Starting phenix.real_space_refine
on Sat May 17 22:39:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3a_62011/05_2025/9k3a_62011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3a_62011/05_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_62011/05_2025/9k3a_62011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3a_62011/05_2025/9k3a_62011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3a_62011/05_2025/9k3a_62011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3a_62011/05_2025/9k3a_62011.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.26, per 1000 atoms: 0.57
  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: 4.32
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 2.07
  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: 5.22

  Time building geometry restraints manager: 4.96 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:             1.450
  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:             0.020
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     36.470
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.620
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (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
 TRP   0.017   0.001   TRP A 424 
 HIS   0.008   0.001   HIS A 717 
 PHE   0.035   0.002   PHE A 742 
 TYR   0.014   0.001   TYR A 380 
 ARG   0.020   0.001   ARG A1083 

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

*********************** 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  : 1.940 
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: 0.3248
  time to fit residues: 193.3237
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  : 1.685 
-------------------------------------------------------------------------------
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 172 optimal weight:    0.8980
   chunk 154 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 104 optimal weight:    8.9990
   chunk 82 optimal weight:    8.9990
   chunk 159 optimal weight:    0.5980
   chunk 61 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   chunk 185 optimal weight:    0.0570
   overall best weight:    1.7102

-------------------------------------------------------------------------------
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 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: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.167824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.127435 restraints weight = 19593.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.127797 restraints weight = 14181.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.128649 restraints weight = 15205.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  16409  Z= 0.150
  Angle     :  0.583  13.251  22223  Z= 0.297
  Chirality :  0.041   0.229   2506
  Planarity :  0.006   0.081   2908
  Dihedral  :  4.805  82.694   2222
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.16 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.19), residues: 2008
  helix:  2.20 (0.15), residues: 1136
  sheet: -0.29 (0.60), residues: 82
  loop : -1.11 (0.22), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 424 
 HIS   0.005   0.001   HIS A  40 
 PHE   0.024   0.001   PHE A 742 
 TYR   0.015   0.001   TYR B1425 
 ARG   0.010   0.001   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04672 (  876)
  hydrogen bonds       : angle       4.21390 ( 2562)
  SS BOND              : bond        0.00376 (    1)
  SS BOND              : angle       1.38666 (    2)
  covalent geometry    : bond        0.00354 (16408)
  covalent geometry    : angle       0.58297 (22221)

*********************** 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
  459 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 415
  time to evaluate  : 1.659 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8615 (t70) cc_final: 0.8271 (t0)
REVERT: A  328 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7642 (mm-30)
REVERT: A  639 LYS cc_start: 0.7982 (tppt) cc_final: 0.7572 (tppt)
REVERT: A  740 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6966 (ttm110)
REVERT: A  874 PHE cc_start: 0.8403 (m-80) cc_final: 0.8146 (m-80)
REVERT: B  899 MET cc_start: 0.8296 (tmm) cc_final: 0.8002 (ppp)
REVERT: B 1181 GLU cc_start: 0.7152 (pt0) cc_final: 0.6747 (pt0)
REVERT: B 1584 ASP cc_start: 0.8402 (p0) cc_final: 0.8109 (p0)
REVERT: B 1658 ASP cc_start: 0.7732 (t0) cc_final: 0.7464 (t0)
  outliers start: 44
  outliers final: 29
  residues processed: 439
  average time/residue: 0.2999
  time to fit residues: 191.0483
Evaluate side-chains
  416 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 387
  time to evaluate  : 1.683 
-------------------------------------------------------------------------------
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  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  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 1271 SER
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 198 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 138 optimal weight:   10.0000
   chunk 99 optimal weight:    1.9990
   chunk 201 optimal weight:    5.9990
   chunk 180 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 178 optimal weight:    4.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 ASN
A 538 HIS
A 744 ASN
B 187 GLN
B 194 ASN
B 222 ASN
B 348 ASN
B 998 ASN
B1602 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.171700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.131766 restraints weight = 19866.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.130518 restraints weight = 14114.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.131353 restraints weight = 14901.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  16409  Z= 0.214
  Angle     :  0.614  13.304  22223  Z= 0.307
  Chirality :  0.043   0.176   2506
  Planarity :  0.006   0.093   2908
  Dihedral  :  4.773  89.268   2218
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.29 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.19), residues: 2008
  helix:  2.13 (0.15), residues: 1129
  sheet: -0.50 (0.55), residues: 94
  loop : -1.11 (0.22), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 424 
 HIS   0.006   0.001   HIS A  40 
 PHE   0.016   0.002   PHE A 742 
 TYR   0.019   0.002   TYR B 466 
 ARG   0.009   0.001   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05147 (  876)
  hydrogen bonds       : angle       4.20520 ( 2562)
  SS BOND              : bond        0.00367 (    1)
  SS BOND              : angle       1.18941 (    2)
  covalent geometry    : bond        0.00516 (16408)
  covalent geometry    : angle       0.61370 (22221)

