Starting phenix.real_space_refine
on Tue Mar  3 22:21:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7op3_13012/03_2026/7op3_13012.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7op3_13012/03_2026/7op3_13012.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2026/7op3_13012.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2026/7op3_13012.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2026/7op3_13012.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2026/7op3_13012.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5709      2.51       5
     N    1460      2.21       5
     O    1549      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8772
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1100, 8758
          Classifications: {'peptide': 1100}
          Link IDs: {'PTRANS': 55, 'TRANS': 1044}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'SPM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.03, per 1000 atoms: 0.23
  Number of scatterers: 8772
  At special positions: 0
  Unit cell: (90.688, 92.352, 132.288, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1549      8.00
     N    1460      7.00
     C    5709      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 337.5 milliseconds
  

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2082

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      46.2% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 229 through 239
    Processing helix  chain 'A' and resid 246 through 251
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 4.233A  pdb=" N   TYR A 255 " --> pdb=" O   TYR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 363 through 368
    Processing helix  chain 'A' and resid 383 through 392
      removed outlier: 3.633A  pdb=" N   VAL A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 410
      removed outlier: 3.612A  pdb=" N   VAL A 401 " --> pdb=" O   TYR A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 446
      removed outlier: 3.632A  pdb=" N   SER A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 519
    Processing helix  chain 'A' and resid 529 through 534
      removed outlier: 3.644A  pdb=" N   ASP A 533 " --> pdb=" O   SER A 529 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS A 534 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 529 through 534'
    Processing helix  chain 'A' and resid 571 through 577
      removed outlier: 3.903A  pdb=" N   SER A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 618
      removed outlier: 4.166A  pdb=" N   PHE A 593 " --> pdb=" O   TYR A 589 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 605 " --> pdb=" O   CYS A 601 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 616 " --> pdb=" O   VAL A 612 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 617 " --> pdb=" O   ASN A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 636
      removed outlier: 3.717A  pdb=" N   LEU A 632 " --> pdb=" O   ALA A 628 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR A 633 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 644
    Processing helix  chain 'A' and resid 645 through 658
    Processing helix  chain 'A' and resid 665 through 671
      removed outlier: 4.276A  pdb=" N   ASN A 669 " --> pdb=" O   PRO A 665 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   VAL A 670 " --> pdb=" O   GLN A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 674
      No H-bonds generated for 'chain 'A' and resid 672 through 674'
    Processing helix  chain 'A' and resid 748 through 757
    Processing helix  chain 'A' and resid 773 through 782
      removed outlier: 3.979A  pdb=" N   LYS A 778 " --> pdb=" O   PRO A 774 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   MET A 779 " --> pdb=" O   LEU A 775 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   PHE A 780 " --> pdb=" O   GLU A 776 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLU A 781 " --> pdb=" O   VAL A 777 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   PHE A 782 " --> pdb=" O   LYS A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 785
      No H-bonds generated for 'chain 'A' and resid 783 through 785'
    Processing helix  chain 'A' and resid 867 through 872
    Processing helix  chain 'A' and resid 882 through 891
    Processing helix  chain 'A' and resid 904 through 908
      removed outlier: 3.741A  pdb=" N   ASN A 907 " --> pdb=" O   PRO A 904 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A 908 " --> pdb=" O   LYS A 905 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 904 through 908'
    Processing helix  chain 'A' and resid 915 through 921
      removed outlier: 3.591A  pdb=" N   VAL A 919 " --> pdb=" O   THR A 915 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A 921 " --> pdb=" O   ASP A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 949
    Processing helix  chain 'A' and resid 960 through 972
      removed outlier: 3.599A  pdb=" N   SER A 966 " --> pdb=" O   ARG A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1052
    Processing helix  chain 'A' and resid 1054 through 1064
    Processing helix  chain 'A' and resid 1072 through 1086
    Processing helix  chain 'A' and resid 1099 through 1106
      removed outlier: 3.568A  pdb=" N   LEU A1103 " --> pdb=" O   ASP A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1167
