Starting phenix.real_space_refine
on Tue Jul 29 10:27:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7v_38128/07_2025/8x7v_38128.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7v_38128/07_2025/8x7v_38128.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x7v_38128/07_2025/8x7v_38128.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7v_38128/07_2025/8x7v_38128.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7v_38128/07_2025/8x7v_38128.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7v_38128/07_2025/8x7v_38128.cif"
  }
  resolution = 3.01
  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=   0.035
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      88      5.16       5
     C    7121      2.51       5
     N    1964      2.21       5
     O    2029      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11202
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 976, 7666
          Classifications: {'peptide': 976}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 36, 'TRANS': 939}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "B"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 780
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 6, 'TRANS': 86}
    Chain: "C"
      Number of atoms: 2756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2756
          Classifications: {'peptide': 349}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 332}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 7.18, per 1000 atoms: 0.64
  Number of scatterers: 11202
  At special positions: 0
  Unit cell: (97.9, 108.9, 134.2, 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      88     16.00
     O    2029      8.00
     N    1964      7.00
     C    7121      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: 2.64
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2674

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 12 sheets defined
      45.9% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 70
      removed outlier: 4.331A  pdb=" N   GLY A  64 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A  65 " --> pdb=" O   SER A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 91
    Processing helix  chain 'A' and resid 97 through 104
      removed outlier: 3.523A  pdb=" N   ALA A 104 " --> pdb=" O   GLU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 118
    Processing helix  chain 'A' and resid 118 through 133
    Processing helix  chain 'A' and resid 136 through 150
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.621A  pdb=" N   ARG A 250 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 269
    Processing helix  chain 'A' and resid 291 through 306
    Processing helix  chain 'A' and resid 321 through 327
      removed outlier: 3.771A  pdb=" N   LYS A 327 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 340
      removed outlier: 3.971A  pdb=" N   TRP A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 351
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 3.759A  pdb=" N   LEU A 367 " --> pdb=" O   PHE A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 3.907A  pdb=" N   ASN A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 410 through 418
    Processing helix  chain 'A' and resid 473 through 483
    Processing helix  chain 'A' and resid 497 through 511
      removed outlier: 3.544A  pdb=" N   LEU A 501 " --> pdb=" O   THR A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 542
    Processing helix  chain 'A' and resid 547 through 555
    Processing helix  chain 'A' and resid 557 through 565
    Processing helix  chain 'A' and resid 585 through 598
    Processing helix  chain 'A' and resid 618 through 625
      removed outlier: 3.889A  pdb=" N   LYS A 622 " --> pdb=" O   SER A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 640
      removed outlier: 4.254A  pdb=" N   MET A 633 " --> pdb=" O   HIS A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 654
      Proline residue:  A 648  - end of helix
    Processing helix  chain 'A' and resid 660 through 674
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 696 through 705
    Processing helix  chain 'A' and resid 716 through 728
      removed outlier: 3.556A  pdb=" N   LEU A 720 " --> pdb=" O   GLN A 716 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   GLN A 728 " --> pdb=" O   SER A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 762
    Processing helix  chain 'A' and resid 764 through 780
    Processing helix  chain 'A' and resid 794 through 807
      removed outlier: 4.292A  pdb=" N   HIS A 807 " --> pdb=" O   ALA A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 828
      removed outlier: 4.859A  pdb=" N   GLN A 827 " --> pdb=" O   PRO A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 829 through 836
      removed outlier: 3.915A  pdb=" N   VAL A 833 " --> pdb=" O   LEU A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 862
    Processing helix  chain 'A' and resid 879 through 893
    Processing helix  chain 'A' and resid 907 through 920
      Proline residue:  A 913  - end of helix
      removed outlier: 3.825A  pdb=" N   VAL A 920 " --> pdb=" O   ASP A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 936 through 950
    Processing helix  chain 'A' and resid 963 through 976
      removed outlier: 3.643A  pdb=" N   GLY A 967 " --> pdb=" O   LEU A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1005
      removed outlier: 3.515A  pdb=" N   MET A1005 " --> pdb=" O   ALA A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1033
    Processing helix  chain 'A' and resid 1050 through 1064
    Processing helix  chain 'A' and resid 1077 through 1090
      removed outlier: 3.684A  pdb=" N   GLY A1081 " --> pdb=" O   LEU A1077 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL A1082 " --> pdb=" O   GLY A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1107 through 1121
    Processing helix  chain 'A' and resid 1135 through 1148
      removed outlier: 3.524A  pdb=" N   CYS A1148 " --> pdb=" O   SER A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1177
    Processing helix  chain 'A' and resid 1192 through 1200
