Starting phenix.real_space_refine
on Sat Jun 14 14:12:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3a_62011/06_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_62011/06_2025/9k3a_62011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3a_62011/06_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-5710/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: 9.06, per 1000 atoms: 0.56
  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: 3.91
  Conformation dependent library (CDL) restraints added in 2.2 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: 2.06
  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: 6.07

  Time building geometry restraints manager: 4.54 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.160
  Process input model:                     38.370
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.850
-------------------------------------------------------------------------------
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  : 1.781 
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: 0.3233
  time to fit residues: 193.7838
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  : 1.624 
-------------------------------------------------------------------------------
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 = 19593.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.127799 restraints weight = 14181.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.128651 restraints weight = 15203.604|
|-----------------------------------------------------------------------------|
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  : 1.864 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8614 (t70) cc_final: 0.8271 (t0)
REVERT: A  328 GLU cc_start: 0.7919 (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: 0.6748 (pt0)
REVERT: B 1584 ASP cc_start: 0.8402 (p0) cc_final: 0.8109 (p0)
REVERT: B 1658 ASP cc_start: 0.7733 (t0) cc_final: 0.7464 (t0)
  outliers start: 44
  outliers final: 29
  residues processed: 439
  average time/residue: 0.2993
  time to fit residues: 191.2206
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  : 1.667 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 138 optimal weight:   10.0000
   chunk 99 optimal weight:    2.9990
   chunk 201 optimal weight:    5.9990
   chunk 180 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 178 optimal weight:    3.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 527 ASN
A 538 HIS
B 187 GLN
B 194 ASN
B 222 ASN
B 348 ASN
B 998 ASN
B1602 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.170330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.130570 restraints weight = 19767.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.130365 restraints weight = 12487.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.130574 restraints weight = 14494.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  16409  Z= 0.192
  Angle     :  0.593  12.780  22223  Z= 0.297
  Chirality :  0.042   0.172   2506
  Planarity :  0.005   0.089   2908
  Dihedral  :  4.711  88.043   2218
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.95 %
    Favored  : 79.76 %
  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:  1.24 (0.19), residues: 2008
  helix:  2.18 (0.15), residues: 1129
  sheet: -0.45 (0.55), residues: 92
  loop : -1.09 (0.22), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 424 
 HIS   0.006   0.001   HIS A  40 
 PHE   0.016   0.001   PHE A 742 
 TYR   0.015   0.002   TYR B 466 
 ARG   0.010   0.001   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04935 (  876)
  hydrogen bonds       : angle       4.14793 ( 2562)
  SS BOND              : bond        0.00371 (    1)
  SS BOND              : angle       1.18398 (    2)
  covalent geometry    : bond        0.00463 (16408)
  covalent geometry    : angle       0.59253 (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
  475 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 417
  time to evaluate  : 1.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8628 (t70) cc_final: 0.8357 (t70)
REVERT: A  328 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7712 (mm-30)
REVERT: A  518 ASN cc_start: 0.8644 (m-40) cc_final: 0.8252 (m110)
REVERT: A  639 LYS cc_start: 0.8139 (tppt) cc_final: 0.7622 (tppt)
REVERT: B  509 ARG cc_start: 0.6535 (ttm-80) cc_final: 0.6204 (mtp85)
REVERT: B  881 ASP cc_start: 0.7506 (m-30) cc_final: 0.7251 (m-30)
REVERT: B 1104 ASP cc_start: 0.8453 (m-30) cc_final: 0.8238 (m-30)
REVERT: B 1116 ASP cc_start: 0.7620 (t0) cc_final: 0.7202 (t0)