      removed outlier: 3.744A  pdb=" N   GLU A1135 " --> pdb=" O   ARG A1131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1168 through 1172
    Processing helix  chain 'A' and resid 1176 through 1187
      removed outlier: 3.736A  pdb=" N   LEU A1181 " --> pdb=" O   ASP A1177 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A1187 " --> pdb=" O   ILE A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1196
    Processing helix  chain 'A' and resid 1215 through 1242
      removed outlier: 3.635A  pdb=" N   VAL A1220 " --> pdb=" O   ARG A1216 " (cutoff:3.500A)
      Proline residue:  A1221  - end of helix
      removed outlier: 3.550A  pdb=" N   GLN A1242 " --> pdb=" O   VAL A1238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1281
      removed outlier: 3.549A  pdb=" N   THR A1264 " --> pdb=" O   ASN A1260 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR A1265 " --> pdb=" O   SER A1261 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A1266 " --> pdb=" O   GLU A1262 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER A1270 " --> pdb=" O   LEU A1266 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A1277 " --> pdb=" O   GLU A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1314
      removed outlier: 4.204A  pdb=" N   LEU A1298 " --> pdb=" O   THR A1294 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA A1300 " --> pdb=" O   PRO A1296 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR A1308 " --> pdb=" O   THR A1304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1317 through 1324
      removed outlier: 4.002A  pdb=" N   GLU A1321 " --> pdb=" O   TYR A1317 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   PHE A1322 " --> pdb=" O   TRP A1318 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET A1323 " --> pdb=" O   LEU A1319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1329 through 1354
    Processing helix  chain 'A' and resid 1354 through 1365
    Processing helix  chain 'A' and resid 1377 through 1389
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210
      removed outlier: 3.723A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE A 218 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A 274 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A 221 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A 272 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 290
      removed outlier: 4.188A  pdb=" N   SER A 322 " --> pdb=" O   ARG A 286 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   LYS A 288 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 320 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   TYR A 290 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   ARG A 318 " --> pdb=" O   TYR A 290 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG A 321 " --> pdb=" O   TYR A 332 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 338 " --> pdb=" O   HIS A 333 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 450 through 451
    Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474
      removed outlier: 6.884A  pdb=" N   VAL A 559 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 510
      removed outlier: 6.735A  pdb=" N   VAL A 506 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   VAL A 496 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   VAL A 508 " --> pdb=" O   CYS A 494 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   CYS A 494 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   ILE A 495 " --> pdb=" O   ILE A 544 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 660 through 662
      removed outlier: 6.401A  pdb=" N   GLY A1109 " --> pdb=" O   PHE A1123 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   SER A1125 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   SER A1111 " --> pdb=" O   SER A1125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 676 through 677
    Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 697
      removed outlier: 7.450A  pdb=" N   ILE A 930 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ILE A 695 " --> pdb=" O   PHE A 928 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   PHE A 928 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   VAL A 697 " --> pdb=" O   VAL A 926 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   VAL A 926 " --> pdb=" O   VAL A 697 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ASP A 924 " --> pdb=" O   THR A 900 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   CYS A 898 " --> pdb=" O   VAL A 926 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   PHE A 928 " --> pdb=" O   ILE A 896 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE A 896 " --> pdb=" O   PHE A 928 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ILE A 930 " --> pdb=" O   ARG A 894 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ARG A 894 " --> pdb=" O   ILE A 930 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 955 through 956
      removed outlier: 6.582A  pdb=" N   MET A 955 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ILE A1039 " --> pdb=" O   LYS A1066 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   TYR A1068 " --> pdb=" O   ILE A1039 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   VAL A1041 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 981 through 984

    353 hydrogen bonds defined for protein.
