Starting phenix.real_space_refine
on Tue Mar 11 22:35:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gqo_51510/03_2025/9gqo_51510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gqo_51510/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gqo_51510/03_2025/9gqo_51510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gqo_51510/03_2025/9gqo_51510.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gqo_51510/03_2025/9gqo_51510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gqo_51510/03_2025/9gqo_51510.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.38, per 1000 atoms: 0.65
  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: 1.79
  Conformation dependent library (CDL) restraints added in 926.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 5 sheets defined
      50.6% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  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: 1.96

  Time building geometry restraints manager: 2.12 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:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.500
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.650
-------------------------------------------------------------------------------
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= 0.240
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (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
 TRP   0.012   0.002   TRP A 703 
 HIS   0.002   0.000   HIS A 437 
 PHE   0.013   0.001   PHE A 707 
 TYR   0.020   0.001   TYR A   4 
 ARG   0.004   0.000   ARG A 187 

*********************** 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  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.1506 (pt0)
REVERT: A  445 MET cc_start: 0.5896 (tpt) cc_final: 0.5448 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2027
  time to fit residues: 23.0146
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  : 0.790 
-------------------------------------------------------------------------------
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 74 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0370
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 719 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.051381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.042043 restraints weight = 51587.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 8.33
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1470

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= 0.210
  Angle     :  0.720  11.811   9212  Z= 0.365
  Chirality :  0.043   0.219   1102
  Planarity :  0.005   0.048   1175
  Dihedral  :  5.026  29.103    930
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 35.08 %
    Favored  : 61.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.28), residues: 876
  helix: -0.19 (0.26), residues: 388
  sheet:  0.15 (0.60), residues: 78
  loop : -1.34 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 552 
 PHE   0.016   0.001   PHE A 403 
 TYR   0.014   0.001   TYR A 497 
 ARG   0.008   0.000   ARG A 187 

*********************** 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
  96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.4509 (mmm) cc_final: 0.4273 (mmm)
REVERT: A  547 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8352 (tmm)
REVERT: A  640 MET cc_start: 0.9183 (tpt) cc_final: 0.8953 (tpt)
REVERT: A  754 MET cc_start: 0.8021 (mmt) cc_final: 0.7811 (mmp)
REVERT: A  862 LEU cc_start: 0.9514 (mt) cc_final: 0.9220 (pp)
REVERT: A  867 MET cc_start: 0.8979 (ptt) cc_final: 0.8731 (mmm)
  outliers start: 27
  outliers final: 8
  residues processed: 91
  average time/residue: 0.2073
  time to fit residues: 25.5721
Evaluate side-chains
  69 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  416 GLU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  547 MET
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 77 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 24 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 798 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.051254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.041518 restraints weight = 53171.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 8.38
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6811  Z= 0.200
  Angle     :  0.704   8.918   9212  Z= 0.350
  Chirality :  0.042   0.179   1102
  Planarity :  0.004   0.054   1175
  Dihedral  :  4.919  18.917    927
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 33.98 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.28), residues: 876
  helix:  0.00 (0.26), residues: 388
  sheet: -0.47 (0.62), residues: 77
  loop : -1.43 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 703 
 HIS   0.002   0.001   HIS A 552 
 PHE   0.013   0.001   PHE A 403 
 TYR   0.013   0.001   TYR A 497 
 ARG   0.003   0.000   ARG A 187 

*********************** 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
  100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 62
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 LEU cc_start: 0.9417 (mt) cc_final: 0.9011 (pp)
REVERT: A  280 MET cc_start: 0.9068 (mmt) cc_final: 0.8797 (mmt)
REVERT: A  397 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.9023 (mp0)
REVERT: A  445 MET cc_start: 0.8360 (tpp) cc_final: 0.8012 (tpp)
REVERT: A  500 MET cc_start: 0.4948 (mmm) cc_final: 0.4592 (mmm)
REVERT: A  523 MET cc_start: 0.8672 (mpp) cc_final: 0.8221 (mmp)
REVERT: A  566 MET cc_start: 0.7439 (tpp) cc_final: 0.7220 (tpp)
REVERT: A  729 MET cc_start: 0.8611 (mmm) cc_final: 0.8109 (mmm)
REVERT: A  754 MET cc_start: 0.8336 (mmt) cc_final: 0.8047 (mmp)
REVERT: A  786 MET cc_start: 0.7754 (mmm) cc_final: 0.7329 (mmt)
REVERT: A  862 LEU cc_start: 0.9534 (mt) cc_final: 0.9232 (pp)
REVERT: A  867 MET cc_start: 0.8902 (ptt) cc_final: 0.8647 (mmm)
  outliers start: 38
  outliers final: 21
  residues processed: 94
  average time/residue: 0.2105
  time to fit residues: 27.2414
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  : 0.812 
-------------------------------------------------------------------------------
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  116 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  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  789 THR
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  799 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    0.2980
   chunk 37 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0570
   overall best weight:    1.4704

