Starting phenix.real_space_refine
on Thu Jul  2 04:55:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gqo_51510/07_2026/9gqo_51510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gqo_51510/07_2026/9gqo_51510.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gqo_51510/07_2026/9gqo_51510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gqo_51510/07_2026/9gqo_51510.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gqo_51510/07_2026/9gqo_51510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gqo_51510/07_2026/9gqo_51510.map"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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: 7
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       1      5.49       5
     Mg      1      5.21       5
     S      34      5.16       5
     C    4284      2.51       5
     N    1111      2.21       5
     O    1284      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6716
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 880, 6710
          Classifications: {'peptide': 880}
          Link IDs: {'PTRANS': 29, 'TRANS': 850}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 5
          Ad-hoc single atom residues: {' CA': 1}
          Unusual residues: {' MG': 1, 'PO3': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 1
  Time building chain proxies: 1.52, per 1000 atoms: 0.23
  Number of scatterers: 6716
  At special positions: 0
  Unit cell: (71.17, 86.698, 142.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      1     19.99
     S      34     16.00
     P       1     15.00
     Mg      1     11.99
     O    1284      8.00
     N    1111      7.00
     C    4284      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 340.3 milliseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1632

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 5 sheets defined
      50.6% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 15
      removed outlier: 4.251A  pdb=" N   GLN A  14 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A  15 " --> pdb=" O   THR A  11 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 10 through 15'
    Processing helix  chain 'A' and resid 23 through 35
      removed outlier: 3.659A  pdb=" N   VAL A  27 " --> pdb=" O   THR A  23 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   LYS A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLN A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   GLU A  32 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 55
      removed outlier: 3.597A  pdb=" N   THR A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 72
      removed outlier: 4.070A  pdb=" N   LEU A  68 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   VAL A  69 " --> pdb=" O   ILE A  65 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLN A  70 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 99
      removed outlier: 3.990A  pdb=" N   LEU A  86 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 161 through 164
    Processing helix  chain 'A' and resid 213 through 223
      removed outlier: 3.590A  pdb=" N   LEU A 221 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 4.260A  pdb=" N   ARG A 234 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   LYS A 235 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 255
      removed outlier: 3.879A  pdb=" N   LEU A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 255 " --> pdb=" O   CYS A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 263
      removed outlier: 3.937A  pdb=" N   LEU A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 290
      removed outlier: 3.670A  pdb=" N   ASN A 277 " --> pdb=" O   THR A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 311
      removed outlier: 4.277A  pdb=" N   SER A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   SER A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 305 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
    Processing helix  chain 'A' and resid 362 through 366
    Processing helix  chain 'A' and resid 369 through 380
    Processing helix  chain 'A' and resid 394 through 407
      removed outlier: 3.712A  pdb=" N   ASN A 407 " --> pdb=" O   PHE A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.046A  pdb=" N   ILE A 414 " --> pdb=" O   ASP A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 458
    Processing helix  chain 'A' and resid 474 through 488
    Processing helix  chain 'A' and resid 529 through 541
      removed outlier: 4.266A  pdb=" N   ALA A 533 " --> pdb=" O   GLU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 562
      removed outlier: 4.866A  pdb=" N   GLY A 560 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG A 561 " --> pdb=" O   GLN A 557 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 581