      removed outlier: 4.444A  pdb=" N   TYR A1196 " --> pdb=" O   GLU A1192 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS A1199 " --> pdb=" O   ARG A1195 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN A1200 " --> pdb=" O   TYR A1196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 47
    Processing helix  chain 'B' and resid 56 through 64
    Processing helix  chain 'B' and resid 69 through 78
    Processing helix  chain 'B' and resid 99 through 124
    Processing helix  chain 'C' and resid 154 through 169
      removed outlier: 4.159A  pdb=" N   THR C 158 " --> pdb=" O   PHE C 154 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU C 159 " --> pdb=" O   TRP C 155 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY C 169 " --> pdb=" O   ARG C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 254
    Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 408
      removed outlier: 6.545A  pdb=" N   VAL A 283 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   VAL A 429 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   HIS A 285 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 320
      removed outlier: 3.501A  pdb=" N   ASP A 362 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 714
      removed outlier: 3.749A  pdb=" N   ARG A 737 " --> pdb=" O   VAL A 710 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP A 739 " --> pdb=" O   LEU A 712 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ILE A 736 " --> pdb=" O   ASP A 787 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 788 " --> pdb=" O   MET A 816 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 815 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLY A 845 " --> pdb=" O   PHE A 817 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU A 871 " --> pdb=" O   SER A 898 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A 902 " --> pdb=" O   LEU A 873 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU A 931 " --> pdb=" O   LEU A 901 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER A 959 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET A 986 " --> pdb=" O   LEU A 956 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU A1043 " --> pdb=" O   LEU A1013 " (cutoff:3.500A)
      removed outlier: 9.324A  pdb=" N   THR A1073 " --> pdb=" O   LEU A1042 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   LEU A1044 " --> pdb=" O   THR A1073 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   LEU A1072 " --> pdb=" O   LYS A1102 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   LEU A1101 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1155 through 1156
    Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 55
      removed outlier: 3.526A  pdb=" N   LEU B  80 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 321
      removed outlier: 8.540A  pdb=" N   ASP C 321 " --> pdb=" O   MET C 280 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ILE C 282 " --> pdb=" O   ASP C 321 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS C 276 " --> pdb=" O   THR C 571 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR C 571 " --> pdb=" O   LYS C 276 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU C 278 " --> pdb=" O   GLN C 569 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL C 567 " --> pdb=" O   MET C 280 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   ILE C 282 " --> pdb=" O   ALA C 565 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ALA C 565 " --> pdb=" O   ILE C 282 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   CYS C 547 " --> pdb=" O   GLY C 560 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 291 through 294
      removed outlier: 3.859A  pdb=" N   ALA C 291 " --> pdb=" O   CYS C 304 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 339 through 342
      removed outlier: 3.514A  pdb=" N   THR C 339 " --> pdb=" O   GLY C 352 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   GLY C 352 " --> pdb=" O   THR C 339 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL C 361 " --> pdb=" O   GLU C 373 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLU C 373 " --> pdb=" O   VAL C 361 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ASP C 363 " --> pdb=" O   VAL C 371 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL C 371 " --> pdb=" O   ASP C 363 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 382 through 388
      removed outlier: 3.774A  pdb=" N   ALA C 384 " --> pdb=" O   SER C 397 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL C 402 " --> pdb=" O   PHE C 398 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL C 403 " --> pdb=" O   ASP C 416 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   ASP C 416 " --> pdb=" O   VAL C 403 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ILE C 405 " --> pdb=" O   VAL C 414 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 426 through 430
      removed outlier: 3.773A  pdb=" N   SER C 426 " --> pdb=" O   GLY C 437 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLY C 437 " --> pdb=" O   SER C 426 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU C 455 " --> pdb=" O   CYS C 445 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 465 through 468
      removed outlier: 4.213A  pdb=" N   SER C 465 " --> pdb=" O   GLY C 478 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY C 478 " --> pdb=" O   SER C 465 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLY C 498 " --> pdb=" O   GLN C 484 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU C 486 " --> pdb=" O   MET C 496 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   MET C 496 " --> pdb=" O   LEU C 486 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 504 through 509
      removed outlier: 3.582A  pdb=" N   TRP C 516 " --> pdb=" O   TYR C 528 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY C 520 " --> pdb=" O   PHE C 524 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   PHE C 524 " --> pdb=" O   GLY C 520 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE C 537 " --> pdb=" O   VAL C 527 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   SER C 529 " --> pdb=" O   LYS C 535 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   LYS C 535 " --> pdb=" O   SER C 529 " (cutoff:3.500A)

    519 hydrogen bonds defined for protein.
