Starting phenix.real_space_refine
on Wed Sep 17 07:45:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gqo_51510/09_2025/9gqo_51510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gqo_51510/09_2025/9gqo_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_51510/09_2025/9gqo_51510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gqo_51510/09_2025/9gqo_51510.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gqo_51510/09_2025/9gqo_51510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gqo_51510/09_2025/9gqo_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-2.0-5805/lib/python3.9/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, 6
          Unusual residues: {' CA': 1, ' MG': 1, 'PO3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.88, per 1000 atoms: 0.28
  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: 0.53
  Conformation dependent library (CDL) restraints added in 408.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.20
  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: 1.10

  Time building geometry restraints manager: 0.68 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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.730
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
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 aren 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
  covalent geometry    : bond        0.00347 ( 6811)
  covalent geometry    : angle       0.71422 ( 9212)
  hydrogen bonds       : bond        0.24841 (  304)
  hydrogen bonds       : angle       8.52586 (  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  : 0.270 
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: 0.5449 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0773
  time to fit residues: 8.8495
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  : 0.268 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  89 ASN
A 719 ASN
A 798 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.056496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.050106 restraints weight = 63661.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 6.38
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1599

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= 0.151
  Angle     :  0.721  12.255   9212  Z= 0.366
  Chirality :  0.043   0.191   1102
  Planarity :  0.005   0.048   1175
  Dihedral  :  5.069  29.250    930
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 34.67 %
    Favored  : 60.91 %
  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 aren not related in a simple way.
  whole: -1.03 (0.28), residues: 876
  helix: -0.15 (0.26), residues: 388
  sheet:  0.13 (0.60), residues: 78
  loop : -1.32 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 187 
 TYR   0.015   0.001   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
  covalent geometry    : bond        0.00322 ( 6811)
  covalent geometry    : angle       0.72071 ( 9212)
  hydrogen bonds       : bond        0.05288 (  304)
  hydrogen bonds       : angle       5.72654 (  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  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.8933 (tpp) cc_final: 0.7202 (tpp)
REVERT: A  500 MET cc_start: 0.4618 (mmm) cc_final: 0.4365 (mmm)
REVERT: A  566 MET cc_start: 0.7234 (tpp) cc_final: 0.6962 (tpp)
REVERT: A  754 MET cc_start: 0.8096 (mmt) cc_final: 0.7889 (mmp)
REVERT: A  862 LEU cc_start: 0.9535 (mt) cc_final: 0.9219 (pp)
  outliers start: 32
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0857
  time to fit residues: 10.9652
Evaluate side-chains
  71 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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  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:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0050
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    1.5198

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3495 r_free = 0.3495 target = 0.052879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.045522 restraints weight = 60150.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 6.81
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2145

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= 0.154
  Angle     :  0.708   8.766   9212  Z= 0.353
  Chirality :  0.042   0.185   1102
  Planarity :  0.004   0.057   1175
  Dihedral  :  5.020  19.513    927
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 18.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 34.67 %
    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 aren not related in a simple way.
  whole: -1.02 (0.28), residues: 876
  helix:  0.04 (0.26), residues: 388
  sheet: -0.12 (0.63), residues: 72
  loop : -1.44 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 187 
 TYR   0.014   0.001   TYR A 497 
 PHE   0.010   0.001   PHE A 685 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6811)
  covalent geometry    : angle       0.70760 ( 9212)
  hydrogen bonds       : bond        0.04503 (  304)
  hydrogen bonds       : angle       5.32624 (  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
  94 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 63
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 LEU cc_start: 0.9383 (mt) cc_final: 0.8990 (pp)
REVERT: A  280 MET cc_start: 0.8837 (mmt) cc_final: 0.8592 (mmt)
REVERT: A  318 LYS cc_start: 0.8465 (tptp) cc_final: 0.8246 (tptp)
REVERT: A  397 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.9029 (mp0)
REVERT: A  445 MET cc_start: 0.8169 (tpp) cc_final: 0.7684 (tpp)
REVERT: A  500 MET cc_start: 0.5157 (mmm) cc_final: 0.4793 (mmm)
REVERT: A  566 MET cc_start: 0.7548 (tpp) cc_final: 0.7217 (tpp)
REVERT: A  640 MET cc_start: 0.9141 (tpt) cc_final: 0.8929 (tpt)
REVERT: A  754 MET cc_start: 0.8334 (mmt) cc_final: 0.8098 (mmt)
REVERT: A  786 MET cc_start: 0.7512 (mmm) cc_final: 0.7155 (mmt)
REVERT: A  793 LEU cc_start: 0.9586 (mm) cc_final: 0.9384 (mm)
REVERT: A  862 LEU cc_start: 0.9578 (mt) cc_final: 0.9252 (pp)
REVERT: A  867 MET cc_start: 0.8726 (mmm) cc_final: 0.8510 (ptp)
  outliers start: 31
  outliers final: 20
  residues processed: 89
  average time/residue: 0.0848
  time to fit residues: 10.3105
Evaluate side-chains
  79 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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  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  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  697 PHE
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:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0070
   chunk 22 optimal weight:    8.9990
   overall best weight:    0.7202

