Starting phenix.real_space_refine
on Tue Jun 10 03:15:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d45_46549/06_2025/9d45_46549.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d45_46549/06_2025/9d45_46549.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d45_46549/06_2025/9d45_46549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d45_46549/06_2025/9d45_46549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d45_46549/06_2025/9d45_46549.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d45_46549/06_2025/9d45_46549.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.015
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      1      5.21       5
     S      59      5.16       5
     C    7177      2.51       5
     N    1822      2.21       5
     O    2059      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11123
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9508
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1160, 9497
          Classifications: {'peptide': 1160}
          Link IDs: {'PTRANS': 44, 'TRANS': 1115}
      Conformer: "B"
        Number of residues, atoms: 1160, 9497
          Classifications: {'peptide': 1160}
          Link IDs: {'PTRANS': 44, 'TRANS': 1115}
          bond proxies already assigned to first conformer: 9695
    Chain: "B"
      Number of atoms: 1404
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 171, 1393
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 6, 'TRANS': 164}
      Conformer: "B"
        Number of residues, atoms: 171, 1393
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 6, 'TRANS': 164}
          bond proxies already assigned to first conformer: 1416
    Chain: "C"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 178
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 3, 'TRANS': 19}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  APHE A 580 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 580 " occ=0.50
    residue:
      pdb=" N  AARG B  78 " occ=0.36
      ... (20 atoms not shown)
      pdb=" NH2BARG B  78 " occ=0.64
  Time building chain proxies: 12.93, per 1000 atoms: 1.16
  Number of scatterers: 11123
  At special positions: 0
  Unit cell: (83.426, 103.25, 123.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      59     16.00
     P       5     15.00
     Mg      1     11.99
     O    2059      8.00
     N    1822      7.00
     C    7177      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: 2.95
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2622

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 1 sheets defined
      77.3% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
      removed outlier: 3.643A  pdb=" N   ILE A   9 " --> pdb=" O   GLY A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 38
    Processing helix  chain 'A' and resid 41 through 53
      removed outlier: 3.931A  pdb=" N   ASN A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 73
    Processing helix  chain 'A' and resid 79 through 96
    Processing helix  chain 'A' and resid 102 through 121
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.660A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 141 through 150
    Processing helix  chain 'A' and resid 153 through 172
    Processing helix  chain 'A' and resid 176 through 182
      removed outlier: 3.618A  pdb=" N   ARG A 182 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 196 through 204
      removed outlier: 3.564A  pdb=" N   ILE A 202 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 214
      removed outlier: 3.693A  pdb=" N   THR A 211 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS A 214 " --> pdb=" O   TRP A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 235
      Proline residue:  A 226  - end of helix
    Processing helix  chain 'A' and resid 236 through 249
      removed outlier: 4.162A  pdb=" N   THR A 249 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 3.670A  pdb=" N   ILE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 273
    Processing helix  chain 'A' and resid 276 through 293
    Processing helix  chain 'A' and resid 297 through 310
      removed outlier: 3.565A  pdb=" N   TYR A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 323
    Processing helix  chain 'A' and resid 334 through 347
    Processing helix  chain 'A' and resid 348 through 355
      Proline residue:  A 353  - end of helix
    Processing helix  chain 'A' and resid 360 through 374
    Processing helix  chain 'A' and resid 377 through 382
    Processing helix  chain 'A' and resid 384 through 394
    Processing helix  chain 'A' and resid 397 through 403
      removed outlier: 4.043A  pdb=" N   LYS A 403 " --> pdb=" O   PRO A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 416
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 427 through 436
      removed outlier: 4.174A  pdb=" N   PHE A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ILE A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 464
    Processing helix  chain 'A' and resid 464 through 482
    Processing helix  chain 'A' and resid 482 through 490
    Processing helix  chain 'A' and resid 498 through 525
      removed outlier: 3.643A  pdb=" N   ALA A 504 " --> pdb=" O   PRO A 500 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ILE A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
    Processing helix  chain 'A' and resid 556 through 575
      removed outlier: 3.948A  pdb=" N   LYS A 562 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   LEU A 569 " --> pdb=" O   GLN A 565 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   MET A 573 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 590
    Processing helix  chain 'A' and resid 598 through 602
      removed outlier: 4.037A  pdb=" N   GLU A 601 " --> pdb=" O   ASN A 598 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ARG A 602 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 598 through 602'