*********************** 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
  480 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 422
  time to evaluate  : 1.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8633 (t70) cc_final: 0.8369 (t70)
REVERT: A  328 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: A  518 ASN cc_start: 0.8637 (m-40) cc_final: 0.8301 (m110)
REVERT: A  639 LYS cc_start: 0.8176 (tppt) cc_final: 0.7663 (tppt)
REVERT: A  740 ARG cc_start: 0.7353 (ttm110) cc_final: 0.7152 (ttm110)
REVERT: B  139 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8588 (mm-30)
REVERT: B  509 ARG cc_start: 0.6555 (ttm-80) cc_final: 0.6217 (mtp85)
REVERT: B  917 ASP cc_start: 0.7804 (t0) cc_final: 0.7554 (t0)
REVERT: B 1104 ASP cc_start: 0.8487 (m-30) cc_final: 0.8278 (m-30)
REVERT: B 1116 ASP cc_start: 0.7627 (t0) cc_final: 0.7183 (t0)
REVERT: B 1121 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7518 (m-30)
REVERT: B 1177 GLU cc_start: 0.6614 (pp20) cc_final: 0.5956 (pp20)
REVERT: B 1181 GLU cc_start: 0.7335 (pt0) cc_final: 0.6279 (pt0)
REVERT: B 1454 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8630 (tt0)
REVERT: B 1492 ASP cc_start: 0.7932 (t0) cc_final: 0.7710 (t70)
REVERT: B 1522 LYS cc_start: 0.8807 (mtpp) cc_final: 0.8483 (mtpt)
REVERT: B 1658 ASP cc_start: 0.8192 (t0) cc_final: 0.7956 (t0)
  outliers start: 58
  outliers final: 34
  residues processed: 452
  average time/residue: 0.2958
  time to fit residues: 194.1096
Evaluate side-chains
  442 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 407
  time to evaluate  : 1.684 
-------------------------------------------------------------------------------
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  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  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  843 LEU
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  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  871 VAL
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
Chi-restraints excluded: chain B residue 1506 LEU
Chi-restraints excluded: chain B residue 1525 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 167 optimal weight:    3.9990
   chunk 187 optimal weight:    1.9990
   chunk 136 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 137 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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
B 194 ASN
B 892 ASN
B 998 ASN
B1131 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.170164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.130201 restraints weight = 19777.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.129799 restraints weight = 12960.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.130304 restraints weight = 13769.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16409  Z= 0.137
  Angle     :  0.551  11.750  22223  Z= 0.276
  Chirality :  0.040   0.219   2506
  Planarity :  0.005   0.082   2908
  Dihedral  :  4.552  86.806   2218
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.48 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.19), residues: 2008
  helix:  2.28 (0.15), residues: 1129
  sheet: -0.59 (0.51), residues: 103
  loop : -0.99 (0.23), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 424 
 HIS   0.004   0.001   HIS A  40 
 PHE   0.015   0.001   PHE A 742 
 TYR   0.014   0.001   TYR B 466 
 ARG   0.010   0.000   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04487 (  876)
  hydrogen bonds       : angle       3.97466 ( 2562)
  SS BOND              : bond        0.00384 (    1)
  SS BOND              : angle       1.05695 (    2)
  covalent geometry    : bond        0.00322 (16408)
  covalent geometry    : angle       0.55059 (22221)

