Starting phenix.real_space_refine
on Thu Sep 18 11:04:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3a_62011/09_2025/9k3a_62011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3a_62011/09_2025/9k3a_62011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k3a_62011/09_2025/9k3a_62011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3a_62011/09_2025/9k3a_62011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3a_62011/09_2025/9k3a_62011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3a_62011/09_2025/9k3a_62011.cif"
  }
  resolution = 3.6
  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=   0.002
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      48      5.16       5
     C   10107      2.51       5
     N    2851      2.21       5
     O    3116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16122
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 973, 7756
          Classifications: {'peptide': 973}
          Link IDs: {'CIS': 1, 'PTRANS': 35, 'TRANS': 936}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 8366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1071, 8366
          Classifications: {'peptide': 1071}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 72, 'TRANS': 997}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.96, per 1000 atoms: 0.25
  Number of scatterers: 16122
  At special positions: 0
  Unit cell: (193.67, 138.03, 153.01, 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      48     16.00
     O    3116      8.00
     N    2851      7.00
     C   10107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   5 " - pdb=" SG  CYS B1715 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 729.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3868

  Finding SS restraints...
    Secondary structure from input PDB file:
      93 helices and 12 sheets defined
      59.9% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 46
      removed outlier: 3.609A  pdb=" N   SER A  46 " --> pdb=" O   LYS A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 83
      removed outlier: 3.517A  pdb=" N   LEU A  82 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 97
      removed outlier: 3.671A  pdb=" N   LEU A  93 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 157
      removed outlier: 3.502A  pdb=" N   VAL A 128 " --> pdb=" O   ASP A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 177
    Processing helix  chain 'A' and resid 178 through 186
    Processing helix  chain 'A' and resid 189 through 211
    Processing helix  chain 'A' and resid 213 through 229
    Processing helix  chain 'A' and resid 229 through 241
    Processing helix  chain 'A' and resid 244 through 251
    Processing helix  chain 'A' and resid 255 through 269
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.835A  pdb=" N   VAL A 297 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 320
      removed outlier: 3.911A  pdb=" N   LEU A 312 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLU A 313 " --> pdb=" O   PRO A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 332
    Processing helix  chain 'A' and resid 332 through 343
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 365 through 376
      removed outlier: 3.575A  pdb=" N   PHE A 369 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 390
      removed outlier: 3.906A  pdb=" N   ASN A 384 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 408
    Processing helix  chain 'A' and resid 414 through 423
    Processing helix  chain 'A' and resid 428 through 435
      removed outlier: 3.980A  pdb=" N   LYS A 432 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ASP A 433 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 440
    Processing helix  chain 'A' and resid 448 through 453
    Processing helix  chain 'A' and resid 455 through 463
      removed outlier: 3.572A  pdb=" N   ALA A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 482
      removed outlier: 3.564A  pdb=" N   SER A 482 " --> pdb=" O   MET A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 504
      removed outlier: 4.049A  pdb=" N   LYS A 504 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 510
      removed outlier: 3.524A  pdb=" N   ARG A 510 " --> pdb=" O   LEU A 507 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 507 through 510'
    Processing helix  chain 'A' and resid 511 through 530
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 535 through 550
      removed outlier: 3.588A  pdb=" N   SER A 544 " --> pdb=" O   MET A 540 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 582
      removed outlier: 3.762A  pdb=" N   GLY A 582 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 612
      removed outlier: 4.374A  pdb=" N   GLY A 609 " --> pdb=" O   LYS A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 631
      removed outlier: 3.534A  pdb=" N   ALA A 617 " --> pdb=" O   ASP A 613 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A 618 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 651
      removed outlier: 3.953A  pdb=" N   TYR A 644 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   VAL A 645 " --> pdb=" O   ALA A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 679
    Processing helix  chain 'A' and resid 683 through 696
      removed outlier: 3.905A  pdb=" N   LEU A 688 " --> pdb=" O   GLY A 684 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA A 689 " --> pdb=" O   ALA A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 722
    Processing helix  chain 'A' and resid 731 through 739
      removed outlier: 3.711A  pdb=" N   ILE A 735 " --> pdb=" O   THR A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 749
      removed outlier: 3.631A  pdb=" N   GLN A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 760
    Processing helix  chain 'A' and resid 761 through 772
      removed outlier: 4.488A  pdb=" N   TYR A 767 " --> pdb=" O   LYS A 763 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   ALA A 768 " --> pdb=" O   PHE A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 790
      removed outlier: 4.266A  pdb=" N   LEU A 789 " --> pdb=" O   ASN A 785 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR A 790 " --> pdb=" O   GLN A 786 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 785 through 790'
    Processing helix  chain 'A' and resid 810 through 813
      removed outlier: 4.529A  pdb=" N   GLY A 813 " --> pdb=" O   ASP A 810 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 810 through 813'
    Processing helix  chain 'A' and resid 865 through 874
    Processing helix  chain 'A' and resid 913 through 919
    Processing helix  chain 'A' and resid 970 through 975
    Processing helix  chain 'A' and resid 981 through 987
    Processing helix  chain 'A' and resid 993 through 1001
      removed outlier: 3.587A  pdb=" N   THR A 997 " --> pdb=" O   ARG A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1028
      removed outlier: 3.562A  pdb=" N   ARG A1024 " --> pdb=" O   VAL A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1070