    1035 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: 1.41

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2729
        1.34 -     1.46: 2104
        1.46 -     1.58: 4078
        1.58 -     1.70: 0
        1.70 -     1.81: 79
  Bond restraints: 8990
  Sorted by residual:
  bond pdb=" C   TRP A1295 "
       pdb=" N   PRO A1296 "
    ideal  model  delta    sigma   weight residual
    1.334  1.372 -0.038 2.34e-02 1.83e+03 2.64e+00
  bond pdb=" CB  ARG A1366 "
       pdb=" CG  ARG A1366 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 2.00e+00
  bond pdb=" CB  TYR A1037 "
       pdb=" CG  TYR A1037 "
    ideal  model  delta    sigma   weight residual
    1.512  1.542 -0.030 2.20e-02 2.07e+03 1.84e+00
  bond pdb=" C   ARG A1285 "
       pdb=" N   PRO A1286 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.017 1.28e-02 6.10e+03 1.72e+00
  bond pdb=" CA  THR A 394 "
       pdb=" CB  THR A 394 "
    ideal  model  delta    sigma   weight residual
    1.526  1.546 -0.020 1.53e-02 4.27e+03 1.69e+00
  ... (remaining 8985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 11734
        1.75 -     3.50: 373
        3.50 -     5.25: 64
        5.25 -     7.00: 27
        7.00 -     8.75: 9
  Bond angle restraints: 12207
  Sorted by residual:
  angle pdb=" CA  THR A 394 "
        pdb=" CB  THR A 394 "
        pdb=" CG2 THR A 394 "
      ideal   model   delta    sigma   weight residual
     110.50  117.05   -6.55 1.70e+00 3.46e-01 1.48e+01
  angle pdb=" N   TYR A1037 "
        pdb=" CA  TYR A1037 "
        pdb=" C   TYR A1037 "
      ideal   model   delta    sigma   weight residual
     111.36  115.40   -4.04 1.09e+00 8.42e-01 1.37e+01
  angle pdb=" C   PHE A 782 "
        pdb=" N   THR A 783 "
        pdb=" CA  THR A 783 "
      ideal   model   delta    sigma   weight residual
     121.54  128.41   -6.87 1.91e+00 2.74e-01 1.29e+01
  angle pdb=" N   TRP A 350 "
        pdb=" CA  TRP A 350 "
        pdb=" CB  TRP A 350 "
      ideal   model   delta    sigma   weight residual
     110.16  115.16   -5.00 1.48e+00 4.57e-01 1.14e+01
  angle pdb=" N   ARG A 292 "
        pdb=" CA  ARG A 292 "
        pdb=" C   ARG A 292 "
      ideal   model   delta    sigma   weight residual
     109.81  117.27   -7.46 2.21e+00 2.05e-01 1.14e+01
  ... (remaining 12202 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4768
       17.62 -    35.23: 463
       35.23 -    52.85: 87
       52.85 -    70.47: 14
       70.47 -    88.08: 8
  Dihedral angle restraints: 5340
    sinusoidal: 2123
      harmonic: 3217
  Sorted by residual:
  dihedral pdb=" CA  VAL A 453 "
           pdb=" C   VAL A 453 "
           pdb=" N   PHE A 454 "
           pdb=" CA  PHE A 454 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.01   18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  ARG A1285 "
           pdb=" C   ARG A1285 "
           pdb=" N   PRO A1286 "
           pdb=" CA  PRO A1286 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.11  -18.89     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CB  GLU A1293 "
           pdb=" CG  GLU A1293 "
           pdb=" CD  GLU A1293 "
           pdb=" OE1 GLU A1293 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.08  -88.08     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 5337 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1170
       0.068 -    0.135: 200
       0.135 -    0.203: 15
       0.203 -    0.270: 3
       0.270 -    0.338: 3
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" CB  ILE A 660 "
            pdb=" CA  ILE A 660 "
            pdb=" CG1 ILE A 660 "
            pdb=" CG2 ILE A 660 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CB  ILE A 220 "
            pdb=" CA  ILE A 220 "
            pdb=" CG1 ILE A 220 "
            pdb=" CG2 ILE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CB  THR A 263 "
            pdb=" CA  THR A 263 "
            pdb=" OG1 THR A 263 "
            pdb=" CG2 THR A 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1388 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 350 "    0.028 2.00e-02 2.50e+03   3.46e-02 2.98e+01
        pdb=" CG  TRP A 350 "   -0.091 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 350 "    0.049 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 350 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 350 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 350 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 350 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 350 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 350 "    0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 350 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1037 "    0.028 2.00e-02 2.50e+03   1.97e-02 7.79e+00