REVERT: B 1121 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7585 (m-30)
REVERT: B 1181 GLU cc_start: 0.7266 (pt0) cc_final: 0.6851 (pt0)
REVERT: B 1492 ASP cc_start: 0.7899 (t0) cc_final: 0.7698 (t70)
  outliers start: 58
  outliers final: 34
  residues processed: 448
  average time/residue: 0.3155
  time to fit residues: 206.0878
Evaluate side-chains
  440 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 405
  time to evaluate  : 1.880 
-------------------------------------------------------------------------------
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  870 THR
Chi-restraints excluded: chain B residue  998 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
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:    0.6980
   chunk 167 optimal weight:    5.9990
   chunk 187 optimal weight:    6.9990
   chunk 136 optimal weight:    0.0170
   chunk 16 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 137 optimal weight:    7.9990
   chunk 93 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   overall best weight:    1.0420

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.173245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.132675 restraints weight = 19778.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.132508 restraints weight = 13668.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.132937 restraints weight = 12588.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  16409  Z= 0.120
  Angle     :  0.539  11.255  22223  Z= 0.271
  Chirality :  0.040   0.215   2506
  Planarity :  0.005   0.078   2908
  Dihedral  :  4.532  89.288   2218
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.03 %
    Favored  : 79.14 %
  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:  1.47 (0.19), residues: 2008
  helix:  2.35 (0.15), residues: 1128
  sheet: -0.52 (0.51), residues: 103
  loop : -0.95 (0.23), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 424 
 HIS   0.004   0.001   HIS A 717 
 PHE   0.015   0.001   PHE A 742 
 TYR   0.021   0.001   TYR B 466 
 ARG   0.010   0.000   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04294 (  876)
  hydrogen bonds       : angle       3.92224 ( 2562)
  SS BOND              : bond        0.00397 (    1)
  SS BOND              : angle       1.03680 (    2)
  covalent geometry    : bond        0.00277 (16408)
  covalent geometry    : angle       0.53916 (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
  464 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 414
  time to evaluate  : 1.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8628 (t70) cc_final: 0.8297 (t0)
REVERT: A  156 MET cc_start: 0.7665 (tpp) cc_final: 0.7425 (tmm)
REVERT: A  438 GLU cc_start: 0.7467 (mp0) cc_final: 0.7236 (mp0)
REVERT: A  518 ASN cc_start: 0.8555 (m-40) cc_final: 0.8093 (m110)
REVERT: A  527 ASN cc_start: 0.8759 (t0) cc_final: 0.8537 (t0)
REVERT: A  639 LYS cc_start: 0.8198 (tppt) cc_final: 0.7716 (tppt)
REVERT: A  747 MET cc_start: 0.8220 (tpp) cc_final: 0.7895 (tpp)
REVERT: B  509 ARG cc_start: 0.6552 (ttm-80) cc_final: 0.6197 (mtp85)
REVERT: B  881 ASP cc_start: 0.7531 (m-30) cc_final: 0.7260 (m-30)
REVERT: B 1104 ASP cc_start: 0.8464 (m-30) cc_final: 0.8229 (m-30)
REVERT: B 1116 ASP cc_start: 0.7628 (t0) cc_final: 0.7125 (t0)
REVERT: B 1121 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7631 (m-30)
REVERT: B 1177 GLU cc_start: 0.6612 (pp20) cc_final: 0.5961 (pp20)
REVERT: B 1181 GLU cc_start: 0.7290 (pt0) cc_final: 0.6205 (pt0)
REVERT: B 1253 ASP cc_start: 0.8563 (t0) cc_final: 0.7781 (m-30)
  outliers start: 50
  outliers final: 34
  residues processed: 443
  average time/residue: 0.3062
  time to fit residues: 199.3266
Evaluate side-chains
  432 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 397
  time to evaluate  : 1.662 
-------------------------------------------------------------------------------
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  320 ASN
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  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  200 SER
Chi-restraints excluded: chain B residue  244 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  871 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 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 126 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 59 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0070
   chunk 7 optimal weight:    4.9990
   chunk 167 optimal weight:    4.9990
   chunk 176 optimal weight:    5.9990
   chunk 163 optimal weight:   50.0000
