Starting phenix.real_space_refine
on Sun Aug 24 15:03:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t3k_41004/08_2025/8t3k_41004_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t3k_41004/08_2025/8t3k_41004.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t3k_41004/08_2025/8t3k_41004_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t3k_41004/08_2025/8t3k_41004_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t3k_41004/08_2025/8t3k_41004.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t3k_41004/08_2025/8t3k_41004.map"
  }
  resolution = 3.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.014 sd=   0.031
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: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      41      5.16       5
     C    6537      2.51       5
     N    1630      2.21       5
     O    1818      1.98       5
     H    9730      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19768
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 10675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 10675
          Classifications: {'peptide': 663}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 649}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 8634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 8634
          Classifications: {'peptide': 541}
          Link IDs: {'PTRANS': 19, 'TRANS': 521}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 268
          Unusual residues: {'ATP': 1, 'POV': 7}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 130
          Unresolved non-hydrogen angles: 166
          Unresolved non-hydrogen dihedrals: 120
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'POV:plan-2': 3, 'POV:plan-3': 3, 'POV:plan-1': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "C"
      Number of atoms: 191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 191
          Unusual residues: {'ATP': 1, 'POV': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 186
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-3': 3, 'POV:plan-2': 2}
          Unresolved non-hydrogen planarities: 34
  Time building chain proxies: 3.92, per 1000 atoms: 0.20
  Number of scatterers: 19768
  At special positions: 0
  Unit cell: (76.346, 98.991, 157.221, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      41     16.00
     P      12     15.00
     O    1818      8.00
     N    1630      7.00
     C    6537      6.00
     H    9730      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.15
  Conformation dependent library (CDL) restraints added in 611.4 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2234

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 8 sheets defined
      63.8% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'D' and resid 2 through 12
      removed outlier: 3.507A  pdb=" N   THR D   6 " --> pdb=" O   LYS D   2 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 45
      removed outlier: 3.878A  pdb=" N   GLY D  35 " --> pdb=" O   ALA D  31 " (cutoff:3.500A)
      Proline residue:  D  36  - end of helix
    Processing helix  chain 'D' and resid 48 through 52
      removed outlier: 3.656A  pdb=" N   GLU D  51 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 141
    Processing helix  chain 'D' and resid 142 through 195
      removed outlier: 3.575A  pdb=" N   ILE D 146 " --> pdb=" O   TYR D 142 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   LYS D 147 " --> pdb=" O   GLN D 143 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   GLY D 148 " --> pdb=" O   PRO D 144 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLN D 170 " --> pdb=" O   PHE D 166 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   HIS D 171 " --> pdb=" O   GLN D 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 203
      removed outlier: 3.975A  pdb=" N   PHE D 201 " --> pdb=" O   PRO D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 214
      removed outlier: 3.520A  pdb=" N   VAL D 209 " --> pdb=" O   PRO D 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 230
    Processing helix  chain 'D' and resid 230 through 249
    Processing helix  chain 'D' and resid 250 through 258
    Processing helix  chain 'D' and resid 259 through 295
      removed outlier: 4.227A  pdb=" N   TYR D 276 " --> pdb=" O   ARG D 272 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ILE D 281 " --> pdb=" O   TYR D 277 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ILE D 284 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 310 through 335
      removed outlier: 3.924A  pdb=" N   GLU D 314 " --> pdb=" O   GLU D 310 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   SER D 321 " --> pdb=" O   GLU D 317 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 361