    Processing helix  chain 'A' and resid 603 through 627
      removed outlier: 3.902A  pdb=" N   ALA A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 633
      removed outlier: 3.726A  pdb=" N   LEU A 631 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS A 633 " --> pdb=" O   GLU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 646
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 650 through 668
    Processing helix  chain 'A' and resid 672 through 686
      removed outlier: 3.502A  pdb=" N   ARG A 676 " --> pdb=" O   MET A 672 " (cutoff:3.500A)
      Proline residue:  A 683  - end of helix
    Processing helix  chain 'A' and resid 687 through 689
      No H-bonds generated for 'chain 'A' and resid 687 through 689'
    Processing helix  chain 'A' and resid 690 through 697
    Processing helix  chain 'A' and resid 699 through 708
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'A' and resid 733 through 751
    Processing helix  chain 'A' and resid 752 through 765
    Processing helix  chain 'A' and resid 769 through 785
      Proline residue:  A 782  - end of helix
    Processing helix  chain 'A' and resid 787 through 801
    Processing helix  chain 'A' and resid 802 through 807
      removed outlier: 6.221A  pdb=" N   ASP A 805 " --> pdb=" O   HIS A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 813
      No H-bonds generated for 'chain 'A' and resid 811 through 813'
    Processing helix  chain 'A' and resid 814 through 823
      removed outlier: 3.624A  pdb=" N   LYS A 819 " --> pdb=" O   GLN A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 848
      removed outlier: 3.550A  pdb=" N   MET A 847 " --> pdb=" O   HIS A 843 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   GLN A 848 " --> pdb=" O   MET A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 878
      removed outlier: 3.705A  pdb=" N   ALA A 854 " --> pdb=" O   LEU A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 885
      removed outlier: 4.026A  pdb=" N   TYR A 883 " --> pdb=" O   GLY A 879 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   LEU A 885 " --> pdb=" O   VAL A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 897
      removed outlier: 3.557A  pdb=" N   SER A 895 " --> pdb=" O   LEU A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 922
    Processing helix  chain 'A' and resid 922 through 929
    Processing helix  chain 'A' and resid 934 through 968
      Proline residue:  A 940  - end of helix
      Proline residue:  A 944  - end of helix
      removed outlier: 3.857A  pdb=" N   GLU A 948 " --> pdb=" O   PRO A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 1002
      removed outlier: 3.584A  pdb=" N   MET A 977 " --> pdb=" O   ASP A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1029
      removed outlier: 3.524A  pdb=" N   ARG A1024 " --> pdb=" O   GLN A1020 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS A1025 " --> pdb=" O   MET A1021 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ILE A1026 " --> pdb=" O   GLU A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1047
      Proline residue:  A1036  - end of helix
    Processing helix  chain 'A' and resid 1049 through 1068
      removed outlier: 3.973A  pdb=" N   THR A1065 " --> pdb=" O   LYS A1061 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   SER A1066 " --> pdb=" O   CYS A1062 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   LEU A1068 " --> pdb=" O   LEU A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1090
      removed outlier: 3.800A  pdb=" N   MET A1083 " --> pdb=" O   THR A1079 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LYS A1084 " --> pdb=" O   PHE A1080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1095
      No H-bonds generated for 'chain 'A' and resid 1093 through 1095'
    Processing helix  chain 'A' and resid 1096 through 1118
      removed outlier: 3.508A  pdb=" N   HIS A1101 " --> pdb=" O   LYS A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1130
      removed outlier: 3.924A  pdb=" N   ARG A1122 " --> pdb=" O   TYR A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1144
    Processing helix  chain 'A' and resid 1146 through 1164
    Processing helix  chain 'B' and resid 24 through 34
    Processing helix  chain 'B' and resid 78 through 83
      removed outlier: 3.567A  pdb=" N   TYR B  81 " --> pdb=" O  AARG B  78 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE B  83 " --> pdb=" O   GLY B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 112
      removed outlier: 4.026A  pdb=" N   TYR B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
      Proline residue:  B 104  - end of helix
    Processing helix  chain 'B' and resid 139 through 144
    Processing helix  chain 'B' and resid 160 through 172
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 56
      removed outlier: 7.046A  pdb=" N   PHE B  13 " --> pdb=" O   ASP B  64 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   TRP B  66 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LEU B  15 " --> pdb=" O   TRP B  66 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   THR B  68 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU B  17 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   ILE B  89 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   MET B  91 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL B  18 " --> pdb=" O   MET B  91 " (cutoff:3.500A)
      removed outlier: 8.798A  pdb=" N   ASP B  93 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ALA B  88 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   CYS B 122 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ILE B  90 " --> pdb=" O   CYS B 122 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   ASN B 124 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   PHE B  92 " --> pdb=" O   ASN B 124 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN B 147 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)

    684 hydrogen bonds defined for protein.
