Starting phenix.real_space_refine
on Mon Jun 16 01:02:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pr3_17833/06_2025/8pr3_17833.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pr3_17833/06_2025/8pr3_17833.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pr3_17833/06_2025/8pr3_17833.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pr3_17833/06_2025/8pr3_17833.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pr3_17833/06_2025/8pr3_17833.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pr3_17833/06_2025/8pr3_17833.cif"
  }
  resolution = 3.9
  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=   0.001
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      72      5.16       5
     C   11319      2.51       5
     N    3146      2.21       5
     O    3351      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17888
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 880
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 1, 'TRANS': 103}
    Chain: "C"
      Number of atoms: 886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 886
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "f"
      Number of atoms: 3449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3449
          Classifications: {'peptide': 420}
          Link IDs: {'PTRANS': 12, 'TRANS': 407}
          Chain breaks: 1
    Chain: "h"
      Number of atoms: 2897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2897
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 17, 'TRANS': 353}
    Chain: "j"
      Number of atoms: 2428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2428
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 12, 'TRANS': 286}
          Chain breaks: 1
    Chain: "m"
      Number of atoms: 4321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4321
          Classifications: {'peptide': 523}
          Link IDs: {'PTRANS': 13, 'TRANS': 509}
          Chain breaks: 3
    Chain: "o"
      Number of atoms: 2897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2897
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 17, 'TRANS': 353}
    Chain: "E"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 65
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "F"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 65
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 10.77, per 1000 atoms: 0.60
  Number of scatterers: 17888
  At special positions: 0
  Unit cell: (119.667, 124.962, 173.676, 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      72     16.00
     O    3351      8.00
     N    3146      7.00
     C   11319      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.46
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4240