    Processing helix  chain 'D' and resid 368 through 383
    Processing helix  chain 'D' and resid 385 through 412
      removed outlier: 4.940A  pdb=" N   GLU D 397 " --> pdb=" O   PHE D 393 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   LEU D 398 " --> pdb=" O   SER D 394 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ALA D 399 " --> pdb=" O   LYS D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 468 through 477
      removed outlier: 3.731A  pdb=" N   LEU D 473 " --> pdb=" O   LYS D 469 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 495 through 497
      No H-bonds generated for 'chain 'D' and resid 495 through 497'
    Processing helix  chain 'D' and resid 498 through 504
    Processing helix  chain 'D' and resid 519 through 526
    Processing helix  chain 'D' and resid 533 through 544
      removed outlier: 3.540A  pdb=" N   LYS D 537 " --> pdb=" O   GLU D 533 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   GLN D 542 " --> pdb=" O   ASN D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 545 through 549
    Processing helix  chain 'D' and resid 568 through 584
    Processing helix  chain 'D' and resid 598 through 600
      No H-bonds generated for 'chain 'D' and resid 598 through 600'
    Processing helix  chain 'D' and resid 601 through 614
      removed outlier: 3.639A  pdb=" N   ILE D 605 " --> pdb=" O   THR D 601 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL D 611 " --> pdb=" O   LYS D 607 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN D 614 " --> pdb=" O   ASP D 610 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 649 through 655
      removed outlier: 3.568A  pdb=" N   LEU D 654 " --> pdb=" O   GLU D 650 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 655 through 664
      removed outlier: 3.849A  pdb=" N   TYR D 659 " --> pdb=" O   GLU D 655 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU D 664 " --> pdb=" O   GLN D 660 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 14
      removed outlier: 6.513A  pdb=" N   PHE C  11 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   PHE C  12 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA C  14 " --> pdb=" O   TRP C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 33
      removed outlier: 3.553A  pdb=" N   ALA C  22 " --> pdb=" O   ARG C  18 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ILE C  23 " --> pdb=" O   TYR C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 49
      removed outlier: 4.058A  pdb=" N   LYS C  38 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 103
      removed outlier: 3.862A  pdb=" N   HIS C  80 " --> pdb=" O   TYR C  76 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA C  86 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 144
      removed outlier: 3.528A  pdb=" N   LEU C 117 " --> pdb=" O   ARG C 113 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY C 121 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   THR C 122 " --> pdb=" O   MET C 118 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   LEU C 125 " --> pdb=" O   GLY C 121 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE C 136 " --> pdb=" O   THR C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 156
    Processing helix  chain 'C' and resid 160 through 167
    Processing helix  chain 'C' and resid 167 through 207
      removed outlier: 4.207A  pdb=" N   VAL C 171 " --> pdb=" O   ILE C 167 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS C 182 " --> pdb=" O   LEU C 178 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLU C 185 " --> pdb=" O   SER C 181 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   GLU C 189 " --> pdb=" O   GLU C 185 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 214
    Processing helix  chain 'C' and resid 216 through 243
      removed outlier: 4.255A  pdb=" N   ILE C 241 " --> pdb=" O   LYS C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 270
      removed outlier: 3.576A  pdb=" N   THR C 248 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER C 256 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 274 through 288
      removed outlier: 3.511A  pdb=" N   LEU C 278 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 315
      removed outlier: 4.293A  pdb=" N   MET C 292 " --> pdb=" O   MET C 288 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   PHE C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLY C 296 " --> pdb=" O   MET C 292 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ASN C 306 " --> pdb=" O   MET C 302 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   ALA C 307 " --> pdb=" O   GLN C 303 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASP C 310 " --> pdb=" O   ASN C 306 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   VAL C 312 " --> pdb=" O   SER C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 377 through 385