    1503 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: 4.64

  Time building geometry restraints manager: 3.19 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3093
        1.33 -     1.45: 1871
        1.45 -     1.57: 6359
        1.57 -     1.69: 0
        1.69 -     1.81: 123
  Bond restraints: 11446
  Sorted by residual:
  bond pdb=" N   PHE A 744 "
       pdb=" CA  PHE A 744 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.29e-02 6.01e+03 8.02e+00
  bond pdb=" N   ARG A 136 "
       pdb=" CA  ARG A 136 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.31e-02 5.83e+03 6.98e+00
  bond pdb=" N   LEU A 135 "
       pdb=" CA  LEU A 135 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.21e-02 6.83e+03 6.05e+00
  bond pdb=" N   MET A 133 "
       pdb=" CA  MET A 133 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.42e-02 4.96e+03 5.74e+00
  bond pdb=" N   ARG A 746 "
       pdb=" CA  ARG A 746 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.029 1.31e-02 5.83e+03 4.77e+00
  ... (remaining 11441 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 15006
        1.57 -     3.15: 401
        3.15 -     4.72: 70
        4.72 -     6.29: 19
        6.29 -     7.86: 5
  Bond angle restraints: 15501
  Sorted by residual:
  angle pdb=" N   GLU B  61 "
        pdb=" CA  GLU B  61 "
        pdb=" CB  GLU B  61 "
      ideal   model   delta    sigma   weight residual
     110.30  115.78   -5.48 1.54e+00 4.22e-01 1.27e+01
  angle pdb=" C   ASP B  60 "
        pdb=" N   GLU B  61 "
        pdb=" CA  GLU B  61 "
      ideal   model   delta    sigma   weight residual
     120.68  114.75    5.93 1.70e+00 3.46e-01 1.22e+01
  angle pdb=" C   PHE A 744 "
        pdb=" CA  PHE A 744 "
        pdb=" CB  PHE A 744 "
      ideal   model   delta    sigma   weight residual
     109.52  114.90   -5.38 1.58e+00 4.01e-01 1.16e+01
  angle pdb=" CA  TRP A1198 "
        pdb=" CB  TRP A1198 "
        pdb=" CG  TRP A1198 "
      ideal   model   delta    sigma   weight residual
     113.60  108.07    5.53 1.90e+00 2.77e-01 8.48e+00
  angle pdb=" C   LYS A 242 "
        pdb=" N   PHE A 243 "
        pdb=" CA  PHE A 243 "
      ideal   model   delta    sigma   weight residual
     121.14  116.26    4.88 1.75e+00 3.27e-01 7.76e+00
  ... (remaining 15496 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 6238
       17.08 -    34.16: 507
       34.16 -    51.24: 99
       51.24 -    68.32: 16
       68.32 -    85.40: 11
  Dihedral angle restraints: 6871
    sinusoidal: 2768
      harmonic: 4103
  Sorted by residual:
  dihedral pdb=" CD  ARG A 746 "
           pdb=" NE  ARG A 746 "
           pdb=" CZ  ARG A 746 "
           pdb=" NH1 ARG A 746 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   37.62  -37.62     1      1.00e+01 1.00e-02 2.00e+01
  dihedral pdb=" CA  TRP A1187 "
           pdb=" C   TRP A1187 "
           pdb=" N   HIS A1188 "
           pdb=" CA  HIS A1188 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  GLU A 246 "
           pdb=" C   GLU A 246 "
           pdb=" N   GLU A 247 "
           pdb=" CA  GLU A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 6868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1316
       0.045 -    0.089: 300
       0.089 -    0.134: 117
       0.134 -    0.179: 10
       0.179 -    0.224: 3
  Chirality restraints: 1746
  Sorted by residual:
  chirality pdb=" CA  LEU A 135 "
            pdb=" N   LEU A 135 "
            pdb=" C   LEU A 135 "
            pdb=" CB  LEU A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  TRP A1187 "
            pdb=" N   TRP A1187 "
            pdb=" C   TRP A1187 "
            pdb=" CB  TRP A1187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  ILE C 451 "
            pdb=" CA  ILE C 451 "
            pdb=" CG1 ILE C 451 "
            pdb=" CG2 ILE C 451 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.09e-01
  ... (remaining 1743 not shown)

  Planarity restraints: 1965
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 746 "    0.662 9.50e-02 1.11e+02   2.97e-01 5.37e+01
        pdb=" NE  ARG A 746 "   -0.039 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 746 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 746 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 746 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 132 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.64e+00
        pdb=" C   ASN A 132 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASN A 132 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 133 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 657 "   -0.031 5.00e-02 4.00e+02   4.71e-02 3.54e+00
        pdb=" N   PRO A 658 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 658 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 658 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1962 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 110
        2.64 -     3.20: 9906
        3.20 -     3.77: 16292
        3.77 -     4.33: 22037
        4.33 -     4.90: 36854
  Nonbonded interactions: 85199