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 17 sheets defined
      51.9% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.80
  Creating SS restraints...
    Processing helix  chain 'B' and resid 26 through 47
    Processing helix  chain 'B' and resid 55 through 128
      removed outlier: 3.626A  pdb=" N   ASN B  61 " --> pdb=" O   PRO B  57 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL B  78 " --> pdb=" O   GLN B  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 47
    Processing helix  chain 'C' and resid 55 through 128
      removed outlier: 3.873A  pdb=" N   ASN C  61 " --> pdb=" O   PRO C  57 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   VAL C  62 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   THR C  92 " --> pdb=" O   GLU C  88 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS C 107 " --> pdb=" O   GLN C 103 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE C 109 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 561 through 572
    Processing helix  chain 'f' and resid 577 through 586
    Processing helix  chain 'f' and resid 588 through 592
      removed outlier: 3.578A  pdb=" N   LEU f 591 " --> pdb=" O   PHE f 588 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE f 592 " --> pdb=" O   ASN f 589 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'f' and resid 588 through 592'
    Processing helix  chain 'f' and resid 596 through 604
      removed outlier: 4.267A  pdb=" N   ALA f 600 " --> pdb=" O   HIS f 596 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 604 through 625
      removed outlier: 4.060A  pdb=" N   VAL f 625 " --> pdb=" O   ASP f 621 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 630 through 637
      removed outlier: 3.768A  pdb=" N   LYS f 634 " --> pdb=" O   SER f 630 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 642 through 670
    Processing helix  chain 'f' and resid 676 through 691
    Processing helix  chain 'f' and resid 692 through 694
      No H-bonds generated for 'chain 'f' and resid 692 through 694'
    Processing helix  chain 'f' and resid 695 through 710
      removed outlier: 3.509A  pdb=" N   PHE f 699 " --> pdb=" O   THR f 695 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 740 through 754
      removed outlier: 3.765A  pdb=" N   ILE f 744 " --> pdb=" O   LEU f 740 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 761 through 773
    Processing helix  chain 'f' and resid 774 through 798
      removed outlier: 3.571A  pdb=" N   ALA f 778 " --> pdb=" O   LEU f 774 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER f 780 " --> pdb=" O   PRO f 776 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG f 798 " --> pdb=" O   LYS f 794 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 799 through 804
      removed outlier: 3.740A  pdb=" N   SER f 802 " --> pdb=" O   ASN f 799 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   LEU f 803 " --> pdb=" O   THR f 800 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 805 through 820
    Processing helix  chain 'f' and resid 828 through 863
      removed outlier: 3.665A  pdb=" N   TYR f 832 " --> pdb=" O   LYS f 828 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL f 833 " --> pdb=" O   LEU f 829 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLN f 834 " --> pdb=" O   ASP f 830 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 870 through 891
      removed outlier: 3.705A  pdb=" N   HIS f 891 " --> pdb=" O   ASP f 887 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 895 through 923
      removed outlier: 3.661A  pdb=" N   GLU f 906 " --> pdb=" O   LYS f 902 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 986 through 995
      removed outlier: 3.926A  pdb=" N   LYS f 990 " --> pdb=" O   MET f 986 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   MET f 991 " --> pdb=" O   PHE f 987 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   VAL f 992 " --> pdb=" O   ALA f 988 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   VAL f 993 " --> pdb=" O   TRP f 989 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 1013 through 1018
    Processing helix  chain 'f' and resid 1030 through 1039
      removed outlier: 3.889A  pdb=" N   ALA f1039 " --> pdb=" O   GLU f1035 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 574 through 579
    Processing helix  chain 'h' and resid 583 through 608
      removed outlier: 3.917A  pdb=" N   GLU h 603 " --> pdb=" O   ARG h 599 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   GLU h 604 " --> pdb=" O   ALA h 600 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLU h 605 " --> pdb=" O   ASP h 601 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ALA h 606 " --> pdb=" O   ALA h 602 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 66 through 76
      removed outlier: 3.674A  pdb=" N   LYS j  73 " --> pdb=" O   THR j  69 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 112 through 117
      removed outlier: 4.691A  pdb=" N   GLY j 117 " --> pdb=" O   TYR j 114 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 118 through 123
      removed outlier: 3.654A  pdb=" N   ALA j 122 " --> pdb=" O   LEU j 118 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 141 through 143
      No H-bonds generated for 'chain 'j' and resid 141 through 143'
    Processing helix  chain 'j' and resid 144 through 161
      removed outlier: 4.241A  pdb=" N   SER j 148 " --> pdb=" O   THR j 144 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASP j 161 " --> pdb=" O   ARG j 157 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 168 through 183
    Processing helix  chain 'j' and resid 233 through 236
    Processing helix  chain 'j' and resid 237 through 243
      removed outlier: 3.566A  pdb=" N   GLU j 243 " --> pdb=" O   VAL j 239 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 247 through 266
      removed outlier: 3.517A  pdb=" N   HIS j 257 " --> pdb=" O   PHE j 253 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 279 through 293
    Processing helix  chain 'j' and resid 320 through 325
      removed outlier: 3.798A  pdb=" N   GLU j 325 " --> pdb=" O   ILE j 322 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 358 through 373
      removed outlier: 3.694A  pdb=" N   GLN j 373 " --> pdb=" O   LEU j 369 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 270 through 287
      removed outlier: 3.697A  pdb=" N   GLU m 274 " --> pdb=" O   THR m 270 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLU m 282 " --> pdb=" O   TRP m 278 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 323 through 337
      Proline residue:  m 334  - end of helix
    Processing helix  chain 'm' and resid 340 through 347
      removed outlier: 4.005A  pdb=" N   LEU m 344 " --> pdb=" O   PRO m 340 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 349 through 364
    Processing helix  chain 'm' and resid 373 through 400
    Processing helix  chain 'm' and resid 401 through 404
      removed outlier: 3.506A  pdb=" N   VAL m 404 " --> pdb=" O   LEU m 401 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 401 through 404'
    Processing helix  chain 'm' and resid 405 through 439
      removed outlier: 3.508A  pdb=" N   PHE m 409 " --> pdb=" O   ALA m 405 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 456 through 484
      removed outlier: 5.392A  pdb=" N   GLN m 472 " --> pdb=" O   LYS m 468 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL m 479 " --> pdb=" O   GLN m 475 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 514 through 532
    Processing helix  chain 'm' and resid 539 through 569
    Processing helix  chain 'm' and resid 570 through 575
    Processing helix  chain 'm' and resid 577 through 588
    Processing helix  chain 'm' and resid 589 through 593
      removed outlier: 3.825A  pdb=" N   VAL m 593 " --> pdb=" O   ALA m 590 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 594 through 601
      removed outlier: 3.575A  pdb=" N   ILE m 601 " --> pdb=" O   ILE m 597 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 602 through 623
      removed outlier: 3.702A  pdb=" N   THR m 606 " --> pdb=" O   ARG m 602 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   GLN m 607 " --> pdb=" O   GLU m 603 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 630 through 638
      removed outlier: 4.183A  pdb=" N   LYS m 634 " --> pdb=" O   SER m 630 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 642 through 670
    Processing helix  chain 'm' and resid 672 through 676
    Processing helix  chain 'm' and resid 678 through 693
      removed outlier: 3.585A  pdb=" N   LEU m 682 " --> pdb=" O   GLU m 678 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS m 692 " --> pdb=" O   SER m 688 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 695 through 710
      removed outlier: 3.504A  pdb=" N   PHE m 699 " --> pdb=" O   THR m 695 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASN m 710 " --> pdb=" O   VAL m 706 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 742 through 754
      removed outlier: 4.156A  pdb=" N   LEU m 746 " --> pdb=" O   GLU m 742 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 761 through 798
      Proline residue:  m 776  - end of helix
    Processing helix  chain 'm' and resid 799 through 802
      removed outlier: 3.517A  pdb=" N   SER m 802 " --> pdb=" O   ASN m 799 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 799 through 802'
    Processing helix  chain 'm' and resid 805 through 821
      removed outlier: 3.628A  pdb=" N   LYS m 809 " --> pdb=" O   VAL m 805 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LYS m 810 " --> pdb=" O   ALA m 806 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU m 811 " --> pdb=" O   GLY m 807 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ALA m 821 " --> pdb=" O   ALA m 817 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 828 through 854
      removed outlier: 3.571A  pdb=" N   TYR m 832 " --> pdb=" O   LYS m 828 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   GLN m 834 " --> pdb=" O   ASP m 830 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR m 839 " --> pdb=" O   ARG m 835 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE m 852 " --> pdb=" O   ASP m 848 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE m 853 " --> pdb=" O   ASP m 849 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 574 through 579
      removed outlier: 3.553A  pdb=" N   VAL o 579 " --> pdb=" O   GLU o 575 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 583 through 608
      removed outlier: 4.500A  pdb=" N   ALA o 593 " --> pdb=" O   GLY o 589 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 430 through 439
    Processing helix  chain 'F' and resid 430 through 439
      removed outlier: 3.565A  pdb=" N   LYS F 439 " --> pdb=" O   SER F 435 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'f' and resid 718 through 723
    Processing sheet with id=AA2, first strand: chain 'h' and resid 239 through 245
      removed outlier: 5.463A  pdb=" N   LEU h 241 " --> pdb=" O   ASP h 572 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   ASP h 572 " --> pdb=" O   LEU h 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'h' and resid 256 through 261
      removed outlier: 4.345A  pdb=" N   CYS h 258 " --> pdb=" O   SER h 272 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL h 286 " --> pdb=" O   TYR h 273 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLY h 285 " --> pdb=" O   CYS h 305 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'h' and resid 309 through 314
    Processing sheet with id=AA5, first strand: chain 'h' and resid 358 through 365
      removed outlier: 3.915A  pdb=" N   CYS h 360 " --> pdb=" O   ILE h 375 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   LYS h 380 " --> pdb=" O   SER h 376 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP h 394 " --> pdb=" O   SER h 383 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'h' and resid 408 through 412
      removed outlier: 6.876A  pdb=" N   GLY h 424 " --> pdb=" O   THR h 409 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   MET h 411 " --> pdb=" O   VAL h 422 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   VAL h 422 " --> pdb=" O   MET h 411 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   VAL h 430 " --> pdb=" O   MET h 445 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   MET h 445 " --> pdb=" O   VAL h 430 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   THR h 432 " --> pdb=" O   SER h 443 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'h' and resid 453 through 458
      removed outlier: 3.557A  pdb=" N   PHE h 471 " --> pdb=" O   TRP h 483 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TYR h 492 " --> pdb=" O   LEU h 482 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'h' and resid 501 through 506
      removed outlier: 4.975A  pdb=" N   ASP h 503 " --> pdb=" O   VAL h 517 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL h 517 " --> pdb=" O   ASP h 503 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET h 505 " --> pdb=" O   ALA h 515 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA h 515 " --> pdb=" O   MET h 505 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP h 518 " --> pdb=" O   ARG h 522 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ARG h 522 " --> pdb=" O   ASP h 518 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA h 537 " --> pdb=" O   LEU h 525 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'j' and resid 86 through 94
      removed outlier: 6.061A  pdb=" N   ASN j  56 " --> pdb=" O   LEU j 132 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ILE j 134 " --> pdb=" O   ASN j  56 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   LEU j  58 " --> pdb=" O   ILE j 134 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL j 136 " --> pdb=" O   LEU j  58 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   PHE j  60 " --> pdb=" O   VAL j 136 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ASP j 138 " --> pdb=" O   PHE j  60 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE j 270 " --> pdb=" O   VAL j 229 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'o' and resid 239 through 245
      removed outlier: 3.651A  pdb=" N   SER o 240 " --> pdb=" O   ASP o 572 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   ILE o 570 " --> pdb=" O   ASN o 242 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   GLN o 244 " --> pdb=" O   ILE o 568 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ILE o 568 " --> pdb=" O   GLN o 244 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'o' and resid 256 through 261
      removed outlier: 6.272A  pdb=" N   SER o 272 " --> pdb=" O   SER o 257 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LEU o 259 " --> pdb=" O   VAL o 270 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL o 270 " --> pdb=" O   LEU o 259 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   TRP o 261 " --> pdb=" O   LEU o 268 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   LEU o 268 " --> pdb=" O   TRP o 261 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU o 288 " --> pdb=" O   ALA o 271 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL o 286 " --> pdb=" O   TYR o 273 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TYR o 301 " --> pdb=" O   VAL o 289 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'o' and resid 309 through 314
    Processing sheet with id=AB4, first strand: chain 'o' and resid 358 through 365
      removed outlier: 3.871A  pdb=" N   CYS o 360 " --> pdb=" O   ILE o 375 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LYS o 380 " --> pdb=" O   SER o 376 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'o' and resid 399 through 400
    Processing sheet with id=AB6, first strand: chain 'o' and resid 411 through 412
      removed outlier: 7.016A  pdb=" N   VAL o 430 " --> pdb=" O   MET o 445 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   MET o 445 " --> pdb=" O   VAL o 430 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR o 432 " --> pdb=" O   SER o 443 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'o' and resid 453 through 458
      removed outlier: 3.591A  pdb=" N   TYR o 492 " --> pdb=" O   LEU o 482 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'o' and resid 501 through 506
      removed outlier: 6.865A  pdb=" N   VAL o 517 " --> pdb=" O   TYR o 502 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   VAL o 504 " --> pdb=" O   ALA o 515 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ALA o 515 " --> pdb=" O   VAL o 504 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   TRP o 506 " --> pdb=" O   LEU o 513 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   LEU o 513 " --> pdb=" O   TRP o 506 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASP o 518 " --> pdb=" O   ARG o 522 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   ARG o 522 " --> pdb=" O   ASP o 518 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA o 537 " --> pdb=" O   LEU o 525 " (cutoff:3.500A)