    Processing helix  chain 'A' and resid 1072 through 1083
      removed outlier: 4.550A  pdb=" N   GLN A1081 " --> pdb=" O   LEU A1077 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1090
      removed outlier: 3.841A  pdb=" N   ASP A1089 " --> pdb=" O   ASN A1086 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1114
      removed outlier: 4.242A  pdb=" N   GLU A1111 " --> pdb=" O   ARG A1107 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ILE A1112 " --> pdb=" O   ARG A1108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 138 through 146
    Processing helix  chain 'B' and resid 180 through 186
    Processing helix  chain 'B' and resid 212 through 224
    Processing helix  chain 'B' and resid 241 through 249
    Processing helix  chain 'B' and resid 308 through 314
      removed outlier: 3.717A  pdb=" N   ILE B 312 " --> pdb=" O   THR B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 354
      removed outlier: 3.577A  pdb=" N   ARG B 344 " --> pdb=" O   ASP B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 381
      removed outlier: 3.512A  pdb=" N   PHE B 380 " --> pdb=" O   ASP B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 403
    Processing helix  chain 'B' and resid 587 through 594
    Processing helix  chain 'B' and resid 604 through 612
      removed outlier: 3.680A  pdb=" N   VAL B 608 " --> pdb=" O   PRO B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 633
    Processing helix  chain 'B' and resid 635 through 639
      removed outlier: 3.629A  pdb=" N   LEU B 639 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 874 through 884
    Processing helix  chain 'B' and resid 896 through 899
    Processing helix  chain 'B' and resid 908 through 916
    Processing helix  chain 'B' and resid 932 through 957
    Processing helix  chain 'B' and resid 959 through 979
      removed outlier: 3.733A  pdb=" N   ALA B 978 " --> pdb=" O   ARG B 974 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 999 through 1004
    Processing helix  chain 'B' and resid 1007 through 1016
    Processing helix  chain 'B' and resid 1025 through 1029
    Processing helix  chain 'B' and resid 1035 through 1046
    Processing helix  chain 'B' and resid 1074 through 1083
    Processing helix  chain 'B' and resid 1087 through 1094
    Processing helix  chain 'B' and resid 1102 through 1108
    Processing helix  chain 'B' and resid 1151 through 1165
    Processing helix  chain 'B' and resid 1166 through 1168
      No H-bonds generated for 'chain 'B' and resid 1166 through 1168'
    Processing helix  chain 'B' and resid 1175 through 1188
    Processing helix  chain 'B' and resid 1193 through 1204
    Processing helix  chain 'B' and resid 1206 through 1210
    Processing helix  chain 'B' and resid 1213 through 1259
    Processing helix  chain 'B' and resid 1452 through 1462
    Processing helix  chain 'B' and resid 1465 through 1470
      removed outlier: 3.743A  pdb=" N   GLU B1470 " --> pdb=" O   PRO B1466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1498 through 1513
    Processing helix  chain 'B' and resid 1514 through 1526
    Processing helix  chain 'B' and resid 1539 through 1554
    Processing helix  chain 'B' and resid 1559 through 1578
    Processing helix  chain 'B' and resid 1592 through 1594
      No H-bonds generated for 'chain 'B' and resid 1592 through 1594'
    Processing helix  chain 'B' and resid 1608 through 1627
    Processing helix  chain 'B' and resid 1630 through 1707
      removed outlier: 3.675A  pdb=" N   ASN B1634 " --> pdb=" O   ILE B1630 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 426 through 427
    Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 568
      removed outlier: 3.911A  pdb=" N   GLU A 566 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLU A 681 " --> pdb=" O   LYS A 562 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 800 through 803
    Processing sheet with id=AA4, first strand: chain 'A' and resid 823 through 824
    Processing sheet with id=AA5, first strand: chain 'B' and resid 424 through 426
    Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 470
      removed outlier: 3.833A  pdb=" N   ARG B 717 " --> pdb=" O   GLY B 474 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 856 through 860
      removed outlier: 3.513A  pdb=" N   ARG B 857 " --> pdb=" O   GLU B 869 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 919 through 921
    Processing sheet with id=AA9, first strand: chain 'B' and resid 996 through 998
      removed outlier: 6.472A  pdb=" N   ARG B1125 " --> pdb=" O   LEU B1115 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1032 through 1033
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1424 through 1430
      removed outlier: 5.656A  pdb=" N   VAL B1430 " --> pdb=" O   GLN B1477 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   GLN B1477 " --> pdb=" O   VAL B1430 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ASN B1600 " --> pdb=" O   GLU B1482 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   LEU B1484 " --> pdb=" O   VAL B1598 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL B1598 " --> pdb=" O   LEU B1484 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1447 through 1450

    876 hydrogen bonds defined for protein.
    2562 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: 3.19

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.44: 6860
        1.44 -     1.65: 9452
        1.65 -     1.87: 95
        1.87 -     2.09: 0
        2.09 -     2.31: 1
  Bond restraints: 16408
  Sorted by residual:
  bond pdb=" N   PRO B 599 "
       pdb=" CD  PRO B 599 "
    ideal  model  delta    sigma   weight residual
    1.473  2.310 -0.837 1.40e-02 5.10e+03 3.57e+03
  bond pdb=" N   PRO B 472 "
       pdb=" CA  PRO B 472 "
    ideal  model  delta    sigma   weight residual
    1.472  1.367  0.105 1.34e-02 5.57e+03 6.13e+01
  bond pdb=" N   SER A 702 "
       pdb=" CA  SER A 702 "
    ideal  model  delta    sigma   weight residual
    1.458  1.532 -0.074 1.33e-02 5.65e+03 3.13e+01
  bond pdb=" N   GLY B 474 "
       pdb=" CA  GLY B 474 "
    ideal  model  delta    sigma   weight residual
    1.449  1.524 -0.075 1.45e-02 4.76e+03 2.69e+01
  bond pdb=" C   PRO A 700 "
       pdb=" N   ILE A 701 "
    ideal  model  delta    sigma   weight residual
    1.329  1.392 -0.062 1.22e-02 6.72e+03 2.59e+01
  ... (remaining 16403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.05: 22190
       11.05 -    22.11: 21
       22.11 -    33.16: 7
       33.16 -    44.22: 2
       44.22 -    55.27: 1
  Bond angle restraints: 22221
  Sorted by residual:
  angle pdb=" N   THR B 359 "
        pdb=" CA  THR B 359 "
        pdb=" C   THR B 359 "
      ideal   model   delta    sigma   weight residual
     111.87  167.14  -55.27 1.41e+00 5.03e-01 1.54e+03
  angle pdb=" CA  PRO B 599 "
        pdb=" N   PRO B 599 "
        pdb=" CD  PRO B 599 "
      ideal   model   delta    sigma   weight residual
     112.00   75.90   36.10 1.40e+00 5.10e-01 6.65e+02
  angle pdb=" N   GLY B 481 "
        pdb=" CA  GLY B 481 "
        pdb=" C   GLY B 481 "