    2022 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.60

  Time building geometry restraints manager: 3.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3509
        1.34 -     1.46: 2588
        1.46 -     1.58: 5175
        1.58 -     1.70: 13
        1.70 -     1.82: 92
  Bond restraints: 11377
  Sorted by residual:
  bond pdb=" N   ILE A 434 "
       pdb=" CA  ILE A 434 "
    ideal  model  delta    sigma   weight residual
    1.454  1.497 -0.043 1.19e-02 7.06e+03 1.28e+01
  bond pdb=" N   ASN A1006 "
       pdb=" CA  ASN A1006 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.29e-02 6.01e+03 1.00e+01
  bond pdb=" N   GLN A1004 "
       pdb=" CA  GLN A1004 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.042 1.34e-02 5.57e+03 9.61e+00
  bond pdb=" N   ASN A 648 "
       pdb=" CA  ASN A 648 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.028 1.15e-02 7.56e+03 5.89e+00
  bond pdb=" C2  GTP B 201 "
       pdb=" N3  GTP B 201 "
    ideal  model  delta    sigma   weight residual
    1.380  1.332  0.048 2.00e-02 2.50e+03 5.85e+00
  ... (remaining 11372 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 15233
        2.14 -     4.29: 145
        4.29 -     6.43: 41
        6.43 -     8.58: 9
        8.58 -    10.72: 8
  Bond angle restraints: 15436
  Sorted by residual:
  angle pdb=" N   GLN A 233 "
        pdb=" CA  GLN A 233 "
        pdb=" C   GLN A 233 "
      ideal   model   delta    sigma   weight residual
     111.14  107.01    4.13 1.08e+00 8.57e-01 1.46e+01
  angle pdb=" C   LEU A 232 "
        pdb=" N   GLN A 233 "
        pdb=" CA  GLN A 233 "
      ideal   model   delta    sigma   weight residual
     120.44  115.38    5.06 1.36e+00 5.41e-01 1.38e+01
  angle pdb=" PB  GTP B 201 "
        pdb=" O3B GTP B 201 "
        pdb=" PG  GTP B 201 "
      ideal   model   delta    sigma   weight residual
     120.50  131.22  -10.72 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" N   ARG B 142 "
        pdb=" CA  ARG B 142 "
        pdb=" C   ARG B 142 "
      ideal   model   delta    sigma   weight residual
     111.69  107.30    4.39 1.23e+00 6.61e-01 1.27e+01
  angle pdb=" O1B GTP B 201 "
        pdb=" PB  GTP B 201 "
        pdb=" O2B GTP B 201 "
      ideal   model   delta    sigma   weight residual
     109.50  119.81  -10.31 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 15431 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.99: 6543
       27.99 -    55.99: 276
       55.99 -    83.98: 31
       83.98 -   111.97: 8
      111.97 -   139.96: 3
  Dihedral angle restraints: 6861
    sinusoidal: 2830
      harmonic: 4031
  Sorted by residual:
  dihedral pdb=" C8  GTP B 201 "
           pdb=" C1' GTP B 201 "
           pdb=" N9  GTP B 201 "
           pdb=" O4' GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -35.37  139.96     1      2.00e+01 2.50e-03 4.24e+01
  dihedral pdb=" O3B GTP B 201 "
           pdb=" O3A GTP B 201 "
           pdb=" PB  GTP B 201 "
           pdb=" PA  GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  168.31  122.77     1      2.00e+01 2.50e-03 3.70e+01
  dihedral pdb=" O3A GTP B 201 "
           pdb=" O3B GTP B 201 "
           pdb=" PB  GTP B 201 "
           pdb=" PG  GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21 -170.97  114.77     1      2.00e+01 2.50e-03 3.41e+01
  ... (remaining 6858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1355
       0.043 -    0.086: 306
       0.086 -    0.129: 74
       0.129 -    0.171: 4
       0.171 -    0.214: 3
  Chirality restraints: 1742
  Sorted by residual:
  chirality pdb=" CB  ILE B  45 "
            pdb=" CA  ILE B  45 "
            pdb=" CG1 ILE B  45 "
            pdb=" CG2 ILE B  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" C2' GTP B 201 "
            pdb=" C1' GTP B 201 "
            pdb=" C3' GTP B 201 "
            pdb=" O2' GTP B 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.67    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  ILE A 896 "
            pdb=" CA  ILE A 896 "
            pdb=" CG1 ILE A 896 "
            pdb=" CG2 ILE A 896 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.30e-01
  ... (remaining 1739 not shown)

  Planarity restraints: 1935
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 141 "    0.013 2.00e-02 2.50e+03   2.52e-02 6.34e+00
        pdb=" C   HIS B 141 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   HIS B 141 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ARG B 142 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 943 "    0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO A 944 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 944 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 944 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 173 "   -0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO B 174 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 174 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 174 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1932 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1003