        pdb=" CG  TYR A1037 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1037 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1037 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1037 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1037 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1037 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A1037 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 868 "    0.041 5.00e-02 4.00e+02   6.10e-02 5.95e+00
        pdb=" N   PRO A 869 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 869 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 869 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2235
        2.80 -     3.33: 8195
        3.33 -     3.85: 14383
        3.85 -     4.38: 15972
        4.38 -     4.90: 27952
  Nonbonded interactions: 68737
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 669 "
            pdb=" OG  SER A1143 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OH  TYR A 331 "
            pdb=" O   VAL A 371 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG  SER A1001 "
            pdb=" O   ASN A1003 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   LYS A 673 "
            pdb=" OG  SER A1089 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   SER A 949 "
            pdb=" OG  SER A 949 "
     model   vdw
     2.315 3.040
  ... (remaining 68732 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.430
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
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      :  0.004   0.042   8990  Z= 0.165
  Angle     :  0.776   8.749  12207  Z= 0.398
  Chirality :  0.052   0.338   1391
  Planarity :  0.006   0.061   1523
  Dihedral  : 14.575  88.082   3258
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.24), residues: 1088
  helix:  0.28 (0.24), residues: 437
  sheet: -0.72 (0.52), residues: 101
  loop : -1.80 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 576 
 TYR   0.042   0.002   TYR A1037 
 PHE   0.042   0.002   PHE A 780 
 TRP   0.091   0.002   TRP A 350 
 HIS   0.004   0.001   HIS A1052 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8990)
  covalent geometry    : angle       0.77559 (12207)
  hydrogen bonds       : bond        0.14052 (  353)
  hydrogen bonds       : angle       6.01784 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.330 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0714
  time to fit residues: 11.0870
Evaluate side-chains
  82 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:   30.0000
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 530 HIS
A1242 GLN
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.192325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 128)---------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.126781 restraints weight = 10600.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.126065 restraints weight = 7447.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.125409 restraints weight = 7047.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.125481 restraints weight = 6418.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.125956 restraints weight = 5990.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   8990  Z= 0.265
  Angle     :  0.659   7.394  12207  Z= 0.338
  Chirality :  0.047   0.217   1391
  Planarity :  0.005   0.048   1523
  Dihedral  :  5.150  53.322   1210
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 11.62 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.25), residues: 1088
  helix:  0.26 (0.24), residues: 459
  sheet: -0.94 (0.48), residues: 120
  loop : -1.78 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 227 
 TYR   0.016   0.002   TYR A1343 
 PHE   0.019   0.002   PHE A 780 
 TRP   0.013   0.001   TRP A 350 
 HIS   0.006   0.001   HIS A1352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 8990)
  covalent geometry    : angle       0.65876 (12207)
  hydrogen bonds       : bond        0.04190 (  353)
  hydrogen bonds       : angle       5.07995 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  578 MET cc_start: 0.8044 (mtp) cc_final: 0.7774 (mtt)
REVERT: A  945 GLU cc_start: 0.7967 (tt0) cc_final: 0.7762 (tt0)
  outliers start: 8
  outliers final: 7
  residues processed: 99
  average time/residue: 0.0634
  time to fit residues: 9.6751
Evaluate side-chains
  95 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue 1387 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0070
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.195891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.123834 restraints weight = 10501.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.127323 restraints weight = 5994.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.129373 restraints weight = 4347.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130354 restraints weight = 3667.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.131352 restraints weight = 3337.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8990  Z= 0.127
