  Chirality :  0.044   0.181   1859
  Planarity :  0.004   0.048   2197
  Dihedral  :  4.454  19.356   1676
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.92 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -1.79 (0.21), residues: 1547
  helix:  0.83 (0.23), residues: 535
  sheet: -2.06 (0.36), residues: 175
  loop : -2.48 (0.19), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  97 
 TYR   0.018   0.001   TYR B 383 
 PHE   0.017   0.001   PHE B 124 
 TRP   0.007   0.001   TRP B 133 
 HIS   0.006   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (12275)
  covalent geometry    : angle       0.59280 (16752)
  hydrogen bonds       : bond        0.03915 (  365)
  hydrogen bonds       : angle       3.85668 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7486 (p)
REVERT: A  601 THR cc_start: 0.9190 (m) cc_final: 0.8740 (p)
REVERT: A  697 GLU cc_start: 0.7704 (pm20) cc_final: 0.6615 (tm-30)
REVERT: B  691 TRP cc_start: 0.6911 (m100) cc_final: 0.6456 (m100)
  outliers start: 26
  outliers final: 23
  residues processed: 121
  average time/residue: 0.0763
  time to fit residues: 15.0675
Evaluate side-chains
  122 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  315 GLU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0670
   chunk 83 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
A 627 HIS
B 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.179579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.163193 restraints weight = 12990.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.160927 restraints weight = 33455.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.133915 restraints weight = 38114.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.124792 restraints weight = 30917.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124085 restraints weight = 23117.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12275  Z= 0.114
  Angle     :  0.563  11.424  16752  Z= 0.280
  Chirality :  0.042   0.168   1859
  Planarity :  0.004   0.047   2197
  Dihedral  :  4.257  18.174   1676
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.64 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -1.65 (0.21), residues: 1547
  helix:  1.00 (0.23), residues: 537
  sheet: -1.93 (0.37), residues: 175
  loop : -2.44 (0.19), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  97 
 TYR   0.019   0.001   TYR B 383 
 PHE   0.011   0.001   PHE B 124 
 TRP   0.007   0.001   TRP A  31 
 HIS   0.005   0.001   HIS A 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12275)
  covalent geometry    : angle       0.56340 (16752)
  hydrogen bonds       : bond        0.03259 (  365)
  hydrogen bonds       : angle       3.69430 ( 1041)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A  601 THR cc_start: 0.9154 (m) cc_final: 0.8712 (p)
REVERT: A  697 GLU cc_start: 0.7747 (pm20) cc_final: 0.6638 (tm-30)
REVERT: B  594 MET cc_start: 0.6321 (ptt) cc_final: 0.5007 (ptp)
REVERT: B  691 TRP cc_start: 0.6902 (m100) cc_final: 0.6470 (m100)
  outliers start: 23
  outliers final: 21
  residues processed: 118
  average time/residue: 0.0740
  time to fit residues: 14.1200
Evaluate side-chains
  122 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 144 optimal weight:    5.9990
   chunk 137 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 114 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0060
   chunk 107 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 138 optimal weight:   10.0000
   overall best weight:    1.3202

-------------------------------------------------------------------------------
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 = 0.3879 r_free = 0.3879 target = 0.177158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.162266 restraints weight = 13014.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.126448 restraints weight = 32167.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.121559 restraints weight = 35144.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.121064 restraints weight = 29519.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.120961 restraints weight = 24235.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12275  Z= 0.155
  Angle     :  0.599  12.187  16752  Z= 0.299
  Chirality :  0.044   0.211   1859
  Planarity :  0.004   0.049   2197
  Dihedral  :  4.389  19.327   1676
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.64 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    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: -1.68 (0.21), residues: 1547
  helix:  0.98 (0.23), residues: 534
  sheet: -1.97 (0.38), residues: 169
  loop : -2.46 (0.19), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 495 
 TYR   0.020   0.001   TYR B 383 
 PHE   0.016   0.001   PHE B 124 
 TRP   0.007   0.001   TRP B 133 
 HIS   0.004   0.001   HIS B 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (12275)
  covalent geometry    : angle       0.59875 (16752)
  hydrogen bonds       : bond        0.03837 (  365)
  hydrogen bonds       : angle       3.82746 ( 1041)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1585.83 seconds
wall clock time: 28 minutes 15.35 seconds (1695.35 seconds total)