Starting phenix.real_space_refine
on Tue Jun 10 18:38:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xjt_38405/06_2025/8xjt_38405.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xjt_38405/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xjt_38405/06_2025/8xjt_38405.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xjt_38405/06_2025/8xjt_38405.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xjt_38405/06_2025/8xjt_38405.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xjt_38405/06_2025/8xjt_38405.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.62, per 1000 atoms: 0.64
  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: 2.88
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.31
  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: 3.39

  Time building geometry restraints manager: 3.44 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:             0.950
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     29.910
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.820
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.023   0.003   TRP B 133 
 HIS   0.016   0.002   HIS A 627 
 PHE   0.039   0.003   PHE B 124 
 TYR   0.040   0.004   TYR A 398 
 ARG   0.020   0.001   ARG B 265 

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

*********************** 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  : 1.196 
Fit side-chains
   revert: symmetry clash
REVERT: A  594 MET cc_start: 0.7362 (ttm) cc_final: 0.7105 (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: 0.6792 (m100)
  outliers start: 9
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1880
  time to fit residues: 37.4240
Evaluate side-chains
  102 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
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 130 optimal weight:   40.0000
   chunk 116 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 139 optimal weight:    9.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3892 r_free = 0.3892 target = 0.178246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.162217 restraints weight = 13014.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.126829 restraints weight = 34756.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.122354 restraints weight = 32289.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12275  Z= 0.150
  Angle     :  0.640   9.242  16752  Z= 0.331
  Chirality :  0.045   0.170   1859
  Planarity :  0.005   0.062   2197
  Dihedral  :  6.002  78.120   1679
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.19), residues: 1547
  helix: -1.25 (0.20), residues: 545
  sheet: -2.44 (0.36), residues: 174
  loop : -2.79 (0.19), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 133 
 HIS   0.008   0.001   HIS A 627 
 PHE   0.013   0.001   PHE B 124 
 TYR   0.011   0.001   TYR A 104 
 ARG   0.002   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04553 (  365)
  hydrogen bonds       : angle       4.63344 ( 1041)
  covalent geometry    : bond        0.00357 (12275)
  covalent geometry    : angle       0.64031 (16752)

*********************** 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
  120 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
REVERT: A  700 GLU cc_start: 0.7857 (mp0) cc_final: 0.7640 (mp0)
REVERT: B  701 ASP cc_start: 0.8024 (p0) cc_final: 0.7636 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 117
  average time/residue: 0.2032
  time to fit residues: 37.0501
Evaluate side-chains
  106 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
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  425 THR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  216 SER
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 64 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 357 HIS
A 645 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.178181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.161306 restraints weight = 13070.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.159259 restraints weight = 31435.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.131212 restraints weight = 35725.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12275  Z= 0.134
  Angle     :  0.587   7.914  16752  Z= 0.300
  Chirality :  0.043   0.160   1859
  Planarity :  0.005   0.060   2197
  Dihedral  :  5.015  20.759   1676
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.89 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.20), residues: 1547
  helix: -0.29 (0.22), residues: 528
  sheet: -2.44 (0.36), residues: 174
  loop : -2.60 (0.19), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 133 
 HIS   0.009   0.001   HIS A 627 
 PHE   0.015   0.001   PHE B 124 
 TYR   0.011   0.001   TYR B 104 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04072 (  365)
  hydrogen bonds       : angle       4.15495 ( 1041)
  covalent geometry    : bond        0.00325 (12275)
  covalent geometry    : angle       0.58695 (16752)

*********************** 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
  124 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  631 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7911 (mm-30)
REVERT: A  697 GLU cc_start: 0.7756 (pm20) cc_final: 0.6678 (tm-30)
REVERT: A  700 GLU cc_start: 0.8001 (mp0) cc_final: 0.7751 (mp0)
REVERT: B  701 ASP cc_start: 0.8120 (p0) cc_final: 0.7762 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 120
  average time/residue: 0.1950
  time to fit residues: 36.7887
Evaluate side-chains
  112 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
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  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  631 GLU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  585 GLN
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 22 optimal weight:    7.9990
   chunk 148 optimal weight:    8.9990
   chunk 106 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9990
   chunk 153 optimal weight:    0.0020
   chunk 107 optimal weight:    5.9990
   chunk 119 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    1.1994