   chunk 86 optimal weight:   10.0000
   chunk 169 optimal weight:    0.8980
   overall best weight:    3.3804

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 ASN
B 187 GLN
B 194 ASN
B 222 ASN
** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 969 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.164243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.124309 restraints weight = 20178.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.123767 restraints weight = 13146.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.124310 restraints weight = 15373.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  16409  Z= 0.223
  Angle     :  0.613  12.377  22223  Z= 0.305
  Chirality :  0.043   0.190   2506
  Planarity :  0.005   0.101   2908
  Dihedral  :  4.512  78.060   2217
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.22 %
    Favored  : 77.55 %
  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:  1.28 (0.19), residues: 2008
  helix:  2.21 (0.15), residues: 1125
  sheet: -0.66 (0.53), residues: 93
  loop : -1.03 (0.22), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 711 
 HIS   0.007   0.001   HIS A  40 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.016   0.002   TYR B 466 
 ARG   0.011   0.001   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05032 (  876)
  hydrogen bonds       : angle       4.11155 ( 2562)
  SS BOND              : bond        0.00373 (    1)
  SS BOND              : angle       1.07943 (    2)
  covalent geometry    : bond        0.00536 (16408)
  covalent geometry    : angle       0.61342 (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
  475 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 418
  time to evaluate  : 1.682 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8640 (t70) cc_final: 0.8382 (t70)
REVERT: A  161 MET cc_start: 0.8268 (pmm) cc_final: 0.7612 (pmm)
REVERT: A  338 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7475 (mt-10)
REVERT: A  397 GLU cc_start: 0.8495 (tp30) cc_final: 0.8203 (tm-30)
REVERT: A  510 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7042 (mmp-170)
REVERT: A  518 ASN cc_start: 0.8550 (m-40) cc_final: 0.8128 (m110)
REVERT: A  527 ASN cc_start: 0.8940 (t0) cc_final: 0.8466 (t0)
REVERT: A  628 SER cc_start: 0.8254 (m) cc_final: 0.7990 (p)
REVERT: A  639 LYS cc_start: 0.8169 (tppt) cc_final: 0.7651 (tppt)
REVERT: A  671 TYR cc_start: 0.9129 (m-80) cc_final: 0.8612 (m-80)
REVERT: B  509 ARG cc_start: 0.6631 (ttm-80) cc_final: 0.6221 (mtp85)
REVERT: B  616 PHE cc_start: 0.6648 (m-80) cc_final: 0.6439 (m-80)
REVERT: B  717 ARG cc_start: 0.8037 (mtp-110) cc_final: 0.7614 (mtp-110)
REVERT: B  879 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8906 (tt)
REVERT: B  881 ASP cc_start: 0.7498 (m-30) cc_final: 0.7264 (m-30)
REVERT: B  899 MET cc_start: 0.8284 (tmm) cc_final: 0.7986 (ppp)
REVERT: B  917 ASP cc_start: 0.7634 (t0) cc_final: 0.7277 (t0)
REVERT: B 1116 ASP cc_start: 0.7733 (t0) cc_final: 0.7196 (t0)
REVERT: B 1121 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7550 (m-30)
REVERT: B 1156 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8141 (ttp-110)
REVERT: B 1181 GLU cc_start: 0.7339 (pt0) cc_final: 0.6953 (pt0)
REVERT: B 1522 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8566 (mtpt)
  outliers start: 57
  outliers final: 38
  residues processed: 449
  average time/residue: 0.3084
  time to fit residues: 202.2845
Evaluate side-chains
  436 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 396
  time to evaluate  : 1.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLN
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  226 ASP
Chi-restraints excluded: chain A residue  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  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  992 VAL
Chi-restraints excluded: chain A residue 1010 THR
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1271 SER
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 162 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 157 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 188 optimal weight:    6.9990
   chunk 164 optimal weight:    5.9990
   chunk 169 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0980
   overall best weight:    1.8188

-------------------------------------------------------------------------------
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
A 841 ASN
B 194 ASN