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3512 r_free = 0.3512 target = 0.053561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.046171 restraints weight = 59967.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 6.88
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2391

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= 0.124
  Angle     :  0.678  10.471   9212  Z= 0.335
  Chirality :  0.042   0.143   1102
  Planarity :  0.004   0.042   1175
  Dihedral  :  4.914  19.121    927
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 34.39 %
    Favored  : 61.60 %
  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 aren not related in a simple way.
  whole: -0.92 (0.29), residues: 876
  helix:  0.18 (0.26), residues: 388
  sheet: -0.59 (0.57), residues: 89
  loop : -1.36 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 187 
 TYR   0.013   0.001   TYR A 497 
 PHE   0.011   0.001   PHE A 403 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6811)
  covalent geometry    : angle       0.67821 ( 9212)
  hydrogen bonds       : bond        0.04008 (  304)
  hydrogen bonds       : angle       5.02575 (  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
  94 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 65
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 LEU cc_start: 0.9405 (mt) cc_final: 0.8994 (pp)
REVERT: A  271 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8462 (tmm)
REVERT: A  344 MET cc_start: 0.8600 (tpp) cc_final: 0.8338 (tpp)
REVERT: A  356 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8745 (mtmt)
REVERT: A  397 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9101 (mp0)
REVERT: A  433 MET cc_start: 0.8415 (tmm) cc_final: 0.8132 (tmm)
REVERT: A  445 MET cc_start: 0.8652 (tpp) cc_final: 0.8299 (tpp)
REVERT: A  500 MET cc_start: 0.5119 (mmm) cc_final: 0.4789 (mmm)
REVERT: A  566 MET cc_start: 0.7739 (tpp) cc_final: 0.7274 (tpp)
REVERT: A  653 MET cc_start: 0.9166 (tpt) cc_final: 0.8504 (tpt)
REVERT: A  786 MET cc_start: 0.7802 (mmm) cc_final: 0.7310 (mmt)
REVERT: A  789 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8888 (t)
REVERT: A  793 LEU cc_start: 0.9607 (mm) cc_final: 0.9369 (mm)
REVERT: A  862 LEU cc_start: 0.9522 (mt) cc_final: 0.9230 (pp)
REVERT: A  867 MET cc_start: 0.8770 (mmm) cc_final: 0.8508 (ptp)
  outliers start: 29
  outliers final: 20
  residues processed: 88
  average time/residue: 0.0814
  time to fit residues: 9.9756
Evaluate side-chains
  81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  294 LEU
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  421 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:    0.6980
   chunk 47 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 61 optimal weight:    0.2980
   chunk 77 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3519 r_free = 0.3519 target = 0.053864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.046407 restraints weight = 60747.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 6.95
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6811  Z= 0.118
  Angle     :  0.682  12.216   9212  Z= 0.332
  Chirality :  0.041   0.163   1102
  Planarity :  0.004   0.041   1175
  Dihedral  :  4.823  18.142    927
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 35.08 %
    Favored  : 60.77 %
  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 aren not related in a simple way.
  whole: -0.98 (0.29), residues: 876
  helix:  0.14 (0.26), residues: 390
  sheet: -0.77 (0.57), residues: 83
  loop : -1.38 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 119 
 TYR   0.012   0.001   TYR A 497 
 PHE   0.013   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
  covalent geometry    : bond        0.00260 ( 6811)
  covalent geometry    : angle       0.68240 ( 9212)
  hydrogen bonds       : bond        0.03767 (  304)
  hydrogen bonds       : angle       4.91267 (  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
  91 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8314 (tmm)
REVERT: A  280 MET cc_start: 0.9132 (mmt) cc_final: 0.8841 (mmt)
REVERT: A  344 MET cc_start: 0.8607 (tpp) cc_final: 0.8285 (tpp)
REVERT: A  397 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.9113 (mp0)
REVERT: A  433 MET cc_start: 0.8413 (tmm) cc_final: 0.8016 (tmm)
REVERT: A  445 MET cc_start: 0.8668 (tpp) cc_final: 0.8282 (tpp)
REVERT: A  500 MET cc_start: 0.5124 (mmm) cc_final: 0.4785 (mmm)
REVERT: A  547 MET cc_start: 0.9287 (ttp) cc_final: 0.8715 (tmm)
REVERT: A  566 MET cc_start: 0.7937 (tpp) cc_final: 0.7374 (tpp)
REVERT: A  653 MET cc_start: 0.9183 (tpt) cc_final: 0.8611 (tpt)
REVERT: A  754 MET cc_start: 0.8543 (mmt) cc_final: 0.8329 (mmt)
REVERT: A  786 MET cc_start: 0.7717 (mmm) cc_final: 0.7282 (mmt)
REVERT: A  789 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8960 (t)
REVERT: A  793 LEU cc_start: 0.9524 (mm) cc_final: 0.9315 (mm)
REVERT: A  862 LEU cc_start: 0.9527 (mt) cc_final: 0.9234 (pp)
  outliers start: 30
  outliers final: 19
  residues processed: 85
  average time/residue: 0.0801
  time to fit residues: 9.5203
Evaluate side-chains
  81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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  397 GLU
Chi-restraints excluded: chain A residue  421 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:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0170
   chunk 57 optimal weight:    0.0870
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 64 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3511 r_free = 0.3511 target = 0.051045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.042731 restraints weight = 55513.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 7.30
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2830