    978 hydrogen bonds defined for protein.
    2877 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.84

  Time building geometry restraints manager: 5.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 5769
        1.34 -     1.46: 4115
        1.46 -     1.58: 8247
        1.58 -     1.71: 1
        1.71 -     1.83: 118
  Bond restraints: 18250
  Sorted by residual:
  bond pdb=" C   ILE m 601 "
       pdb=" N   ARG m 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.296  0.036 1.40e-02 5.10e+03 6.73e+00
  bond pdb=" N   SER E 438 "
       pdb=" CA  SER E 438 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.31e-02 5.83e+03 5.90e+00
  bond pdb=" CB  GLU B 121 "
       pdb=" CG  GLU B 121 "
    ideal  model  delta    sigma   weight residual
    1.520  1.585 -0.065 3.00e-02 1.11e+03 4.70e+00
  bond pdb=" CB  GLN f 610 "
       pdb=" CG  GLN f 610 "
    ideal  model  delta    sigma   weight residual
    1.520  1.583 -0.063 3.00e-02 1.11e+03 4.35e+00
  bond pdb=" CB  GLN f 605 "
       pdb=" CG  GLN f 605 "
    ideal  model  delta    sigma   weight residual
    1.520  1.577 -0.057 3.00e-02 1.11e+03 3.65e+00
  ... (remaining 18245 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.40: 24438
        4.40 -     8.80: 205
        8.80 -    13.20: 37
       13.20 -    17.60: 8
       17.60 -    22.00: 3
  Bond angle restraints: 24691
  Sorted by residual:
  angle pdb=" CB  MET f 662 "
        pdb=" CG  MET f 662 "
        pdb=" SD  MET f 662 "
      ideal   model   delta    sigma   weight residual
     112.70  131.58  -18.88 3.00e+00 1.11e-01 3.96e+01
  angle pdb=" CA  LEU m 357 "
        pdb=" CB  LEU m 357 "
        pdb=" CG  LEU m 357 "
      ideal   model   delta    sigma   weight residual
     116.30  138.30  -22.00 3.50e+00 8.16e-02 3.95e+01
  angle pdb=" CA  LEU m 393 "
        pdb=" CB  LEU m 393 "
        pdb=" CG  LEU m 393 "
      ideal   model   delta    sigma   weight residual
     116.30  138.02  -21.72 3.50e+00 8.16e-02 3.85e+01
  angle pdb=" N   LEU E 437 "
        pdb=" CA  LEU E 437 "
        pdb=" C   LEU E 437 "
      ideal   model   delta    sigma   weight residual
     111.14  117.74   -6.60 1.08e+00 8.57e-01 3.73e+01
  angle pdb=" N   ASN F 434 "
        pdb=" CA  ASN F 434 "
        pdb=" C   ASN F 434 "
      ideal   model   delta    sigma   weight residual
     111.36  105.38    5.98 1.09e+00 8.42e-01 3.01e+01
  ... (remaining 24686 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 9299
       17.81 -    35.62: 1325
       35.62 -    53.42: 312
       53.42 -    71.23: 70
       71.23 -    89.04: 29
  Dihedral angle restraints: 11035
    sinusoidal: 4522
      harmonic: 6513
  Sorted by residual:
  dihedral pdb=" CA  PHE m 339 "
           pdb=" C   PHE m 339 "
           pdb=" N   PRO m 340 "
           pdb=" CA  PRO m 340 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.52  -24.48     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CA  MET o 445 "
           pdb=" C   MET o 445 "
           pdb=" N   PHE o 446 "
           pdb=" CA  PHE o 446 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.40   22.60     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  GLU o 444 "
           pdb=" C   GLU o 444 "
           pdb=" N   MET o 445 "
           pdb=" CA  MET o 445 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.08   21.92     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 11032 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1960
       0.052 -    0.103: 601
       0.103 -    0.155: 133
       0.155 -    0.206: 34
       0.206 -    0.258: 7
  Chirality restraints: 2735
  Sorted by residual:
  chirality pdb=" CB  ILE j 134 "
            pdb=" CA  ILE j 134 "
            pdb=" CG1 ILE j 134 "
            pdb=" CG2 ILE j 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CB  ILE m 698 "
            pdb=" CA  ILE m 698 "
            pdb=" CG1 ILE m 698 "
            pdb=" CG2 ILE m 698 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CB  VAL m 381 "
            pdb=" CA  VAL m 381 "
            pdb=" CG1 VAL m 381 "
            pdb=" CG2 VAL m 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 2732 not shown)