        2.74 -     3.28: 11735
        3.28 -     3.82: 19280
        3.82 -     4.36: 22275
        4.36 -     4.90: 38672
  Nonbonded interactions: 92965
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 148 "
            pdb=" OD1 ASP B 150 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   LYS A 522 "
            pdb=" OH  TYR A 531 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OE1 GLN A  30 "
            pdb=" OH  TYR B  81 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   TRP A 121 "
            pdb=" NH2 ARG A 182 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NE2 HIS B  32 "
            pdb=" O   PHE B 159 "
     model   vdw
     2.269 3.120
  ... (remaining 92960 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=0.36 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:             2.870
  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:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     37.270
  Find NCS groups from input model:        0.130
  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:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
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   0.048  11377  Z= 0.140
  Angle     :  0.610  10.723  15436  Z= 0.295
  Chirality :  0.039   0.214   1742
  Planarity :  0.003   0.038   1935
  Dihedral  : 15.676 139.964   4239
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 12.01 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.23), residues: 1348
  helix:  1.97 (0.17), residues: 898
  sheet: -0.16 (0.79), residues: 40
  loop : -0.48 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 150 
 HIS   0.003   0.001   HIS A 652 
 PHE   0.019   0.001   PHE A 660 
 TYR   0.021   0.001   TYR A 796 
 ARG   0.007   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16043 (  684)
  hydrogen bonds       : angle       5.38158 ( 2022)
  covalent geometry    : bond        0.00272 (11377)
  covalent geometry    : angle       0.61026 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 1.337 
Fit side-chains
REVERT: B  142 ARG cc_start: 0.8530 (mtt180) cc_final: 0.7955 (mmm160)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.2510
  time to fit residues: 23.9380
Evaluate side-chains
  60 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  900 LYS
Chi-restraints excluded: chain A residue 1023 MET
Chi-restraints excluded: chain A residue 1045 ILE
Chi-restraints excluded: chain A residue 1049 ASP
Chi-restraints excluded: chain A residue 1073 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A1006 ASN
A1069 ASN
A1072 ASN
** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.080553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.049760 restraints weight = 71067.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 4.56
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8830
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11377  Z= 0.176
  Angle     :  0.569   7.533  15436  Z= 0.287
  Chirality :  0.040   0.157   1742
  Planarity :  0.004   0.041   1935
  Dihedral  :  8.004 142.291   1501
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.65 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.23), residues: 1348
  helix:  1.97 (0.17), residues: 931
  sheet: -0.10 (0.74), residues: 42
  loop : -0.61 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 150 
 HIS   0.005   0.001   HIS A1019 
 PHE   0.040   0.001   PHE A1080 
 TYR   0.019   0.001   TYR A 796 
 ARG   0.004   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04528 (  684)
  hydrogen bonds       : angle       4.27116 ( 2022)
  covalent geometry    : bond        0.00416 (11377)
  covalent geometry    : angle       0.56919 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8416 (ttm)
REVERT: B  142 ARG cc_start: 0.8632 (mtt180) cc_final: 0.8170 (mmm-85)
  outliers start: 11
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2099
  time to fit residues: 21.7984
Evaluate side-chains
  62 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain C residue  120 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 104 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 115 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0980
   chunk 13 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.081512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.050731 restraints weight = 79249.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 4.78
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11377  Z= 0.121
  Angle     :  0.508   7.054  15436  Z= 0.257
  Chirality :  0.038   0.178   1742
  Planarity :  0.003   0.043   1935
  Dihedral  :  7.611 143.522   1489
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 10.25 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.23), residues: 1348
  helix:  2.06 (0.17), residues: 929
  sheet:  0.13 (0.74), residues: 42
  loop : -0.55 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 150 
 HIS   0.002   0.000   HIS A 496 
 PHE   0.018   0.001   PHE A 660 
 TYR   0.014   0.001   TYR A 796 