      removed outlier: 3.582A  pdb=" N   MET A 581 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 4.328A  pdb=" N   GLU A 591 " --> pdb=" O   ASP A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 614
      removed outlier: 3.593A  pdb=" N   ILE A 607 " --> pdb=" O   ASN A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 626
      No H-bonds generated for 'chain 'A' and resid 624 through 626'
    Processing helix  chain 'A' and resid 627 through 634
    Processing helix  chain 'A' and resid 644 through 651
    Processing helix  chain 'A' and resid 660 through 701
      removed outlier: 4.292A  pdb=" N   VAL A 664 " --> pdb=" O   PHE A 660 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ILE A 681 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ALA A 682 " --> pdb=" O   LYS A 678 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU A 684 " --> pdb=" O   SER A 680 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU A 701 " --> pdb=" O   PHE A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 720
      removed outlier: 3.504A  pdb=" N   LEU A 713 " --> pdb=" O   ALA A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 750 through 776
      removed outlier: 4.362A  pdb=" N   ALA A 756 " --> pdb=" O   GLY A 752 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   SER A 759 " --> pdb=" O   ARG A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 798
      removed outlier: 3.830A  pdb=" N   ALA A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE A 788 " --> pdb=" O   VAL A 784 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR A 789 " --> pdb=" O   ALA A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 803
    Processing helix  chain 'A' and resid 817 through 836
      removed outlier: 3.664A  pdb=" N   LEU A 836 " --> pdb=" O   GLY A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 877
      removed outlier: 3.587A  pdb=" N   ILE A 871 " --> pdb=" O   MET A 867 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 119
    Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 139
      removed outlier: 3.958A  pdb=" N   LEU A 196 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   LYS A 158 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLY A 200 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   SER A 156 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      removed outlier: 8.441A  pdb=" N   GLY A 202 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   SER A 154 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   PHE A 204 " --> pdb=" O   PHE A 152 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   PHE A 152 " --> pdb=" O   PHE A 204 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   VAL A 206 " --> pdb=" O   ARG A 150 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ARG A 150 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP A 148 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LEU A 157 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574
      removed outlier: 6.457A  pdb=" N   LEU A 573 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 8.930A  pdb=" N   TYR A 596 " --> pdb=" O   THR A 545 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   MET A 547 " --> pdb=" O   TYR A 596 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   ILE A 331 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   ILE A 548 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   THR A 333 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   THR A 618 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   VAL A 638 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   MET A 620 " --> pdb=" O   VAL A 638 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   MET A 640 " --> pdb=" O   MET A 620 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   GLY A 622 " --> pdb=" O   MET A 640 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   LEU A 655 " --> pdb=" O   GLY A 637 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   ALA A 639 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 350
      removed outlier: 5.181A  pdb=" N   VAL A 346 " --> pdb=" O   ILE A 524 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ILE A 524 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   LEU A 517 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   TYR A 497 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 350
      removed outlier: 5.181A  pdb=" N   VAL A 346 " --> pdb=" O   ILE A 524 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ILE A 524 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR A 460 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   GLY A 519 " --> pdb=" O   TYR A 460 " (cutoff:3.500A)

    308 hydrogen bonds defined for protein.
    894 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.42

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2207