  Planarity restraints: 3192
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE m 339 "   -0.041 2.00e-02 2.50e+03   8.06e-02 6.49e+01
        pdb=" C   PHE m 339 "    0.139 2.00e-02 2.50e+03
        pdb=" O   PHE m 339 "   -0.052 2.00e-02 2.50e+03
        pdb=" N   PRO m 340 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG f1003 "   -0.291 9.50e-02 1.11e+02   1.31e-01 1.05e+01
        pdb=" NE  ARG f1003 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG f1003 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG f1003 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG f1003 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP f 849 "    0.015 2.00e-02 2.50e+03   2.92e-02 8.56e+00
        pdb=" CG  ASP f 849 "   -0.051 2.00e-02 2.50e+03
        pdb=" OD1 ASP f 849 "    0.019 2.00e-02 2.50e+03
        pdb=" OD2 ASP f 849 "    0.017 2.00e-02 2.50e+03
  ... (remaining 3189 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 4967
        2.80 -     3.33: 16656
        3.33 -     3.85: 31462
        3.85 -     4.38: 33640
        4.38 -     4.90: 57977
  Nonbonded interactions: 144702
  Sorted by model distance:
  nonbonded pdb=" OG  SER h 475 "
            pdb=" OD1 ASP h 477 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG1 THR h 454 "
            pdb=" O   TYR h 502 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   ILE j 287 "
            pdb=" OG1 THR j 291 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   GLU m 783 "
            pdb=" OG1 THR m 787 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   SER j 127 "
            pdb=" OG1 THR j 131 "
     model   vdw
     2.314 3.040
  ... (remaining 144697 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = (chain 'C' and resid 24 through 128)
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'h'
  selection = chain 'o'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     41.370
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
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      :  0.006   0.065  18250  Z= 0.268
  Angle     :  1.079  22.004  24691  Z= 0.544
  Chirality :  0.054   0.258   2735
  Planarity :  0.006   0.131   3192
  Dihedral  : 17.802  89.039   6795
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.01 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 26.56 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.20 (0.16), residues: 2193
  helix: -0.49 (0.14), residues: 1061
  sheet: -0.84 (0.28), residues: 335
  loop : -0.95 (0.20), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP h 552 
 HIS   0.011   0.001   HIS o 400 
 PHE   0.033   0.002   PHE m 843 
 TYR   0.022   0.002   TYR h 301 
 ARG   0.015   0.001   ARG f1020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15997 (  978)
  hydrogen bonds       : angle       6.54056 ( 2877)
  covalent geometry    : bond        0.00590 (18250)
  covalent geometry    : angle       1.07887 (24691)

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

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

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 216
  time to evaluate  : 2.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   96 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7823 (ttp80)
REVERT: B  122 LEU cc_start: 0.9081 (mt) cc_final: 0.8615 (tp)
REVERT: C   98 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8906 (ttmm)
REVERT: C  103 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8957 (pp30)
REVERT: C  123 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8792 (tp-100)
REVERT: j  103 ARG cc_start: 0.8329 (mmp-170) cc_final: 0.7784 (mmm160)
REVERT: o  310 MET cc_start: 0.8528 (ptp) cc_final: 0.8293 (ptp)
REVERT: o  400 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6458 (t-90)
  outliers start: 13
  outliers final: 8
  residues processed: 226
  average time/residue: 0.3864
  time to fit residues: 127.2966
Evaluate side-chains
  197 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 188
  time to evaluate  : 3.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain f residue  713 VAL
Chi-restraints excluded: chain f residue  755 TRP
Chi-restraints excluded: chain f residue  993 VAL
Chi-restraints excluded: chain j residue  239 VAL
Chi-restraints excluded: chain m residue  576 LYS
Chi-restraints excluded: chain o residue  381 ILE
Chi-restraints excluded: chain o residue  400 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 184 optimal weight:   10.0000
   chunk 165 optimal weight:    0.0370
   chunk 92 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 111 optimal weight:   10.0000
   chunk 88 optimal weight:    0.7980
   chunk 171 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   chunk 104 optimal weight:    5.9990
   chunk 127 optimal weight:    5.9990
   chunk 198 optimal weight:    3.9990
   overall best weight:    1.9664

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
f 916 GLN
** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
j 373 GLN
** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
o 469 HIS
** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.080800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.058620 restraints weight = 69872.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.060465 restraints weight = 35867.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.061688 restraints weight = 23689.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18250  Z= 0.157
  Angle     :  0.614  11.206  24691  Z= 0.316
  Chirality :  0.041   0.145   2735
  Planarity :  0.004   0.049   3192
  Dihedral  :  4.836  46.606   2426
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.33 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 23.78 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.18), residues: 2193
  helix:  1.05 (0.16), residues: 1067
  sheet: -0.77 (0.26), residues: 383
  loop : -0.41 (0.22), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP j 143 
 HIS   0.004   0.001   HIS m 473 
 PHE   0.014   0.001   PHE m 843 
 TYR   0.014   0.001   TYR o 502 
 ARG   0.004   0.000   ARG j 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04595 (  978)
  hydrogen bonds       : angle       4.62415 ( 2877)
  covalent geometry    : bond        0.00332 (18250)
  covalent geometry    : angle       0.61376 (24691)

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

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

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 199
  time to evaluate  : 2.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  107 LYS cc_start: 0.9363 (tmmt) cc_final: 0.9017 (tptt)
REVERT: C  123 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8781 (tp-100)
REVERT: f  605 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: f  610 GLN cc_start: 0.8320 (tp40) cc_final: 0.8078 (tp40)
REVERT: f  991 MET cc_start: 0.8367 (ptp) cc_final: 0.7965 (ptp)
REVERT: f 1026 MET cc_start: 0.8000 (mmm) cc_final: 0.7159 (tpp)
REVERT: j  126 GLU cc_start: 0.9007 (pp20) cc_final: 0.8807 (pp20)
REVERT: j  162 LYS cc_start: 0.8741 (mttt) cc_final: 0.8514 (mtpt)
REVERT: j  163 MET cc_start: 0.6919 (pmm) cc_final: 0.6667 (pmm)
REVERT: m  413 MET cc_start: 0.9152 (ppp) cc_final: 0.8850 (ppp)
REVERT: m  846 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8608 (mmtm)
REVERT: o  400 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6299 (t70)
REVERT: o  567 GLN cc_start: 0.8551 (pm20) cc_final: 0.8323 (pm20)
  outliers start: 44
  outliers final: 31
  residues processed: 233
  average time/residue: 0.3297
  time to fit residues: 114.2316
Evaluate side-chains
  205 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 2.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain C residue   45 HIS
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain f residue  713 VAL
Chi-restraints excluded: chain f residue  746 LEU
Chi-restraints excluded: chain f residue  845 GLU
Chi-restraints excluded: chain f residue  993 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  396 MET
Chi-restraints excluded: chain h residue  411 MET
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  123 VAL
Chi-restraints excluded: chain j residue  156 LEU
Chi-restraints excluded: chain j residue  239 VAL
Chi-restraints excluded: chain j residue  258 LEU
Chi-restraints excluded: chain m residue  339 PHE
Chi-restraints excluded: chain m residue  576 LYS
Chi-restraints excluded: chain m residue  653 GLN
Chi-restraints excluded: chain m residue  760 VAL
Chi-restraints excluded: chain o residue  286 VAL
Chi-restraints excluded: chain o residue  305 CYS
Chi-restraints excluded: chain o residue  344 VAL
Chi-restraints excluded: chain o residue  360 CYS
Chi-restraints excluded: chain o residue  381 ILE
Chi-restraints excluded: chain o residue  400 HIS
Chi-restraints excluded: chain o residue  430 VAL
Chi-restraints excluded: chain o residue  436 HIS
Chi-restraints excluded: chain o residue  453 ILE
Chi-restraints excluded: chain o residue  525 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 159 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 156 optimal weight:    0.8980
   chunk 133 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 202 optimal weight:    2.9990
   chunk 185 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
** C  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 ASN
C  93 GLN
f1009 HIS
** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.080694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.058662 restraints weight = 69581.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.060535 restraints weight = 35680.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.061738 restraints weight = 23315.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18250  Z= 0.136
  Angle     :  0.580  12.901  24691  Z= 0.293
  Chirality :  0.041   0.154   2735
  Planarity :  0.004   0.063   3192
  Dihedral  :  4.393  43.234   2420
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.37 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.98 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.18), residues: 2193
  helix:  1.62 (0.16), residues: 1073
  sheet: -0.81 (0.26), residues: 385
  loop : -0.16 (0.23), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP o 483 
 HIS   0.016   0.001   HIS m 769 
 PHE   0.020   0.001   PHE B 108 
 TYR   0.012   0.001   TYR o 502 
 ARG   0.016   0.000   ARG f 709 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  978)
  hydrogen bonds       : angle       4.31580 ( 2877)
  covalent geometry    : bond        0.00294 (18250)
  covalent geometry    : angle       0.57992 (24691)