*********************** 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
  473 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 419
  time to evaluate  : 1.732 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8629 (t70) cc_final: 0.8301 (t0)
REVERT: A  161 MET cc_start: 0.8257 (pmm) cc_final: 0.7430 (pmm)
REVERT: A  438 GLU cc_start: 0.7475 (mp0) cc_final: 0.7242 (mp0)
REVERT: A  518 ASN cc_start: 0.8639 (m-40) cc_final: 0.8209 (m110)
REVERT: A  527 ASN cc_start: 0.8824 (t0) cc_final: 0.8484 (t0)
REVERT: A  639 LYS cc_start: 0.8200 (tppt) cc_final: 0.7708 (tppt)
REVERT: A  747 MET cc_start: 0.8218 (tpp) cc_final: 0.7894 (tpp)
REVERT: B  509 ARG cc_start: 0.6584 (ttm-80) cc_final: 0.6218 (mtp85)
REVERT: B  616 PHE cc_start: 0.6410 (m-80) cc_final: 0.6059 (m-80)
REVERT: B  704 ASP cc_start: 0.8526 (t70) cc_final: 0.8302 (t0)
REVERT: B  881 ASP cc_start: 0.7535 (m-30) cc_final: 0.7261 (m-30)
REVERT: B 1104 ASP cc_start: 0.8464 (m-30) cc_final: 0.8217 (m-30)
REVERT: B 1116 ASP cc_start: 0.7617 (t0) cc_final: 0.7138 (t0)
REVERT: B 1121 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7613 (m-30)
REVERT: B 1177 GLU cc_start: 0.6589 (pp20) cc_final: 0.5931 (pp20)
REVERT: B 1181 GLU cc_start: 0.7337 (pt0) cc_final: 0.6311 (pt0)
REVERT: B 1253 ASP cc_start: 0.8565 (t0) cc_final: 0.7773 (m-30)
REVERT: B 1522 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8505 (mtpt)
REVERT: B 1658 ASP cc_start: 0.8130 (t0) cc_final: 0.7892 (t0)
  outliers start: 54
  outliers final: 37
  residues processed: 448
  average time/residue: 0.3032
  time to fit residues: 198.0456
Evaluate side-chains
  439 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 401
  time to evaluate  : 1.843 
-------------------------------------------------------------------------------
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  313 GLU
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  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  920 MET
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  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  600 GLU
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
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 1179 LEU
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
Chi-restraints excluded: chain B residue 1506 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 126 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 59 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 167 optimal weight:    6.9990
   chunk 176 optimal weight:    7.9990
   chunk 163 optimal weight:    9.9990
   chunk 86 optimal weight:    8.9990
   chunk 169 optimal weight:    2.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 ASN
** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 ASN
B 222 ASN
B 496 ASN
** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 969 GLN
B1131 ASN
B1554 ASN
** B1564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.158179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.119765 restraints weight = 20309.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.118411 restraints weight = 13593.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.119924 restraints weight = 12299.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  16409  Z= 0.337
  Angle     :  0.721  13.921  22223  Z= 0.359
  Chirality :  0.046   0.189   2506
  Planarity :  0.006   0.113   2908
  Dihedral  :  4.743  67.697   2217
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.39 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.19), residues: 2008
  helix:  1.85 (0.15), residues: 1117
  sheet: -0.77 (0.53), residues: 93
  loop : -1.16 (0.22), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 711 
 HIS   0.007   0.002   HIS B1267 
 PHE   0.021   0.002   PHE A 369 
 TYR   0.028   0.002   TYR B 466 
 ARG   0.012   0.001   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05888 (  876)
  hydrogen bonds       : angle       4.44089 ( 2562)
  SS BOND              : bond        0.00331 (    1)
  SS BOND              : angle       1.16689 (    2)
  covalent geometry    : bond        0.00808 (16408)
  covalent geometry    : angle       0.72076 (22221)