      ideal   model   delta    sigma   weight residual
     111.18   78.47   32.71 1.54e+00 4.22e-01 4.51e+02
  angle pdb=" C   ASP B1584 "
        pdb=" CA  ASP B1584 "
        pdb=" CB  ASP B1584 "
      ideal   model   delta    sigma   weight residual
     111.48  148.66  -37.18 1.91e+00 2.74e-01 3.79e+02
  angle pdb=" N   PRO B 599 "
        pdb=" CD  PRO B 599 "
        pdb=" CG  PRO B 599 "
      ideal   model   delta    sigma   weight residual
     103.20   75.50   27.70 1.50e+00 4.44e-01 3.41e+02
  ... (remaining 22216 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 8733
       17.98 -    35.96: 1089
       35.96 -    53.95: 222
       53.95 -    71.93: 39
       71.93 -    89.91: 17
  Dihedral angle restraints: 10100
    sinusoidal: 4153
      harmonic: 5947
  Sorted by residual:
  dihedral pdb=" N   THR B 359 "
           pdb=" C   THR B 359 "
           pdb=" CA  THR B 359 "
           pdb=" CB  THR B 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40   83.48   39.92     0      2.50e+00 1.60e-01 2.55e+02
  dihedral pdb=" C   ASN B 357 "
           pdb=" N   ASN B 357 "
           pdb=" CA  ASN B 357 "
           pdb=" CB  ASN B 357 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -161.65   39.05     0      2.50e+00 1.60e-01 2.44e+02
  dihedral pdb=" C   THR B 359 "
           pdb=" N   THR B 359 "
           pdb=" CA  THR B 359 "
           pdb=" CB  THR B 359 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00  -83.31  -38.69     0      2.50e+00 1.60e-01 2.40e+02
  ... (remaining 10097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.353: 2496
       0.353 -    0.706: 5
       0.706 -    1.059: 3
       1.059 -    1.413: 0
       1.413 -    1.766: 2
  Chirality restraints: 2506
  Sorted by residual:
  chirality pdb=" CA  THR B 359 "
            pdb=" N   THR B 359 "
            pdb=" C   THR B 359 "
            pdb=" CB  THR B 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    0.76    1.77 2.00e-01 2.50e+01 7.79e+01
  chirality pdb=" CA  ASN B 357 "
            pdb=" N   ASN B 357 "
            pdb=" C   ASN B 357 "
            pdb=" CB  ASN B 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.83    1.68 2.00e-01 2.50e+01 7.06e+01
  chirality pdb=" CA  ASP B1584 "
            pdb=" N   ASP B1584 "
            pdb=" C   ASP B1584 "
            pdb=" CB  ASP B1584 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.59    0.92 2.00e-01 2.50e+01 2.12e+01
  ... (remaining 2503 not shown)

  Planarity restraints: 2908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 703 "    0.850 9.50e-02 1.11e+02   3.81e-01 8.81e+01
        pdb=" NE  ARG A 703 "   -0.051 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 703 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 703 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 703 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 598 "    0.185 5.00e-02 4.00e+02   2.05e-01 6.75e+01
        pdb=" N   PRO B 599 "   -0.348 5.00e-02 4.00e+02
        pdb=" CA  PRO B 599 "    0.090 5.00e-02 4.00e+02
        pdb=" CD  PRO B 599 "    0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 700 "   -0.026 2.00e-02 2.50e+03   5.61e-02 3.14e+01
        pdb=" C   PRO A 700 "    0.097 2.00e-02 2.50e+03
        pdb=" O   PRO A 700 "   -0.038 2.00e-02 2.50e+03
        pdb=" N   ILE A 701 "   -0.032 2.00e-02 2.50e+03
  ... (remaining 2905 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 64
        2.38 -     3.01: 9267
        3.01 -     3.64: 23873
        3.64 -     4.27: 34646
        4.27 -     4.90: 58635
  Nonbonded interactions: 126485
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 704 "
            pdb=" CG2 ILE A 704 "
     model   vdw
     1.754 3.460
  nonbonded pdb=" OD2 ASP B 638 "
            pdb=" NH2 ARG B 717 "
     model   vdw
     1.781 3.120
  nonbonded pdb=" CB  THR B 471 "
            pdb=" O   LYS B 473 "
     model   vdw
     1.812 3.470
  nonbonded pdb=" N   GLY B 481 "
            pdb=" O   GLY B 481 "
     model   vdw
     1.853 2.496
  nonbonded pdb=" N   LYS B 358 "
            pdb=" O   LYS B 358 "
     model   vdw
     2.009 2.496
  ... (remaining 126480 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.910
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  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:   20.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.837  16409  Z= 0.523
  Angle     :  1.108  55.270  22223  Z= 0.699
  Chirality :  0.077   1.766   2506
  Planarity :  0.011   0.381   2908
  Dihedral  : 16.141  89.910   6229
  Min Nonbonded Distance : 1.754

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 16.72 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.72 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.19), residues: 2008
  helix:  2.17 (0.16), residues: 1103
  sheet: -0.18 (0.55), residues: 96
  loop : -1.14 (0.21), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A1083 
 TYR   0.014   0.001   TYR A 380 
 PHE   0.035   0.002   PHE A 742 
 TRP   0.017   0.001   TRP A 424 
 HIS   0.008   0.001   HIS A 717 

Details of bonding type rmsd
  covalent geometry    : bond        0.00790 (16408)
  covalent geometry    : angle       1.10775 (22221)
  SS BOND              : bond        0.00489 (    1)
  SS BOND              : angle       1.59749 (    2)
  hydrogen bonds       : bond        0.14361 (  876)
  hydrogen bonds       : angle       5.25235 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 407
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8596 (t70) cc_final: 0.8243 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 411
  average time/residue: 0.1501
  time to fit residues: 89.0434
Evaluate side-chains
  405 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 400
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue 1508 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    9.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 200 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    5.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 ASN
A 744 ASN
A 786 GLN
A 812 ASN
A 979 ASN
A1029 ASN
A1100 GLN
B 187 GLN
B 194 ASN
B 233 GLN
B 348 ASN
B 496 ASN
B 716 GLN
B1131 ASN
** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1437 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.182006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.140462 restraints weight = 19748.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.142605 restraints weight = 13533.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.143121 restraints weight = 11299.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.143611 restraints weight = 8154.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.143861 restraints weight = 7165.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  16409  Z= 0.147
  Angle     :  0.580  13.433  22223  Z= 0.295
  Chirality :  0.041   0.228   2506
  Planarity :  0.006   0.080   2908
  Dihedral  :  4.792  82.593   2222
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.38 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.19), residues: 2008