B1131 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.168109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.127072 restraints weight = 20016.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.127462 restraints weight = 13588.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.127666 restraints weight = 12767.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16409  Z= 0.142
  Angle     :  0.562  11.524  22223  Z= 0.279
  Chirality :  0.041   0.327   2506
  Planarity :  0.005   0.080   2908
  Dihedral  :  4.326  68.975   2216
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.56 %
    Favored  : 77.44 %
  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:  1.45 (0.19), residues: 2008
  helix:  2.35 (0.15), residues: 1124
  sheet: -0.68 (0.53), residues: 93
  loop : -0.94 (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 468 
 PHE   0.013   0.001   PHE A 742 
 TYR   0.022   0.001   TYR A 546 
 ARG   0.006   0.000   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 (  876)
  hydrogen bonds       : angle       3.92350 ( 2562)
  SS BOND              : bond        0.00384 (    1)
  SS BOND              : angle       0.97688 (    2)
  covalent geometry    : bond        0.00337 (16408)
  covalent geometry    : angle       0.56156 (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
  457 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 404
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8672 (t70) cc_final: 0.8318 (t0)
REVERT: A  438 GLU cc_start: 0.7539 (mp0) cc_final: 0.7220 (mp0)
REVERT: A  518 ASN cc_start: 0.8538 (m-40) cc_final: 0.8091 (m110)
REVERT: A  527 ASN cc_start: 0.8787 (t0) cc_final: 0.8347 (t0)
REVERT: A  628 SER cc_start: 0.8246 (m) cc_final: 0.7969 (p)
REVERT: A  639 LYS cc_start: 0.8196 (tppt) cc_final: 0.7652 (tppt)
REVERT: A  747 MET cc_start: 0.8265 (tpp) cc_final: 0.7974 (tpp)
REVERT: B  509 ARG cc_start: 0.6663 (ttm-80) cc_final: 0.6168 (mtp85)
REVERT: B  598 ASN cc_start: 0.8583 (m-40) cc_final: 0.8229 (m-40)
REVERT: B  646 ASP cc_start: 0.7693 (p0) cc_final: 0.7425 (p0)
REVERT: B  704 ASP cc_start: 0.8669 (t70) cc_final: 0.8401 (t0)
REVERT: B  879 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8887 (tt)
REVERT: B  881 ASP cc_start: 0.7572 (m-30) cc_final: 0.7284 (m-30)
REVERT: B 1104 ASP cc_start: 0.8457 (m-30) cc_final: 0.8172 (m-30)
REVERT: B 1116 ASP cc_start: 0.7701 (t0) cc_final: 0.7142 (t0)
REVERT: B 1121 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7659 (m-30)
REVERT: B 1181 GLU cc_start: 0.7390 (pt0) cc_final: 0.7068 (pt0)
REVERT: B 1253 ASP cc_start: 0.8567 (t0) cc_final: 0.7765 (m-30)
REVERT: B 1492 ASP cc_start: 0.7973 (t0) cc_final: 0.7762 (t70)
REVERT: B 1522 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8613 (mtpt)
  outliers start: 53
  outliers final: 38
  residues processed: 433
  average time/residue: 0.3098
  time to fit residues: 196.1201
Evaluate side-chains
  430 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 390
  time to evaluate  : 1.748 
-------------------------------------------------------------------------------
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  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  547 LEU
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  920 MET
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  194 ASN
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  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1271 SER
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 194 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 158 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 151 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 137 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 107 optimal weight:    0.0470
   chunk 181 optimal weight:   10.0000
   chunk 195 optimal weight:    1.9990
   overall best weight:    1.3282

-------------------------------------------------------------------------------
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 194 ASN
** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 998 ASN
B1131 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.170527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.131213 restraints weight = 20030.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.129130 restraints weight = 15222.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.131130 restraints weight = 13928.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2283

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= 0.127
  Angle     :  0.555  10.771  22223  Z= 0.274
  Chirality :  0.040   0.274   2506
  Planarity :  0.005   0.090   2908
  Dihedral  :  4.182  59.879   2216