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

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

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 197
  time to evaluate  : 1.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 MET cc_start: 0.6046 (mmt) cc_final: 0.3654 (tpt)
REVERT: B   96 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7970 (ttp80)
REVERT: B  107 LYS cc_start: 0.9378 (tmmt) cc_final: 0.8935 (tptt)
REVERT: C  123 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8768 (tp-100)
REVERT: f  605 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: f  610 GLN cc_start: 0.8467 (tp40) cc_final: 0.8022 (tp40)
REVERT: f  986 MET cc_start: 0.8493 (tpp) cc_final: 0.7950 (tmm)
REVERT: f 1026 MET cc_start: 0.8176 (mmm) cc_final: 0.7747 (tpp)
REVERT: j  126 GLU cc_start: 0.9034 (pp20) cc_final: 0.8810 (pp20)
REVERT: j  289 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7099 (t70)
REVERT: m  622 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9206 (ttmt)
REVERT: o  426 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8083 (tt0)
REVERT: o  503 ASP cc_start: 0.8454 (m-30) cc_final: 0.8115 (m-30)
REVERT: o  567 GLN cc_start: 0.8601 (pm20) cc_final: 0.8308 (pm20)
  outliers start: 66
  outliers final: 41
  residues processed: 252
  average time/residue: 0.3255
  time to fit residues: 122.3244
Evaluate side-chains
  219 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 175
  time to evaluate  : 2.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain C residue   28 ARG
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain f residue  713 VAL
Chi-restraints excluded: chain f residue  746 LEU
Chi-restraints excluded: chain f residue  755 TRP
Chi-restraints excluded: chain f residue  823 VAL
Chi-restraints excluded: chain f residue  845 GLU
Chi-restraints excluded: chain f residue  888 LEU
Chi-restraints excluded: chain f residue  993 VAL
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  411 MET
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  102 THR
Chi-restraints excluded: chain j residue  239 VAL
Chi-restraints excluded: chain j residue  240 LEU
Chi-restraints excluded: chain j residue  245 ASP
Chi-restraints excluded: chain j residue  258 LEU
Chi-restraints excluded: chain j residue  274 VAL
Chi-restraints excluded: chain j residue  289 HIS
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  339 PHE
Chi-restraints excluded: chain m residue  472 GLN
Chi-restraints excluded: chain m residue  482 ARG
Chi-restraints excluded: chain m residue  576 LYS
Chi-restraints excluded: chain m residue  577 ASN
Chi-restraints excluded: chain m residue  622 LYS
Chi-restraints excluded: chain m residue  641 LEU
Chi-restraints excluded: chain m residue  653 GLN
Chi-restraints excluded: chain m residue  760 VAL
Chi-restraints excluded: chain o residue  311 SER
Chi-restraints excluded: chain o residue  381 ILE
Chi-restraints excluded: chain o residue  415 VAL
Chi-restraints excluded: chain o residue  426 GLU
Chi-restraints excluded: chain o residue  436 HIS
Chi-restraints excluded: chain o residue  453 ILE
Chi-restraints excluded: chain o residue  561 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 86 optimal weight:    7.9990
   chunk 158 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 191 optimal weight:    0.4980
   chunk 189 optimal weight:    1.9990
   chunk 206 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
j 255 GLN
** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.080079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.058140 restraints weight = 69745.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.059987 restraints weight = 35807.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.061162 restraints weight = 23476.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18250  Z= 0.151
  Angle     :  0.586  13.811  24691  Z= 0.293
  Chirality :  0.041   0.185   2735
  Planarity :  0.003   0.041   3192
  Dihedral  :  4.251  41.346   2418
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.33 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.09 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  1.03 (0.18), residues: 2193
  helix:  1.86 (0.16), residues: 1072
  sheet: -0.87 (0.26), residues: 385
  loop : -0.07 (0.24), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP o 483 
 HIS   0.014   0.001   HIS m 769 
 PHE   0.011   0.001   PHE h 471 
 TYR   0.013   0.001   TYR o 502 
 ARG   0.005   0.000   ARG m 786 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  978)
  hydrogen bonds       : angle       4.22005 ( 2877)
  covalent geometry    : bond        0.00327 (18250)
  covalent geometry    : angle       0.58580 (24691)