      removed outlier: 4.517A  pdb=" N   ILE C 381 " --> pdb=" O   LYS C 377 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU C 384 " --> pdb=" O   ILE C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 413
    Processing helix  chain 'C' and resid 427 through 433
    Processing helix  chain 'C' and resid 452 through 458
      removed outlier: 3.997A  pdb=" N   ASP C 456 " --> pdb=" O   HIS C 452 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   HIS C 458 " --> pdb=" O   GLU C 454 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 477 through 491
      removed outlier: 3.824A  pdb=" N   ALA C 491 " --> pdb=" O   ARG C 487 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 521
    Processing helix  chain 'C' and resid 555 through 561
      removed outlier: 3.844A  pdb=" N   ALA C 561 " --> pdb=" O   GLN C 557 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 567 through 571
      removed outlier: 3.545A  pdb=" N   TYR C 570 " --> pdb=" O   ARG C 567 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 65 through 66
    Processing sheet with id=AA2, first strand: chain 'D' and resid 110 through 111
      removed outlier: 4.074A  pdb=" N   ILE D 119 " --> pdb=" O   ARG D 126 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ARG D 126 " --> pdb=" O   ILE D 119 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 430 through 433
    Processing sheet with id=AA4, first strand: chain 'D' and resid 506 through 508
    Processing sheet with id=AA5, first strand: chain 'D' and resid 634 through 638
      removed outlier: 3.695A  pdb=" N   GLU D 644 " --> pdb=" O   VAL D 636 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ASP D 638 " --> pdb=" O   ILE D 642 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   ILE D 642 " --> pdb=" O   ASP D 638 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 360 through 361
      removed outlier: 4.223A  pdb=" N   VAL C 342 " --> pdb=" O   GLU C 392 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   GLU C 392 " --> pdb=" O   VAL C 342 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 366 through 369
      removed outlier: 7.385A  pdb=" N   LEU C 496 " --> pdb=" O   PHE C 527 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   LEU C 529 " --> pdb=" O   LEU C 496 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU C 498 " --> pdb=" O   LEU C 529 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 544 through 546
      removed outlier: 7.123A  pdb=" N   VAL C 544 " --> pdb=" O   ALA C 551 " (cutoff:3.500A)

    565 hydrogen bonds defined for protein.
    1653 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: 4.71

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 3229
        1.04 -     1.23: 6734
        1.23 -     1.43: 3923
        1.43 -     1.62: 5969
        1.62 -     1.81: 90
  Bond restraints: 19945
  Sorted by residual:
  bond pdb=" NE1 TRP C 413 "
       pdb=" HE1 TRP C 413 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" NE1 TRP C  16 "
       pdb=" HE1 TRP C  16 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" NE1 TRP D 266 "
       pdb=" HE1 TRP D 266 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" NE1 TRP C 290 "
       pdb=" HE1 TRP C 290 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" NE1 TRP D 354 "
       pdb=" HE1 TRP D 354 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  ... (remaining 19940 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.01: 35754
       13.01 -    26.02: 12
       26.02 -    39.03: 2
       39.03 -    52.04: 1
       52.04 -    65.05: 1
  Bond angle restraints: 35770
  Sorted by residual:
  angle pdb=" CA  GLU C 465 "
        pdb=" N   GLU C 465 "
        pdb=" H   GLU C 465 "
      ideal   model   delta    sigma   weight residual
     114.00  179.05  -65.05 3.00e+00 1.11e-01 4.70e+02
  angle pdb=" CA  ASN C 353 "
        pdb=" N   ASN C 353 "
        pdb=" H   ASN C 353 "
      ideal   model   delta    sigma   weight residual
     114.00  153.47  -39.47 3.00e+00 1.11e-01 1.73e+02
  angle pdb=" CA  ALA C 451 "
        pdb=" N   ALA C 451 "
        pdb=" H   ALA C 451 "
      ideal   model   delta    sigma   weight residual
     114.00  151.05  -37.05 3.00e+00 1.11e-01 1.53e+02
  angle pdb=" CA  SER C 476 "
        pdb=" N   SER C 476 "
        pdb=" H   SER C 476 "
      ideal   model   delta    sigma   weight residual
     114.00   80.75   33.25 3.00e+00 1.11e-01 1.23e+02
  angle pdb=" O13 POV D 701 "
        pdb=" P   POV D 701 "
        pdb=" O14 POV D 701 "
      ideal   model   delta    sigma   weight residual
     121.11  101.06   20.05 3.00e+00 1.11e-01 4.46e+01
  ... (remaining 35765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.75: 8690