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= 0.117
  Angle     :  0.687  12.771   9212  Z= 0.333
  Chirality :  0.041   0.167   1102
  Planarity :  0.004   0.039   1175
  Dihedral  :  4.769  18.143    927
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 36.46 %
    Favored  : 59.53 %
  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 aren not related in a simple way.
  whole: -1.00 (0.29), residues: 876
  helix:  0.19 (0.26), residues: 390
  sheet: -0.80 (0.57), residues: 83
  loop : -1.45 (0.32), residues: 403

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   0.010   0.001   PHE A 403 
 TRP   0.010   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6811)
  covalent geometry    : angle       0.68734 ( 9212)
  hydrogen bonds       : bond        0.03551 (  304)
  hydrogen bonds       : angle       4.79434 (  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
  90 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 61
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 MET cc_start: 0.9036 (mmt) cc_final: 0.8802 (mmt)
REVERT: A  397 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.9006 (mp0)
REVERT: A  433 MET cc_start: 0.8271 (tmm) cc_final: 0.7837 (tmm)
REVERT: A  445 MET cc_start: 0.8640 (tpp) cc_final: 0.8287 (tpp)
REVERT: A  500 MET cc_start: 0.5142 (mmm) cc_final: 0.4788 (mmm)
REVERT: A  566 MET cc_start: 0.7821 (tpp) cc_final: 0.7344 (tpp)
REVERT: A  653 MET cc_start: 0.9106 (tpt) cc_final: 0.8553 (tpt)
REVERT: A  689 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8953 (mt)
REVERT: A  786 MET cc_start: 0.7410 (mmm) cc_final: 0.7157 (mmt)
REVERT: A  789 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8925 (t)
REVERT: A  862 LEU cc_start: 0.9511 (mt) cc_final: 0.9198 (pp)
REVERT: A  867 MET cc_start: 0.8863 (ptt) cc_final: 0.8565 (mmm)
  outliers start: 29
  outliers final: 19
  residues processed: 85
  average time/residue: 0.0779
  time to fit residues: 9.2808
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  : 0.268 
-------------------------------------------------------------------------------
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  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  421 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  689 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0870
   chunk 36 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0170
   chunk 42 optimal weight:   20.0000
   overall best weight:    2.6202