 ARG   0.005   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  684)
  hydrogen bonds       : angle       4.03108 ( 2022)
  covalent geometry    : bond        0.00270 (11377)
  covalent geometry    : angle       0.50835 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 1.309 
Fit side-chains
REVERT: B  142 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8217 (mmm160)
  outliers start: 9
  outliers final: 5
  residues processed: 62
  average time/residue: 0.2135
  time to fit residues: 21.3390
Evaluate side-chains
  59 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  970 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 134 optimal weight:    0.6980
   chunk 72 optimal weight:    0.3980
   chunk 129 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.081035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.050512 restraints weight = 66757.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 4.43
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11377  Z= 0.135
  Angle     :  0.514   7.213  15436  Z= 0.258
  Chirality :  0.038   0.188   1742
  Planarity :  0.003   0.039   1935
  Dihedral  :  7.646 145.762   1489
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.65 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.23), residues: 1348
  helix:  2.08 (0.17), residues: 930
  sheet:  0.32 (0.75), residues: 42
  loop : -0.53 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 150 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.019   0.001   PHE A 660 
 TYR   0.015   0.001   TYR A 796 
 ARG   0.004   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  684)
  hydrogen bonds       : angle       4.00164 ( 2022)
  covalent geometry    : bond        0.00317 (11377)
  covalent geometry    : angle       0.51427 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 1.381 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8486 (ttm)
REVERT: A  282 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7746 (mtm)
REVERT: A 1154 MET cc_start: 0.6852 (mmm) cc_final: 0.6569 (mmp)
REVERT: B   36 GLU cc_start: 0.8574 (pp20) cc_final: 0.7955 (pp20)
REVERT: B  142 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8248 (mmm160)
  outliers start: 12
  outliers final: 7
  residues processed: 64
  average time/residue: 0.2721
  time to fit residues: 27.0259
Evaluate side-chains
  64 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 131 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0020
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 989 GLN
** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.081347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.050369 restraints weight = 87700.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 5.00
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2801
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11377  Z= 0.116
  Angle     :  0.497   7.370  15436  Z= 0.249
  Chirality :  0.038   0.176   1742
  Planarity :  0.003   0.041   1935
  Dihedral  :  7.654 146.731   1489
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.17 %
    Favored  : 88.55 %
  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:  2.07 (0.23), residues: 1348
  helix:  2.16 (0.17), residues: 930
  sheet:  0.55 (0.76), residues: 42
  loop : -0.54 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 150 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.018   0.001   PHE A 660 
 TYR   0.013   0.001   TYR A 796 
 ARG   0.003   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03583 (  684)
  hydrogen bonds       : angle       3.90441 ( 2022)
  covalent geometry    : bond        0.00267 (11377)
  covalent geometry    : angle       0.49661 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 1.405 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8530 (ttm)
REVERT: A  282 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7670 (mtm)
REVERT: A  405 VAL cc_start: 0.9060 (m) cc_final: 0.8800 (p)
REVERT: B   36 GLU cc_start: 0.8599 (pp20) cc_final: 0.7956 (pp20)
REVERT: B  142 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8210 (mmm160)
  outliers start: 15
  outliers final: 8
  residues processed: 69
  average time/residue: 0.2318
  time to fit residues: 24.9169
Evaluate side-chains
  66 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0170
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A1085 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.081676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.050641 restraints weight = 90145.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 5.08
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11377  Z= 0.109
  Angle     :  0.503   7.572  15436  Z= 0.251
  Chirality :  0.038   0.174   1742
  Planarity :  0.003   0.039   1935
  Dihedral  :  7.630 146.247   1489
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.25 %
    Favored  : 88.39 %
  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:  2.07 (0.24), residues: 1348
  helix:  2.16 (0.17), residues: 938
  sheet:  0.46 (0.76), residues: 42
  loop : -0.59 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 150 