        1.35 -     1.46: 1372
        1.46 -     1.58: 3169
        1.58 -     1.70: 0
        1.70 -     1.82: 63
  Bond restraints: 6811
  Sorted by residual:
  bond pdb=" O2  PO3 A1002 "
       pdb=" P   PO3 A1002 "
    ideal  model  delta    sigma   weight residual
    1.604  1.509  0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" O1  PO3 A1002 "
       pdb=" P   PO3 A1002 "
    ideal  model  delta    sigma   weight residual
    1.604  1.509  0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" O3  PO3 A1002 "
       pdb=" P   PO3 A1002 "
    ideal  model  delta    sigma   weight residual
    1.601  1.510  0.091 2.00e-02 2.50e+03 2.07e+01
  bond pdb=" N   ILE A   3 "
       pdb=" CA  ILE A   3 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.17e-02 7.31e+03 6.40e+00
  bond pdb=" N   GLU A   2 "
       pdb=" CA  GLU A   2 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.15e+00
  ... (remaining 6806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 8962
        1.89 -     3.77: 195
        3.77 -     5.66: 42
        5.66 -     7.55: 10
        7.55 -     9.43: 3
  Bond angle restraints: 9212
  Sorted by residual:
  angle pdb=" CB  LYS A  40 "
        pdb=" CG  LYS A  40 "
        pdb=" CD  LYS A  40 "
      ideal   model   delta    sigma   weight residual
     111.30  120.73   -9.43 2.30e+00 1.89e-01 1.68e+01
  angle pdb=" N   VAL A 378 "
        pdb=" CA  VAL A 378 "
        pdb=" C   VAL A 378 "
      ideal   model   delta    sigma   weight residual
     113.42  108.64    4.78 1.17e+00 7.31e-01 1.67e+01
  angle pdb=" CA  MET A 868 "
        pdb=" CB  MET A 868 "
        pdb=" CG  MET A 868 "
      ideal   model   delta    sigma   weight residual
     114.10  120.89   -6.79 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" C   LEU A 104 "
        pdb=" N   ASP A 105 "
        pdb=" CA  ASP A 105 "
      ideal   model   delta    sigma   weight residual
     125.66  131.81   -6.15 1.85e+00 2.92e-01 1.11e+01
  angle pdb=" CA  TYR A   4 "
        pdb=" CB  TYR A   4 "
        pdb=" CG  TYR A   4 "
      ideal   model   delta    sigma   weight residual
     113.90  119.72   -5.82 1.80e+00 3.09e-01 1.04e+01
  ... (remaining 9207 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 3447
       17.81 -    35.63: 545
       35.63 -    53.44: 128
       53.44 -    71.25: 21
       71.25 -    89.06: 12
  Dihedral angle restraints: 4153
    sinusoidal: 1627
      harmonic: 2526
  Sorted by residual:
  dihedral pdb=" CA  MET A 271 "
           pdb=" C   MET A 271 "
           pdb=" N   ALA A 272 "
           pdb=" CA  ALA A 272 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.35   24.65     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CD  ARG A   5 "
           pdb=" NE  ARG A   5 "
           pdb=" CZ  ARG A   5 "
           pdb=" NH1 ARG A   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   36.04  -36.04     1      1.00e+01 1.00e-02 1.84e+01
  dihedral pdb=" CA  THR A 165 "
           pdb=" C   THR A 165 "
           pdb=" N   GLY A 166 "
           pdb=" CA  GLY A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.10   20.90     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 4150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 850
       0.045 -    0.091: 198
       0.091 -    0.136: 51
       0.136 -    0.182: 2
       0.182 -    0.227: 1
  Chirality restraints: 1102
  Sorted by residual:
  chirality pdb=" CA  ILE A   3 "
            pdb=" N   ILE A   3 "
            pdb=" C   ILE A   3 "
            pdb=" CB  ILE A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  THR A 165 "
            pdb=" N   THR A 165 "
            pdb=" C   THR A 165 "
            pdb=" CB  THR A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  MET A 470 "
            pdb=" N   MET A 470 "
            pdb=" C   MET A 470 "
            pdb=" CB  MET A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 1099 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A   5 "   -0.644 9.50e-02 1.11e+02   2.89e-01 5.08e+01
        pdb=" NE  ARG A   5 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG A   5 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A   5 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A   5 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 178 "    0.042 5.00e-02 4.00e+02   6.33e-02 6.42e+00
        pdb=" N   PRO A 179 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 179 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 179 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 391 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" CD  GLU A 391 "    0.025 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 391 "   -0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 391 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 137