  Angle     :  0.543   7.473  12207  Z= 0.276
  Chirality :  0.043   0.189   1391
  Planarity :  0.004   0.039   1523
  Dihedral  :  4.907  56.728   1210
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.04 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.26), residues: 1088
  helix:  0.72 (0.25), residues: 458
  sheet: -0.80 (0.47), residues: 123
  loop : -1.73 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1070 
 TYR   0.015   0.002   TYR A1343 
 PHE   0.018   0.001   PHE A 536 
 TRP   0.013   0.001   TRP A 350 
 HIS   0.005   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8990)
  covalent geometry    : angle       0.54299 (12207)
  hydrogen bonds       : bond        0.03414 (  353)
  hydrogen bonds       : angle       4.72183 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  578 MET cc_start: 0.8064 (mtp) cc_final: 0.7824 (mtt)
REVERT: A  868 MET cc_start: 0.4673 (OUTLIER) cc_final: 0.4385 (mtm)
REVERT: A  945 GLU cc_start: 0.8119 (tt0) cc_final: 0.7865 (tt0)
  outliers start: 15
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0800
  time to fit residues: 12.3330
Evaluate side-chains
  102 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  868 MET
Chi-restraints excluded: chain A residue  887 TYR
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue 1037 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 57 optimal weight:   40.0000
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A1257 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 = 0.4175 r_free = 0.4175 target = 0.192177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.120861 restraints weight = 10762.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125110 restraints weight = 6935.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125064 restraints weight = 4312.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125082 restraints weight = 4355.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.125232 restraints weight = 4207.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8990  Z= 0.218
  Angle     :  0.602   7.470  12207  Z= 0.306
  Chirality :  0.045   0.210   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.988  59.220   1210
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.56 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.26), residues: 1088
  helix:  0.62 (0.24), residues: 456
  sheet: -0.90 (0.47), residues: 123
  loop : -1.75 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 438 
 TYR   0.015   0.002   TYR A1343 
 PHE   0.036   0.002   PHE A 462 
 TRP   0.013   0.001   TRP A 350 
 HIS   0.005   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 8990)
  covalent geometry    : angle       0.60162 (12207)
  hydrogen bonds       : bond        0.03657 (  353)
  hydrogen bonds       : angle       4.77837 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 91
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  868 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.4451 (mtm)
REVERT: A  945 GLU cc_start: 0.8172 (tt0) cc_final: 0.7914 (tt0)
REVERT: A  982 MET cc_start: 0.7818 (mtp) cc_final: 0.7500 (ttm)
REVERT: A 1187 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8570 (mp)
  outliers start: 32
  outliers final: 20
  residues processed: 117
  average time/residue: 0.0681
  time to fit residues: 12.3293
Evaluate side-chains
  108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  868 MET
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue 1037 TYR
Chi-restraints excluded: chain A residue 1039 ILE
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1210 VAL
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Chi-restraints excluded: chain A residue 1387 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 8 optimal weight:    0.0370
   chunk 64 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:   30.0000
   chunk 95 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 60 optimal weight:    9.9990
   chunk 80 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.195316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.124384 restraints weight = 10629.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.127324 restraints weight = 6321.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.128415 restraints weight = 4646.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.129354 restraints weight = 3863.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.129602 restraints weight = 3996.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8990  Z= 0.118
  Angle     :  0.532   6.377  12207  Z= 0.271
  Chirality :  0.042   0.186   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.776  54.052   1210
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.63 %
    Favored  : 79.98 %
  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 are not related in a simple way.