  helix:  2.22 (0.15), residues: 1136
  sheet: -0.27 (0.60), residues: 82
  loop : -1.10 (0.22), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 476 
 TYR   0.016   0.001   TYR B1425 
 PHE   0.024   0.001   PHE A 742 
 TRP   0.013   0.001   TRP A 424 
 HIS   0.005   0.001   HIS A 717 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (16408)
  covalent geometry    : angle       0.57975 (22221)
  SS BOND              : bond        0.00376 (    1)
  SS BOND              : angle       1.36037 (    2)
  hydrogen bonds       : bond        0.04587 (  876)
  hydrogen bonds       : angle       4.19738 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 414
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8625 (t70) cc_final: 0.8301 (t0)
REVERT: A  328 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: A  639 LYS cc_start: 0.7947 (tppt) cc_final: 0.7535 (tppt)
REVERT: A  740 ARG cc_start: 0.7323 (ttm110) cc_final: 0.6944 (ttm110)
REVERT: B  899 MET cc_start: 0.8296 (tmm) cc_final: 0.7999 (ppp)
REVERT: B 1181 GLU cc_start: 0.7161 (pt0) cc_final: 0.6760 (pt0)
REVERT: B 1584 ASP cc_start: 0.8439 (p0) cc_final: 0.8155 (p0)
REVERT: B 1658 ASP cc_start: 0.7868 (t0) cc_final: 0.7615 (t0)
  outliers start: 42
  outliers final: 27
  residues processed: 436
  average time/residue: 0.1259
  time to fit residues: 80.2798
Evaluate side-chains
  418 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 391
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  320 ASN
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue 1010 THR
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  885 THR
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1442 GLU
Chi-restraints excluded: chain B residue 1490 THR
Chi-restraints excluded: chain B residue 1497 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 144 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 183 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 162 optimal weight:    9.9990
   chunk 89 optimal weight:    7.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 HIS
A1081 GLN
B 187 GLN
B 194 ASN
B 222 ASN
B 348 ASN
B 998 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.174462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.134970 restraints weight = 20131.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.133424 restraints weight = 14114.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.134915 restraints weight = 13736.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.135775 restraints weight = 9103.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.136233 restraints weight = 8099.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16409  Z= 0.164
  Angle     :  0.571  12.480  22223  Z= 0.285
  Chirality :  0.041   0.177   2506
  Planarity :  0.005   0.085   2908
  Dihedral  :  4.623  87.365   2218
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.95 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.19), residues: 2008
  helix:  2.25 (0.15), residues: 1129
  sheet: -0.43 (0.55), residues: 92
  loop : -1.04 (0.22), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B1626 
 TYR   0.014   0.002   TYR B 466 
 PHE   0.017   0.001   PHE A 742 
 TRP   0.010   0.001   TRP A 424 
 HIS   0.005   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (16408)
  covalent geometry    : angle       0.57048 (22221)
  SS BOND              : bond        0.00391 (    1)
  SS BOND              : angle       1.16209 (    2)
  hydrogen bonds       : bond        0.04681 (  876)
  hydrogen bonds       : angle       4.06520 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 404
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8654 (t70) cc_final: 0.8310 (t0)
REVERT: A  156 MET cc_start: 0.8087 (tpp) cc_final: 0.7487 (tpp)
REVERT: A  328 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7595 (mm-30)
REVERT: A  518 ASN cc_start: 0.8562 (m-40) cc_final: 0.8153 (m110)
REVERT: A  639 LYS cc_start: 0.8166 (tppt) cc_final: 0.7669 (tppt)
REVERT: B  509 ARG cc_start: 0.6499 (ttm-80) cc_final: 0.6185 (mtp85)
REVERT: B  717 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7543 (mtp-110)
REVERT: B  881 ASP cc_start: 0.7558 (m-30) cc_final: 0.7276 (m-30)
REVERT: B 1116 ASP cc_start: 0.7580 (t0) cc_final: 0.7150 (t0)
REVERT: B 1121 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7581 (m-30)
REVERT: B 1181 GLU cc_start: 0.7258 (pt0) cc_final: 0.6833 (pt0)
REVERT: B 1658 ASP cc_start: 0.8032 (t0) cc_final: 0.7818 (t0)
  outliers start: 52
  outliers final: 32
  residues processed: 432
  average time/residue: 0.1297
  time to fit residues: 82.5030
Evaluate side-chains
  421 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 388
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  320 ASN
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  840 VAL
Chi-restraints excluded: chain A residue 1010 THR
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  194 ASN
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  998 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 181 optimal weight:    0.0270
   chunk 168 optimal weight:    0.7980
   chunk 164 optimal weight:    9.9990
   chunk 81 optimal weight:   30.0000
   chunk 99 optimal weight:    0.9980
   chunk 91 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 178 optimal weight:    6.9990
   overall best weight:    1.3640

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 ASN
A 538 HIS
B 187 GLN
B 194 ASN
B 892 ASN
B 998 ASN
B1131 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.175706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.136158 restraints weight = 20040.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.135052 restraints weight = 13977.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.136966 restraints weight = 13698.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.137244 restraints weight = 9191.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.137990 restraints weight = 8324.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  16409  Z= 0.129
  Angle     :  0.537  11.162  22223  Z= 0.269
  Chirality :  0.040   0.211   2506
  Planarity :  0.005   0.079   2908
  Dihedral  :  4.513  89.995   2218
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.03 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.19), residues: 2008
  helix:  2.35 (0.15), residues: 1129
  sheet: -0.53 (0.51), residues: 103
  loop : -0.95 (0.23), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B1626 
 TYR   0.012   0.001   TYR B 466 
 PHE   0.015   0.001   PHE A 742 
 TRP   0.011   0.001   TRP A 424 
 HIS   0.004   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (16408)
  covalent geometry    : angle       0.53663 (22221)
  SS BOND              : bond        0.00388 (    1)
  SS BOND              : angle       1.05172 (    2)
  hydrogen bonds       : bond        0.04333 (  876)
  hydrogen bonds       : angle       3.91430 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  461 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 409
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8645 (t70) cc_final: 0.8294 (t0)