       26.75 -    53.51: 636
       53.51 -    80.26: 107
       80.26 -   107.02: 16
      107.02 -   133.77: 11
  Dihedral angle restraints: 9460
    sinusoidal: 5307
      harmonic: 4153
  Sorted by residual:
  dihedral pdb=" CA  GLU D 558 "
           pdb=" C   GLU D 558 "
           pdb=" N   PRO D 559 "
           pdb=" CA  PRO D 559 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.68   21.32     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" C29 POV D 704 "
           pdb="C210 POV D 704 "
           pdb="C211 POV D 704 "
           pdb="C212 POV D 704 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -113.98 -133.77     1      3.00e+01 1.11e-03 1.80e+01
  dihedral pdb=" C29 POV D 707 "
           pdb="C210 POV D 707 "
           pdb="C211 POV D 707 "
           pdb="C212 POV D 707 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -114.83 -132.92     1      3.00e+01 1.11e-03 1.79e+01
  ... (remaining 9457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1306
       0.060 -    0.121: 173
       0.121 -    0.181: 22
       0.181 -    0.242: 5
       0.242 -    0.302: 5
  Chirality restraints: 1511
  Sorted by residual:
  chirality pdb=" C3' ATP C 607 "
            pdb=" C2' ATP C 607 "
            pdb=" C4' ATP C 607 "
            pdb=" O3' ATP C 607 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.94    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" C3' ATP D 708 "
            pdb=" C2' ATP D 708 "
            pdb=" C4' ATP D 708 "
            pdb=" O3' ATP D 708 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.93    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" C2' ATP C 607 "
            pdb=" C1' ATP C 607 "
            pdb=" C3' ATP C 607 "
            pdb=" O2' ATP C 607 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.14e+00
  ... (remaining 1508 not shown)

  Planarity restraints: 2859
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV D 707 "    0.088 2.00e-02 2.50e+03   2.55e-01 6.49e+02
        pdb=" C29 POV D 707 "   -0.329 2.00e-02 2.50e+03
        pdb="C210 POV D 707 "    0.360 2.00e-02 2.50e+03
        pdb="C211 POV D 707 "   -0.119 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV C 605 "    0.135 2.00e-02 2.50e+03   2.33e-01 5.45e+02
        pdb=" C29 POV C 605 "   -0.301 2.00e-02 2.50e+03
        pdb="C210 POV C 605 "    0.301 2.00e-02 2.50e+03
        pdb="C211 POV C 605 "   -0.135 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV D 701 "   -0.126 2.00e-02 2.50e+03   2.14e-01 4.60e+02
        pdb=" C29 POV D 701 "    0.275 2.00e-02 2.50e+03
        pdb="C210 POV D 701 "   -0.276 2.00e-02 2.50e+03
        pdb="C211 POV D 701 "    0.127 2.00e-02 2.50e+03
  ... (remaining 2856 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 888
        2.09 -     2.71: 31354
        2.71 -     3.34: 56439
        3.34 -     3.97: 75125
        3.97 -     4.60: 112389
  Nonbonded interactions: 276195
  Sorted by model distance:
  nonbonded pdb="HD12 ILE D 302 "
            pdb=" HH  TYR C 434 "
     model   vdw
     1.458 2.270
  nonbonded pdb=" HE2 MET D 185 "
            pdb=" HE1 PHE D 407 "
     model   vdw
     1.546 2.270
  nonbonded pdb=" OE1 GLU D 314 "
            pdb=" H   GLU D 314 "
     model   vdw
     1.560 2.450
  nonbonded pdb=" HB2 PRO C 334 "
            pdb="HD11 ILE C 495 "
     model   vdw
     1.588 2.440
  nonbonded pdb="HH11 ARG D 629 "
            pdb=" HH  TYR D 658 "
     model   vdw
     1.597 2.100
  ... (remaining 276190 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=1.00 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:             11.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.130
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     21.100
  Find NCS groups from input model:        0.070
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
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      :  0.008   0.198  10215  Z= 0.396
  Angle     :  1.059  20.046  13715  Z= 0.519
  Chirality :  0.046   0.302   1511
  Planarity :  0.012   0.255   1694
  Dihedral  : 20.306 133.770   3961
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 22.97 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.24), residues: 1190
  helix: -0.10 (0.19), residues: 727
  sheet: -2.12 (0.56), residues: 77
  loop : -2.50 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 212 
 TYR   0.023   0.002   TYR C 434 
 PHE   0.018   0.002   PHE C  59 
 TRP   0.012   0.001   TRP C  78 
 HIS   0.003   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00755 (10215)
  covalent geometry    : angle       1.05875 (13715)
  hydrogen bonds       : bond        0.13763 (  565)