 HIS   0.006   0.001   HIS A1019 
 PHE   0.053   0.001   PHE A1080 
 TYR   0.012   0.001   TYR A 796 
 ARG   0.004   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03471 (  684)
  hydrogen bonds       : angle       3.84792 ( 2022)
  covalent geometry    : bond        0.00247 (11377)
  covalent geometry    : angle       0.50292 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 1.253 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8523 (ttm)
REVERT: A  282 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7628 (mtm)
REVERT: A  405 VAL cc_start: 0.9032 (m) cc_final: 0.8767 (p)
REVERT: B   36 GLU cc_start: 0.8572 (pp20) cc_final: 0.7921 (pp20)
REVERT: B  142 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8219 (mmm160)
  outliers start: 16
  outliers final: 10
  residues processed: 69
  average time/residue: 0.2028
  time to fit residues: 22.5730
Evaluate side-chains
  70 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1004 GLN
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 128 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 109 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 92 optimal weight:    0.0060
   overall best weight:    0.5996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.081727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.050776 restraints weight = 91209.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 5.12
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11377  Z= 0.108
  Angle     :  0.500   8.118  15436  Z= 0.249
  Chirality :  0.038   0.171   1742
  Planarity :  0.003   0.039   1935
  Dihedral  :  7.594 145.527   1489
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.57 %
    Favored  : 88.31 %
  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:  2.14 (0.24), residues: 1348
  helix:  2.20 (0.17), residues: 938
  sheet:  0.43 (0.76), residues: 42
  loop : -0.53 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 150 
 HIS   0.004   0.001   HIS A1019 
 PHE   0.019   0.001   PHE A 660 
 TYR   0.011   0.001   TYR A 796 
 ARG   0.003   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  684)
  hydrogen bonds       : angle       3.80000 ( 2022)
  covalent geometry    : bond        0.00243 (11377)
  covalent geometry    : angle       0.50012 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.282 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8524 (ttm)
REVERT: A  282 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7576 (mtm)
REVERT: A  405 VAL cc_start: 0.9028 (m) cc_final: 0.8764 (p)
REVERT: B   36 GLU cc_start: 0.8551 (pp20) cc_final: 0.7937 (pp20)
REVERT: B  142 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8238 (mmm160)
  outliers start: 13
  outliers final: 11
  residues processed: 66
  average time/residue: 0.2168
  time to fit residues: 23.0964
Evaluate side-chains
  70 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1004 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 7 optimal weight:    0.0870
   chunk 133 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 989 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.081966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.051272 restraints weight = 82497.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 4.86
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11377  Z= 0.104
  Angle     :  0.497   8.495  15436  Z= 0.247
  Chirality :  0.037   0.163   1742
  Planarity :  0.003   0.038   1935
  Dihedral  :  7.529 144.176   1489
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.57 %
    Favored  : 88.31 %
  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:  2.20 (0.24), residues: 1348
  helix:  2.24 (0.17), residues: 939
  sheet:  0.51 (0.76), residues: 42
  loop : -0.50 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 150 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.019   0.001   PHE A 660 
 TYR   0.010   0.001   TYR A 796 
 ARG   0.004   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03296 (  684)
  hydrogen bonds       : angle       3.74806 ( 2022)
  covalent geometry    : bond        0.00235 (11377)
  covalent geometry    : angle       0.49715 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 1.148 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8492 (ttm)
REVERT: A  282 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7556 (mtm)
REVERT: B   36 GLU cc_start: 0.8539 (pp20) cc_final: 0.7896 (pp20)
REVERT: B  142 ARG cc_start: 0.8635 (mtt180) cc_final: 0.8218 (mmm160)
  outliers start: 13
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1924
  time to fit residues: 20.8190
Evaluate side-chains
  70 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1004 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 107 optimal weight:    7.9990
   chunk 127 optimal weight:    0.6980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.081715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.051175 restraints weight = 68691.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 4.53
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11377  Z= 0.113