REVERT: A  156 MET cc_start: 0.8042 (tpp) cc_final: 0.7723 (tpp)
REVERT: A  328 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7639 (mm-30)
REVERT: A  438 GLU cc_start: 0.7492 (mp0) cc_final: 0.7267 (mp0)
REVERT: A  518 ASN cc_start: 0.8537 (m-40) cc_final: 0.8113 (m110)
REVERT: A  527 ASN cc_start: 0.8802 (t0) cc_final: 0.8486 (t0)
REVERT: A  639 LYS cc_start: 0.8206 (tppt) cc_final: 0.7761 (tppt)
REVERT: B  509 ARG cc_start: 0.6509 (ttm-80) cc_final: 0.6195 (mtp85)
REVERT: B  881 ASP cc_start: 0.7532 (m-30) cc_final: 0.7264 (m-30)
REVERT: B 1116 ASP cc_start: 0.7625 (t0) cc_final: 0.7121 (t0)
REVERT: B 1121 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7562 (m-30)
REVERT: B 1177 GLU cc_start: 0.6559 (pp20) cc_final: 0.5940 (pp20)
REVERT: B 1181 GLU cc_start: 0.7290 (pt0) cc_final: 0.6197 (pt0)
REVERT: B 1231 ILE cc_start: 0.9051 (mm) cc_final: 0.8832 (mt)
REVERT: B 1658 ASP cc_start: 0.8068 (t0) cc_final: 0.7812 (t0)
  outliers start: 52
  outliers final: 34
  residues processed: 438
  average time/residue: 0.1290
  time to fit residues: 83.2463
Evaluate side-chains
  424 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 389
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  320 ASN
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  590 SER
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  998 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 187 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 146 optimal weight:   20.0000
   chunk 114 optimal weight:    0.9990
   chunk 65 optimal weight:    9.9990
   chunk 140 optimal weight:    0.0000
   chunk 168 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 165 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   overall best weight:    2.7992

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 ASN
A 538 HIS
B 187 GLN
B 222 ASN
** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 969 GLN
B 998 ASN
B1602 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.168691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.128660 restraints weight = 20052.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.128310 restraints weight = 12525.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.128849 restraints weight = 13928.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.129661 restraints weight = 9848.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.130679 restraints weight = 8284.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  16409  Z= 0.189
  Angle     :  0.586  11.819  22223  Z= 0.290
  Chirality :  0.042   0.325   2506
  Planarity :  0.005   0.092   2908
  Dihedral  :  4.453  82.809   2217
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.65 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.19), residues: 2008
  helix:  2.33 (0.15), residues: 1124
  sheet: -0.68 (0.51), residues: 103
  loop : -0.99 (0.23), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 717 
 TYR   0.014   0.002   TYR B 694 
 PHE   0.014   0.001   PHE A 742 
 TRP   0.008   0.001   TRP A 424 
 HIS   0.005   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (16408)
  covalent geometry    : angle       0.58548 (22221)
  SS BOND              : bond        0.00367 (    1)
  SS BOND              : angle       1.05705 (    2)
  hydrogen bonds       : bond        0.04717 (  876)
  hydrogen bonds       : angle       3.98837 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 404
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8666 (t70) cc_final: 0.8300 (t0)
REVERT: A  161 MET cc_start: 0.8347 (pmm) cc_final: 0.7989 (pmm)
REVERT: A  338 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7499 (mt-10)
REVERT: A  518 ASN cc_start: 0.8588 (m-40) cc_final: 0.8102 (m110)
REVERT: A  527 ASN cc_start: 0.8846 (t0) cc_final: 0.8453 (t0)
REVERT: A  639 LYS cc_start: 0.8163 (tppt) cc_final: 0.7644 (tppt)
REVERT: A  747 MET cc_start: 0.8252 (tpp) cc_final: 0.7963 (tpp)
REVERT: B  509 ARG cc_start: 0.6626 (ttm-80) cc_final: 0.6246 (mtp85)
REVERT: B  588 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7637 (ttp80)
REVERT: B  646 ASP cc_start: 0.7819 (p0) cc_final: 0.7526 (p0)
REVERT: B  879 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8908 (tt)
REVERT: B  881 ASP cc_start: 0.7536 (m-30) cc_final: 0.7275 (m-30)
REVERT: B  899 MET cc_start: 0.8233 (tmm) cc_final: 0.7891 (ppp)
REVERT: B 1116 ASP cc_start: 0.7695 (t0) cc_final: 0.7158 (t0)
REVERT: B 1121 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7570 (m-30)
REVERT: B 1181 GLU cc_start: 0.7409 (pt0) cc_final: 0.7021 (pt0)
REVERT: B 1522 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8512 (mtpt)
REVERT: B 1658 ASP cc_start: 0.8089 (t0) cc_final: 0.7825 (t0)
  outliers start: 58
  outliers final: 41
  residues processed: 434
  average time/residue: 0.1320
  time to fit residues: 84.3115
Evaluate side-chains
  426 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 383
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  226 ASP
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  320 ASN
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  840 VAL
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1010 THR
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 159 optimal weight:    8.9990
   chunk 190 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 163 optimal weight:    0.0040
   chunk 143 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    3.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 GLN
** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 969 GLN
** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1131 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.163376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.123658 restraints weight = 20022.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.123207 restraints weight = 12600.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.124645 restraints weight = 11509.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.124929 restraints weight = 8703.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.125369 restraints weight = 7847.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  16409  Z= 0.232
  Angle     :  0.626  12.662  22223  Z= 0.311
  Chirality :  0.043   0.271   2506
  Planarity :  0.005   0.092   2908
  Dihedral  :  4.471  64.690   2216
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.56 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.19), residues: 2008
  helix:  2.15 (0.15), residues: 1120
  sheet: -0.73 (0.53), residues: 93
  loop : -1.05 (0.22), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 717 
 TYR   0.022   0.002   TYR A 546 
 PHE   0.014   0.002   PHE A 723 
 TRP   0.009   0.001   TRP A 879 
 HIS   0.005   0.001   HIS B1267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (16408)
  covalent geometry    : angle       0.62574 (22221)
  SS BOND              : bond        0.00370 (    1)
  SS BOND              : angle       1.08046 (    2)
  hydrogen bonds       : bond        0.05144 (  876)