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.177586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.163973 restraints weight = 12998.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.127622 restraints weight = 28035.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123867 restraints weight = 31044.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12275  Z= 0.147
  Angle     :  0.587   9.418  16752  Z= 0.299
  Chirality :  0.044   0.179   1859
  Planarity :  0.004   0.056   2197
  Dihedral  :  4.816  19.434   1676
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.77 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.20), residues: 1547
  helix:  0.11 (0.23), residues: 535
  sheet: -2.39 (0.36), residues: 173
  loop : -2.57 (0.19), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 571 
 HIS   0.008   0.001   HIS A 627 
 PHE   0.016   0.001   PHE B 124 
 TYR   0.011   0.001   TYR A 398 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  365)
  hydrogen bonds       : angle       4.00901 ( 1041)
  covalent geometry    : bond        0.00359 (12275)
  covalent geometry    : angle       0.58727 (16752)

*********************** 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: 26
    poor density    : 102
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7362 (mm-30)
REVERT: A  631 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7473 (mm-30)
REVERT: A  697 GLU cc_start: 0.7716 (pm20) cc_final: 0.6662 (tm-30)
REVERT: A  701 ASP cc_start: 0.8483 (t0) cc_final: 0.8200 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1787
  time to fit residues: 35.9919
Evaluate side-chains
  115 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
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   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  315 GLU
Chi-restraints excluded: chain A residue  425 THR
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  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  559 MET
Chi-restraints excluded: chain B residue  716 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 129 optimal weight:   30.0000
   chunk 2 optimal weight:    0.9980
   chunk 132 optimal weight:   30.0000
   chunk 98 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 595 ASN
A 645 HIS
A 710 GLN
C 846 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.179147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.169269 restraints weight = 12907.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.129562 restraints weight = 36330.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.124820 restraints weight = 36024.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1867

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= 0.118
  Angle     :  0.550   7.450  16752  Z= 0.279
  Chirality :  0.042   0.173   1859
  Planarity :  0.004   0.053   2197
  Dihedral  :  4.557  18.614   1676
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.81 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.21), residues: 1547
  helix:  0.42 (0.23), residues: 535
  sheet: -2.19 (0.36), residues: 175
  loop : -2.53 (0.19), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  31 
 HIS   0.008   0.001   HIS A 627 
 PHE   0.011   0.001   PHE B 124 
 TYR   0.010   0.001   TYR B 104 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03518 (  365)
  hydrogen bonds       : angle       3.80857 ( 1041)
  covalent geometry    : bond        0.00284 (12275)
  covalent geometry    : angle       0.55038 (16752)

*********************** 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
  123 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  631 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7889 (mm-30)
REVERT: A  697 GLU cc_start: 0.7721 (pm20) cc_final: 0.6635 (tm-30)
REVERT: A  700 GLU cc_start: 0.8219 (tp30) cc_final: 0.7781 (mt-10)
REVERT: A  701 ASP cc_start: 0.8716 (t0) cc_final: 0.8157 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 116
  average time/residue: 0.1773
  time to fit residues: 33.5002
Evaluate side-chains
  112 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  338 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  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  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 106 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 109 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 134 optimal weight:   20.0000
   chunk 70 optimal weight:    3.9990
   chunk 147 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 129 optimal weight:   30.0000
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0070
   overall best weight:    1.3602

-------------------------------------------------------------------------------
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 = 0.3875 r_free = 0.3875 target = 0.176654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.161495 restraints weight = 13122.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.124844 restraints weight = 33165.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.121466 restraints weight = 35206.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1856

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= 0.159
  Angle     :  0.587   7.031  16752  Z= 0.298
  Chirality :  0.044   0.171   1859
  Planarity :  0.004   0.053   2197
  Dihedral  :  4.621  20.246   1676
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.68 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.21), residues: 1547
  helix:  0.52 (0.23), residues: 533
  sheet: -2.21 (0.36), residues: 175
  loop : -2.53 (0.20), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 133 
 HIS   0.007   0.001   HIS A 627 
 PHE   0.018   0.001   PHE B 124 
 TYR   0.012   0.001   TYR A 398 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  365)
  hydrogen bonds       : angle       3.87501 ( 1041)
  covalent geometry    : bond        0.00392 (12275)
  covalent geometry    : angle       0.58684 (16752)