        2.65 -     3.21: 6907
        3.21 -     3.78: 10744
        3.78 -     4.34: 14411
        4.34 -     4.90: 22082
  Nonbonded interactions: 54281
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 334 "
            pdb="MG    MG A1003 "
     model   vdw
     2.090 2.170
  nonbonded pdb=" O3  PO3 A1002 "
            pdb="MG    MG A1003 "
     model   vdw
     2.099 2.170
  nonbonded pdb=" O   THR A 336 "
            pdb="MG    MG A1003 "
     model   vdw
     2.132 2.170
  nonbonded pdb=" OG1 THR A 549 "
            pdb=" O1  PO3 A1002 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER A 680 "
            pdb=" O   ALA A 724 "
     model   vdw
     2.240 3.040
  ... (remaining 54276 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.730
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095   6811  Z= 0.176
  Angle     :  0.714   9.434   9212  Z= 0.386
  Chirality :  0.042   0.227   1102
  Planarity :  0.009   0.289   1175
  Dihedral  : 18.403  89.063   2521
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 39.92 %
    Favored  : 59.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.28), residues: 876
  helix: -0.53 (0.26), residues: 390
  sheet:  0.15 (0.61), residues: 72
  loop : -1.35 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 187 
 TYR   0.020   0.001   TYR A   4 
 PHE   0.013   0.001   PHE A 707 
 TRP   0.012   0.002   TRP A 703 
 HIS   0.002   0.000   HIS A 437 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.18 ( 6811)
  covalent geometry    : angle       0.71422 /  0.39 ( 9212)
  hydrogen bonds       : bond        0.24841 / 16.00 (  304)
  hydrogen bonds       : angle       8.52586 /  5.72 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.1506 (pt0)
REVERT: A  445 MET cc_start: 0.5896 (tpt) cc_final: 0.5448 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0832
  time to fit residues: 9.5597
Evaluate side-chains
  61 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  89 ASN
A 719 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.056558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.050160 restraints weight = 63521.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 6.39
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6811  Z= 0.156
  Angle     :  0.720  11.841   9212  Z= 0.366
  Chirality :  0.043   0.223   1102
  Planarity :  0.004   0.048   1175
  Dihedral  :  5.107  29.325    930
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 34.53 %
    Favored  : 61.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.28), residues: 876
  helix: -0.19 (0.26), residues: 388
  sheet:  0.13 (0.60), residues: 78
  loop : -1.33 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 187 
 TYR   0.015   0.002   TYR A 497 
 PHE   0.016   0.001   PHE A 403 
 TRP   0.007   0.001   TRP A 703 
 HIS   0.003   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.16 ( 6811)
  covalent geometry    : angle       0.72013 /  0.37 ( 9212)
  hydrogen bonds       : bond        0.05331 /  3.55 (  304)
  hydrogen bonds       : angle       5.72687 /  3.85 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 69
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 LEU cc_start: 0.9343 (mt) cc_final: 0.8968 (pp)
REVERT: A  344 MET cc_start: 0.8969 (tpp) cc_final: 0.7661 (tpp)
REVERT: A  500 MET cc_start: 0.4634 (mmm) cc_final: 0.4381 (mmm)
REVERT: A  547 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8637 (tmm)
REVERT: A  566 MET cc_start: 0.7227 (tpp) cc_final: 0.6959 (tpp)
REVERT: A  754 MET cc_start: 0.8077 (mmt) cc_final: 0.7864 (mmp)
REVERT: A  862 LEU cc_start: 0.9534 (mt) cc_final: 0.9214 (pp)
  outliers start: 32
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0801
  time to fit residues: 10.3915
Evaluate side-chains
  73 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  547 MET
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0270
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    1.5644

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 798 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.052824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.045426 restraints weight = 60453.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 6.88
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6811  Z= 0.157
  Angle     :  0.710   9.066   9212  Z= 0.354
  Chirality :  0.042   0.172   1102
  Planarity :  0.004   0.054   1175
  Dihedral  :  5.042  19.610    927
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 34.25 %
    Favored  : 61.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.28), residues: 876
  helix: -0.01 (0.26), residues: 388
  sheet: -0.56 (0.62), residues: 77
  loop : -1.43 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 187 
 TYR   0.014   0.001   TYR A 497 
 PHE   0.012   0.001   PHE A 707 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.16 ( 6811)