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 358 "
            pdb=" OE1 GLN C 374 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" NH1 ARG C 415 "
            pdb=" O   ASP C 416 "
     model   vdw
     2.152 3.120
  nonbonded pdb=" NH2 ARG A 513 "
            pdb=" O   ALA A 563 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" OE2 GLU C 541 "
            pdb=" OH  TYR C 568 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG  SER A 642 "
            pdb=" OD1 ASP A 644 "
     model   vdw
     2.199 3.040
  ... (remaining 85194 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     30.840
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
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      :  0.003   0.037  11446  Z= 0.160
  Angle     :  0.646   7.863  15501  Z= 0.342
  Chirality :  0.044   0.224   1746
  Planarity :  0.008   0.297   1965
  Dihedral  : 13.389  85.402   4197
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.32 %
    Favored  : 99.60 %
  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:  0.16 (0.22), residues: 1396
  helix:  1.05 (0.21), residues: 602
  sheet: -0.09 (0.31), residues: 285
  loop : -0.81 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 115 
 HIS   0.009   0.001   HIS A 627 
 PHE   0.031   0.002   PHE A 243 
 TYR   0.011   0.002   TYR C 420 
 ARG   0.005   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17376 (  519)
  hydrogen bonds       : angle       6.15355 ( 1503)
  covalent geometry    : bond        0.00335 (11446)
  covalent geometry    : angle       0.64616 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  745 PRO cc_start: 0.7357 (Cg_endo) cc_final: 0.7109 (Cg_exo)
REVERT: A  912 MET cc_start: 0.7428 (mtm) cc_final: 0.7108 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2616
  time to fit residues: 68.1876
Evaluate side-chains
  128 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 127 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 HIS
A 629 HIS
** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 838 ASN
** A 955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS
A1188 HIS
C 487 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.203311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.161454 restraints weight = 12212.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.4263 rms_B_bonded: 2.50
r_work: 0.4012 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  11446  Z= 0.304
  Angle     :  0.818  10.274  15501  Z= 0.421
  Chirality :  0.051   0.199   1746
  Planarity :  0.006   0.044   1965
  Dihedral  :  5.358  28.733   1515
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.86 %
    Favored  : 88.28 %
  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: -0.19 (0.22), residues: 1396
  helix:  0.82 (0.20), residues: 601
  sheet: -0.13 (0.31), residues: 275
  loop : -1.17 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP C 516 
 HIS   0.011   0.002   HIS A 627 
 PHE   0.027   0.003   PHE A 335 
 TYR   0.023   0.003   TYR C 528 
 ARG   0.008   0.001   ARG C 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07427 (  519)
  hydrogen bonds       : angle       5.25355 ( 1503)
  covalent geometry    : bond        0.00744 (11446)
  covalent geometry    : angle       0.81828 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  323 GLU cc_start: 0.7439 (mp0) cc_final: 0.7025 (mp0)
REVERT: A  745 PRO cc_start: 0.7363 (Cg_endo) cc_final: 0.7110 (Cg_exo)
REVERT: A  838 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8196 (t0)
REVERT: A  863 HIS cc_start: 0.7065 (t70) cc_final: 0.6639 (t70)
  outliers start: 23
  outliers final: 18
  residues processed: 155
  average time/residue: 0.2294
  time to fit residues: 51.3094
Evaluate side-chains
  150 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  838 ASN
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1022 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1094 SER
Chi-restraints excluded: chain A residue 1198 TRP
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  303 THR
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  426 SER
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  495 HIS
Chi-restraints excluded: chain C residue  549 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 139 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 126 optimal weight:    5.9990
   chunk 123 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0010
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 ASN
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS
A1152 ASN
A1188 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.208079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.165241 restraints weight = 12054.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.4328 rms_B_bonded: 2.79
r_work: 0.4107 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11446  Z= 0.122
  Angle     :  0.561   7.901  15501  Z= 0.291
  Chirality :  0.042   0.171   1746
  Planarity :  0.004   0.039   1965
  Dihedral  :  4.722  20.178   1515
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.85 %
    Favored  : 84.96 %