*********************** 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
  125 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7276 (mm-30)
REVERT: A  631 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7685 (mm-30)
REVERT: A  697 GLU cc_start: 0.7772 (pm20) cc_final: 0.6680 (tm-30)
REVERT: A  701 ASP cc_start: 0.8740 (t0) cc_final: 0.8365 (t0)
  outliers start: 27
  outliers final: 23
  residues processed: 117
  average time/residue: 0.1734
  time to fit residues: 33.9732
Evaluate side-chains
  121 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
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  315 GLU
Chi-restraints excluded: chain A residue  338 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  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  631 GLU
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 147 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   chunk 139 optimal weight:   20.0000
   chunk 29 optimal weight:    2.9990
   chunk 132 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.176358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.159164 restraints weight = 13129.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.124302 restraints weight = 35388.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.120292 restraints weight = 32921.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1918

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= 0.161
  Angle     :  0.586   6.993  16752  Z= 0.299
  Chirality :  0.044   0.171   1859
  Planarity :  0.004   0.053   2197
  Dihedral  :  4.629  20.492   1676
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.84 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.21), residues: 1547
  helix:  0.60 (0.23), residues: 537
  sheet: -2.25 (0.36), residues: 175
  loop : -2.57 (0.19), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 571 
 HIS   0.006   0.001   HIS A 627 
 PHE   0.016   0.001   PHE B 124 
 TYR   0.011   0.001   TYR A 398 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  365)
  hydrogen bonds       : angle       3.85207 ( 1041)
  covalent geometry    : bond        0.00400 (12275)
  covalent geometry    : angle       0.58621 (16752)

*********************** 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
  130 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7452 (mm-30)
REVERT: A  631 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7986 (mm-30)
REVERT: A  697 GLU cc_start: 0.7782 (pm20) cc_final: 0.6574 (tm-30)
REVERT: A  700 GLU cc_start: 0.8190 (tp30) cc_final: 0.7711 (mt-10)
REVERT: A  701 ASP cc_start: 0.8667 (t0) cc_final: 0.8007 (t0)
  outliers start: 28
  outliers final: 24
  residues processed: 121
  average time/residue: 0.1782
  time to fit residues: 34.8927
Evaluate side-chains
  126 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
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  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  338 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  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  631 GLU
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  559 MET
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 58 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 141 optimal weight:   30.0000
   chunk 45 optimal weight:    0.0070
   chunk 115 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 153 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 152 optimal weight:    9.9990
   overall best weight:    2.1604

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.173637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.157944 restraints weight = 13169.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.121888 restraints weight = 32918.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.116307 restraints weight = 34405.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  12275  Z= 0.232
  Angle     :  0.660   7.228  16752  Z= 0.338
  Chirality :  0.046   0.171   1859
  Planarity :  0.005   0.055   2197
  Dihedral  :  4.899  22.206   1676
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.04 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.20), residues: 1547
  helix:  0.49 (0.23), residues: 537
  sheet: -2.34 (0.35), residues: 177
  loop : -2.66 (0.19), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 133 
 HIS   0.006   0.001   HIS A 627 
 PHE   0.025   0.002   PHE B 124 
 TYR   0.016   0.002   TYR A 398 
 ARG   0.003   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04831 (  365)
  hydrogen bonds       : angle       4.08960 ( 1041)
  covalent geometry    : bond        0.00580 (12275)
  covalent geometry    : angle       0.66022 (16752)

*********************** 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: 31
    poor density    : 93
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7283 (mm-30)
REVERT: A  362 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7449 (p)
REVERT: A  631 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7910 (mm-30)
REVERT: A  697 GLU cc_start: 0.7770 (pm20) cc_final: 0.6295 (tm-30)
REVERT: A  701 ASP cc_start: 0.8731 (t0) cc_final: 0.8258 (t0)
  outliers start: 31
  outliers final: 26
  residues processed: 116
  average time/residue: 0.1880
  time to fit residues: 35.4769
Evaluate side-chains
  121 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
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  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  338 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  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  631 GLU
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  559 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 14 optimal weight:   20.0000
   chunk 118 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 96 optimal weight:    7.9990
   chunk 111 optimal weight:    0.8980
   chunk 135 optimal weight:   30.0000
   chunk 13 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.179143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.163857 restraints weight = 13006.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.126569 restraints weight = 31436.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.122388 restraints weight = 31932.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2110

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= 0.111
  Angle     :  0.550   7.716  16752  Z= 0.277
  Chirality :  0.042   0.171   1859
  Planarity :  0.004   0.050   2197
  Dihedral  :  4.422  19.087   1676
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.00 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.21), residues: 1547
  helix:  0.78 (0.23), residues: 535
  sheet: -2.19 (0.35), residues: 182
  loop : -2.49 (0.20), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  31 
 HIS   0.007   0.001   HIS A 627 
 PHE   0.012   0.001   PHE B 124 
 TYR   0.009   0.001   TYR B 104 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03271 (  365)
  hydrogen bonds       : angle       3.68435 ( 1041)
  covalent geometry    : bond        0.00267 (12275)
  covalent geometry    : angle       0.54950 (16752)