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.61 %
    Favored  : 77.49 %
  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:  1.59 (0.20), residues: 2008
  helix:  2.47 (0.15), residues: 1116
  sheet: -0.70 (0.49), residues: 103
  loop : -0.83 (0.23), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A 717 
 PHE   0.028   0.001   PHE A 742 
 TYR   0.017   0.001   TYR A 546 
 ARG   0.007   0.000   ARG B 717 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04265 (  876)
  hydrogen bonds       : angle       3.82694 ( 2562)
  SS BOND              : bond        0.00416 (    1)
  SS BOND              : angle       0.93733 (    2)
  covalent geometry    : bond        0.00296 (16408)
  covalent geometry    : angle       0.55466 (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
  452 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 401
  time to evaluate  : 1.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8657 (t70) cc_final: 0.8256 (t0)
REVERT: A  338 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7372 (mt-10)
REVERT: A  518 ASN cc_start: 0.8577 (m-40) cc_final: 0.8131 (m110)
REVERT: A  527 ASN cc_start: 0.8725 (t0) cc_final: 0.8411 (t0)
REVERT: A  549 LYS cc_start: 0.8662 (mmpt) cc_final: 0.8097 (mmpt)
REVERT: A  639 LYS cc_start: 0.8216 (tppt) cc_final: 0.7792 (tppt)
REVERT: B  509 ARG cc_start: 0.6559 (ttm-80) cc_final: 0.6115 (mtp85)
REVERT: B  598 ASN cc_start: 0.8630 (m-40) cc_final: 0.8149 (m-40)
REVERT: B  879 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8889 (tt)
REVERT: B  881 ASP cc_start: 0.7459 (m-30) cc_final: 0.7190 (m-30)
REVERT: B  899 MET cc_start: 0.8148 (tmm) cc_final: 0.7828 (ppp)
REVERT: B 1065 ARG cc_start: 0.8619 (ptp-170) cc_final: 0.8275 (mtt180)
REVERT: B 1078 TYR cc_start: 0.9363 (t80) cc_final: 0.9156 (t80)
REVERT: B 1116 ASP cc_start: 0.7655 (t0) cc_final: 0.7106 (t0)
REVERT: B 1121 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7744 (m-30)
REVERT: B 1181 GLU cc_start: 0.7322 (pt0) cc_final: 0.7014 (pt0)
REVERT: B 1253 ASP cc_start: 0.8570 (t0) cc_final: 0.7785 (m-30)
REVERT: B 1522 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8623 (mtpt)
  outliers start: 51
  outliers final: 37
  residues processed: 433
  average time/residue: 0.3176
  time to fit residues: 201.3007
Evaluate side-chains
  425 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 386
  time to evaluate  : 1.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  194 ASN
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue  998 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 1202 ASP
Chi-restraints excluded: chain B residue 1256 SER
Chi-restraints excluded: chain B residue 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 199 optimal weight:    2.9990
   chunk 116 optimal weight:    6.9990
   chunk 84 optimal weight:   10.0000
   chunk 100 optimal weight:    0.0070
   chunk 154 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.9378

-------------------------------------------------------------------------------
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 538 HIS
A 841 ASN
B 187 GLN
B 194 ASN
B1131 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.172869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.131811 restraints weight = 19911.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.133005 restraints weight = 13668.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.133312 restraints weight = 12573.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16409  Z= 0.116
  Angle     :  0.551  10.382  22223  Z= 0.273
  Chirality :  0.040   0.259   2506
  Planarity :  0.005   0.077   2908
  Dihedral  :  4.098  53.839   2216
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.18 %
    Favored  : 77.21 %
  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:  1.69 (0.20), residues: 2008
  helix:  2.55 (0.15), residues: 1112
  sheet: -0.64 (0.49), residues: 103
  loop : -0.76 (0.23), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A 717 
 PHE   0.026   0.001   PHE A 742 
 TYR   0.014   0.001   TYR A 546 
 ARG   0.008   0.000   ARG A 999 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  876)
  hydrogen bonds       : angle       3.76191 ( 2562)
  SS BOND              : bond        0.00419 (    1)
  SS BOND              : angle       0.86603 (    2)
  covalent geometry    : bond        0.00267 (16408)
  covalent geometry    : angle       0.55107 (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
  441 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 395