  hydrogen bonds       : angle       4.16106 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  463 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 403
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8679 (t70) cc_final: 0.8403 (t70)
REVERT: A  156 MET cc_start: 0.8156 (tpp) cc_final: 0.7751 (tpp)
REVERT: A  338 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7498 (mt-10)
REVERT: A  518 ASN cc_start: 0.8595 (m-40) cc_final: 0.8159 (m110)
REVERT: A  527 ASN cc_start: 0.8946 (t0) cc_final: 0.8362 (t0)
REVERT: A  549 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8129 (mmpt)
REVERT: A  628 SER cc_start: 0.8361 (m) cc_final: 0.8099 (p)
REVERT: A  639 LYS cc_start: 0.8189 (tppt) cc_final: 0.7650 (tppt)
REVERT: A  671 TYR cc_start: 0.9128 (m-80) cc_final: 0.8727 (m-80)
REVERT: A  717 HIS cc_start: 0.7885 (t-90) cc_final: 0.7549 (t-90)
REVERT: B  139 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8586 (mm-30)
REVERT: B  509 ARG cc_start: 0.6881 (ttm-80) cc_final: 0.6377 (mtp85)
REVERT: B  588 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7761 (ttp80)
REVERT: B  598 ASN cc_start: 0.8521 (m-40) cc_final: 0.8125 (m-40)
REVERT: B  879 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8849 (tt)
REVERT: B  881 ASP cc_start: 0.7579 (m-30) cc_final: 0.7332 (m-30)
REVERT: B 1065 ARG cc_start: 0.8693 (ptp-170) cc_final: 0.8336 (mtt180)
REVERT: B 1116 ASP cc_start: 0.7795 (t0) cc_final: 0.7352 (t0)
REVERT: B 1121 ASP cc_start: 0.8078 (m-30) cc_final: 0.7624 (m-30)
REVERT: B 1156 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8200 (ttp-110)
REVERT: B 1181 GLU cc_start: 0.7443 (pt0) cc_final: 0.7129 (pt0)
REVERT: B 1522 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8612 (mtpt)
REVERT: B 1627 ASN cc_start: 0.8299 (m110) cc_final: 0.8057 (m110)
  outliers start: 60
  outliers final: 44
  residues processed: 435
  average time/residue: 0.1202
  time to fit residues: 76.7429
Evaluate side-chains
  417 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 372
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  226 ASP
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  320 ASN
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  840 VAL
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  920 MET
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1010 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1271 SER
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 158 optimal weight:    0.9990
   chunk 65 optimal weight:    9.9990
   chunk 200 optimal weight:    6.9990
   chunk 67 optimal weight:    0.3980
   chunk 142 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 199 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 192 optimal weight:    5.9990
   chunk 183 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 ASN
B 969 GLN
B 998 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.171603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.131395 restraints weight = 19934.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.131365 restraints weight = 14000.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.132253 restraints weight = 14373.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.132901 restraints weight = 9849.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.133393 restraints weight = 8572.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16409  Z= 0.117
  Angle     :  0.556  11.500  22223  Z= 0.275
  Chirality :  0.040   0.237   2506
  Planarity :  0.005   0.081   2908
  Dihedral  :  4.226  57.603   2216
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.41 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.19), residues: 2008
  helix:  2.46 (0.15), residues: 1117
  sheet: -0.77 (0.49), residues: 103
  loop : -0.86 (0.23), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 872 
 TYR   0.016   0.001   TYR A 546 
 PHE   0.039   0.001   PHE A 742 
 TRP   0.013   0.001   TRP A 424 
 HIS   0.004   0.001   HIS A 717 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (16408)
  covalent geometry    : angle       0.55547 (22221)
  SS BOND              : bond        0.00415 (    1)
  SS BOND              : angle       0.93653 (    2)
  hydrogen bonds       : bond        0.04265 (  876)
  hydrogen bonds       : angle       3.84572 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 407
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8642 (t70) cc_final: 0.8257 (t0)
REVERT: A  161 MET cc_start: 0.8336 (pmm) cc_final: 0.8078 (ptt)
REVERT: A  248 LEU cc_start: 0.8074 (mt) cc_final: 0.7830 (mt)
REVERT: A  438 GLU cc_start: 0.7622 (mp0) cc_final: 0.7400 (mp0)
REVERT: A  518 ASN cc_start: 0.8530 (m-40) cc_final: 0.8033 (m110)
REVERT: A  527 ASN cc_start: 0.8710 (t0) cc_final: 0.8422 (t0)
REVERT: A  549 LYS cc_start: 0.8656 (mmpt) cc_final: 0.8092 (mmpt)
REVERT: A  639 LYS cc_start: 0.8292 (tppt) cc_final: 0.7552 (tppt)
REVERT: A  643 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7194 (mt-10)
REVERT: A  671 TYR cc_start: 0.9060 (m-80) cc_final: 0.8679 (m-80)
REVERT: A  717 HIS cc_start: 0.7831 (t-90) cc_final: 0.7448 (t-90)
REVERT: A  747 MET cc_start: 0.8260 (tpp) cc_final: 0.7948 (tpp)
REVERT: B  139 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8514 (mm-30)
REVERT: B  509 ARG cc_start: 0.6686 (ttm-80) cc_final: 0.6249 (mtp85)
REVERT: B  598 ASN cc_start: 0.8526 (m-40) cc_final: 0.8208 (m-40)
REVERT: B  704 ASP cc_start: 0.8662 (t70) cc_final: 0.8383 (t0)
REVERT: B  716 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8685 (mt0)
REVERT: B  879 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8891 (tt)
REVERT: B  881 ASP cc_start: 0.7549 (m-30) cc_final: 0.7277 (m-30)
REVERT: B  899 MET cc_start: 0.8185 (tmm) cc_final: 0.7848 (ppp)
REVERT: B 1078 TYR cc_start: 0.9347 (t80) cc_final: 0.9141 (t80)
REVERT: B 1116 ASP cc_start: 0.7633 (t0) cc_final: 0.7097 (t0)
REVERT: B 1121 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7626 (m-30)
REVERT: B 1181 GLU cc_start: 0.7379 (pt0) cc_final: 0.7092 (pt0)
REVERT: B 1253 ASP cc_start: 0.8559 (t0) cc_final: 0.7870 (m-30)
REVERT: B 1522 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8643 (mtpt)
REVERT: B 1658 ASP cc_start: 0.8159 (t0) cc_final: 0.7899 (t0)
  outliers start: 46
  outliers final: 36
  residues processed: 434
  average time/residue: 0.1449
  time to fit residues: 91.9177
Evaluate side-chains
  426 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 387
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  320 ASN
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  920 MET
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  716 GLN
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  998 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 129 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 86 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 112 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 ASN
B 222 ASN
B 892 ASN
B 969 GLN
** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.169582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.130212 restraints weight = 20014.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.128590 restraints weight = 14719.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.130177 restraints weight = 14028.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.131066 restraints weight = 9473.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.131550 restraints weight = 8424.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16409  Z= 0.140
  Angle     :  0.565  10.983  22223  Z= 0.279
  Chirality :  0.041   0.221   2506
  Planarity :  0.005   0.091   2908
  Dihedral  :  4.161  50.248   2216
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.63 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.19), residues: 2008
  helix:  2.47 (0.15), residues: 1116
  sheet: -0.76 (0.49), residues: 103
  loop : -0.84 (0.23), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B1626 
 TYR   0.015   0.001   TYR A 546 
 PHE   0.038   0.001   PHE A 742 
 TRP   0.030   0.001   TRP A 711 
 HIS   0.004   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (16408)
  covalent geometry    : angle       0.56477 (22221)
  SS BOND              : bond        0.00407 (    1)
  SS BOND              : angle       0.92641 (    2)
  hydrogen bonds       : bond        0.04345 (  876)
  hydrogen bonds       : angle       3.85518 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 396
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8649 (t70) cc_final: 0.8284 (t0)
REVERT: A  156 MET cc_start: 0.8107 (tpp) cc_final: 0.7597 (tmm)
REVERT: A  248 LEU cc_start: 0.8086 (mt) cc_final: 0.7823 (mt)
REVERT: A  338 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7365 (mt-10)
REVERT: A  518 ASN cc_start: 0.8595 (m-40) cc_final: 0.8135 (m110)
REVERT: A  527 ASN cc_start: 0.8723 (t0) cc_final: 0.8144 (t0)
REVERT: A  549 LYS cc_start: 0.8660 (mmpt) cc_final: 0.8058 (mmpt)
REVERT: A  628 SER cc_start: 0.8225 (m) cc_final: 0.7917 (p)
REVERT: A  639 LYS cc_start: 0.8293 (tppt) cc_final: 0.7720 (tppt)
REVERT: A  671 TYR cc_start: 0.9042 (m-80) cc_final: 0.8645 (m-80)
REVERT: A  717 HIS cc_start: 0.7899 (t-90) cc_final: 0.7617 (t-90)
REVERT: B  139 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8520 (mm-30)
REVERT: B  509 ARG cc_start: 0.6759 (ttm-80) cc_final: 0.6340 (mtp85)
REVERT: B  598 ASN cc_start: 0.8590 (m-40) cc_final: 0.8193 (m-40)
REVERT: B  717 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8014 (ttm110)
REVERT: B  879 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8902 (tt)
REVERT: B  881 ASP cc_start: 0.7484 (m-30) cc_final: 0.7221 (m-30)
REVERT: B 1078 TYR cc_start: 0.9359 (t80) cc_final: 0.9108 (t80)
REVERT: B 1116 ASP cc_start: 0.7695 (t0) cc_final: 0.7252 (t0)
REVERT: B 1121 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7632 (m-30)
REVERT: B 1181 GLU cc_start: 0.7295 (pt0) cc_final: 0.6993 (pt0)
REVERT: B 1253 ASP cc_start: 0.8585 (t0) cc_final: 0.7895 (m-30)
REVERT: B 1522 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8636 (mtpt)
REVERT: B 1658 ASP cc_start: 0.8163 (t0) cc_final: 0.7891 (t0)
  outliers start: 49
  outliers final: 40
  residues processed: 423
  average time/residue: 0.1271
  time to fit residues: 78.2514
Evaluate side-chains
  429 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 387
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  920 MET
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 141 optimal weight:    8.9990
   chunk 195 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 168 optimal weight:    4.9990
   chunk 193 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 200 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 ASN
** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 998 ASN
** B1013 GLN ** 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 = 0.3908 r_free = 0.3908 target = 0.180900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.140804 restraints weight = 19860.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.140500 restraints weight = 12970.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.141446 restraints weight = 13573.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.142054 restraints weight = 8914.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.142634 restraints weight = 7679.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16409  Z= 0.182
  Angle     :  0.598  11.303  22223  Z= 0.295
  Chirality :  0.042   0.216   2506
  Planarity :  0.005   0.086   2908
  Dihedral  :  4.183  41.934   2216
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.92 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.19), residues: 2008
  helix:  2.43 (0.15), residues: 1113
  sheet: -0.79 (0.51), residues: 94
  loop : -0.88 (0.23), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 999 
 TYR   0.017   0.001   TYR B 466 
 PHE   0.033   0.002   PHE A 742 
 TRP   0.043   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (16408)
  covalent geometry    : angle       0.59784 (22221)
  SS BOND              : bond        0.00389 (    1)
  SS BOND              : angle       0.94718 (    2)
  hydrogen bonds       : bond        0.04643 (  876)
  hydrogen bonds       : angle       3.95369 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 397
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8670 (t70) cc_final: 0.8300 (t0)
REVERT: A  161 MET cc_start: 0.8367 (pmm) cc_final: 0.8102 (ptt)
REVERT: A  239 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7997 (tp30)
REVERT: A  248 LEU cc_start: 0.8090 (mt) cc_final: 0.7749 (mt)
REVERT: A  338 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: A  518 ASN cc_start: 0.8517 (m-40) cc_final: 0.8061 (m110)
REVERT: A  527 ASN cc_start: 0.8790 (t0) cc_final: 0.8189 (t0)
REVERT: A  549 LYS cc_start: 0.8692 (mmpt) cc_final: 0.8094 (mmpt)
REVERT: A  628 SER cc_start: 0.8304 (m) cc_final: 0.8004 (p)
REVERT: A  639 LYS cc_start: 0.8301 (tppt) cc_final: 0.7602 (tppt)
REVERT: A  643 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7477 (mt-10)
REVERT: A  671 TYR cc_start: 0.8991 (m-80) cc_final: 0.8603 (m-80)
REVERT: A  717 HIS cc_start: 0.7961 (t-90) cc_final: 0.7578 (t-90)
REVERT: A  999 ARG cc_start: 0.8273 (ttp80) cc_final: 0.8002 (ttp80)
REVERT: B  139 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8541 (mm-30)
REVERT: B  509 ARG cc_start: 0.6727 (ttm-80) cc_final: 0.6355 (mtp85)
REVERT: B  598 ASN cc_start: 0.8561 (m-40) cc_final: 0.8156 (m-40)
REVERT: B  646 ASP cc_start: 0.7783 (p0) cc_final: 0.7512 (p0)
REVERT: B  704 ASP cc_start: 0.8724 (t70) cc_final: 0.8483 (t0)
REVERT: B  879 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8931 (tt)
REVERT: B  881 ASP cc_start: 0.7476 (m-30) cc_final: 0.7236 (m-30)
REVERT: B  899 MET cc_start: 0.8149 (tmm) cc_final: 0.7819 (ppp)
REVERT: B 1065 ARG cc_start: 0.8612 (ptp-170) cc_final: 0.8295 (mtt180)
REVERT: B 1078 TYR cc_start: 0.9377 (t80) cc_final: 0.9103 (t80)
REVERT: B 1104 ASP cc_start: 0.8544 (m-30) cc_final: 0.8231 (m-30)
REVERT: B 1116 ASP cc_start: 0.7772 (t0) cc_final: 0.7361 (t0)
REVERT: B 1121 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7565 (m-30)
REVERT: B 1181 GLU cc_start: 0.7291 (pt0) cc_final: 0.7008 (pt0)