  hydrogen bonds       : angle       6.78620 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   99 PHE cc_start: 0.7681 (t80) cc_final: 0.7426 (t80)
REVERT: D  652 MET cc_start: 0.2693 (mmp) cc_final: 0.2206 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 128
  average time/residue: 0.2605
  time to fit residues: 45.7458
Evaluate side-chains
  111 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
D 523 ASN
C 271 ASN
C 282 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.129411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.106840 restraints weight = 64163.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 2.11
r_work: 0.3926 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3810 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10215  Z= 0.175
  Angle     :  0.575   5.781  13715  Z= 0.315
  Chirality :  0.039   0.147   1511
  Planarity :  0.005   0.046   1694
  Dihedral  : 16.346 173.094   1681
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 24.34 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.24), residues: 1190
  helix:  0.20 (0.19), residues: 732
  sheet: -2.42 (0.58), residues: 73
  loop : -2.31 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 223 
 TYR   0.017   0.002   TYR C  19 
 PHE   0.024   0.002   PHE D 323 
 TRP   0.010   0.001   TRP C  78 
 HIS   0.004   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10215)
  covalent geometry    : angle       0.57495 (13715)
  hydrogen bonds       : bond        0.04912 (  565)
  hydrogen bonds       : angle       5.11824 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  254 PHE cc_start: 0.6804 (t80) cc_final: 0.6563 (m-80)
REVERT: C    2 PHE cc_start: 0.6069 (p90) cc_final: 0.5778 (p90)
  outliers start: 9
  outliers final: 4
  residues processed: 121
  average time/residue: 0.2581
  time to fit residues: 42.9639
Evaluate side-chains
  114 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0770
   chunk 73 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
C 282 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.130150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.107753 restraints weight = 64159.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.4041 rms_B_bonded: 2.10
r_work: 0.3940 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10215  Z= 0.135
  Angle     :  0.524   5.665  13715  Z= 0.287
  Chirality :  0.038   0.147   1511
  Planarity :  0.004   0.043   1694
  Dihedral  : 15.209 174.426   1680
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 24.34 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.25), residues: 1190
  helix:  0.58 (0.20), residues: 730
  sheet: -2.48 (0.59), residues: 73
  loop : -2.22 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 362 
 TYR   0.015   0.001   TYR C  19 
 PHE   0.022   0.001   PHE D 323 
 TRP   0.011   0.001   TRP C  78 
 HIS   0.004   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10215)
  covalent geometry    : angle       0.52405 (13715)
  hydrogen bonds       : bond        0.04178 (  565)
  hydrogen bonds       : angle       4.72907 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  254 PHE cc_start: 0.6681 (t80) cc_final: 0.6460 (m-80)
  outliers start: 10
  outliers final: 5
  residues processed: 120
  average time/residue: 0.2212
  time to fit residues: 36.4199
Evaluate side-chains
  113 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  256 SER
Chi-restraints excluded: chain C residue  298 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 10 optimal weight:    0.2980
   chunk 98 optimal weight:    5.9990
   chunk 117 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 282 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.129966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.107563 restraints weight = 64054.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 2.10
r_work: 0.3935 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3816 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10215  Z= 0.137
  Angle     :  0.516   5.633  13715  Z= 0.282
  Chirality :  0.037   0.146   1511
  Planarity :  0.004   0.043   1694
  Dihedral  : 14.872 174.971   1680
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 23.56 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.25), residues: 1190
  helix:  0.64 (0.20), residues: 732
  sheet: -2.58 (0.57), residues: 78
  loop : -2.13 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 362 
 TYR   0.015   0.001   TYR C  19 
 PHE   0.022   0.001   PHE D 323 
 TRP   0.011   0.001   TRP C  78 
 HIS   0.003   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10215)
  covalent geometry    : angle       0.51611 (13715)
  hydrogen bonds       : bond        0.04066 (  565)
  hydrogen bonds       : angle       4.61272 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  254 PHE cc_start: 0.6658 (t80) cc_final: 0.6438 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 118