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

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

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 187
  time to evaluate  : 2.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  107 LYS cc_start: 0.9387 (tmmt) cc_final: 0.8979 (tptt)
REVERT: B  123 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8525 (mt0)
REVERT: C  123 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8757 (tp-100)
REVERT: f  605 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: f  610 GLN cc_start: 0.8481 (tp40) cc_final: 0.7949 (tp40)
REVERT: f  624 LYS cc_start: 0.9537 (mmmm) cc_final: 0.8942 (mmmm)
REVERT: f  987 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.3918 (p90)
REVERT: f 1026 MET cc_start: 0.8177 (mmm) cc_final: 0.7513 (tpp)
REVERT: j  277 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8138 (mp0)
REVERT: j  289 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7103 (t70)
REVERT: m  579 ASN cc_start: 0.9047 (m110) cc_final: 0.8690 (t0)
REVERT: m  622 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9198 (ttmt)
REVERT: m  691 MET cc_start: 0.9140 (tpp) cc_final: 0.8929 (tpp)
REVERT: o  244 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7572 (tm-30)
REVERT: o  445 MET cc_start: 0.8924 (tpp) cc_final: 0.8702 (tpp)
REVERT: o  503 ASP cc_start: 0.8365 (m-30) cc_final: 0.7941 (m-30)
  outliers start: 71
  outliers final: 50
  residues processed: 246
  average time/residue: 0.3267
  time to fit residues: 120.0697
Evaluate side-chains
  224 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 169
  time to evaluate  : 1.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain C residue   28 ARG
Chi-restraints excluded: chain C residue   45 HIS
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain f residue  608 LEU
Chi-restraints excluded: chain f residue  713 VAL
Chi-restraints excluded: chain f residue  746 LEU
Chi-restraints excluded: chain f residue  755 TRP
Chi-restraints excluded: chain f residue  845 GLU
Chi-restraints excluded: chain f residue  888 LEU
Chi-restraints excluded: chain f residue  987 PHE
Chi-restraints excluded: chain f residue  993 VAL
Chi-restraints excluded: chain f residue 1040 VAL
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  411 MET
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  102 THR
Chi-restraints excluded: chain j residue  134 ILE
Chi-restraints excluded: chain j residue  144 THR
Chi-restraints excluded: chain j residue  239 VAL
Chi-restraints excluded: chain j residue  240 LEU
Chi-restraints excluded: chain j residue  245 ASP
Chi-restraints excluded: chain j residue  258 LEU
Chi-restraints excluded: chain j residue  274 VAL
Chi-restraints excluded: chain j residue  277 GLU
Chi-restraints excluded: chain j residue  289 HIS
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  339 PHE
Chi-restraints excluded: chain m residue  352 LYS
Chi-restraints excluded: chain m residue  472 GLN
Chi-restraints excluded: chain m residue  484 LEU
Chi-restraints excluded: chain m residue  557 ILE
Chi-restraints excluded: chain m residue  577 ASN
Chi-restraints excluded: chain m residue  622 LYS
Chi-restraints excluded: chain m residue  641 LEU
Chi-restraints excluded: chain m residue  653 GLN
Chi-restraints excluded: chain m residue  760 VAL
Chi-restraints excluded: chain o residue  244 GLN
Chi-restraints excluded: chain o residue  286 VAL
Chi-restraints excluded: chain o residue  311 SER
Chi-restraints excluded: chain o residue  344 VAL
Chi-restraints excluded: chain o residue  381 ILE
Chi-restraints excluded: chain o residue  415 VAL
Chi-restraints excluded: chain o residue  436 HIS
Chi-restraints excluded: chain o residue  453 ILE
Chi-restraints excluded: chain o residue  465 VAL
Chi-restraints excluded: chain o residue  561 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   chunk 208 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 126 optimal weight:   20.0000
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 205 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
j 221 HIS
j 255 GLN
** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
o 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.078846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.056568 restraints weight = 72260.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.058319 restraints weight = 37904.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.059428 restraints weight = 25358.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  18250  Z= 0.265
  Angle     :  0.673  12.534  24691  Z= 0.343
  Chirality :  0.043   0.165   2735
  Planarity :  0.004   0.046   3192
  Dihedral  :  4.390  31.228   2414
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.10 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 24.60 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.18), residues: 2193
  helix:  1.83 (0.16), residues: 1066
  sheet: -1.21 (0.25), residues: 395
  loop :  0.02 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP m 755 
 HIS   0.010   0.001   HIS m 769 
 PHE   0.012   0.002   PHE f 739 
 TYR   0.017   0.002   TYR o 502 
 ARG   0.009   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04220 (  978)
  hydrogen bonds       : angle       4.42337 ( 2877)
  covalent geometry    : bond        0.00574 (18250)
  covalent geometry    : angle       0.67334 (24691)

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

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

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 172
  time to evaluate  : 1.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   96 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7996 (ttp80)
REVERT: B  107 LYS cc_start: 0.9426 (tmmt) cc_final: 0.9017 (tptt)
REVERT: C  107 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.8560 (ptpp)
REVERT: C  123 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8795 (tp-100)
REVERT: f  605 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7953 (tm-30)
REVERT: f  610 GLN cc_start: 0.8467 (tp40) cc_final: 0.7783 (tp40)
REVERT: f  987 PHE cc_start: 0.5734 (OUTLIER) cc_final: 0.4033 (p90)
REVERT: f 1026 MET cc_start: 0.8562 (mmm) cc_final: 0.8019 (mmm)
REVERT: j   90 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.8272 (p90)
REVERT: j  277 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8158 (mp0)
REVERT: j  289 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7169 (t70)
REVERT: m  602 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8167 (mmm-85)
REVERT: m  622 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9274 (ttmt)
REVERT: m  691 MET cc_start: 0.9136 (tpp) cc_final: 0.8912 (tpp)
REVERT: o  244 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7643 (tm-30)
REVERT: o  265 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6829 (m-80)
  outliers start: 84
  outliers final: 56
  residues processed: 242
  average time/residue: 0.3282
  time to fit residues: 117.6422
Evaluate side-chains
  223 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 159
  time to evaluate  : 2.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  128 HIS
Chi-restraints excluded: chain C residue   28 ARG
Chi-restraints excluded: chain C residue   45 HIS
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  107 LYS
Chi-restraints excluded: chain f residue  608 LEU
Chi-restraints excluded: chain f residue  713 VAL
Chi-restraints excluded: chain f residue  717 ILE
Chi-restraints excluded: chain f residue  746 LEU
Chi-restraints excluded: chain f residue  755 TRP
Chi-restraints excluded: chain f residue  815 LEU
Chi-restraints excluded: chain f residue  823 VAL
Chi-restraints excluded: chain f residue  845 GLU
Chi-restraints excluded: chain f residue  888 LEU
Chi-restraints excluded: chain f residue  987 PHE
Chi-restraints excluded: chain f residue  993 VAL
Chi-restraints excluded: chain f residue 1040 VAL
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  411 MET
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue   90 TYR
Chi-restraints excluded: chain j residue  134 ILE
Chi-restraints excluded: chain j residue  144 THR
Chi-restraints excluded: chain j residue  239 VAL
Chi-restraints excluded: chain j residue  240 LEU
Chi-restraints excluded: chain j residue  245 ASP
Chi-restraints excluded: chain j residue  258 LEU
Chi-restraints excluded: chain j residue  274 VAL
Chi-restraints excluded: chain j residue  277 GLU
Chi-restraints excluded: chain j residue  289 HIS
Chi-restraints excluded: chain m residue  339 PHE
Chi-restraints excluded: chain m residue  352 LYS
Chi-restraints excluded: chain m residue  472 GLN
Chi-restraints excluded: chain m residue  557 ILE
Chi-restraints excluded: chain m residue  577 ASN
Chi-restraints excluded: chain m residue  622 LYS
Chi-restraints excluded: chain m residue  760 VAL
Chi-restraints excluded: chain o residue  244 GLN
Chi-restraints excluded: chain o residue  265 TYR
Chi-restraints excluded: chain o residue  286 VAL
Chi-restraints excluded: chain o residue  305 CYS
Chi-restraints excluded: chain o residue  311 SER
Chi-restraints excluded: chain o residue  344 VAL
Chi-restraints excluded: chain o residue  360 CYS
Chi-restraints excluded: chain o residue  415 VAL
Chi-restraints excluded: chain o residue  418 VAL
Chi-restraints excluded: chain o residue  436 HIS
Chi-restraints excluded: chain o residue  453 ILE
Chi-restraints excluded: chain o residue  465 VAL
Chi-restraints excluded: chain o residue  475 SER
Chi-restraints excluded: chain o residue  561 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 120 optimal weight:    0.0060
   chunk 183 optimal weight:    3.9990
   chunk 121 optimal weight:    8.9990
   chunk 124 optimal weight:    9.9990
   chunk 206 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    2.0002