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 552 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.051405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.044290 restraints weight = 62940.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 6.68
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6811  Z= 0.213
  Angle     :  0.765  13.616   9212  Z= 0.381
  Chirality :  0.043   0.182   1102
  Planarity :  0.004   0.041   1175
  Dihedral  :  4.977  20.901    927
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 20.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 36.46 %
    Favored  : 59.12 %
  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 aren not related in a simple way.
  whole: -1.08 (0.28), residues: 876
  helix:  0.11 (0.26), residues: 397
  sheet: -0.06 (0.61), residues: 71
  loop : -1.68 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 187 
 TYR   0.012   0.001   TYR A 497 
 PHE   0.009   0.001   PHE A 359 
 TRP   0.010   0.001   TRP A 703 
 HIS   0.003   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 6811)
  covalent geometry    : angle       0.76547 ( 9212)
  hydrogen bonds       : bond        0.03857 (  304)
  hydrogen bonds       : angle       5.07502 (  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: 32
    poor density    : 58
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.8931 (pmm) cc_final: 0.8657 (pmm)
REVERT: A  344 MET cc_start: 0.8473 (tpp) cc_final: 0.7921 (tpp)
REVERT: A  397 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9059 (mp0)
REVERT: A  433 MET cc_start: 0.8669 (tmm) cc_final: 0.8184 (tmm)
REVERT: A  445 MET cc_start: 0.8698 (tpp) cc_final: 0.8316 (tpp)
REVERT: A  500 MET cc_start: 0.5391 (mmm) cc_final: 0.5018 (mmm)
REVERT: A  566 MET cc_start: 0.7887 (tpp) cc_final: 0.7300 (tpp)
REVERT: A  653 MET cc_start: 0.9164 (tpt) cc_final: 0.8599 (tpt)
REVERT: A  689 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8933 (mp)
REVERT: A  696 LEU cc_start: 0.9449 (tt) cc_final: 0.9175 (pp)
REVERT: A  786 MET cc_start: 0.7535 (mmm) cc_final: 0.7222 (mmt)
REVERT: A  789 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9150 (t)
REVERT: A  853 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7547 (pm20)
REVERT: A  862 LEU cc_start: 0.9531 (mt) cc_final: 0.9297 (pp)
REVERT: A  867 MET cc_start: 0.9099 (ptt) cc_final: 0.8837 (mmm)
  outliers start: 32
  outliers final: 21
  residues processed: 87
  average time/residue: 0.0800
  time to fit residues: 9.6954
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  : 0.235 
-------------------------------------------------------------------------------
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  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  441 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  689 LEU
Chi-restraints excluded: chain A residue  745 ASN
Chi-restraints excluded: chain A residue  789 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:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3487 r_free = 0.3487 target = 0.052361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.045080 restraints weight = 62593.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 6.82
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3151

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= 0.134
  Angle     :  0.730  14.134   9212  Z= 0.356
  Chirality :  0.042   0.153   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.982  19.119    927
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 36.88 %
    Favored  : 59.12 %
  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 aren not related in a simple way.
  whole: -0.98 (0.28), residues: 876
  helix:  0.19 (0.26), residues: 394
  sheet: -0.31 (0.61), residues: 69
  loop : -1.54 (0.31), residues: 413