  whole: -0.67 (0.26), residues: 1088
  helix:  0.90 (0.25), residues: 456
  sheet: -0.64 (0.49), residues: 117
  loop : -1.68 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1070 
 TYR   0.015   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A 462 
 TRP   0.012   0.001   TRP A 350 
 HIS   0.004   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8990)
  covalent geometry    : angle       0.53229 (12207)
  hydrogen bonds       : bond        0.03173 (  353)
  hydrogen bonds       : angle       4.49096 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  868 MET cc_start: 0.4797 (OUTLIER) cc_final: 0.4568 (mtm)
REVERT: A  945 GLU cc_start: 0.8126 (tt0) cc_final: 0.7884 (tt0)
REVERT: A 1187 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 111
  average time/residue: 0.0737
  time to fit residues: 12.2250
Evaluate side-chains
  104 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  868 MET
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue 1037 TYR
Chi-restraints excluded: chain A residue 1039 ILE
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1210 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A1257 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 = 0.4192 r_free = 0.4192 target = 0.194346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.121565 restraints weight = 10557.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.125163 restraints weight = 5975.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.127169 restraints weight = 4332.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.128467 restraints weight = 3639.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.128905 restraints weight = 3313.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8990  Z= 0.137
  Angle     :  0.545   6.930  12207  Z= 0.275
  Chirality :  0.043   0.167   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.716  52.178   1210
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.74 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.26), residues: 1088
  helix:  0.96 (0.25), residues: 455
  sheet: -0.73 (0.47), residues: 123
  loop : -1.69 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1070 
 TYR   0.016   0.001   TYR A 255 
 PHE   0.015   0.001   PHE A 536 
 TRP   0.014   0.001   TRP A 350 
 HIS   0.005   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8990)
  covalent geometry    : angle       0.54450 (12207)
  hydrogen bonds       : bond        0.03212 (  353)
  hydrogen bonds       : angle       4.46586 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  868 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.4600 (mtm)
REVERT: A  945 GLU cc_start: 0.8135 (tt0) cc_final: 0.7891 (tt0)
  outliers start: 25
  outliers final: 18
  residues processed: 106
  average time/residue: 0.0696
  time to fit residues: 11.6871
Evaluate side-chains
  97 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  868 MET
Chi-restraints excluded: chain A residue  954 VAL
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue 1037 TYR
Chi-restraints excluded: chain A residue 1039 ILE
Chi-restraints excluded: chain A residue 1210 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:   30.0000
   chunk 64 optimal weight:    6.9990
   chunk 105 optimal weight:    0.5980
   chunk 103 optimal weight:    0.8980
   chunk 62 optimal weight:   20.0000
   chunk 89 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A1257 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 = 0.4179 r_free = 0.4179 target = 0.193054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.120004 restraints weight = 10565.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.123609 restraints weight = 6018.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.125702 restraints weight = 4377.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.126780 restraints weight = 3674.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.127513 restraints weight = 3339.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8990  Z= 0.180
  Angle     :  0.579   7.501  12207  Z= 0.293
  Chirality :  0.044   0.167   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.788  51.445   1210
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.05 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 1088
  helix:  0.84 (0.25), residues: 457
  sheet: -0.71 (0.47), residues: 123
  loop : -1.73 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 438 
 TYR   0.015   0.002   TYR A1343 
 PHE   0.015   0.001   PHE A 536 
 TRP   0.013   0.001   TRP A 350 
 HIS   0.004   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 8990)
  covalent geometry    : angle       0.57933 (12207)
  hydrogen bonds       : bond        0.03453 (  353)
  hydrogen bonds       : angle       4.56919 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 83
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  232 ILE cc_start: 0.4755 (OUTLIER) cc_final: 0.4479 (mp)
REVERT: A  868 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4591 (mtm)
REVERT: A  928 PHE cc_start: 0.2254 (OUTLIER) cc_final: 0.1432 (m-10)
REVERT: A  945 GLU cc_start: 0.8203 (tt0) cc_final: 0.7957 (tt0)
REVERT: A  982 MET cc_start: 0.7811 (mtp) cc_final: 0.7425 (ttm)