  average time/residue: 0.2320
  time to fit residues: 38.1453
Evaluate side-chains
  113 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 76 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0770
   chunk 114 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
D 319 ASN
** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 282 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.130266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.108026 restraints weight = 63459.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 2.09
r_work: 0.3950 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3830 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10215  Z= 0.116
  Angle     :  0.493   5.693  13715  Z= 0.269
  Chirality :  0.037   0.147   1511
  Planarity :  0.004   0.042   1694
  Dihedral  : 14.326 175.335   1680
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 23.17 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.26), residues: 1190
  helix:  0.85 (0.20), residues: 733
  sheet: -2.57 (0.57), residues: 78
  loop : -2.13 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 572 
 TYR   0.013   0.001   TYR C  19 
 PHE   0.019   0.001   PHE D 323 
 TRP   0.011   0.001   TRP C  78 
 HIS   0.003   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10215)
  covalent geometry    : angle       0.49340 (13715)
  hydrogen bonds       : bond        0.03816 (  565)
  hydrogen bonds       : angle       4.41973 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  323 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.5666 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 127
  average time/residue: 0.2222
  time to fit residues: 39.0667
Evaluate side-chains
  119 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  323 PHE
Chi-restraints excluded: chain D residue  331 ASN
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  563 LYS
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  203 GLU
Chi-restraints excluded: chain C residue  256 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 105 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 102 optimal weight:   20.0000
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 ASN
C 282 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.128876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.106090 restraints weight = 63527.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.14
r_work: 0.3911 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10215  Z= 0.189
  Angle     :  0.544   5.740  13715  Z= 0.299
  Chirality :  0.038   0.142   1511
  Planarity :  0.004   0.043   1694
  Dihedral  : 14.041 176.264   1680
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 23.26 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.25), residues: 1190
  helix:  0.45 (0.19), residues: 736
  sheet: -2.72 (0.56), residues: 78
  loop : -2.19 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 186 
 TYR   0.021   0.002   TYR C  19 
 PHE   0.024   0.002   PHE D 323 
 TRP   0.012   0.001   TRP C  78 
 HIS   0.004   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (10215)
  covalent geometry    : angle       0.54440 (13715)
  hydrogen bonds       : bond        0.04226 (  565)
  hydrogen bonds       : angle       4.58858 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  196 MET cc_start: 0.8778 (mmt) cc_final: 0.8384 (mmt)
REVERT: D  323 PHE cc_start: 0.5954 (OUTLIER) cc_final: 0.5683 (t80)
REVERT: D  540 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7278 (tp)
  outliers start: 21
  outliers final: 17
  residues processed: 129
  average time/residue: 0.2315
  time to fit residues: 41.6539
Evaluate side-chains
  126 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  323 PHE
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  435 VAL
Chi-restraints excluded: chain D residue  540 LEU
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  203 GLU
Chi-restraints excluded: chain C residue  233 GLN
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  248 THR
Chi-restraints excluded: chain C residue  256 SER
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 117 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 106 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 282 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.127866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.104970 restraints weight = 64510.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 2.18
r_work: 0.3890 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10215  Z= 0.230
  Angle     :  0.587   5.732  13715  Z= 0.323
  Chirality :  0.040   0.159   1511
  Planarity :  0.005   0.047   1694
  Dihedral  : 14.196 173.910   1680