*********************** 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
  502 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 432
  time to evaluate  : 1.747 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8683 (t70) cc_final: 0.8417 (t70)
REVERT: A  302 ARG cc_start: 0.8971 (ttp-170) cc_final: 0.8755 (ttp-170)
REVERT: A  338 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7478 (mt-10)
REVERT: A  397 GLU cc_start: 0.8613 (tp30) cc_final: 0.8258 (tm-30)
REVERT: A  441 ASN cc_start: 0.7835 (m-40) cc_final: 0.7629 (t0)
REVERT: A  510 ARG cc_start: 0.7914 (mtt90) cc_final: 0.6953 (mmt180)
REVERT: A  518 ASN cc_start: 0.8653 (m-40) cc_final: 0.8220 (m110)
REVERT: A  527 ASN cc_start: 0.8988 (t0) cc_final: 0.8547 (t0)
REVERT: A  549 LYS cc_start: 0.8553 (mmpt) cc_final: 0.7846 (mmpt)
REVERT: A  628 SER cc_start: 0.8446 (m) cc_final: 0.8223 (p)
REVERT: A  639 LYS cc_start: 0.8149 (tppt) cc_final: 0.7619 (tppt)
REVERT: A  671 TYR cc_start: 0.9172 (m-80) cc_final: 0.8642 (m-80)
REVERT: A  725 PHE cc_start: 0.6899 (p90) cc_final: 0.6667 (p90)
REVERT: A 1079 GLU cc_start: 0.6619 (tp30) cc_final: 0.6411 (tp30)
REVERT: B  352 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7267 (ttt-90)
REVERT: B  509 ARG cc_start: 0.6823 (ttm-80) cc_final: 0.6309 (mtp85)
REVERT: B  598 ASN cc_start: 0.8617 (m-40) cc_final: 0.8266 (m-40)
REVERT: B  717 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7628 (mtp-110)
REVERT: B  917 ASP cc_start: 0.7587 (t0) cc_final: 0.7183 (t0)
REVERT: B 1065 ARG cc_start: 0.8737 (ptp-170) cc_final: 0.8400 (mtt180)
REVERT: B 1116 ASP cc_start: 0.7859 (t0) cc_final: 0.7379 (t0)
REVERT: B 1121 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7515 (m-30)
REVERT: B 1627 ASN cc_start: 0.8460 (m110) cc_final: 0.8219 (m110)
REVERT: B 1658 ASP cc_start: 0.8123 (t0) cc_final: 0.7869 (t0)
  outliers start: 70
  outliers final: 49
  residues processed: 473
  average time/residue: 0.3189
  time to fit residues: 218.4949
Evaluate side-chains
  436 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 386
  time to evaluate  : 1.697 
-------------------------------------------------------------------------------
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  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  364 THR
Chi-restraints excluded: chain A residue  401 VAL
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  551 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  871 THR
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  244 SER
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  400 TRP
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  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 1200 VAL
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1271 SER
Chi-restraints excluded: chain B residue 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Chi-restraints excluded: chain B residue 1506 LEU
Chi-restraints excluded: chain B residue 1632 THR
Chi-restraints excluded: chain B residue 1687 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 162 optimal weight:    7.9990
   chunk 89 optimal weight:    9.9990
   chunk 81 optimal weight:    0.8980
   chunk 96 optimal weight:    9.9990
   chunk 157 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 188 optimal weight:    4.9990
   chunk 164 optimal weight:    1.9990
   chunk 169 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 HIS
A 841 ASN
B 194 ASN
B 969 GLN
B 998 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.166442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.126225 restraints weight = 20054.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.125721 restraints weight = 14289.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.126736 restraints weight = 14557.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16409  Z= 0.140
  Angle     :  0.575  12.648  22223  Z= 0.286
  Chirality :  0.041   0.328   2506
  Planarity :  0.005   0.085   2908
  Dihedral  :  4.400  58.838   2216
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.75 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.19), residues: 2008
  helix:  2.21 (0.15), residues: 1118
  sheet: -0.82 (0.49), residues: 103
  loop : -0.98 (0.23), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 711 
 HIS   0.004   0.001   HIS A  40 
 PHE   0.015   0.001   PHE A 262 
 TYR   0.022   0.001   TYR A 546 
 ARG   0.007   0.000   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04641 (  876)
  hydrogen bonds       : angle       4.03666 ( 2562)
  SS BOND              : bond        0.00392 (    1)
  SS BOND              : angle       0.98350 (    2)
  covalent geometry    : bond        0.00324 (16408)
  covalent geometry    : angle       0.57500 (22221)