-------------------------------------------------------------------------------
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 = 0.3486 r_free = 0.3486 target = 0.052621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.045308 restraints weight = 60911.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 6.76
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6811  Z= 0.202
  Angle     :  0.699  10.132   9212  Z= 0.348
  Chirality :  0.042   0.167   1102
  Planarity :  0.004   0.043   1175
  Dihedral  :  4.905  18.473    927
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 34.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.29), residues: 876
  helix:  0.22 (0.26), residues: 382
  sheet: -0.57 (0.62), residues: 76
  loop : -1.39 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 552 
 PHE   0.009   0.001   PHE A  12 
 TYR   0.013   0.001   TYR A 497 
 ARG   0.007   0.000   ARG A 187 

*********************** 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
  91 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.8748 (tpp) cc_final: 0.8453 (tpp)
REVERT: A  397 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9067 (mp0)
REVERT: A  433 MET cc_start: 0.8386 (tmm) cc_final: 0.8129 (tmm)
REVERT: A  445 MET cc_start: 0.8491 (tpp) cc_final: 0.8108 (tpp)
REVERT: A  500 MET cc_start: 0.5159 (mmm) cc_final: 0.4800 (mmm)
REVERT: A  523 MET cc_start: 0.8450 (mpp) cc_final: 0.8109 (mmt)
REVERT: A  566 MET cc_start: 0.7644 (tpp) cc_final: 0.7296 (tpp)
REVERT: A  729 MET cc_start: 0.8973 (mmm) cc_final: 0.8626 (mmm)
REVERT: A  754 MET cc_start: 0.8593 (mmt) cc_final: 0.8246 (mmt)
REVERT: A  786 MET cc_start: 0.7704 (mmm) cc_final: 0.7214 (mmt)
REVERT: A  862 LEU cc_start: 0.9561 (mt) cc_final: 0.9263 (pp)
REVERT: A  867 MET cc_start: 0.8964 (ptt) cc_final: 0.8639 (mmm)
  outliers start: 30
  outliers final: 24
  residues processed: 86
  average time/residue: 0.1710
  time to fit residues: 20.6291
Evaluate side-chains
  80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 55
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  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  607 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  782 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  799 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 3 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 64 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.052609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.045366 restraints weight = 61054.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 6.77
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6811  Z= 0.190
  Angle     :  0.695  12.435   9212  Z= 0.342
  Chirality :  0.042   0.179   1102
  Planarity :  0.004   0.040   1175
  Dihedral  :  4.895  18.974    927
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 18.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 35.64 %
    Favored  : 60.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.29), residues: 876
  helix:  0.23 (0.27), residues: 381
  sheet: -0.09 (0.61), residues: 72
  loop : -1.46 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 552 
 PHE   0.011   0.001   PHE A 707 
 TYR   0.012   0.001   TYR A 497 
 ARG   0.011   0.000   ARG A 261 

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

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 60
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.9080 (mp0)
REVERT: A  433 MET cc_start: 0.8451 (tmm) cc_final: 0.8062 (tmm)
REVERT: A  445 MET cc_start: 0.8656 (tpp) cc_final: 0.8276 (tpp)
REVERT: A  500 MET cc_start: 0.5243 (mmm) cc_final: 0.4865 (mmm)
REVERT: A  523 MET cc_start: 0.8237 (mpp) cc_final: 0.7954 (mmt)
REVERT: A  536 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.9117 (mp0)
REVERT: A  566 MET cc_start: 0.7928 (tpp) cc_final: 0.7493 (tpp)
REVERT: A  653 MET cc_start: 0.9152 (tpt) cc_final: 0.8398 (tpt)
REVERT: A  729 MET cc_start: 0.9027 (mmm) cc_final: 0.8740 (mmm)
REVERT: A  754 MET cc_start: 0.8570 (mmt) cc_final: 0.8369 (mmt)
REVERT: A  786 MET cc_start: 0.7770 (mmm) cc_final: 0.7297 (mmt)
REVERT: A  789 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9087 (t)
REVERT: A  862 LEU cc_start: 0.9544 (mt) cc_final: 0.9260 (pp)
REVERT: A  867 MET cc_start: 0.8965 (ptt) cc_final: 0.8634 (mmm)
  outliers start: 30
  outliers final: 19
  residues processed: 84
  average time/residue: 0.1811
  time to fit residues: 21.1663
Evaluate side-chains
  78 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  792 ILE
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 1 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0270
   chunk 56 optimal weight:    0.4980
   chunk 69 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0040
   overall best weight:    0.3050