  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:  0.38 (0.23), residues: 1396
  helix:  1.36 (0.21), residues: 607
  sheet: -0.01 (0.32), residues: 280
  loop : -0.89 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1198 
 HIS   0.006   0.001   HIS A1012 
 PHE   0.025   0.001   PHE A 243 
 TYR   0.011   0.001   TYR A  63 
 ARG   0.004   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04541 (  519)
  hydrogen bonds       : angle       4.68695 ( 1503)
  covalent geometry    : bond        0.00263 (11446)
  covalent geometry    : angle       0.56071 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  745 PRO cc_start: 0.6910 (Cg_endo) cc_final: 0.6671 (Cg_exo)
REVERT: A  863 HIS cc_start: 0.7160 (t70) cc_final: 0.6747 (t70)
  outliers start: 27
  outliers final: 17
  residues processed: 151
  average time/residue: 0.2310
  time to fit residues: 50.8224
Evaluate side-chains
  144 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1044 LEU
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1152 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain C residue  426 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0170
   chunk 16 optimal weight:    0.0370
   chunk 47 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.0102

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

Flipped N/Q/H residues before XYZ refinement:
A 285 HIS
A 502 HIS
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1152 ASN
A1188 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.209555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.165533 restraints weight = 12167.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.4315 rms_B_bonded: 2.81
r_work: 0.4078 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11446  Z= 0.129
  Angle     :  0.569   9.955  15501  Z= 0.291
  Chirality :  0.042   0.178   1746
  Planarity :  0.004   0.040   1965
  Dihedral  :  4.604  20.261   1515
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.04 %
    Favored  : 82.62 %
  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:  0.49 (0.23), residues: 1396
  helix:  1.46 (0.21), residues: 608
  sheet:  0.05 (0.32), residues: 278
  loop : -0.84 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 516 
 HIS   0.006   0.001   HIS A 238 
 PHE   0.022   0.001   PHE A 243 
 TYR   0.011   0.001   TYR A  63 
 ARG   0.005   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04568 (  519)
  hydrogen bonds       : angle       4.59097 ( 1503)
  covalent geometry    : bond        0.00292 (11446)
  covalent geometry    : angle       0.56946 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  745 PRO cc_start: 0.6848 (Cg_endo) cc_final: 0.6588 (Cg_exo)
REVERT: A  863 HIS cc_start: 0.7153 (t70) cc_final: 0.6736 (t70)
REVERT: A 1086 CYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7815 (t)
REVERT: A 1111 CYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5815 (p)
REVERT: B   36 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7761 (mt)
REVERT: B  109 MET cc_start: 0.7823 (mtp) cc_final: 0.7598 (mtp)
REVERT: C  165 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7457 (mmm-85)
  outliers start: 29
  outliers final: 20
  residues processed: 149
  average time/residue: 0.2789
  time to fit residues: 62.1096
Evaluate side-chains
  153 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1044 LEU
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1111 CYS
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  247 ILE
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  426 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 30 optimal weight:    0.0570
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 128 optimal weight:    0.5980
   chunk 1 optimal weight:    0.2980
   chunk 32 optimal weight:    0.1980
   chunk 98 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 137 optimal weight:    0.8980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS
A1152 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.207149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.164856 restraints weight = 12135.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.4429 rms_B_bonded: 2.70
r_work: 0.4200 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11446  Z= 0.100
  Angle     :  0.515   8.648  15501  Z= 0.264
  Chirality :  0.040   0.175   1746
  Planarity :  0.004   0.038   1965
  Dihedral  :  4.327  18.984   1515
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.68 %
    Favored  : 81.89 %
  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:  0.74 (0.23), residues: 1396
  helix:  1.65 (0.21), residues: 603
  sheet:  0.18 (0.32), residues: 282
  loop : -0.66 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 668 
 HIS   0.005   0.001   HIS A 238 
 PHE   0.025   0.001   PHE A 243 
 TYR   0.008   0.001   TYR A  63 
 ARG   0.005   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03671 (  519)
  hydrogen bonds       : angle       4.39633 ( 1503)
  covalent geometry    : bond        0.00212 (11446)
  covalent geometry    : angle       0.51463 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6665 (mt)