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   0.015   0.001   PHE A 403 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6811)
  covalent geometry    : angle       0.73024 ( 9212)
  hydrogen bonds       : bond        0.03657 (  304)
  hydrogen bonds       : angle       4.90857 (  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
  87 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 58
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.8871 (pmm) cc_final: 0.8584 (pmm)
REVERT: A  344 MET cc_start: 0.8514 (tpp) cc_final: 0.7914 (tpp)
REVERT: A  397 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9052 (mp0)
REVERT: A  433 MET cc_start: 0.8649 (tmm) cc_final: 0.8109 (tmm)
REVERT: A  445 MET cc_start: 0.8783 (tpp) cc_final: 0.8442 (tpp)
REVERT: A  500 MET cc_start: 0.5372 (mmm) cc_final: 0.4929 (mmm)
REVERT: A  566 MET cc_start: 0.8149 (tpp) cc_final: 0.7477 (tpp)
REVERT: A  581 MET cc_start: 0.6804 (ptt) cc_final: 0.6551 (ptt)
REVERT: A  640 MET cc_start: 0.9062 (tpt) cc_final: 0.8740 (tpt)
REVERT: A  653 MET cc_start: 0.9107 (tpt) cc_final: 0.8535 (tpt)
REVERT: A  689 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.9010 (mt)
REVERT: A  696 LEU cc_start: 0.9409 (tt) cc_final: 0.9102 (pp)
REVERT: A  754 MET cc_start: 0.8332 (mmp) cc_final: 0.7962 (mmp)
REVERT: A  786 MET cc_start: 0.7381 (mmm) cc_final: 0.7081 (mmt)
REVERT: A  789 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9099 (t)
REVERT: A  862 LEU cc_start: 0.9526 (mt) cc_final: 0.9291 (pp)
  outliers start: 29
  outliers final: 20
  residues processed: 84
  average time/residue: 0.0806
  time to fit residues: 9.3237
Evaluate side-chains
  79 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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  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  683 TYR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  799 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:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 74 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3493 r_free = 0.3493 target = 0.052480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.045189 restraints weight = 62251.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 6.85
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3262