  Angle     :  0.498   7.938  15436  Z= 0.249
  Chirality :  0.038   0.152   1742
  Planarity :  0.003   0.038   1935
  Dihedral  :  7.525 144.519   1489
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.49 %
    Favored  : 88.23 %
  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:  2.27 (0.23), residues: 1348
  helix:  2.29 (0.17), residues: 933
  sheet:  0.60 (0.75), residues: 42
  loop : -0.42 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 150 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.019   0.001   PHE A 660 
 TYR   0.011   0.001   TYR A 796 
 ARG   0.003   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03363 (  684)
  hydrogen bonds       : angle       3.76327 ( 2022)
  covalent geometry    : bond        0.00260 (11377)
  covalent geometry    : angle       0.49827 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 1.389 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8517 (ttm)
REVERT: A  282 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7557 (mtm)
REVERT: B   36 GLU cc_start: 0.8583 (pp20) cc_final: 0.7935 (pp20)
REVERT: B  142 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8206 (mmm160)
  outliers start: 15
  outliers final: 11
  residues processed: 69
  average time/residue: 0.2183
  time to fit residues: 24.2377
Evaluate side-chains
  70 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1004 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 113 optimal weight:    7.9990
   chunk 116 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 119 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 90 optimal weight:    0.0470
   chunk 69 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.6278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.082574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.052385 restraints weight = 65424.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 4.36
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11377  Z= 0.107
  Angle     :  0.504   7.797  15436  Z= 0.249
  Chirality :  0.038   0.194   1742
  Planarity :  0.003   0.038   1935
  Dihedral  :  7.507 144.155   1489
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.73 %
    Favored  : 88.15 %
  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:  2.29 (0.23), residues: 1348
  helix:  2.32 (0.17), residues: 927
  sheet:  0.68 (0.76), residues: 42
  loop : -0.43 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 150 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.019   0.001   PHE A 660 
 TYR   0.011   0.001   TYR A 796 
 ARG   0.003   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03289 (  684)
  hydrogen bonds       : angle       3.73695 ( 2022)
  covalent geometry    : bond        0.00246 (11377)
  covalent geometry    : angle       0.50444 (15436)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.351 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8523 (ttm)
REVERT: A  282 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7564 (mtm)
REVERT: A  395 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8241 (m-30)
REVERT: B   36 GLU cc_start: 0.8541 (pp20) cc_final: 0.7906 (pp20)
REVERT: B  142 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8199 (mmm160)
  outliers start: 13
  outliers final: 10
  residues processed: 66
  average time/residue: 0.2140
  time to fit residues: 22.6028
Evaluate side-chains
  69 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  623 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1004 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0770
   chunk 16 optimal weight:    0.4980
   chunk 49 optimal weight:    0.0970
   chunk 61 optimal weight:    0.8980
   chunk 30 optimal weight:    0.2980
   chunk 76 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0010
   chunk 24 optimal weight:    0.0970
   overall best weight:    0.1140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.083559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.053492 restraints weight = 65322.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 4.50
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11377  Z= 0.093
  Angle     :  0.491   8.087  15436  Z= 0.243
  Chirality :  0.037   0.184   1742
  Planarity :  0.003   0.039   1935
  Dihedral  :  7.356 139.287   1489
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.81 %
    Favored  : 88.15 %
  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:  2.43 (0.24), residues: 1348
  helix:  2.42 (0.17), residues: 924
  sheet:  0.77 (0.76), residues: 42
  loop : -0.34 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 121 
 HIS   0.003   0.001   HIS A1019 
 PHE   0.019   0.001   PHE A 660 
 TYR   0.008   0.001   TYR A 762 
 ARG   0.003   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02949 (  684)
  hydrogen bonds       : angle       3.61577 ( 2022)
  covalent geometry    : bond        0.00189 (11377)
  covalent geometry    : angle       0.49106 (15436)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5360.52 seconds
wall clock time: 94 minutes 33.58 seconds (5673.58 seconds total)