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.053767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.046466 restraints weight = 59557.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 6.78
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2944

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= 0.167
  Angle     :  0.696  13.236   9212  Z= 0.338
  Chirality :  0.042   0.167   1102
  Planarity :  0.004   0.039   1175
  Dihedral  :  4.807  19.188    927
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 36.88 %
    Favored  : 59.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.29), residues: 876
  helix:  0.25 (0.27), residues: 381
  sheet: -0.74 (0.58), residues: 83
  loop : -1.44 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 703 
 HIS   0.003   0.001   HIS A 437 
 PHE   0.012   0.001   PHE A 707 
 TYR   0.011   0.001   TYR A 497 
 ARG   0.011   0.001   ARG A 108 

*********************** 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
  85 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 58
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.8799 (tpp) cc_final: 0.8439 (tpp)
REVERT: A  397 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9079 (mp0)
REVERT: A  421 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8276 (pt0)
REVERT: A  433 MET cc_start: 0.8403 (tmm) cc_final: 0.7984 (tmm)
REVERT: A  445 MET cc_start: 0.8661 (tpp) cc_final: 0.8362 (tpp)
REVERT: A  500 MET cc_start: 0.5176 (mmm) cc_final: 0.4809 (mmm)
REVERT: A  536 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.9055 (mp0)
REVERT: A  547 MET cc_start: 0.9048 (ttp) cc_final: 0.8627 (tmm)
REVERT: A  566 MET cc_start: 0.7895 (tpp) cc_final: 0.7481 (tpp)
REVERT: A  653 MET cc_start: 0.9194 (tpt) cc_final: 0.8566 (tpt)
REVERT: A  689 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8971 (mt)
REVERT: A  729 MET cc_start: 0.9013 (mmm) cc_final: 0.8769 (mmm)
REVERT: A  786 MET cc_start: 0.7324 (mmm) cc_final: 0.7046 (mmt)
REVERT: A  789 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9016 (t)
REVERT: A  862 LEU cc_start: 0.9517 (mt) cc_final: 0.9229 (pp)
REVERT: A  867 MET cc_start: 0.8841 (ptt) cc_final: 0.8521 (mmm)
  outliers start: 27
  outliers final: 17
  residues processed: 80
  average time/residue: 0.1671
  time to fit residues: 18.9610
Evaluate side-chains
  78 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  792 ILE
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 1 optimal weight:    0.2980
   chunk 20 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.053635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.046362 restraints weight = 60025.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 6.78
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3071

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= 0.171
  Angle     :  0.696  13.861   9212  Z= 0.337
  Chirality :  0.041   0.162   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.740  18.974    927
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 37.43 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.28), residues: 876
  helix:  0.28 (0.27), residues: 384
  sheet: -0.44 (0.59), residues: 78
  loop : -1.53 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 
 PHE   0.018   0.001   PHE A 403 
 TYR   0.012   0.001   TYR A 497 
 ARG   0.006   0.000   ARG A 261 

*********************** 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
  82 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 LYS cc_start: 0.8515 (tptp) cc_final: 0.8263 (tptp)
REVERT: A  397 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.9121 (mp0)
REVERT: A  421 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8009 (mp0)
REVERT: A  433 MET cc_start: 0.8505 (tmm) cc_final: 0.8010 (tmm)
REVERT: A  445 MET cc_start: 0.8829 (tpp) cc_final: 0.8523 (tpp)
REVERT: A  500 MET cc_start: 0.5143 (mmm) cc_final: 0.4781 (mmm)
REVERT: A  536 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9140 (mp0)
REVERT: A  547 MET cc_start: 0.9333 (ttp) cc_final: 0.8727 (tmm)
REVERT: A  566 MET cc_start: 0.8094 (tpp) cc_final: 0.7597 (tpp)
REVERT: A  653 MET cc_start: 0.9141 (tpt) cc_final: 0.8431 (tpt)
REVERT: A  689 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8921 (mt)
REVERT: A  696 LEU cc_start: 0.9379 (tt) cc_final: 0.9085 (pp)
REVERT: A  729 MET cc_start: 0.8988 (mmm) cc_final: 0.8748 (mmm)
REVERT: A  786 MET cc_start: 0.7484 (mmm) cc_final: 0.7135 (mmt)
REVERT: A  862 LEU cc_start: 0.9456 (mt) cc_final: 0.9182 (pp)
REVERT: A  867 MET cc_start: 0.8952 (ptt) cc_final: 0.8621 (mmm)
  outliers start: 25
  outliers final: 16
  residues processed: 81
  average time/residue: 0.1938
  time to fit residues: 23.3251
Evaluate side-chains
  75 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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  324 THR
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  536 GLU
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  792 ILE
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    0.3980
   chunk 77 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0010
   chunk 84 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    1.0388