  covalent geometry    : angle       0.71019 /  0.35 ( 9212)
  hydrogen bonds       : bond        0.04516 /  2.94 (  304)
  hydrogen bonds       : angle       5.32088 /  3.58 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 61
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.9033 (mp0)
REVERT: A  445 MET cc_start: 0.8193 (tpp) cc_final: 0.7809 (tpp)
REVERT: A  500 MET cc_start: 0.5090 (mmm) cc_final: 0.4687 (mmm)
REVERT: A  566 MET cc_start: 0.7545 (tpp) cc_final: 0.7214 (tpp)
REVERT: A  640 MET cc_start: 0.9303 (tpt) cc_final: 0.9096 (tpt)
REVERT: A  716 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9124 (t0)
REVERT: A  754 MET cc_start: 0.8313 (mmt) cc_final: 0.8072 (mmp)
REVERT: A  786 MET cc_start: 0.7475 (mmm) cc_final: 0.7119 (mmt)
REVERT: A  793 LEU cc_start: 0.9597 (mm) cc_final: 0.9390 (mm)
REVERT: A  862 LEU cc_start: 0.9574 (mt) cc_final: 0.9257 (pp)
  outliers start: 34
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0794
  time to fit residues: 9.7686
Evaluate side-chains
  77 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.053438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.046044 restraints weight = 59970.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 6.85
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6811  Z= 0.123
  Angle     :  0.677   9.982   9212  Z= 0.336
  Chirality :  0.042   0.162   1102
  Planarity :  0.004   0.041   1175
  Dihedral  :  4.956  18.744    927
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 34.67 %
    Favored  : 61.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.29), residues: 876
  helix:  0.10 (0.26), residues: 388
  sheet: -0.33 (0.58), residues: 84
  loop : -1.39 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 187 
 TYR   0.013   0.001   TYR A 497 
 PHE   0.013   0.001   PHE A 403 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.000   HIS A 437 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 6811)
  covalent geometry    : angle       0.67668 /  0.34 ( 9212)
  hydrogen bonds       : bond        0.04031 /  2.68 (  304)
  hydrogen bonds       : angle       5.00003 /  3.36 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 67
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8422 (tmm)
REVERT: A  397 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.9089 (mp0)
REVERT: A  433 MET cc_start: 0.8388 (tmm) cc_final: 0.8108 (tmm)
REVERT: A  445 MET cc_start: 0.8632 (tpp) cc_final: 0.8286 (tpp)
REVERT: A  500 MET cc_start: 0.5075 (mmm) cc_final: 0.4740 (mmm)
REVERT: A  547 MET cc_start: 0.9325 (ttp) cc_final: 0.8743 (tmm)
REVERT: A  566 MET cc_start: 0.7721 (tpp) cc_final: 0.7271 (tpp)
REVERT: A  786 MET cc_start: 0.7785 (mmm) cc_final: 0.7297 (mmt)
REVERT: A  789 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8877 (t)
REVERT: A  793 LEU cc_start: 0.9611 (mm) cc_final: 0.9367 (mm)
REVERT: A  862 LEU cc_start: 0.9523 (mt) cc_final: 0.9238 (pp)
REVERT: A  867 MET cc_start: 0.9075 (ptp) cc_final: 0.8849 (mmm)
  outliers start: 28
  outliers final: 18
  residues processed: 90
  average time/residue: 0.0688
  time to fit residues: 8.7024
Evaluate side-chains
  78 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  782 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0470
   chunk 60 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0370
   chunk 67 optimal weight:    7.9990
   overall best weight:    0.4956

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.053961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.046527 restraints weight = 60633.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 6.95
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6811  Z= 0.122
  Angle     :  0.694  12.463   9212  Z= 0.338
  Chirality :  0.042   0.174   1102
  Planarity :  0.004   0.041   1175
  Dihedral  :  4.858  18.228    927
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 34.94 %
    Favored  : 60.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.29), residues: 876
  helix:  0.08 (0.26), residues: 390
  sheet: -0.85 (0.57), residues: 83
  loop : -1.42 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 261 
 TYR   0.012   0.001   TYR A 497 
 PHE   0.012   0.001   PHE A 707 
 TRP   0.010   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 6811)
  covalent geometry    : angle       0.69416 /  0.34 ( 9212)
  hydrogen bonds       : bond        0.03810 /  2.52 (  304)
  hydrogen bonds       : angle       4.92768 /  3.33 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 58
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.8611 (tpp) cc_final: 0.8379 (tpp)
REVERT: A  397 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.9037 (mp0)
REVERT: A  433 MET cc_start: 0.8307 (tmm) cc_final: 0.7942 (tmm)
REVERT: A  445 MET cc_start: 0.8564 (tpp) cc_final: 0.8235 (tpp)