  time to evaluate  : 1.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8658 (t70) cc_final: 0.8244 (t0)
REVERT: A  438 GLU cc_start: 0.7604 (mp0) cc_final: 0.7348 (mp0)
REVERT: A  518 ASN cc_start: 0.8580 (m-40) cc_final: 0.8093 (m110)
REVERT: A  527 ASN cc_start: 0.8666 (t0) cc_final: 0.8396 (t0)
REVERT: A  549 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8101 (mmpt)
REVERT: A  639 LYS cc_start: 0.8176 (tppt) cc_final: 0.7757 (tppt)
REVERT: A  747 MET cc_start: 0.8235 (tpp) cc_final: 0.7900 (tpp)
REVERT: A  834 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7921 (m-30)
REVERT: A  999 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8074 (ttp80)
REVERT: A 1047 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7276 (mm-30)
REVERT: B  509 ARG cc_start: 0.6527 (ttm-80) cc_final: 0.6105 (mtp85)
REVERT: B  598 ASN cc_start: 0.8618 (m-40) cc_final: 0.8242 (m-40)
REVERT: B  879 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8833 (tt)
REVERT: B  881 ASP cc_start: 0.7477 (m-30) cc_final: 0.7192 (m-30)
REVERT: B  899 MET cc_start: 0.8196 (tmm) cc_final: 0.7865 (ppp)
REVERT: B 1078 TYR cc_start: 0.9349 (t80) cc_final: 0.9115 (t80)
REVERT: B 1116 ASP cc_start: 0.7636 (t0) cc_final: 0.7088 (t0)
REVERT: B 1121 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7924 (m-30)
REVERT: B 1181 GLU cc_start: 0.7244 (pt0) cc_final: 0.6935 (pt0)
REVERT: B 1425 TYR cc_start: 0.8817 (m-80) cc_final: 0.8552 (m-80)
REVERT: B 1522 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8600 (mtpt)
  outliers start: 46
  outliers final: 38
  residues processed: 422
  average time/residue: 0.3202
  time to fit residues: 198.0543
Evaluate side-chains
  424 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 383
  time to evaluate  : 1.742 
-------------------------------------------------------------------------------
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  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  834 ASP
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  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  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue 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 1484 LEU
Chi-restraints excluded: chain B residue 1490 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 150 optimal weight:    0.4980
   chunk 196 optimal weight:    6.9990
   chunk 88 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 110 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 136 optimal weight:    0.8980
   chunk 176 optimal weight:    6.9990
   chunk 92 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   overall best weight:    2.8786

-------------------------------------------------------------------------------
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 744 ASN
A 841 ASN
B 187 GLN
B 194 ASN
B 998 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.160626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.122259 restraints weight = 19868.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.122936 restraints weight = 15658.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.123243 restraints weight = 16431.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  16409  Z= 0.198
  Angle     :  0.615  11.218  22223  Z= 0.304
  Chirality :  0.043   0.254   2506
  Planarity :  0.005   0.102   2908
  Dihedral  :  4.171  42.951   2216
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.24 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (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:  1.54 (0.19), residues: 2008
  helix:  2.43 (0.15), residues: 1112
  sheet: -0.68 (0.49), residues: 103
  loop : -0.83 (0.23), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 711 
 HIS   0.004   0.001   HIS B1267 
 PHE   0.021   0.002   PHE A 742 
 TYR   0.016   0.002   TYR B1550 
 ARG   0.009   0.001   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04783 (  876)
  hydrogen bonds       : angle       3.99352 ( 2562)
  SS BOND              : bond        0.00423 (    1)
  SS BOND              : angle       1.03546 (    2)
  covalent geometry    : bond        0.00477 (16408)
  covalent geometry    : angle       0.61529 (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
  463 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 407
  time to evaluate  : 1.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8708 (t70) cc_final: 0.8323 (t0)
REVERT: A  338 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7308 (mt-10)
REVERT: A  397 GLU cc_start: 0.8500 (tp30) cc_final: 0.7835 (tm-30)