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
j 221 HIS
j 255 GLN
** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m 657 GLN
** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.079980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.057979 restraints weight = 70786.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.059771 restraints weight = 36799.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.060898 restraints weight = 24457.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18250  Z= 0.150
  Angle     :  0.615  14.286  24691  Z= 0.306
  Chirality :  0.041   0.158   2735
  Planarity :  0.003   0.039   3192
  Dihedral  :  4.235  34.102   2412
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.33 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 25.53 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  1.13 (0.19), residues: 2193
  helix:  1.99 (0.16), residues: 1057
  sheet: -1.06 (0.25), residues: 389
  loop :  0.10 (0.24), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP m 755 
 HIS   0.009   0.001   HIS m 769 
 PHE   0.019   0.001   PHE B 108 
 TYR   0.011   0.001   TYR o 502 
 ARG   0.007   0.000   ARG f1003 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  978)
  hydrogen bonds       : angle       4.25349 ( 2877)
  covalent geometry    : bond        0.00329 (18250)
  covalent geometry    : angle       0.61506 (24691)

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

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

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 181
  time to evaluate  : 2.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 MET cc_start: 0.6429 (mpp) cc_final: 0.4208 (tpt)
REVERT: B   96 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7941 (ttp80)
REVERT: B  107 LYS cc_start: 0.9407 (tmmt) cc_final: 0.9007 (tptt)
REVERT: C  103 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8900 (mm-40)
REVERT: C  123 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8779 (tp-100)
REVERT: f  581 MET cc_start: 0.9479 (ttm) cc_final: 0.9224 (mtp)
REVERT: f  605 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: f  610 GLN cc_start: 0.8466 (tp40) cc_final: 0.7736 (tp40)
REVERT: f  624 LYS cc_start: 0.9563 (mmmm) cc_final: 0.8936 (mmmm)
REVERT: f  663 LYS cc_start: 0.8980 (tppt) cc_final: 0.8722 (tppt)
REVERT: f  987 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.4122 (p90)
REVERT: f 1026 MET cc_start: 0.8503 (mmm) cc_final: 0.8019 (mmm)
REVERT: j  163 MET cc_start: 0.7043 (pmm) cc_final: 0.6767 (pmm)
REVERT: j  277 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8159 (mp0)
REVERT: j  289 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7089 (t70)
REVERT: m  413 MET cc_start: 0.9269 (ppp) cc_final: 0.9008 (ppp)
REVERT: m  602 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8133 (mmm-85)
REVERT: m  691 MET cc_start: 0.9132 (tpp) cc_final: 0.8912 (tpp)
REVERT: o  244 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7626 (tm-30)
REVERT: o  445 MET cc_start: 0.8952 (tpp) cc_final: 0.8672 (tpp)
REVERT: o  503 ASP cc_start: 0.8366 (m-30) cc_final: 0.8001 (m-30)
  outliers start: 74
  outliers final: 47
  residues processed: 239
  average time/residue: 0.4074
  time to fit residues: 143.5075
Evaluate side-chains
  216 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 165
  time to evaluate  : 3.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  128 HIS
Chi-restraints excluded: chain C residue   45 HIS
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain f residue  608 LEU
Chi-restraints excluded: chain f residue  713 VAL
Chi-restraints excluded: chain f residue  746 LEU
Chi-restraints excluded: chain f residue  755 TRP
Chi-restraints excluded: chain f residue  801 ILE
Chi-restraints excluded: chain f residue  815 LEU
Chi-restraints excluded: chain f residue  823 VAL
Chi-restraints excluded: chain f residue  845 GLU
Chi-restraints excluded: chain f residue  888 LEU
Chi-restraints excluded: chain f residue  987 PHE
Chi-restraints excluded: chain f residue  993 VAL
Chi-restraints excluded: chain f residue 1040 VAL
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  411 MET
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  144 THR
Chi-restraints excluded: chain j residue  239 VAL
Chi-restraints excluded: chain j residue  240 LEU
Chi-restraints excluded: chain j residue  245 ASP
Chi-restraints excluded: chain j residue  258 LEU
Chi-restraints excluded: chain j residue  274 VAL
Chi-restraints excluded: chain j residue  277 GLU
Chi-restraints excluded: chain j residue  289 HIS
Chi-restraints excluded: chain j residue  328 THR
Chi-restraints excluded: chain m residue  339 PHE
Chi-restraints excluded: chain m residue  352 LYS
Chi-restraints excluded: chain m residue  369 ASN
Chi-restraints excluded: chain m residue  557 ILE
Chi-restraints excluded: chain m residue  577 ASN
Chi-restraints excluded: chain m residue  641 LEU
Chi-restraints excluded: chain m residue  760 VAL
Chi-restraints excluded: chain o residue  244 GLN
Chi-restraints excluded: chain o residue  286 VAL
Chi-restraints excluded: chain o residue  311 SER
Chi-restraints excluded: chain o residue  344 VAL
Chi-restraints excluded: chain o residue  381 ILE
Chi-restraints excluded: chain o residue  415 VAL
Chi-restraints excluded: chain o residue  436 HIS
Chi-restraints excluded: chain o residue  453 ILE
Chi-restraints excluded: chain o residue  465 VAL
Chi-restraints excluded: chain o residue  564 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 201 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   chunk 199 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 127 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 175 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 188 optimal weight:    1.9990
   chunk 155 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f 626 GLN
** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
j 255 GLN
** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.079717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.057862 restraints weight = 69385.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.059687 restraints weight = 35402.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.060874 restraints weight = 23169.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18250  Z= 0.124
  Angle     :  0.619  14.437  24691  Z= 0.304
  Chirality :  0.042   0.219   2735
  Planarity :  0.003   0.039   3192
  Dihedral  :  4.091  29.664   2412
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.46 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 26.35 %
    Favored  : 70.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  1.23 (0.19), residues: 2193
  helix:  2.06 (0.16), residues: 1057
  sheet: -1.01 (0.25), residues: 389
  loop :  0.18 (0.24), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP o 483 
 HIS   0.008   0.001   HIS m 769 
 PHE   0.013   0.001   PHE h 471 
 TYR   0.010   0.001   TYR o 502 
 ARG   0.006   0.000   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03859 (  978)
  hydrogen bonds       : angle       4.15762 ( 2877)
  covalent geometry    : bond        0.00274 (18250)
  covalent geometry    : angle       0.61903 (24691)