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 22.97 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.24), residues: 1190
  helix:  0.07 (0.19), residues: 736
  sheet: -2.83 (0.54), residues: 78
  loop : -2.33 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 487 
 TYR   0.023   0.002   TYR C  76 
 PHE   0.026   0.002   PHE D 323 
 TRP   0.012   0.002   TRP C  78 
 HIS   0.003   0.001   HIS D 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (10215)
  covalent geometry    : angle       0.58698 (13715)
  hydrogen bonds       : bond        0.04514 (  565)
  hydrogen bonds       : angle       4.74296 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  196 MET cc_start: 0.8773 (mmt) cc_final: 0.8347 (mmt)
REVERT: D  323 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5761 (t80)
REVERT: D  540 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7283 (tp)
  outliers start: 34
  outliers final: 26
  residues processed: 141
  average time/residue: 0.2356
  time to fit residues: 46.0099
Evaluate side-chains
  136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  323 PHE
Chi-restraints excluded: chain D residue  331 ASN
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain D residue  368 SER
Chi-restraints excluded: chain D residue  376 VAL
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  435 VAL
Chi-restraints excluded: chain D residue  540 LEU
Chi-restraints excluded: chain D residue  563 LYS
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  123 ASN
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  189 GLU
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  203 GLU
Chi-restraints excluded: chain C residue  233 GLN
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  248 THR
Chi-restraints excluded: chain C residue  256 SER
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 282 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.129275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.106704 restraints weight = 63523.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.4025 rms_B_bonded: 2.12
r_work: 0.3924 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3804 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10215  Z= 0.134
  Angle     :  0.524   5.755  13715  Z= 0.286
  Chirality :  0.037   0.156   1511
  Planarity :  0.004   0.041   1694
  Dihedral  : 13.583 172.030   1680
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 24.14 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.25), residues: 1190
  helix:  0.51 (0.19), residues: 736
  sheet: -2.71 (0.56), residues: 78
  loop : -2.19 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 362 
 TYR   0.017   0.001   TYR C 318 
 PHE   0.017   0.001   PHE D 323 
 TRP   0.013   0.001   TRP C  78 
 HIS   0.003   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10215)
  covalent geometry    : angle       0.52383 (13715)
  hydrogen bonds       : bond        0.04000 (  565)
  hydrogen bonds       : angle       4.48770 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  196 MET cc_start: 0.8772 (mmt) cc_final: 0.8376 (mmt)
REVERT: D  323 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5706 (t80)
REVERT: D  540 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7286 (tp)
  outliers start: 25
  outliers final: 20
  residues processed: 133
  average time/residue: 0.2006
  time to fit residues: 36.8001
Evaluate side-chains
  132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  323 PHE
Chi-restraints excluded: chain D residue  331 ASN
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain D residue  435 VAL
Chi-restraints excluded: chain D residue  540 LEU
Chi-restraints excluded: chain D residue  563 LYS
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  203 GLU
Chi-restraints excluded: chain C residue  233 GLN
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  256 SER
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
C 282 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.129364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.106849 restraints weight = 63413.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 2.11
r_work: 0.3924 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3807 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10215  Z= 0.136
  Angle     :  0.518   6.031  13715  Z= 0.283
  Chirality :  0.037   0.146   1511
  Planarity :  0.004   0.041   1694
  Dihedral  : 13.359 169.659   1680
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 24.63 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.25), residues: 1190
  helix:  0.63 (0.20), residues: 736
  sheet: -2.69 (0.56), residues: 78
  loop : -2.16 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 362 
 TYR   0.016   0.001   TYR C  19 