REVERT: A  500 MET cc_start: 0.5091 (mmm) cc_final: 0.4744 (mmm)
REVERT: A  547 MET cc_start: 0.9020 (ttp) cc_final: 0.8630 (tmm)
REVERT: A  566 MET cc_start: 0.7848 (tpp) cc_final: 0.7361 (tpp)
REVERT: A  581 MET cc_start: 0.6902 (ptt) cc_final: 0.6697 (ptt)
REVERT: A  653 MET cc_start: 0.9256 (tpt) cc_final: 0.8908 (tpp)
REVERT: A  786 MET cc_start: 0.7572 (mmm) cc_final: 0.7158 (mmt)
REVERT: A  789 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8803 (t)
REVERT: A  793 LEU cc_start: 0.9522 (mm) cc_final: 0.9269 (mm)
REVERT: A  862 LEU cc_start: 0.9544 (mt) cc_final: 0.9231 (pp)
  outliers start: 32
  outliers final: 20
  residues processed: 83
  average time/residue: 0.0681
  time to fit residues: 8.0890
Evaluate side-chains
  80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  782 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 57 optimal weight:    0.2980
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 43 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   overall best weight:    1.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.052349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.045151 restraints weight = 63358.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 6.83
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6811  Z= 0.171
  Angle     :  0.717  12.501   9212  Z= 0.356
  Chirality :  0.042   0.180   1102
  Planarity :  0.004   0.040   1175
  Dihedral  :  4.891  19.309    927
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 19.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 36.05 %
    Favored  : 59.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.28), residues: 876
  helix:  0.24 (0.27), residues: 390
  sheet: -0.02 (0.61), residues: 70
  loop : -1.50 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 234 
 TYR   0.011   0.001   TYR A 497 
 PHE   0.009   0.001   PHE A 359 
 TRP   0.009   0.001   TRP A 703 
 HIS   0.003   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.17 ( 6811)
  covalent geometry    : angle       0.71675 /  0.36 ( 9212)
  hydrogen bonds       : bond        0.03835 /  2.56 (  304)
  hydrogen bonds       : angle       5.00243 /  3.39 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.9088 (mp0)
REVERT: A  433 MET cc_start: 0.8483 (tmm) cc_final: 0.8011 (tmm)
REVERT: A  445 MET cc_start: 0.8685 (tpp) cc_final: 0.8312 (tpp)
REVERT: A  500 MET cc_start: 0.5301 (mmm) cc_final: 0.4732 (mmm)
REVERT: A  566 MET cc_start: 0.7976 (tpp) cc_final: 0.7381 (tpp)
REVERT: A  786 MET cc_start: 0.7549 (mmm) cc_final: 0.7283 (mmt)
REVERT: A  789 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.8907 (t)
REVERT: A  793 LEU cc_start: 0.9547 (mm) cc_final: 0.9305 (mm)
REVERT: A  862 LEU cc_start: 0.9567 (mt) cc_final: 0.9271 (pp)
REVERT: A  867 MET cc_start: 0.8985 (mmm) cc_final: 0.8773 (ptp)
  outliers start: 29
  outliers final: 18
  residues processed: 81
  average time/residue: 0.0669
  time to fit residues: 7.8582
Evaluate side-chains
  76 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.049168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.040824 restraints weight = 52874.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 6.97
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6811  Z= 0.142
  Angle     :  0.733  13.681   9212  Z= 0.358
  Chirality :  0.042   0.169   1102
  Planarity :  0.004   0.042   1175
  Dihedral  :  4.930  18.779    927
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 18.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 36.05 %
    Favored  : 59.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.28), residues: 876
  helix:  0.20 (0.26), residues: 390
  sheet: -0.95 (0.57), residues: 81
  loop : -1.47 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 261 
 TYR   0.011   0.001   TYR A 497 
 PHE   0.013   0.001   PHE A 685 
 TRP   0.010   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 ( 6811)
  covalent geometry    : angle       0.73268 /  0.36 ( 9212)
  hydrogen bonds       : bond        0.03712 /  2.49 (  304)
  hydrogen bonds       : angle       5.00058 /  3.39 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 57
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8985 (mp0)
REVERT: A  433 MET cc_start: 0.8421 (tmm) cc_final: 0.7983 (tmm)
REVERT: A  445 MET cc_start: 0.8644 (tpp) cc_final: 0.8330 (tpp)
REVERT: A  500 MET cc_start: 0.5314 (mmm) cc_final: 0.4898 (mmm)
REVERT: A  566 MET cc_start: 0.7851 (tpp) cc_final: 0.7392 (tpp)
REVERT: A  754 MET cc_start: 0.8029 (mmp) cc_final: 0.7617 (mmp)
REVERT: A  786 MET cc_start: 0.7334 (mmm) cc_final: 0.7074 (mmt)
REVERT: A  789 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.8843 (t)
REVERT: A  793 LEU cc_start: 0.9529 (mm) cc_final: 0.9300 (mm)
REVERT: A  853 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7535 (pm20)