*********************** 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
  469 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 417
  time to evaluate  : 1.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8670 (t70) cc_final: 0.8383 (t70)
REVERT: A  338 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7388 (mt-10)
REVERT: A  397 GLU cc_start: 0.8438 (tp30) cc_final: 0.8193 (tm-30)
REVERT: A  518 ASN cc_start: 0.8570 (m-40) cc_final: 0.8142 (m110)
REVERT: A  527 ASN cc_start: 0.8856 (t0) cc_final: 0.8444 (t0)
REVERT: A  549 LYS cc_start: 0.8502 (mmpt) cc_final: 0.7760 (mmpt)
REVERT: A  628 SER cc_start: 0.8278 (m) cc_final: 0.8017 (p)
REVERT: A  639 LYS cc_start: 0.8204 (tppt) cc_final: 0.7745 (tppt)
REVERT: A  671 TYR cc_start: 0.9053 (m-80) cc_final: 0.8688 (m-80)
REVERT: A  717 HIS cc_start: 0.7880 (t-90) cc_final: 0.7492 (t-90)
REVERT: A  725 PHE cc_start: 0.7120 (p90) cc_final: 0.6843 (p90)
REVERT: A  747 MET cc_start: 0.8275 (tpp) cc_final: 0.7986 (tpp)
REVERT: B  352 ARG cc_start: 0.7415 (ttt-90) cc_final: 0.7137 (ttt-90)
REVERT: B  509 ARG cc_start: 0.6791 (ttm-80) cc_final: 0.6306 (mtp85)
REVERT: B  598 ASN cc_start: 0.8611 (m-40) cc_final: 0.8234 (m-40)
REVERT: B  646 ASP cc_start: 0.7830 (p0) cc_final: 0.7589 (p0)
REVERT: B  704 ASP cc_start: 0.8690 (t70) cc_final: 0.8442 (t0)
REVERT: B 1116 ASP cc_start: 0.7763 (t0) cc_final: 0.7316 (t0)
REVERT: B 1121 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7623 (m-30)
REVERT: B 1253 ASP cc_start: 0.8559 (t0) cc_final: 0.7780 (m-30)
REVERT: B 1492 ASP cc_start: 0.8045 (t0) cc_final: 0.7801 (t70)
REVERT: B 1627 ASN cc_start: 0.8234 (m110) cc_final: 0.8010 (m110)
REVERT: B 1658 ASP cc_start: 0.8128 (t0) cc_final: 0.7875 (t0)
  outliers start: 52
  outliers final: 40
  residues processed: 446
  average time/residue: 0.3137
  time to fit residues: 202.5943
Evaluate side-chains
  441 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 400
  time to evaluate  : 1.741 
-------------------------------------------------------------------------------
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  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  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  194 ASN
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  870 THR
Chi-restraints excluded: chain B residue  923 SER
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 1202 ASP
Chi-restraints excluded: chain B residue 1235 VAL
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
Chi-restraints excluded: chain B residue 1506 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 194 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 158 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 151 optimal weight:    0.7980
   chunk 86 optimal weight:    9.9990
   chunk 137 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 181 optimal weight:    9.9990
   chunk 195 optimal weight:    0.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 841 ASN
B 998 ASN
B1131 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.168640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.128218 restraints weight = 19997.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.128518 restraints weight = 14006.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.128943 restraints weight = 13741.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2431

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= 0.118
  Angle     :  0.554  11.401  22223  Z= 0.275
  Chirality :  0.040   0.285   2506
  Planarity :  0.005   0.092   2908
  Dihedral  :  4.235  52.702   2216
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.63 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.20), residues: 2008
  helix:  2.39 (0.15), residues: 1118
  sheet: -0.82 (0.49), residues: 103
  loop : -0.87 (0.23), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A 468 
 PHE   0.014   0.001   PHE A 723 
 TYR   0.014   0.001   TYR B 466 
 ARG   0.007   0.000   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  876)
  hydrogen bonds       : angle       3.87238 ( 2562)
  SS BOND              : bond        0.00432 (    1)
  SS BOND              : angle       0.91287 (    2)
  covalent geometry    : bond        0.00268 (16408)
  covalent geometry    : angle       0.55429 (22221)

*********************** 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
  459 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 405
  time to evaluate  : 1.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8711 (t70) cc_final: 0.8352 (t0)
REVERT: A  438 GLU cc_start: 0.7535 (mp0) cc_final: 0.7243 (mp0)
REVERT: A  518 ASN cc_start: 0.8512 (m-40) cc_final: 0.8072 (m110)
REVERT: A  527 ASN cc_start: 0.8710 (t0) cc_final: 0.8498 (t0)
REVERT: A  639 LYS cc_start: 0.8194 (tppt) cc_final: 0.7721 (tppt)
REVERT: A  671 TYR cc_start: 0.9059 (m-80) cc_final: 0.8668 (m-80)
REVERT: A  717 HIS cc_start: 0.7882 (t-90) cc_final: 0.7566 (t-90)
REVERT: A  725 PHE cc_start: 0.6990 (p90) cc_final: 0.6747 (p90)
REVERT: B  352 ARG cc_start: 0.7436 (ttt-90) cc_final: 0.7165 (ttt-90)
REVERT: B  509 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.6327 (mtp85)
REVERT: B  598 ASN cc_start: 0.8613 (m-40) cc_final: 0.8173 (m-40)
REVERT: B  881 ASP cc_start: 0.7496 (m-30) cc_final: 0.7210 (m-30)
REVERT: B 1102 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (m-30)
REVERT: B 1116 ASP cc_start: 0.7698 (t0) cc_final: 0.7257 (t0)
REVERT: B 1121 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7671 (m-30)
REVERT: B 1253 ASP cc_start: 0.8598 (t0) cc_final: 0.7820 (m-30)
REVERT: B 1492 ASP cc_start: 0.8059 (t0) cc_final: 0.7847 (t70)
REVERT: B 1658 ASP cc_start: 0.8094 (t0) cc_final: 0.7830 (t0)
  outliers start: 54
  outliers final: 37
  residues processed: 433
  average time/residue: 0.3029
  time to fit residues: 191.5314
Evaluate side-chains
  428 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 389
  time to evaluate  : 1.834 
-------------------------------------------------------------------------------
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  139 ILE
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  638 THR
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1004 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  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  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 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
Chi-restraints excluded: chain B residue 1506 LEU
Chi-restraints excluded: chain B residue 1543 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   chunk 199 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 100 optimal weight:    0.0020
   chunk 154 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0670
   chunk 39 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.9730