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

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

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4386 Ramachandran restraints generated.
    2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 183
  time to evaluate  : 2.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  107 LYS cc_start: 0.9388 (tmmt) cc_final: 0.9012 (tptt)
REVERT: B  123 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8621 (mt0)
REVERT: C  103 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8785 (mm-40)
REVERT: C  106 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8301 (mp0)
REVERT: C  128 HIS cc_start: 0.4393 (OUTLIER) cc_final: 0.4053 (p-80)
REVERT: f  581 MET cc_start: 0.9453 (ttm) cc_final: 0.9215 (mtp)
REVERT: f  605 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: f  610 GLN cc_start: 0.8529 (tp40) cc_final: 0.7828 (tp40)
REVERT: f  624 LYS cc_start: 0.9549 (mmmm) cc_final: 0.8927 (mmmm)
REVERT: f  663 LYS cc_start: 0.8976 (tppt) cc_final: 0.8715 (tppt)
REVERT: f 1026 MET cc_start: 0.8445 (mmm) cc_final: 0.8048 (mmm)
REVERT: j  163 MET cc_start: 0.6980 (pmm) cc_final: 0.6714 (pmm)
REVERT: j  277 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8216 (mp0)
REVERT: j  289 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.6950 (t70)
REVERT: m  602 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8120 (mmm-85)
REVERT: m  691 MET cc_start: 0.9148 (tpp) cc_final: 0.8935 (tpp)
REVERT: o  244 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7606 (tm-30)
REVERT: o  445 MET cc_start: 0.8923 (tpp) cc_final: 0.8717 (tpp)
REVERT: o  503 ASP cc_start: 0.8367 (m-30) cc_final: 0.7939 (m-30)
  outliers start: 59
  outliers final: 42
  residues processed: 228
  average time/residue: 0.4182
  time to fit residues: 144.3312
Evaluate side-chains
  217 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 170
  time to evaluate  : 2.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  128 HIS
Chi-restraints excluded: chain C residue   45 HIS
Chi-restraints excluded: chain C residue   76 HIS
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain C residue  128 HIS
Chi-restraints excluded: chain f residue  713 VAL
Chi-restraints excluded: chain f residue  746 LEU
Chi-restraints excluded: chain f residue  755 TRP
Chi-restraints excluded: chain f residue  801 ILE
Chi-restraints excluded: chain f residue  815 LEU
Chi-restraints excluded: chain f residue  823 VAL
Chi-restraints excluded: chain f residue  845 GLU
Chi-restraints excluded: chain f residue  888 LEU
Chi-restraints excluded: chain f residue  993 VAL
Chi-restraints excluded: chain f residue 1040 VAL
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  411 MET
Chi-restraints excluded: chain j residue  134 ILE
Chi-restraints excluded: chain j residue  144 THR
Chi-restraints excluded: chain j residue  239 VAL
Chi-restraints excluded: chain j residue  240 LEU
Chi-restraints excluded: chain j residue  258 LEU
Chi-restraints excluded: chain j residue  274 VAL
Chi-restraints excluded: chain j residue  277 GLU
Chi-restraints excluded: chain j residue  289 HIS
Chi-restraints excluded: chain m residue  557 ILE
Chi-restraints excluded: chain m residue  577 ASN
Chi-restraints excluded: chain m residue  641 LEU
Chi-restraints excluded: chain m residue  760 VAL
Chi-restraints excluded: chain o residue  244 GLN
Chi-restraints excluded: chain o residue  269 LEU
Chi-restraints excluded: chain o residue  286 VAL
Chi-restraints excluded: chain o residue  311 SER
Chi-restraints excluded: chain o residue  381 ILE
Chi-restraints excluded: chain o residue  415 VAL
Chi-restraints excluded: chain o residue  436 HIS
Chi-restraints excluded: chain o residue  453 ILE
Chi-restraints excluded: chain o residue  465 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 55.0746 > 50:
  distance: 48 - 108:  10.546
  distance: 57 - 99:  17.763
  distance: 60 - 96:  22.183
  distance: 67 - 72:  12.413
  distance: 72 - 73:  30.077
  distance: 73 - 74:  19.693
  distance: 74 - 75:  23.708
  distance: 74 - 76:   9.157
  distance: 76 - 77:  12.075
  distance: 77 - 78:  14.019
  distance: 77 - 80:  21.113
  distance: 78 - 79:  17.878
  distance: 78 - 82:   7.587
  distance: 80 - 81:  18.290
  distance: 82 - 83:   6.409
  distance: 83 - 84:  12.786
  distance: 83 - 86:  19.299
  distance: 84 - 85:  14.348
  distance: 84 - 91:  28.106
  distance: 86 - 87:  20.413
  distance: 87 - 88:  22.917
  distance: 88 - 89:   8.207
  distance: 89 - 90:  18.135
  distance: 91 - 92:  14.707
  distance: 92 - 93:  32.825
  distance: 92 - 95:  17.866
  distance: 93 - 94:  27.878
  distance: 93 - 96:  25.964
  distance: 96 - 97:  18.513
  distance: 97 - 98:  17.210
  distance: 98 - 99:  25.812
  distance: 98 - 100:  14.757
  distance: 100 - 101:  13.473
  distance: 101 - 102:   7.544
  distance: 101 - 104:   6.262
  distance: 102 - 103:   7.809
  distance: 102 - 108:  11.864
  distance: 104 - 105:  12.233
  distance: 104 - 106:  24.321
  distance: 105 - 107:   9.600
  distance: 108 - 109:  15.417
  distance: 109 - 112:   3.205
  distance: 110 - 111:  13.104
  distance: 110 - 114:   6.736
  distance: 112 - 113:  16.863
  distance: 114 - 115:   4.478
  distance: 115 - 116:   9.807
  distance: 115 - 118:  15.581
  distance: 116 - 117:  14.735
  distance: 116 - 123:  15.430
  distance: 118 - 119:  14.434
  distance: 119 - 120:  11.286
  distance: 120 - 121:  11.664
  distance: 120 - 122:   9.312
  distance: 123 - 124:   5.269
  distance: 124 - 125:  12.301
  distance: 124 - 127:  11.050
  distance: 125 - 131:   9.264
  distance: 127 - 128:  11.541
  distance: 128 - 129:   5.093
  distance: 129 - 130:  12.370
  distance: 131 - 132:  21.544
  distance: 132 - 133:  20.190
  distance: 132 - 135:  10.842
  distance: 133 - 134:  23.739
  distance: 133 - 142:  29.083
  distance: 135 - 136:  11.009
  distance: 136 - 137:  11.475
  distance: 136 - 138:   7.854
  distance: 137 - 139:  10.906
  distance: 138 - 140:  15.305
  distance: 139 - 141:  17.016
  distance: 140 - 141:   6.220