REVERT: B 1253 ASP cc_start: 0.8587 (t0) cc_final: 0.7897 (m-30)
  outliers start: 48
  outliers final: 42
  residues processed: 425
  average time/residue: 0.1339
  time to fit residues: 82.8908
Evaluate side-chains
  421 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 377
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  920 MET
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  998 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 1200 VAL
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 159 optimal weight:    0.5980
   chunk 109 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 157 optimal weight:    5.9990
   chunk 200 optimal weight:    6.9990
   chunk 121 optimal weight:   20.0000
   chunk 165 optimal weight:    0.6980
   chunk 182 optimal weight:    0.9990
   chunk 198 optimal weight:    1.9990
   chunk 140 optimal weight:    2.9990
   chunk 112 optimal weight:    6.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 ASN
A1064 ASN
** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1013 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.174230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.134364 restraints weight = 19847.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.133674 restraints weight = 12272.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.134374 restraints weight = 14318.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.135518 restraints weight = 9355.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.135986 restraints weight = 7888.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100  16409  Z= 0.157
  Angle     :  0.781  59.198  22223  Z= 0.421
  Chirality :  0.042   0.240   2506
  Planarity :  0.005   0.096   2908
  Dihedral  :  4.200  41.840   2216
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.26 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.19), residues: 2008
  helix:  2.45 (0.15), residues: 1113
  sheet: -0.79 (0.51), residues: 94
  loop : -0.88 (0.23), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.038   0.001   ARG B 508 
 TYR   0.023   0.001   TYR A 546 
 PHE   0.030   0.002   PHE A 742 
 TRP   0.040   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (16408)
  covalent geometry    : angle       0.78144 (22221)
  SS BOND              : bond        0.00372 (    1)
  SS BOND              : angle       0.95821 (    2)
  hydrogen bonds       : bond        0.04562 (  876)
  hydrogen bonds       : angle       3.94525 ( 2562)

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

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

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4016 Ramachandran restraints generated.
    2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  427 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 379
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8658 (t70) cc_final: 0.8277 (t0)
REVERT: A  161 MET cc_start: 0.8390 (pmm) cc_final: 0.8133 (ptt)
REVERT: A  248 LEU cc_start: 0.8091 (mt) cc_final: 0.7752 (mt)
REVERT: A  338 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7401 (mt-10)
REVERT: A  518 ASN cc_start: 0.8494 (m-40) cc_final: 0.8050 (m110)
REVERT: A  527 ASN cc_start: 0.8761 (t0) cc_final: 0.8178 (t0)
REVERT: A  549 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8090 (mmpt)
REVERT: A  628 SER cc_start: 0.8288 (m) cc_final: 0.7987 (p)
REVERT: A  639 LYS cc_start: 0.8288 (tppt) cc_final: 0.7707 (tppt)
REVERT: A  671 TYR cc_start: 0.8996 (m-80) cc_final: 0.8634 (m-80)
REVERT: A  717 HIS cc_start: 0.7963 (t-90) cc_final: 0.7566 (t-90)
REVERT: A  999 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7967 (ttp80)
REVERT: B  139 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8535 (mm-30)
REVERT: B  509 ARG cc_start: 0.6734 (ttm-80) cc_final: 0.6354 (mtp85)
REVERT: B  598 ASN cc_start: 0.8565 (m-40) cc_final: 0.8159 (m-40)
REVERT: B  717 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7831 (ttm110)
REVERT: B  879 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8913 (tt)
REVERT: B  881 ASP cc_start: 0.7438 (m-30) cc_final: 0.7220 (m-30)
REVERT: B  899 MET cc_start: 0.8159 (tmm) cc_final: 0.7825 (ppp)
REVERT: B 1065 ARG cc_start: 0.8604 (ptp-170) cc_final: 0.8282 (mtt180)
REVERT: B 1078 TYR cc_start: 0.9376 (t80) cc_final: 0.9098 (t80)
REVERT: B 1102 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7862 (m-30)
REVERT: B 1116 ASP cc_start: 0.7762 (t0) cc_final: 0.7353 (t0)
REVERT: B 1121 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7558 (m-30)
REVERT: B 1181 GLU cc_start: 0.7282 (pt0) cc_final: 0.7000 (pt0)
REVERT: B 1253 ASP cc_start: 0.8595 (t0) cc_final: 0.7912 (m-30)
  outliers start: 48
  outliers final: 44
  residues processed: 405
  average time/residue: 0.1376
  time to fit residues: 81.5712
Evaluate side-chains
  422 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 375
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  920 MET
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  465 LYS
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1102 ASP
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 1200 VAL
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 140 optimal weight:    0.8980
   chunk 176 optimal weight:    6.9990
   chunk 83 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0670
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 ASN
B 716 GLN
** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1013 GLN ** 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 = 0.3915 r_free = 0.3915 target = 0.181679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.141664 restraints weight = 19836.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.141418 restraints weight = 12749.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.142352 restraints weight = 13383.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.142954 restraints weight = 8754.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.143656 restraints weight = 7570.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.200  16409  Z= 0.189
  Angle     :  0.910  58.783  22223  Z= 0.530
  Chirality :  0.053   1.707   2506
  Planarity :  0.005   0.094   2908
  Dihedral  :  4.215  41.830   2216
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.03 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.19), residues: 2008
  helix:  2.45 (0.15), residues: 1113
  sheet: -0.79 (0.51), residues: 94
  loop : -0.88 (0.23), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.055   0.001   ARG B 508 
 TYR   0.020   0.001   TYR A 546 
 PHE   0.027   0.002   PHE A 742 
 TRP   0.033   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (16408)
  covalent geometry    : angle       0.91030 (22221)
  SS BOND              : bond        0.00364 (    1)
  SS BOND              : angle       0.95844 (    2)
  hydrogen bonds       : bond        0.04537 (  876)
  hydrogen bonds       : angle       3.94810 ( 2562)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2931.98 seconds
wall clock time: 51 minutes 19.06 seconds (3079.06 seconds total)