-------------------------------------------------------------------------------
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
B1131 ASN
B1627 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.171028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.130453 restraints weight = 19876.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.133539 restraints weight = 12874.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.134252 restraints weight = 9595.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16409  Z= 0.118
  Angle     :  0.556  10.919  22223  Z= 0.275
  Chirality :  0.040   0.267   2506
  Planarity :  0.005   0.082   2908
  Dihedral  :  4.131  46.590   2216
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.43 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.20), residues: 2008
  helix:  2.43 (0.15), residues: 1119
  sheet: -0.74 (0.49), residues: 103
  loop : -0.81 (0.23), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 711 
 HIS   0.004   0.001   HIS A 717 
 PHE   0.029   0.001   PHE A 742 
 TYR   0.028   0.001   TYR A 546 
 ARG   0.007   0.000   ARG A 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04154 (  876)
  hydrogen bonds       : angle       3.81592 ( 2562)
  SS BOND              : bond        0.00425 (    1)
  SS BOND              : angle       0.82737 (    2)
  covalent geometry    : bond        0.00272 (16408)
  covalent geometry    : angle       0.55623 (22221)

*********************** 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
  439 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 389
  time to evaluate  : 1.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8692 (t70) cc_final: 0.8248 (t0)
REVERT: A  518 ASN cc_start: 0.8559 (m-40) cc_final: 0.8060 (m110)
REVERT: A  639 LYS cc_start: 0.8191 (tppt) cc_final: 0.7797 (tppt)
REVERT: A  671 TYR cc_start: 0.8983 (m-80) cc_final: 0.8628 (m-80)
REVERT: A  717 HIS cc_start: 0.7898 (t-90) cc_final: 0.7599 (t-90)
REVERT: A  725 PHE cc_start: 0.7029 (p90) cc_final: 0.6796 (p90)
REVERT: B  352 ARG cc_start: 0.7392 (ttt-90) cc_final: 0.7148 (ttt-90)
REVERT: B  509 ARG cc_start: 0.6605 (ttm-80) cc_final: 0.6247 (mtp85)
REVERT: B  598 ASN cc_start: 0.8580 (m-40) cc_final: 0.8197 (m-40)
REVERT: B  646 ASP cc_start: 0.7818 (p0) cc_final: 0.7521 (p0)
REVERT: B  899 MET cc_start: 0.8151 (tmm) cc_final: 0.7818 (ppp)
REVERT: B 1102 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7764 (m-30)
REVERT: B 1104 ASP cc_start: 0.8484 (m-30) cc_final: 0.8221 (m-30)
REVERT: B 1116 ASP cc_start: 0.7629 (t0) cc_final: 0.7154 (t0)
REVERT: B 1121 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7767 (m-30)
REVERT: B 1253 ASP cc_start: 0.8605 (t0) cc_final: 0.7824 (m-30)
REVERT: B 1492 ASP cc_start: 0.8080 (t0) cc_final: 0.7860 (t70)
REVERT: B 1658 ASP cc_start: 0.8002 (t0) cc_final: 0.7728 (t0)
  outliers start: 50
  outliers final: 40
  residues processed: 414
  average time/residue: 0.2946
  time to fit residues: 177.5090
Evaluate side-chains
  394 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 352
  time to evaluate  : 1.883 
-------------------------------------------------------------------------------
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  139 ILE
Chi-restraints excluded: chain A residue  248 LEU
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  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 1004 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  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  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 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
Chi-restraints excluded: chain B residue 1506 LEU
Chi-restraints excluded: chain B residue 1543 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 150 optimal weight:    0.9980
   chunk 196 optimal weight:    5.9990
   chunk 88 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 58 optimal weight:   20.0000
   chunk 136 optimal weight:    0.2980
   chunk 176 optimal weight:    8.9990
   chunk 92 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    2.6586