-------------------------------------------------------------------------------
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 = 0.3510 r_free = 0.3510 target = 0.053001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.045726 restraints weight = 60450.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 6.79
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3200

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= 0.179
  Angle     :  0.715  14.343   9212  Z= 0.349
  Chirality :  0.041   0.167   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.761  18.708    927
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 36.33 %
    Favored  : 60.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.28), residues: 876
  helix:  0.32 (0.26), residues: 385
  sheet: -0.46 (0.59), residues: 78
  loop : -1.55 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 
 PHE   0.017   0.001   PHE A 403 
 TYR   0.013   0.001   TYR A 831 
 ARG   0.004   0.000   ARG A 261 

*********************** 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
  82 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 LYS cc_start: 0.8540 (tptp) cc_final: 0.8264 (tptp)
REVERT: A  344 MET cc_start: 0.8803 (tpp) cc_final: 0.8509 (tpp)
REVERT: A  397 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9059 (mp0)
REVERT: A  421 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7940 (mp0)
REVERT: A  433 MET cc_start: 0.8534 (tmm) cc_final: 0.8015 (tmm)
REVERT: A  445 MET cc_start: 0.8756 (tpp) cc_final: 0.8453 (tpp)
REVERT: A  467 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8391 (pm20)
REVERT: A  500 MET cc_start: 0.5198 (mmm) cc_final: 0.4811 (mmm)
REVERT: A  566 MET cc_start: 0.8133 (tpp) cc_final: 0.7638 (tpp)
REVERT: A  640 MET cc_start: 0.9033 (tpt) cc_final: 0.8728 (tpt)
REVERT: A  653 MET cc_start: 0.9160 (tpt) cc_final: 0.8463 (tpt)
REVERT: A  689 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8929 (mt)
REVERT: A  696 LEU cc_start: 0.9365 (tt) cc_final: 0.9039 (pp)
REVERT: A  729 MET cc_start: 0.9029 (mmm) cc_final: 0.8827 (mmm)
REVERT: A  754 MET cc_start: 0.8191 (mmp) cc_final: 0.7847 (mmp)
REVERT: A  786 MET cc_start: 0.7370 (mmm) cc_final: 0.7013 (mmt)
REVERT: A  862 LEU cc_start: 0.9487 (mt) cc_final: 0.9198 (pp)
REVERT: A  867 MET cc_start: 0.8881 (ptt) cc_final: 0.8672 (mmm)
  outliers start: 25
  outliers final: 19
  residues processed: 79
  average time/residue: 0.1875
  time to fit residues: 20.8613
Evaluate side-chains
  78 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
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  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  421 GLU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  792 ILE
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 31 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0060
   chunk 76 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7596

-------------------------------------------------------------------------------
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 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.053087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.045811 restraints weight = 60565.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 6.80
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3318

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= 0.175
  Angle     :  0.751  14.743   9212  Z= 0.363
  Chirality :  0.042   0.167   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.769  18.925    927
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 36.60 %
    Favored  : 59.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.29), residues: 876
  helix:  0.32 (0.26), residues: 385
  sheet: -0.45 (0.60), residues: 80
  loop : -1.54 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 
 PHE   0.014   0.001   PHE A 403 
 TYR   0.011   0.001   TYR A 497 
 ARG   0.005   0.000   ARG A 187 