REVERT: A  534 MET cc_start: 0.6347 (ttp) cc_final: 0.6039 (ptm)
REVERT: A  745 PRO cc_start: 0.6657 (Cg_endo) cc_final: 0.6413 (Cg_exo)
REVERT: A  863 HIS cc_start: 0.7110 (t70) cc_final: 0.6703 (t70)
REVERT: A 1086 CYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7751 (t)
REVERT: A 1111 CYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5655 (p)
REVERT: C  165 ARG cc_start: 0.7643 (mmt90) cc_final: 0.7320 (mmm-85)
  outliers start: 30
  outliers final: 14
  residues processed: 151
  average time/residue: 0.2232
  time to fit residues: 49.4436
Evaluate side-chains
  147 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1044 LEU
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1111 CYS
Chi-restraints excluded: chain A residue 1152 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  426 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.0370
   chunk 134 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0570
   chunk 41 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 116 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9980
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS
A1152 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.207552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.164911 restraints weight = 12206.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.4431 rms_B_bonded: 2.78
r_work: 0.4206 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11446  Z= 0.099
  Angle     :  0.530   9.564  15501  Z= 0.268
  Chirality :  0.040   0.233   1746
  Planarity :  0.004   0.037   1965
  Dihedral  :  4.217  18.418   1515
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.57 %
    Favored  : 80.84 %
  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:  0.86 (0.23), residues: 1396
  helix:  1.74 (0.21), residues: 603
  sheet:  0.22 (0.32), residues: 275
  loop : -0.58 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 516 
 HIS   0.007   0.001   HIS A 238 
 PHE   0.020   0.001   PHE A 243 
 TYR   0.010   0.001   TYR A 732 
 ARG   0.006   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  519)
  hydrogen bonds       : angle       4.32474 ( 1503)
  covalent geometry    : bond        0.00214 (11446)
  covalent geometry    : angle       0.52966 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 MET cc_start: 0.5244 (ppp) cc_final: 0.3870 (ptp)
REVERT: A  534 MET cc_start: 0.6367 (ttp) cc_final: 0.6042 (ptm)
REVERT: A  745 PRO cc_start: 0.6535 (Cg_endo) cc_final: 0.6290 (Cg_exo)
REVERT: A  863 HIS cc_start: 0.7107 (t70) cc_final: 0.6709 (t70)
REVERT: A 1086 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7701 (t)
REVERT: A 1111 CYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5615 (p)
REVERT: C  165 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7318 (mmm-85)
  outliers start: 32
  outliers final: 20
  residues processed: 156
  average time/residue: 0.2167
  time to fit residues: 50.3745
Evaluate side-chains
  152 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1044 LEU
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1111 CYS
Chi-restraints excluded: chain A residue 1152 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  426 SER
Chi-restraints excluded: chain C residue  525 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 124 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0980
   chunk 112 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 119 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 120 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.201114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.153450 restraints weight = 12470.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.4163 rms_B_bonded: 3.00
r_work: 0.4010 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055  11446  Z= 0.104
  Angle     :  0.535  11.000  15501  Z= 0.268
  Chirality :  0.041   0.209   1746
  Planarity :  0.003   0.036   1965
  Dihedral  :  4.176  18.051   1515
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.25 %
    Favored  : 81.08 %
  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:  0.86 (0.23), residues: 1396
  helix:  1.72 (0.21), residues: 603
  sheet:  0.23 (0.32), residues: 275
  loop : -0.56 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 516 
 HIS   0.008   0.001   HIS A 238 
 PHE   0.021   0.001   PHE A 243 
 TYR   0.009   0.001   TYR A  63 
 ARG   0.006   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  519)
  hydrogen bonds       : angle       4.29775 ( 1503)
  covalent geometry    : bond        0.00229 (11446)
  covalent geometry    : angle       0.53524 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 MET cc_start: 0.4969 (ppp) cc_final: 0.3821 (ptp)
REVERT: A  534 MET cc_start: 0.6571 (ttp) cc_final: 0.6137 (ptm)
REVERT: A  674 GLN cc_start: 0.5325 (OUTLIER) cc_final: 0.4916 (mt0)
REVERT: A  745 PRO cc_start: 0.6574 (Cg_endo) cc_final: 0.6310 (Cg_exo)
REVERT: A  863 HIS cc_start: 0.7161 (t70) cc_final: 0.6625 (t70)
REVERT: A 1086 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7830 (t)