-------------------------------------------------------------------------------
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 998 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.180591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.141696 restraints weight = 20008.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.139242 restraints weight = 12555.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.140396 restraints weight = 14719.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16409  Z= 0.185
  Angle     :  0.602  11.046  22223  Z= 0.297
  Chirality :  0.042   0.255   2506
  Planarity :  0.005   0.102   2908
  Dihedral  :  4.178  42.280   2216
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.43 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.19), residues: 2008
  helix:  2.36 (0.15), residues: 1114
  sheet: -0.74 (0.49), residues: 103
  loop : -0.89 (0.23), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A  40 
 PHE   0.025   0.001   PHE A 742 
 TYR   0.024   0.001   TYR A 546 
 ARG   0.010   0.001   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04682 (  876)
  hydrogen bonds       : angle       3.98545 ( 2562)
  SS BOND              : bond        0.00419 (    1)
  SS BOND              : angle       0.95733 (    2)
  covalent geometry    : bond        0.00445 (16408)
  covalent geometry    : angle       0.60231 (22221)

*********************** 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
  438 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 387
  time to evaluate  : 1.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8720 (t70) cc_final: 0.8348 (t0)
REVERT: A  328 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7072 (mm-30)
REVERT: A  338 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7344 (mt-10)
REVERT: A  518 ASN cc_start: 0.8540 (m-40) cc_final: 0.8078 (m110)
REVERT: A  549 LYS cc_start: 0.8429 (mmpt) cc_final: 0.7635 (mmpt)
REVERT: A  628 SER cc_start: 0.8297 (m) cc_final: 0.8025 (p)
REVERT: A  639 LYS cc_start: 0.8207 (tppt) cc_final: 0.7773 (tppt)
REVERT: A  671 TYR cc_start: 0.8974 (m-80) cc_final: 0.8617 (m-80)
REVERT: A  717 HIS cc_start: 0.7974 (t-90) cc_final: 0.7734 (t-90)
REVERT: A  725 PHE cc_start: 0.6963 (p90) cc_final: 0.6703 (p90)
REVERT: B  139 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8493 (mm-30)
REVERT: B  352 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7259 (ttt-90)
REVERT: B  509 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.6396 (mtp85)
REVERT: B  598 ASN cc_start: 0.8594 (m-40) cc_final: 0.8201 (m-40)
REVERT: B  899 MET cc_start: 0.8165 (tmm) cc_final: 0.7823 (ppp)
REVERT: B 1102 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7811 (m-30)
REVERT: B 1116 ASP cc_start: 0.7747 (t0) cc_final: 0.7412 (t0)
REVERT: B 1121 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7554 (m-30)
REVERT: B 1159 ARG cc_start: 0.6912 (ttm-80) cc_final: 0.6702 (ttm-80)
REVERT: B 1658 ASP cc_start: 0.8092 (t0) cc_final: 0.7887 (t0)
  outliers start: 51
  outliers final: 44
  residues processed: 416
  average time/residue: 0.3280
  time to fit residues: 196.2115
Evaluate side-chains
  411 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 365
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
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  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  669 THR
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1004 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  870 THR
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  885 THR
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 1235 VAL
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Chi-restraints excluded: chain B residue 1506 LEU
Chi-restraints excluded: chain B residue 1543 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 141 optimal weight:    8.9990
   chunk 114 optimal weight:    0.0270
   chunk 167 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 128 optimal weight:    0.4980
   chunk 25 optimal weight:    6.9990
   chunk 142 optimal weight:    5.9990
   chunk 179 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    2.3044