REVERT: A 1186 MET cc_start: 0.8260 (mtt) cc_final: 0.7880 (mtt)
REVERT: A 1263 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7850 (t0)
  outliers start: 29
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0688
  time to fit residues: 11.3424
Evaluate side-chains
  109 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  868 MET
Chi-restraints excluded: chain A residue  928 PHE
Chi-restraints excluded: chain A residue  954 VAL
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue  991 ASP
Chi-restraints excluded: chain A residue 1037 TYR
Chi-restraints excluded: chain A residue 1039 ILE
Chi-restraints excluded: chain A residue 1150 CYS
Chi-restraints excluded: chain A residue 1210 VAL
Chi-restraints excluded: chain A residue 1263 ASN
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 47 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
A1257 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.194494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.122249 restraints weight = 10587.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.126149 restraints weight = 6071.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.127364 restraints weight = 4033.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.127395 restraints weight = 3631.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.127678 restraints weight = 3739.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8990  Z= 0.136
  Angle     :  0.553   8.149  12207  Z= 0.276
  Chirality :  0.043   0.163   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.694  50.541   1210
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.95 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.26), residues: 1088
  helix:  0.97 (0.25), residues: 456
  sheet: -0.61 (0.48), residues: 123
  loop : -1.68 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1070 
 TYR   0.015   0.001   TYR A1317 
 PHE   0.015   0.001   PHE A 536 
 TRP   0.012   0.001   TRP A 350 
 HIS   0.004   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8990)
  covalent geometry    : angle       0.55300 (12207)
  hydrogen bonds       : bond        0.03206 (  353)
  hydrogen bonds       : angle       4.45020 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  623 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8229 (tt)
REVERT: A  868 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.4686 (mtm)
REVERT: A  928 PHE cc_start: 0.2135 (OUTLIER) cc_final: 0.1315 (m-10)
REVERT: A  945 GLU cc_start: 0.8186 (tt0) cc_final: 0.7940 (tt0)
REVERT: A  982 MET cc_start: 0.7773 (mtp) cc_final: 0.7383 (ttm)
REVERT: A 1186 MET cc_start: 0.8242 (mtt) cc_final: 0.7896 (mtt)
REVERT: A 1263 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.7741 (t0)
  outliers start: 33
  outliers final: 25
  residues processed: 111
  average time/residue: 0.0723
  time to fit residues: 12.1496
Evaluate side-chains
  112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 83
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  868 MET
Chi-restraints excluded: chain A residue  928 PHE
Chi-restraints excluded: chain A residue  954 VAL
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue  991 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1037 TYR
Chi-restraints excluded: chain A residue 1039 ILE
Chi-restraints excluded: chain A residue 1150 CYS
Chi-restraints excluded: chain A residue 1210 VAL
Chi-restraints excluded: chain A residue 1263 ASN
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0770
   chunk 40 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0770
   chunk 28 optimal weight:   10.0000
   chunk 88 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
** A1257 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 = 0.4208 r_free = 0.4208 target = 0.196292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.124409 restraints weight = 10460.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.127812 restraints weight = 6053.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.129920 restraints weight = 4433.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.130961 restraints weight = 3748.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.131628 restraints weight = 3416.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8990  Z= 0.107
  Angle     :  0.539   8.378  12207  Z= 0.267
  Chirality :  0.042   0.169   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.567  48.870   1210
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.19 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.26), residues: 1088
  helix:  1.04 (0.25), residues: 464
  sheet: -0.58 (0.48), residues: 123
  loop : -1.76 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 438 
 TYR   0.014   0.001   TYR A1317 
 PHE   0.022   0.001   PHE A1361 
 TRP   0.016   0.001   TRP A 350 
 HIS   0.004   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8990)
  covalent geometry    : angle       0.53889 (12207)
  hydrogen bonds       : bond        0.03015 (  353)
  hydrogen bonds       : angle       4.32788 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  945 GLU cc_start: 0.8066 (tt0) cc_final: 0.7836 (tt0)
REVERT: A  982 MET cc_start: 0.7618 (mtp) cc_final: 0.7338 (ttm)