REVERT: A 1111 CYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5550 (p)
REVERT: C  165 ARG cc_start: 0.7250 (mmt90) cc_final: 0.6905 (mmm-85)
  outliers start: 33
  outliers final: 21
  residues processed: 153
  average time/residue: 0.2114
  time to fit residues: 48.8458
Evaluate side-chains
  152 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  674 GLN
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1044 LEU
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1111 CYS
Chi-restraints excluded: chain A residue 1198 TRP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  247 ILE
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  426 SER
Chi-restraints excluded: chain C residue  525 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 105 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0270
   chunk 73 optimal weight:    2.9990
   chunk 134 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 131 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.8040

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS
A1188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.199464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.151908 restraints weight = 12480.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 3.00
r_work: 0.3994 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
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   0.043  11446  Z= 0.114
  Angle     :  0.549   9.745  15501  Z= 0.277
  Chirality :  0.041   0.191   1746
  Planarity :  0.004   0.038   1965
  Dihedral  :  4.209  18.410   1515
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.57 %
    Favored  : 80.92 %
  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 (0.23), residues: 1396
  helix:  1.68 (0.21), residues: 604
  sheet:  0.20 (0.32), residues: 273
  loop : -0.56 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 115 
 HIS   0.007   0.001   HIS A 238 
 PHE   0.020   0.001   PHE A 243 
 TYR   0.010   0.001   TYR A  63 
 ARG   0.005   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  519)
  hydrogen bonds       : angle       4.32038 ( 1503)
  covalent geometry    : bond        0.00260 (11446)
  covalent geometry    : angle       0.54868 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 MET cc_start: 0.4885 (ppp) cc_final: 0.3729 (ptp)
REVERT: A  323 GLU cc_start: 0.6365 (mp0) cc_final: 0.5316 (tt0)
REVERT: A  534 MET cc_start: 0.6404 (ttp) cc_final: 0.5978 (ptm)
REVERT: A  745 PRO cc_start: 0.6594 (Cg_endo) cc_final: 0.6323 (Cg_exo)
REVERT: A  863 HIS cc_start: 0.7184 (t70) cc_final: 0.6572 (t-90)
REVERT: A 1086 CYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7845 (t)
REVERT: A 1111 CYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5587 (p)
REVERT: C  165 ARG cc_start: 0.7266 (mmt90) cc_final: 0.6912 (mmm-85)
  outliers start: 31
  outliers final: 24
  residues processed: 151
  average time/residue: 0.2063
  time to fit residues: 47.5321
Evaluate side-chains
  155 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1044 LEU
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1111 CYS
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1198 TRP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  247 ILE
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  426 SER
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  566 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 101 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 138 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 135 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.197895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.150374 restraints weight = 12379.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 2.99
r_work: 0.3981 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11446  Z= 0.122
  Angle     :  0.564  10.287  15501  Z= 0.284
  Chirality :  0.042   0.179   1746
  Planarity :  0.004   0.038   1965
  Dihedral  :  4.269  18.873   1515
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.33 %
    Favored  : 80.68 %
  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:  0.77 (0.23), residues: 1396
  helix:  1.62 (0.21), residues: 604
  sheet:  0.17 (0.32), residues: 275
  loop : -0.56 (0.28), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 115 
 HIS   0.008   0.001   HIS A 238 
 PHE   0.020   0.001   PHE A 243 
 TYR   0.011   0.001   TYR C 568 
 ARG   0.005   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  519)
  hydrogen bonds       : angle       4.36663 ( 1503)
  covalent geometry    : bond        0.00281 (11446)
  covalent geometry    : angle       0.56441 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 126
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 MET cc_start: 0.4892 (ppp) cc_final: 0.3717 (ptp)
REVERT: A  534 MET cc_start: 0.6364 (ttp) cc_final: 0.5984 (ptm)
REVERT: A  674 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.5021 (mt0)
REVERT: A  745 PRO cc_start: 0.6600 (Cg_endo) cc_final: 0.6325 (Cg_exo)
REVERT: A  863 HIS cc_start: 0.7108 (t70) cc_final: 0.6550 (t-90)
REVERT: A 1086 CYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7817 (t)