REVERT: A  518 ASN cc_start: 0.8507 (m-40) cc_final: 0.8060 (m110)
REVERT: A  527 ASN cc_start: 0.8833 (t0) cc_final: 0.8292 (t0)
REVERT: A  549 LYS cc_start: 0.8691 (mmpt) cc_final: 0.8103 (mmpt)
REVERT: A  628 SER cc_start: 0.8266 (m) cc_final: 0.8031 (p)
REVERT: A  639 LYS cc_start: 0.8228 (tppt) cc_final: 0.7794 (tppt)
REVERT: A  671 TYR cc_start: 0.9152 (m-80) cc_final: 0.8561 (m-80)
REVERT: A  747 MET cc_start: 0.8323 (tpp) cc_final: 0.8001 (tpp)
REVERT: A  834 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7927 (m-30)
REVERT: A  999 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8066 (ttp80)
REVERT: B  139 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8506 (mm-30)
REVERT: B  509 ARG cc_start: 0.6759 (ttm-80) cc_final: 0.6338 (mtp85)
REVERT: B  598 ASN cc_start: 0.8577 (m-40) cc_final: 0.8200 (m-40)
REVERT: B  879 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8961 (tt)
REVERT: B  881 ASP cc_start: 0.7452 (m-30) cc_final: 0.7228 (m-30)
REVERT: B 1065 ARG cc_start: 0.8623 (ptp-170) cc_final: 0.8311 (mtt180)
REVERT: B 1078 TYR cc_start: 0.9389 (t80) cc_final: 0.9122 (t80)
REVERT: B 1104 ASP cc_start: 0.8531 (m-30) cc_final: 0.8157 (m-30)
REVERT: B 1116 ASP cc_start: 0.7798 (t0) cc_final: 0.7454 (t0)
REVERT: B 1121 ASP cc_start: 0.7986 (m-30) cc_final: 0.7596 (m-30)
REVERT: B 1181 GLU cc_start: 0.7275 (pt0) cc_final: 0.6972 (pt0)
REVERT: B 1522 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8658 (mtpt)
  outliers start: 56
  outliers final: 46
  residues processed: 441
  average time/residue: 0.3107
  time to fit residues: 200.1076
Evaluate side-chains
  434 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 386
  time to evaluate  : 1.801 
-------------------------------------------------------------------------------
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  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  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  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  834 ASP
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  244 SER
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  998 ASN
Chi-restraints excluded: chain B residue 1018 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 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 1632 THR
Chi-restraints excluded: chain B residue 1687 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 141 optimal weight:    8.9990
   chunk 114 optimal weight:    0.9980
   chunk 167 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 128 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 142 optimal weight:    8.9990
   chunk 179 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.5382

-------------------------------------------------------------------------------
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
A 744 ASN
A 841 ASN
B 187 GLN
B 194 ASN
B 969 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.182676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.142902 restraints weight = 19910.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.141260 restraints weight = 13041.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.142267 restraints weight = 14612.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16409  Z= 0.140
  Angle     :  0.582  11.385  22223  Z= 0.288
  Chirality :  0.041   0.242   2506
  Planarity :  0.005   0.078   2908
  Dihedral  :  4.128  40.239   2216
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.75 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.94 %
    Twisted General : 0.00 %

Rama-Z (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:  1.63 (0.19), residues: 2008
  helix:  2.50 (0.15), residues: 1111
  sheet: -0.67 (0.48), residues: 103
  loop : -0.78 (0.23), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A 717 
 PHE   0.024   0.001   PHE A 742 
 TYR   0.030   0.001   TYR A 546 
 ARG   0.008   0.000   ARG B1626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (  876)
  hydrogen bonds       : angle       3.89830 ( 2562)
  SS BOND              : bond        0.00447 (    1)
  SS BOND              : angle       0.94787 (    2)
  covalent geometry    : bond        0.00327 (16408)
  covalent geometry    : angle       0.58201 (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
  433 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 386
  time to evaluate  : 1.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.8646 (t70) cc_final: 0.8277 (t0)
REVERT: A  328 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7251 (mm-30)