REVERT: A  862 LEU cc_start: 0.9532 (mt) cc_final: 0.9235 (pp)
  outliers start: 33
  outliers final: 25
  residues processed: 86
  average time/residue: 0.0700
  time to fit residues: 8.4771
Evaluate side-chains
  84 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 56
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  681 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  745 ASN
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  853 GLU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 80 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 4 optimal weight:    0.1980
   chunk 50 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 716 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.049918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.041585 restraints weight = 53439.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 6.94
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6811  Z= 0.121
  Angle     :  0.729  14.218   9212  Z= 0.352
  Chirality :  0.042   0.167   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.876  18.671    927
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 35.64 %
    Favored  : 59.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.29), residues: 876
  helix:  0.21 (0.26), residues: 390
  sheet: -0.68 (0.58), residues: 79
  loop : -1.36 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 261 
 TYR   0.011   0.001   TYR A 497 
 PHE   0.013   0.001   PHE A 685 
 TRP   0.012   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 6811)
  covalent geometry    : angle       0.72857 /  0.35 ( 9212)
  hydrogen bonds       : bond        0.03621 /  2.41 (  304)
  hydrogen bonds       : angle       4.87926 /  3.31 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 58
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 LYS cc_start: 0.8726 (tptp) cc_final: 0.8369 (tptp)
REVERT: A  397 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9005 (mp0)
REVERT: A  433 MET cc_start: 0.8359 (tmm) cc_final: 0.7899 (tmm)
REVERT: A  445 MET cc_start: 0.8651 (tpp) cc_final: 0.8349 (tpp)
REVERT: A  500 MET cc_start: 0.5249 (mmm) cc_final: 0.4844 (mmm)
REVERT: A  566 MET cc_start: 0.7982 (tpp) cc_final: 0.7484 (tpp)
REVERT: A  581 MET cc_start: 0.6780 (ptt) cc_final: 0.6480 (ptt)
REVERT: A  640 MET cc_start: 0.9104 (tpt) cc_final: 0.8797 (tpt)
REVERT: A  696 LEU cc_start: 0.9347 (tt) cc_final: 0.9050 (pp)
REVERT: A  716 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.9020 (t0)
REVERT: A  754 MET cc_start: 0.8058 (mmp) cc_final: 0.7788 (mmp)
REVERT: A  786 MET cc_start: 0.7272 (mmm) cc_final: 0.6934 (mmt)
REVERT: A  789 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8819 (t)
REVERT: A  793 LEU cc_start: 0.9516 (mm) cc_final: 0.9231 (mm)
REVERT: A  862 LEU cc_start: 0.9516 (mt) cc_final: 0.9226 (pp)
  outliers start: 33
  outliers final: 23
  residues processed: 87
  average time/residue: 0.0701
  time to fit residues: 8.6431
Evaluate side-chains
  81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 55
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  681 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 63 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0970
   chunk 44 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0980
   chunk 10 optimal weight:    0.0030
   overall best weight:    0.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.053425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.045971 restraints weight = 60333.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 6.95
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6811  Z= 0.120
  Angle     :  0.746  14.698   9212  Z= 0.358
  Chirality :  0.042   0.173   1102
  Planarity :  0.004   0.037   1175
  Dihedral  :  4.835  18.770    927
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 35.77 %
    Favored  : 60.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.29), residues: 876
  helix:  0.13 (0.26), residues: 390
  sheet: -0.79 (0.59), residues: 84
  loop : -1.45 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 187 
 TYR   0.011   0.001   TYR A 497 
 PHE   0.014   0.001   PHE A 403 
 TRP   0.012   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 313 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 6811)
  covalent geometry    : angle       0.74613 /  0.36 ( 9212)
  hydrogen bonds       : bond        0.03533 /  2.35 (  304)
  hydrogen bonds       : angle       4.83327 /  3.29 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.8465 (ptt-90)
REVERT: A  318 LYS cc_start: 0.8764 (tptp) cc_final: 0.8389 (tptp)
REVERT: A  397 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9032 (mp0)
REVERT: A  433 MET cc_start: 0.8454 (tmm) cc_final: 0.7926 (tmm)
REVERT: A  445 MET cc_start: 0.8767 (tpp) cc_final: 0.8471 (tpp)