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= 0.129
  Angle     :  0.750  14.540   9212  Z= 0.362
  Chirality :  0.042   0.169   1102
  Planarity :  0.004   0.039   1175
  Dihedral  :  4.943  19.067    927
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 37.15 %
    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 aren not related in a simple way.
  whole: -0.97 (0.28), residues: 876
  helix:  0.20 (0.26), residues: 394
  sheet: -0.71 (0.58), residues: 77
  loop : -1.45 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 187 
 TYR   0.011   0.001   TYR A 497 
 PHE   0.015   0.001   PHE A 403 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6811)
  covalent geometry    : angle       0.74995 ( 9212)
  hydrogen bonds       : bond        0.03598 (  304)
  hydrogen bonds       : angle       4.85186 (  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
  82 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.8862 (pmm) cc_final: 0.8576 (pmm)
REVERT: A  280 MET cc_start: 0.9234 (mmt) cc_final: 0.8960 (mmt)
REVERT: A  318 LYS cc_start: 0.8614 (tptp) cc_final: 0.8253 (tptp)
REVERT: A  344 MET cc_start: 0.8381 (tpp) cc_final: 0.7818 (tpp)
REVERT: A  397 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9088 (mp0)
REVERT: A  433 MET cc_start: 0.8655 (tmm) cc_final: 0.8088 (tmm)
REVERT: A  445 MET cc_start: 0.8837 (tpp) cc_final: 0.8515 (tpp)
REVERT: A  500 MET cc_start: 0.5297 (mmm) cc_final: 0.4872 (mmm)
REVERT: A  566 MET cc_start: 0.8205 (tpp) cc_final: 0.7578 (tpp)
REVERT: A  581 MET cc_start: 0.6896 (ptt) cc_final: 0.6632 (ptt)
REVERT: A  653 MET cc_start: 0.9092 (tpt) cc_final: 0.8504 (tpt)
REVERT: A  689 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8947 (mt)
REVERT: A  696 LEU cc_start: 0.9387 (tt) cc_final: 0.9070 (pp)
REVERT: A  754 MET cc_start: 0.8306 (mmp) cc_final: 0.7838 (mmp)
REVERT: A  786 MET cc_start: 0.7382 (mmm) cc_final: 0.7090 (mmt)
REVERT: A  862 LEU cc_start: 0.9502 (mt) cc_final: 0.9262 (pp)
  outliers start: 23
  outliers final: 18
  residues processed: 81
  average time/residue: 0.0770
  time to fit residues: 8.7080
Evaluate side-chains
  77 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  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  574 THR
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  689 LEU
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  860 LEU
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:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 9 optimal weight:    0.1980
   chunk 5 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 23 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3479 r_free = 0.3479 target = 0.051963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.044663 restraints weight = 62275.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 6.84
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6811  Z= 0.143
  Angle     :  0.773  14.739   9212  Z= 0.373
  Chirality :  0.043   0.179   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.972  19.634    927
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 37.15 %
    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 aren not related in a simple way.
  whole: -0.92 (0.28), residues: 876
  helix:  0.20 (0.26), residues: 399
  sheet: -0.40 (0.62), residues: 69
  loop : -1.45 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 187 
 TYR   0.015   0.001   TYR A 831 
 PHE   0.015   0.001   PHE A 403 
 TRP   0.012   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6811)
  covalent geometry    : angle       0.77257 ( 9212)
  hydrogen bonds       : bond        0.03581 (  304)
  hydrogen bonds       : angle       4.89059 (  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
  80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.8800 (pmm) cc_final: 0.8464 (pmm)
REVERT: A  318 LYS cc_start: 0.8596 (tptp) cc_final: 0.8237 (tptp)
REVERT: A  344 MET cc_start: 0.8311 (tpp) cc_final: 0.7771 (tpp)
REVERT: A  386 ASN cc_start: 0.9131 (p0) cc_final: 0.8914 (p0)
REVERT: A  397 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8948 (mp0)
REVERT: A  433 MET cc_start: 0.8629 (tmm) cc_final: 0.8074 (tmm)
REVERT: A  445 MET cc_start: 0.8805 (tpp) cc_final: 0.8493 (tpp)
REVERT: A  500 MET cc_start: 0.5387 (mmm) cc_final: 0.4940 (mmm)
REVERT: A  566 MET cc_start: 0.8216 (tpp) cc_final: 0.7609 (tpp)
REVERT: A  653 MET cc_start: 0.9108 (tpt) cc_final: 0.8528 (tpt)
REVERT: A  689 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8956 (mt)
REVERT: A  696 LEU cc_start: 0.9389 (tt) cc_final: 0.9067 (pp)
REVERT: A  754 MET cc_start: 0.8306 (mmp) cc_final: 0.7809 (mmp)
REVERT: A  786 MET cc_start: 0.7386 (mmm) cc_final: 0.7017 (mmt)
REVERT: A  862 LEU cc_start: 0.9514 (mt) cc_final: 0.9274 (pp)
  outliers start: 23
  outliers final: 20
  residues processed: 79
  average time/residue: 0.0777
  time to fit residues: 8.5993
Evaluate side-chains
  79 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    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  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  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  683 TYR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  745 ASN
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  860 LEU
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:    6.9990
   chunk 37 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3483 r_free = 0.3483 target = 0.052039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.043934 restraints weight = 50287.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 6.70
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3470

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= 0.132
  Angle     :  0.757  15.063   9212  Z= 0.366
  Chirality :  0.042   0.175   1102
  Planarity :  0.004   0.039   1175
  Dihedral  :  4.964  20.203    927
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 36.88 %
    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 aren not related in a simple way.
  whole: -0.93 (0.29), residues: 876
  helix:  0.20 (0.26), residues: 399
  sheet: -0.77 (0.60), residues: 77
  loop : -1.39 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 187 
 TYR   0.013   0.001   TYR A 831 
 PHE   0.014   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
  covalent geometry    : bond        0.00288 ( 6811)
  covalent geometry    : angle       0.75670 ( 9212)
  hydrogen bonds       : bond        0.03582 (  304)
  hydrogen bonds       : angle       4.83808 (  894)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1355.29 seconds
wall clock time: 24 minutes 8.64 seconds (1448.64 seconds total)