REVERT: A 1111 CYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5643 (p)
REVERT: C  165 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6899 (mmm-85)
  outliers start: 37
  outliers final: 24
  residues processed: 153
  average time/residue: 0.2299
  time to fit residues: 54.9106
Evaluate side-chains
  150 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  674 GLN
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1044 LEU
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1111 CYS
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1198 TRP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  247 ILE
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  426 SER
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  566 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 16 optimal weight:    0.1980
   chunk 75 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 117 optimal weight:    0.0050
   chunk 112 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0570
   chunk 70 optimal weight:    0.0770
   overall best weight:    0.2670

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS
A1188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.203047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.156146 restraints weight = 12294.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.4187 rms_B_bonded: 3.01
r_work: 0.4029 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11446  Z= 0.095
  Angle     :  0.537  11.026  15501  Z= 0.266
  Chirality :  0.041   0.183   1746
  Planarity :  0.003   0.036   1965
  Dihedral  :  4.036  17.493   1515
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.46 %
    Favored  : 80.68 %
  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:  0.90 (0.23), residues: 1396
  helix:  1.69 (0.21), residues: 604
  sheet:  0.27 (0.33), residues: 275
  loop : -0.46 (0.28), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 115 
 HIS   0.008   0.001   HIS A 238 
 PHE   0.021   0.001   PHE A 243 
 TYR   0.007   0.001   TYR A  63 
 ARG   0.006   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03223 (  519)
  hydrogen bonds       : angle       4.23696 ( 1503)
  covalent geometry    : bond        0.00206 (11446)
  covalent geometry    : angle       0.53680 (15501)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 MET cc_start: 0.4936 (ppp) cc_final: 0.3814 (ptp)
REVERT: A  406 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6331 (mt)
REVERT: A  534 MET cc_start: 0.6507 (ttp) cc_final: 0.6105 (ptm)
REVERT: A  674 GLN cc_start: 0.5140 (OUTLIER) cc_final: 0.4757 (mt0)
REVERT: A  745 PRO cc_start: 0.6399 (Cg_endo) cc_final: 0.6066 (Cg_exo)
REVERT: A  798 MET cc_start: 0.7343 (tpp) cc_final: 0.7040 (mmt)
REVERT: A  863 HIS cc_start: 0.7176 (t70) cc_final: 0.6544 (t-90)
REVERT: A 1086 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7793 (t)
REVERT: A 1111 CYS cc_start: 0.6059 (OUTLIER) cc_final: 0.5506 (p)
REVERT: C  165 ARG cc_start: 0.7163 (mmt90) cc_final: 0.6819 (mmm-85)
REVERT: C  282 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7738 (tp)
REVERT: C  479 MET cc_start: 0.7832 (mmm) cc_final: 0.6539 (mmm)
  outliers start: 23
  outliers final: 15
  residues processed: 146
  average time/residue: 0.2517
  time to fit residues: 57.2987
Evaluate side-chains
  147 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 1.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  674 GLN
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1111 CYS
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  426 SER
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  566 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 133 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 94 optimal weight:    0.6980
   chunk 88 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 HIS
A1188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.200867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.153357 restraints weight = 12321.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.4162 rms_B_bonded: 2.98
r_work: 0.4008 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11446  Z= 0.114
  Angle     :  0.561  11.161  15501  Z= 0.278
  Chirality :  0.042   0.181   1746
  Planarity :  0.004   0.038   1965
  Dihedral  :  4.074  18.009   1515
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.87 %
    Favored  : 80.36 %
  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:  0.86 (0.23), residues: 1396
  helix:  1.64 (0.21), residues: 604
  sheet:  0.25 (0.32), residues: 275
  loop : -0.45 (0.28), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 115 
 HIS   0.018   0.001   HIS A 114 
 PHE   0.022   0.001   PHE A 243 
 TYR   0.014   0.001   TYR C 354 
 ARG   0.005   0.000   ARG C 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03656 (  519)
  hydrogen bonds       : angle       4.26165 ( 1503)
  covalent geometry    : bond        0.00265 (11446)
  covalent geometry    : angle       0.56101 (15501)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6827.47 seconds
wall clock time: 119 minutes 53.14 seconds (7193.14 seconds total)