REVERT: A  518 ASN cc_start: 0.8542 (m-40) cc_final: 0.8117 (m110)
REVERT: A  527 ASN cc_start: 0.8799 (t0) cc_final: 0.8231 (t0)
REVERT: A  549 LYS cc_start: 0.8717 (mmpt) cc_final: 0.8092 (mmpt)
REVERT: A  628 SER cc_start: 0.8201 (m) cc_final: 0.7960 (p)
REVERT: A  639 LYS cc_start: 0.8204 (tppt) cc_final: 0.7773 (tppt)
REVERT: A  747 MET cc_start: 0.8303 (tpp) cc_final: 0.7982 (tpp)
REVERT: A  834 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7977 (m-30)
REVERT: A  999 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8093 (ttp80)
REVERT: B  139 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8459 (mm-30)
REVERT: B  509 ARG cc_start: 0.6683 (ttm-80) cc_final: 0.6281 (mtp85)
REVERT: B  598 ASN cc_start: 0.8579 (m-40) cc_final: 0.8188 (m-40)
REVERT: B  879 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8910 (tt)
REVERT: B  881 ASP cc_start: 0.7398 (m-30) cc_final: 0.7183 (m-30)
REVERT: B 1065 ARG cc_start: 0.8595 (ptp-170) cc_final: 0.8273 (mtt180)
REVERT: B 1078 TYR cc_start: 0.9362 (t80) cc_final: 0.9105 (t80)
REVERT: B 1104 ASP cc_start: 0.8479 (m-30) cc_final: 0.8102 (m-30)
REVERT: B 1116 ASP cc_start: 0.7727 (t0) cc_final: 0.7326 (t0)
REVERT: B 1121 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7623 (m-30)
REVERT: B 1181 GLU cc_start: 0.7278 (pt0) cc_final: 0.6982 (pt0)
REVERT: B 1253 ASP cc_start: 0.8644 (t0) cc_final: 0.7840 (m-30)
REVERT: B 1658 ASP cc_start: 0.8181 (t0) cc_final: 0.7897 (t0)
  outliers start: 47
  outliers final: 41
  residues processed: 416
  average time/residue: 0.3380
  time to fit residues: 205.8678
Evaluate side-chains
  425 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 381
  time to evaluate  : 1.719 
-------------------------------------------------------------------------------
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  638 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  834 ASP
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  244 SER
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  621 THR
Chi-restraints excluded: chain B residue  629 GLU
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  871 VAL
Chi-restraints excluded: chain B residue  873 VAL
Chi-restraints excluded: chain B residue  879 LEU
Chi-restraints excluded: chain B residue  923 SER
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue 1018 ASN
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1121 ASP
Chi-restraints excluded: chain B residue 1154 GLU
Chi-restraints excluded: chain B residue 1179 LEU
Chi-restraints excluded: chain B residue 1200 VAL
Chi-restraints excluded: chain B residue 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 163 optimal weight:    0.0030
   chunk 12 optimal weight:    6.9990
   chunk 198 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 154 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 93 optimal weight:    0.4980
   overall best weight:    1.1992

-------------------------------------------------------------------------------
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 538 HIS
A 744 ASN
A 841 ASN
B 969 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.182669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.142942 restraints weight = 19760.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.141440 restraints weight = 12859.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.142254 restraints weight = 14773.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102  16409  Z= 0.171
  Angle     :  0.806  59.200  22223  Z= 0.453
  Chirality :  0.041   0.234   2506
  Planarity :  0.005   0.081   2908
  Dihedral  :  4.130  40.218   2216
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.98 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.05 %
  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:  1.64 (0.19), residues: 2008
  helix:  2.50 (0.15), residues: 1111
  sheet: -0.67 (0.48), residues: 103
  loop : -0.77 (0.23), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 711 
 HIS   0.004   0.001   HIS A 717 
 PHE   0.022   0.001   PHE A 742 
 TYR   0.025   0.001   TYR A 546 
 ARG   0.007   0.000   ARG A 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  876)
  hydrogen bonds       : angle       3.89730 ( 2562)
  SS BOND              : bond        0.00439 (    1)
  SS BOND              : angle       0.95208 (    2)
  covalent geometry    : bond        0.00359 (16408)
  covalent geometry    : angle       0.80606 (22221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6203.32 seconds
wall clock time: 108 minutes 26.73 seconds (6506.73 seconds total)