*********************** 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
  126 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7464 (mm-30)
REVERT: A  362 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7377 (p)
REVERT: A  601 THR cc_start: 0.9194 (m) cc_final: 0.8714 (p)
REVERT: A  631 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7795 (mm-30)
REVERT: A  697 GLU cc_start: 0.7704 (pm20) cc_final: 0.6286 (tm-30)
REVERT: A  701 ASP cc_start: 0.8515 (t0) cc_final: 0.8040 (t0)
REVERT: B  594 MET cc_start: 0.6529 (ptt) cc_final: 0.5168 (ptp)
  outliers start: 24
  outliers final: 21
  residues processed: 120
  average time/residue: 0.1812
  time to fit residues: 35.4254
Evaluate side-chains
  124 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
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  338 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  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  631 GLU
Chi-restraints excluded: chain A residue  702 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 127 optimal weight:    9.9990
   chunk 138 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0570
   chunk 59 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.0104

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.178022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.161177 restraints weight = 13004.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.159335 restraints weight = 32838.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.133084 restraints weight = 35394.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12275  Z= 0.131
  Angle     :  0.567   7.962  16752  Z= 0.285
  Chirality :  0.043   0.170   1859
  Planarity :  0.004   0.053   2197
  Dihedral  :  4.386  18.976   1676
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.32 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.21), residues: 1547
  helix:  0.84 (0.23), residues: 533
  sheet: -2.02 (0.37), residues: 175
  loop : -2.47 (0.19), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  31 
 HIS   0.006   0.001   HIS A 627 
 PHE   0.013   0.001   PHE B 124 
 TYR   0.009   0.001   TYR B 104 
 ARG   0.001   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  365)
  hydrogen bonds       : angle       3.70177 ( 1041)
  covalent geometry    : bond        0.00322 (12275)
  covalent geometry    : angle       0.56669 (16752)

********************** 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
  126 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6769 (mm-30)
REVERT: A  362 VAL cc_start: 0.7286 (OUTLIER) cc_final: 0.7068 (p)
REVERT: A  601 THR cc_start: 0.9166 (m) cc_final: 0.8680 (p)
REVERT: A  631 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7572 (mm-30)
REVERT: A  697 GLU cc_start: 0.7777 (pm20) cc_final: 0.6449 (tm-30)
REVERT: A  701 ASP cc_start: 0.8549 (t0) cc_final: 0.8078 (t0)
  outliers start: 25
  outliers final: 20
  residues processed: 121
  average time/residue: 0.1821
  time to fit residues: 35.7640
Evaluate side-chains
  122 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
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  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  552 LEU
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  631 GLU
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain B residue  174 VAL
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 51 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0050
   chunk 35 optimal weight:    0.9990
   chunk 132 optimal weight:   20.0000
   chunk 122 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 113 optimal weight:    0.0010
   chunk 16 optimal weight:    2.9990
   chunk 150 optimal weight:    0.0040
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.3412

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

Flipped N/Q/H residues before XYZ refinement:
A 645 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 = 0.3931 r_free = 0.3931 target = 0.182376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.173168 restraints weight = 12860.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.139041 restraints weight = 32156.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.131073 restraints weight = 36470.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2413

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= 0.095
  Angle     :  0.534  10.110  16752  Z= 0.265
  Chirality :  0.041   0.170   1859
  Planarity :  0.004   0.048   2197
  Dihedral  :  4.046  16.454   1676
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.96 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.21), residues: 1547
  helix:  1.00 (0.23), residues: 538
  sheet: -1.71 (0.39), residues: 165
  loop : -2.40 (0.19), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 712 
 HIS   0.006   0.000   HIS A 627 
 PHE   0.007   0.001   PHE B 124 
 TYR   0.007   0.001   TYR A 343 
 ARG   0.001   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02732 (  365)
  hydrogen bonds       : angle       3.51706 ( 1041)
  covalent geometry    : bond        0.00221 (12275)
  covalent geometry    : angle       0.53419 (16752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3233.40 seconds
wall clock time: 57 minutes 15.63 seconds (3435.63 seconds total)