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.180752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.141812 restraints weight = 19994.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.139851 restraints weight = 12348.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.140670 restraints weight = 14973.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16409  Z= 0.167
  Angle     :  0.594  11.676  22223  Z= 0.294
  Chirality :  0.042   0.249   2506
  Planarity :  0.005   0.084   2908
  Dihedral  :  4.177  39.133   2216
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.71 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.19), residues: 2008
  helix:  2.32 (0.15), residues: 1117
  sheet: -0.76 (0.49), residues: 103
  loop : -0.86 (0.23), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A  40 
 PHE   0.026   0.001   PHE A 742 
 TYR   0.023   0.001   TYR A 546 
 ARG   0.011   0.001   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  876)
  hydrogen bonds       : angle       3.96782 ( 2562)
  SS BOND              : bond        0.00420 (    1)
  SS BOND              : angle       0.82808 (    2)
  covalent geometry    : bond        0.00401 (16408)
  covalent geometry    : angle       0.59391 (22221)

********************** 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
  429 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 383
  time to evaluate  : 1.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8705 (t70) cc_final: 0.8342 (t0)
REVERT: A  328 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7235 (mm-30)
REVERT: A  338 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: A  518 ASN cc_start: 0.8532 (m-40) cc_final: 0.8088 (m110)
REVERT: A  527 ASN cc_start: 0.8822 (t0) cc_final: 0.8618 (t0)
REVERT: A  628 SER cc_start: 0.8291 (m) cc_final: 0.8022 (p)
REVERT: A  639 LYS cc_start: 0.8200 (tppt) cc_final: 0.7753 (tppt)
REVERT: A  671 TYR cc_start: 0.8945 (m-80) cc_final: 0.8576 (m-80)
REVERT: A  717 HIS cc_start: 0.7993 (t-90) cc_final: 0.7593 (t-90)
REVERT: A  725 PHE cc_start: 0.7024 (p90) cc_final: 0.6735 (p90)
REVERT: A  999 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7964 (ttp80)
REVERT: B  139 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8444 (mm-30)
REVERT: B  352 ARG cc_start: 0.7570 (ttt-90) cc_final: 0.7245 (ttt-90)
REVERT: B  509 ARG cc_start: 0.6766 (ttm-80) cc_final: 0.6394 (mtp85)
REVERT: B  598 ASN cc_start: 0.8590 (m-40) cc_final: 0.8177 (m-40)
REVERT: B  621 THR cc_start: 0.5231 (OUTLIER) cc_final: 0.5017 (m)
REVERT: B  646 ASP cc_start: 0.8021 (p0) cc_final: 0.7646 (p0)
REVERT: B 1102 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7761 (m-30)
REVERT: B 1104 ASP cc_start: 0.8541 (m-30) cc_final: 0.8288 (m-30)
REVERT: B 1116 ASP cc_start: 0.7761 (t0) cc_final: 0.7428 (t0)
REVERT: B 1121 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7544 (m-30)
REVERT: B 1253 ASP cc_start: 0.8651 (t0) cc_final: 0.7850 (m-30)
REVERT: B 1658 ASP cc_start: 0.8101 (t0) cc_final: 0.7813 (t0)
  outliers start: 46
  outliers final: 41
  residues processed: 409
  average time/residue: 0.2999
  time to fit residues: 178.0859
Evaluate side-chains
  408 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 364
  time to evaluate  : 1.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  248 LEU
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  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 1004 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain A residue 1065 TYR
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  870 THR
Chi-restraints excluded: chain B residue  871 VAL
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 1235 VAL
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Chi-restraints excluded: chain B residue 1543 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 163 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 198 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 154 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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 224 ASN
** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.178987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.139032 restraints weight = 19925.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.138551 restraints weight = 13285.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.139186 restraints weight = 14735.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  16409  Z= 0.199
  Angle     :  0.629  11.734  22223  Z= 0.310
  Chirality :  0.043   0.244   2506
  Planarity :  0.005   0.101   2908
  Dihedral  :  4.241  43.475   2216
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.77 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.19), residues: 2008
  helix:  2.26 (0.15), residues: 1116
  sheet: -0.77 (0.48), residues: 103
  loop : -0.90 (0.23), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A  40 
 PHE   0.025   0.002   PHE A 742 
 TYR   0.022   0.002   TYR A 546 
 ARG   0.010   0.001   ARG B 717 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04855 (  876)
  hydrogen bonds       : angle       4.07610 ( 2562)
  SS BOND              : bond        0.00395 (    1)
  SS BOND              : angle       0.93335 (    2)
  covalent geometry    : bond        0.00482 (16408)
  covalent geometry    : angle       0.62942 (22221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5857.78 seconds
wall clock time: 102 minutes 54.35 seconds (6174.35 seconds total)