REVERT: A 1186 MET cc_start: 0.8098 (mtt) cc_final: 0.7773 (mtt)
REVERT: A 1263 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7414 (t0)
  outliers start: 23
  outliers final: 21
  residues processed: 108
  average time/residue: 0.0688
  time to fit residues: 11.5309
Evaluate side-chains
  107 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  954 VAL
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue 1037 TYR
Chi-restraints excluded: chain A residue 1039 ILE
Chi-restraints excluded: chain A residue 1150 CYS
Chi-restraints excluded: chain A residue 1210 VAL
Chi-restraints excluded: chain A residue 1263 ASN
Chi-restraints excluded: chain A residue 1378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:   40.0000
   chunk 102 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 98 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 97 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A1257 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 = 0.4188 r_free = 0.4188 target = 0.194094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.121662 restraints weight = 10545.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.124906 restraints weight = 6190.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.126186 restraints weight = 4407.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.126063 restraints weight = 3692.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.126305 restraints weight = 3861.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8990  Z= 0.156
  Angle     :  0.578  10.138  12207  Z= 0.286
  Chirality :  0.043   0.173   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.651  51.934   1210
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.57 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.26), residues: 1088
  helix:  0.94 (0.24), residues: 463
  sheet: -0.57 (0.48), residues: 123
  loop : -1.76 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 438 
 TYR   0.016   0.001   TYR A1317 
 PHE   0.016   0.001   PHE A 536 
 TRP   0.014   0.001   TRP A 350 
 HIS   0.004   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8990)
  covalent geometry    : angle       0.57837 (12207)
  hydrogen bonds       : bond        0.03265 (  353)
  hydrogen bonds       : angle       4.43969 ( 1035)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  623 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8257 (tt)
REVERT: A  945 GLU cc_start: 0.8186 (tt0) cc_final: 0.7947 (tt0)
REVERT: A  982 MET cc_start: 0.7785 (mtp) cc_final: 0.7406 (ttm)
REVERT: A 1186 MET cc_start: 0.8255 (mtt) cc_final: 0.7922 (mtt)
REVERT: A 1263 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7762 (t0)
  outliers start: 28
  outliers final: 25
  residues processed: 105
  average time/residue: 0.0701
  time to fit residues: 11.4343
Evaluate side-chains
  111 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  662 CYS
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  954 VAL
Chi-restraints excluded: chain A residue  955 MET
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  963 THR
Chi-restraints excluded: chain A residue  991 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1037 TYR
Chi-restraints excluded: chain A residue 1039 ILE
Chi-restraints excluded: chain A residue 1150 CYS
Chi-restraints excluded: chain A residue 1210 VAL
Chi-restraints excluded: chain A residue 1263 ASN
Chi-restraints excluded: chain A residue 1378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 23 optimal weight:    0.0870
   chunk 99 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** A1257 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 = 0.4196 r_free = 0.4196 target = 0.195101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.123041 restraints weight = 10356.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.126220 restraints weight = 6149.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.127535 restraints weight = 4426.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.128270 restraints weight = 3659.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.128570 restraints weight = 3843.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8990  Z= 0.127
  Angle     :  0.561   9.945  12207  Z= 0.276
  Chirality :  0.043   0.164   1391
  Planarity :  0.004   0.036   1523
  Dihedral  :  4.611  52.776   1210
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.88 %
    Favored  : 78.22 %
  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 are not related in a simple way.
  whole: -0.58 (0.26), residues: 1088
  helix:  1.01 (0.24), residues: 461
  sheet: -0.53 (0.48), residues: 123
  loop : -1.71 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1070 
 TYR   0.016   0.001   TYR A1317 
 PHE   0.016   0.001   PHE A 536 
 TRP   0.012   0.001   TRP A 350 
 HIS   0.004   0.001   HIS A 977 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8990)
  covalent geometry    : angle       0.56057 (12207)
  hydrogen bonds       : bond        0.03113 (  353)
  hydrogen bonds       : angle       4.38793 ( 1035)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1624.53 seconds
wall clock time: 28 minutes 41.47 seconds (1721.47 seconds total)