REVERT: A  467 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8414 (pm20)
REVERT: A  500 MET cc_start: 0.5240 (mmm) cc_final: 0.4835 (mmm)
REVERT: A  523 MET cc_start: 0.8766 (mmp) cc_final: 0.8449 (mmp)
REVERT: A  566 MET cc_start: 0.8087 (tpp) cc_final: 0.7582 (tpp)
REVERT: A  581 MET cc_start: 0.6393 (ptt) cc_final: 0.6106 (ptt)
REVERT: A  640 MET cc_start: 0.9073 (tpt) cc_final: 0.8820 (tpt)
REVERT: A  696 LEU cc_start: 0.9330 (tt) cc_final: 0.9044 (pp)
REVERT: A  754 MET cc_start: 0.8110 (mmp) cc_final: 0.7800 (mmp)
REVERT: A  786 MET cc_start: 0.7166 (mmm) cc_final: 0.6814 (mmt)
REVERT: A  789 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8910 (t)
REVERT: A  793 LEU cc_start: 0.9502 (mm) cc_final: 0.9291 (mm)
REVERT: A  862 LEU cc_start: 0.9529 (mt) cc_final: 0.9228 (pp)
  outliers start: 30
  outliers final: 23
  residues processed: 87
  average time/residue: 0.0740
  time to fit residues: 8.8424
Evaluate side-chains
  83 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  681 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  745 ASN
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 72 optimal weight:    9.9990
   chunk 23 optimal weight:    0.4980
   chunk 65 optimal weight:   10.0000
   overall best weight:    1.2584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.052762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.045506 restraints weight = 61661.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 6.79
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6811  Z= 0.136
  Angle     :  0.763  14.930   9212  Z= 0.370
  Chirality :  0.042   0.177   1102
  Planarity :  0.004   0.037   1175
  Dihedral  :  4.865  19.182    927
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 18.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 36.60 %
    Favored  : 59.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.28), residues: 876
  helix:  0.13 (0.26), residues: 395
  sheet: -0.16 (0.64), residues: 65
  loop : -1.55 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 187 
 TYR   0.011   0.001   TYR A 497 
 PHE   0.017   0.001   PHE A 403 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.14 ( 6811)
  covalent geometry    : angle       0.76335 /  0.37 ( 9212)
  hydrogen bonds       : bond        0.03567 /  2.37 (  304)
  hydrogen bonds       : angle       4.89950 /  3.34 (  894)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.8958 (pmm) cc_final: 0.8731 (pmm)
REVERT: A  318 LYS cc_start: 0.8603 (tptp) cc_final: 0.8257 (tptp)
REVERT: A  397 GLU cc_start: 0.9421 (OUTLIER) cc_final: 0.9096 (mp0)
REVERT: A  433 MET cc_start: 0.8607 (tmm) cc_final: 0.8034 (tmm)
REVERT: A  445 MET cc_start: 0.8858 (tpp) cc_final: 0.8571 (tpp)
REVERT: A  500 MET cc_start: 0.5241 (mmm) cc_final: 0.4841 (mmm)
REVERT: A  566 MET cc_start: 0.8186 (tpp) cc_final: 0.7485 (tpp)
REVERT: A  696 LEU cc_start: 0.9379 (tt) cc_final: 0.9075 (pp)
REVERT: A  754 MET cc_start: 0.8415 (mmp) cc_final: 0.8053 (mmp)
REVERT: A  786 MET cc_start: 0.7493 (mmm) cc_final: 0.6984 (mmt)
REVERT: A  789 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9002 (t)
REVERT: A  862 LEU cc_start: 0.9525 (mt) cc_final: 0.9241 (pp)
  outliers start: 26
  outliers final: 23
  residues processed: 83
  average time/residue: 0.0734
  time to fit residues: 8.4269
Evaluate side-chains
  81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 56
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  681 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  745 ASN
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0060
   chunk 41 optimal weight:    0.4980
   chunk 68 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 716 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.052950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.045574 restraints weight = 60338.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 6.85
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6811  Z= 0.123
  Angle     :  0.777  15.185   9212  Z= 0.370
  Chirality :  0.042   0.173   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.820  19.928    927
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 37.15 %
    Favored  : 59.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.28), residues: 876
  helix:  0.17 (0.26), residues: 391
  sheet: -0.50 (0.62), residues: 73
  loop : -1.51 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 187 
 TYR   0.010   0.001   TYR A 497 
 PHE   0.016   0.001   PHE A 403 
 TRP   0.013   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 6811)
  covalent geometry    : angle       0.77682 /  0.37 ( 9212)
  hydrogen bonds       : bond        0.03574 /  2.38 (  304)
  hydrogen bonds       : angle       4.84079 /  3.29 (  894)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1343.16 seconds
wall clock time: 24 minutes 3.45 seconds (1443.45 seconds total)