*********************** 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: 26
    poor density    : 56
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 MET cc_start: 0.8772 (mmm) cc_final: 0.8510 (mmm)
REVERT: A  344 MET cc_start: 0.8834 (tpp) cc_final: 0.8503 (tpp)
REVERT: A  397 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.9049 (mp0)
REVERT: A  421 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7889 (mp0)
REVERT: A  433 MET cc_start: 0.8497 (tmm) cc_final: 0.7967 (tmm)
REVERT: A  445 MET cc_start: 0.8784 (tpp) cc_final: 0.8496 (tpp)
REVERT: A  500 MET cc_start: 0.5159 (mmm) cc_final: 0.4701 (mmm)
REVERT: A  523 MET cc_start: 0.8815 (mmp) cc_final: 0.8575 (mmp)
REVERT: A  566 MET cc_start: 0.8224 (tpp) cc_final: 0.7654 (tpp)
REVERT: A  689 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8925 (mt)
REVERT: A  696 LEU cc_start: 0.9348 (tt) cc_final: 0.9003 (pp)
REVERT: A  754 MET cc_start: 0.8095 (mmp) cc_final: 0.7657 (mmp)
REVERT: A  786 MET cc_start: 0.7317 (mmm) cc_final: 0.6961 (mmt)
REVERT: A  862 LEU cc_start: 0.9488 (mt) cc_final: 0.9095 (pp)
  outliers start: 26
  outliers final: 19
  residues processed: 81
  average time/residue: 0.1689
  time to fit residues: 19.3515
Evaluate side-chains
  78 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  324 THR
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  618 THR
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  873 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.052578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.045314 restraints weight = 61450.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 6.79
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6811  Z= 0.188
  Angle     :  0.757  15.084   9212  Z= 0.367
  Chirality :  0.042   0.175   1102
  Planarity :  0.004   0.037   1175
  Dihedral  :  4.793  19.188    927
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 37.02 %
    Favored  : 59.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.29), residues: 876
  helix:  0.35 (0.26), residues: 385
  sheet: -0.45 (0.60), residues: 80
  loop : -1.54 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 
 PHE   0.014   0.001   PHE A 403 
 TYR   0.011   0.001   TYR A 497 
 ARG   0.004   0.000   ARG A 187 

********************** 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  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.8926 (tpp) cc_final: 0.8602 (tpp)
REVERT: A  397 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.8950 (mp0)
REVERT: A  421 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7815 (mp0)
REVERT: A  433 MET cc_start: 0.8432 (tmm) cc_final: 0.7918 (tmm)
REVERT: A  445 MET cc_start: 0.8655 (tpp) cc_final: 0.8370 (tpp)
REVERT: A  500 MET cc_start: 0.5149 (mmm) cc_final: 0.4789 (mmm)
REVERT: A  523 MET cc_start: 0.8739 (mmp) cc_final: 0.8517 (mmp)
REVERT: A  566 MET cc_start: 0.8280 (tpp) cc_final: 0.7747 (tpp)
REVERT: A  653 MET cc_start: 0.9166 (tpt) cc_final: 0.8489 (tpt)
REVERT: A  689 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (mt)
REVERT: A  696 LEU cc_start: 0.9343 (tt) cc_final: 0.8993 (pp)
REVERT: A  754 MET cc_start: 0.8055 (mmp) cc_final: 0.7610 (mmp)
REVERT: A  786 MET cc_start: 0.7233 (mmm) cc_final: 0.6829 (mmt)
REVERT: A  862 LEU cc_start: 0.9505 (mt) cc_final: 0.9124 (pp)
  outliers start: 23
  outliers final: 20
  residues processed: 78
  average time/residue: 0.1726
  time to fit residues: 19.1050
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  : 0.749 
-------------------------------------------------------------------------------
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  324 THR
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  492 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  681 ILE
Chi-restraints excluded: chain A residue  683 TYR
Chi-restraints excluded: chain A residue  689 LEU
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 38 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 5 optimal weight:    0.3980
   chunk 31 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.052972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.045673 restraints weight = 61010.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 6.84
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6811  Z= 0.177
  Angle     :  0.759  14.986   9212  Z= 0.364
  Chirality :  0.042   0.170   1102
  Planarity :  0.004   0.038   1175
  Dihedral  :  4.786  19.351    927
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 36.46 %
    Favored  : 60.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.29), residues: 876
  helix:  0.38 (0.26), residues: 385
  sheet: -0.48 (0.60), residues: 80
  loop : -1.54 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 703 
 HIS   0.002   0.001   HIS A 437 
 PHE   0.014   0.001   PHE A 403 
 TYR   0.011   0.001   TYR A 497 
 ARG   0.004   0.000   ARG A 187 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2909.78 seconds
wall clock time: 50 minutes 49.16 seconds (3049.16 seconds total)