 PHE   0.019   0.001   PHE D 323 
 TRP   0.012   0.001   TRP C  78 
 HIS   0.002   0.001   HIS D 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10215)
  covalent geometry    : angle       0.51795 (13715)
  hydrogen bonds       : bond        0.03944 (  565)
  hydrogen bonds       : angle       4.43718 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  196 MET cc_start: 0.8766 (mmt) cc_final: 0.8417 (mmt)
REVERT: D  540 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7303 (tp)
  outliers start: 22
  outliers final: 16
  residues processed: 129
  average time/residue: 0.2012
  time to fit residues: 36.5399
Evaluate side-chains
  127 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  331 ASN
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain D residue  368 SER
Chi-restraints excluded: chain D residue  435 VAL
Chi-restraints excluded: chain D residue  540 LEU
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  256 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 86 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
D 183 GLN
D 307 HIS
D 319 ASN
** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 282 ASN
C 557 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.127062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.104325 restraints weight = 64597.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 2.07
r_work: 0.3881 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  10215  Z= 0.295
  Angle     :  0.649   6.077  13715  Z= 0.357
  Chirality :  0.042   0.145   1511
  Planarity :  0.005   0.054   1694
  Dihedral  : 14.276 168.742   1680
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.85 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.24), residues: 1190
  helix: -0.26 (0.18), residues: 742
  sheet: -2.91 (0.54), residues: 78
  loop : -2.45 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 362 
 TYR   0.030   0.003   TYR C  19 
 PHE   0.022   0.002   PHE D 516 
 TRP   0.011   0.002   TRP C  78 
 HIS   0.005   0.001   HIS D 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 (10215)
  covalent geometry    : angle       0.64871 (13715)
  hydrogen bonds       : bond        0.04847 (  565)
  hydrogen bonds       : angle       4.89947 ( 1653)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  196 MET cc_start: 0.8747 (mmt) cc_final: 0.8408 (mmt)
REVERT: D  323 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5809 (t80)
REVERT: D  540 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7250 (tp)
  outliers start: 27
  outliers final: 21
  residues processed: 135
  average time/residue: 0.2247
  time to fit residues: 42.1333
Evaluate side-chains
  131 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  321 SER
Chi-restraints excluded: chain D residue  323 PHE
Chi-restraints excluded: chain D residue  367 VAL
Chi-restraints excluded: chain D residue  368 SER
Chi-restraints excluded: chain D residue  414 ASN
Chi-restraints excluded: chain D residue  435 VAL
Chi-restraints excluded: chain D residue  540 LEU
Chi-restraints excluded: chain D residue  563 LYS
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  189 GLU
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  233 GLN
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  396 THR
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  538 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 67 optimal weight:    0.4980
   chunk 113 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 115 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 282 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.129380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.107148 restraints weight = 64501.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 2.04
r_work: 0.3931 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3816 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10215  Z= 0.123
  Angle     :  0.529   6.369  13715  Z= 0.288
  Chirality :  0.038   0.153   1511
  Planarity :  0.004   0.040   1694
  Dihedral  : 13.374 163.773   1680
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 25.12 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.25), residues: 1190
  helix:  0.53 (0.19), residues: 736
  sheet: -2.79 (0.55), residues: 78
  loop : -2.24 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 362 
 TYR   0.013   0.001   TYR C  76 
 PHE   0.010   0.001   PHE C 150 
 TRP   0.014   0.001   TRP C  10 
 HIS   0.003   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10215)
  covalent geometry    : angle       0.52921 (13715)
  hydrogen bonds       : bond        0.03995 (  565)
  hydrogen bonds       : angle       4.48110 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5374.27 seconds
wall clock time: 91 minutes 48.16 seconds (5508.16 seconds total)