Starting phenix.real_space_refine
on Wed Sep 17 16:30:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6l_50228/09_2025/9f6l_50228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6l_50228/09_2025/9f6l_50228.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6l_50228/09_2025/9f6l_50228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6l_50228/09_2025/9f6l_50228.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6l_50228/09_2025/9f6l_50228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6l_50228/09_2025/9f6l_50228.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.003 sd=   0.101
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Fe      4      7.16       5
     P      26      5.49       5
     S      53      5.16       5
     C    6066      2.51       5
     N    1647      2.21       5
     O    1841      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9639
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1118, 9098
          Classifications: {'peptide': 1118}
          Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1059}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "T"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 246
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 10
          Unusual residues: {' CA': 2, 'SF4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4834  SG  CYS A 651      38.003  19.250  53.220  1.00 99.09           S
  ATOM   4850  SG  CYS A 654      36.437  17.492  47.221  1.00 98.87           S
  ATOM   4916  SG  CYS A 663      42.008  16.185  49.846  1.00 97.49           S
  ATOM   5640  SG  CYS A 747      41.526  21.844  48.347  1.00 94.19           S

  Time building chain proxies: 2.10, per 1000 atoms: 0.22
  Number of scatterers: 9639
  At special positions: 0
  Unit cell: (103.66, 109.5, 109.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      4     26.01
     Ca      2     19.99
     S      53     16.00
     P      26     15.00
     O    1841      8.00
     N    1647      7.00
     C    6066      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: 1.15
  Conformation dependent library (CDL) restraints added in 280.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1301 "
        pdb="FE3  SF4 A1301 " - pdb=" SG  CYS A 663 "
        pdb="FE4  SF4 A1301 " - pdb=" SG  CYS A 747 "
        pdb="FE1  SF4 A1301 " - pdb=" SG  CYS A 651 "
        pdb="FE2  SF4 A1301 " - pdb=" SG  CYS A 654 "
      Number of angles added : 12


  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 12 sheets defined
      48.6% alpha, 17.2% beta
      10 base pairs and 20 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 48
    Processing helix  chain 'A' and resid 112 through 124
    Processing helix  chain 'A' and resid 143 through 147
    Processing helix  chain 'A' and resid 159 through 181
      removed outlier: 3.576A  pdb=" N   LEU A 163 " --> pdb=" O   THR A 159 " (cutoff:3.500A)
      Proline residue:  A 172  - end of helix
    Processing helix  chain 'A' and resid 227 through 237
      removed outlier: 3.522A  pdb=" N   SER A 233 " --> pdb=" O   HIS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 367 through 379
      removed outlier: 3.573A  pdb=" N   PHE A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 407 through 414
    Processing helix  chain 'A' and resid 423 through 432
    Processing helix  chain 'A' and resid 443 through 451
    Processing helix  chain 'A' and resid 451 through 473
      removed outlier: 3.804A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 451 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER A 461 " --> pdb=" O   THR A 457 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A 463 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA A 465 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR A 468 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 482
      removed outlier: 4.014A  pdb=" N   PHE A 477 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 485
      No H-bonds generated for 'chain 'A' and resid 483 through 485'
    Processing helix  chain 'A' and resid 488 through 495
    Processing helix  chain 'A' and resid 496 through 512
      removed outlier: 3.842A  pdb=" N   LEU A 500 " --> pdb=" O   GLY A 496 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   CYS A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 507 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLN A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 571
      removed outlier: 4.157A  pdb=" N   PHE A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 584
    Processing helix  chain 'A' and resid 589 through 593
    Processing helix  chain 'A' and resid 595 through 613
      removed outlier: 3.722A  pdb=" N   VAL A 599 " --> pdb=" O   ASN A 595 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   VAL A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 639
    Processing helix  chain 'A' and resid 647 through 652
      removed outlier: 3.825A  pdb=" N   CYS A 651 " --> pdb=" O   ASP A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 706 through 710
      removed outlier: 3.802A  pdb=" N   LEU A 710 " --> pdb=" O   PHE A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 731
      removed outlier: 4.582A  pdb=" N   ARG A 728 " --> pdb=" O   ALA A 724 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   LYS A 729 " --> pdb=" O   ASP A 725 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA A 730 " --> pdb=" O   TYR A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 786
    Processing helix  chain 'A' and resid 787 through 818
      removed outlier: 4.222A  pdb=" N   TYR A 816 " --> pdb=" O   LEU A 812 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   GLY A 817 " --> pdb=" O   ASN A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 854
      removed outlier: 4.168A  pdb=" N   ILE A 843 " --> pdb=" O   GLY A 839 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   GLN A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE A 853 " --> pdb=" O   LEU A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 905
      removed outlier: 3.764A  pdb=" N   LEU A 897 " --> pdb=" O   PRO A 893 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 899 " --> pdb=" O   ALA A 895 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   MET A 900 " --> pdb=" O   MET A 896 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 901 " --> pdb=" O   LEU A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 994
      removed outlier: 3.772A  pdb=" N   LYS A 983 " --> pdb=" O   LEU A 979 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A 991 " --> pdb=" O   SER A 987 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU A 994 " --> pdb=" O   PHE A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1019
      removed outlier: 4.269A  pdb=" N   LYS A1008 " --> pdb=" O   GLY A1004 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   VAL A1009 " --> pdb=" O   SER A1005 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA A1010 " --> pdb=" O   VAL A1006 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASP A1015 " --> pdb=" O   ASP A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1034
    Processing helix  chain 'A' and resid 1042 through 1047
      removed outlier: 3.558A  pdb=" N   TYR A1046 " --> pdb=" O   LEU A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1065
      removed outlier: 3.676A  pdb=" N   THR A1056 " --> pdb=" O   THR A1052 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ALA A1057 " --> pdb=" O   SER A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1069
    Processing helix  chain 'A' and resid 1097 through 1101
    Processing helix  chain 'A' and resid 1102 through 1114
      removed outlier: 3.507A  pdb=" N   LYS A1112 " --> pdb=" O   HIS A1108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1128
      removed outlier: 4.010A  pdb=" N   ILE A1127 " --> pdb=" O   ASP A1123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1145
      removed outlier: 3.771A  pdb=" N   TYR A1133 " --> pdb=" O   ASP A1129 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LYS A1143 " --> pdb=" O   SER A1139 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A1144 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1152
    Processing helix  chain 'A' and resid 1164 through 1175
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52
      removed outlier: 7.126A  pdb=" N   GLU A  51 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   ALA A  97 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ILE A  87 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   LEU A  63 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 136
      removed outlier: 6.681A  pdb=" N   SER A 156 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   VAL A 131 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ARG A 154 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   THR A 133 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TYR A 152 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ARG A 150 " --> pdb=" O   PRO A 135 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ASN A 151 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   THR A 108 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR A 105 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321
      removed outlier: 3.606A  pdb=" N   PHE A 320 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   GLY A 304 " --> pdb=" O   CYS A 333 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   LEU A 306 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   GLU A 337 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR A 308 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   MET A 294 " --> pdb=" O   ASN A 309 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE A 274 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   THR A 361 " --> pdb=" O   MET A 405 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391
    Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 539
      removed outlier: 6.591A  pdb=" N   GLU A 674 " --> pdb=" O   ASP A 535 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   GLU A 537 " --> pdb=" O   ARG A 672 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   TYR A 539 " --> pdb=" O   GLN A 670 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   GLN A 670 " --> pdb=" O   TYR A 539 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG A 665 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET A 667 " --> pdb=" O   THR A 744 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546
      removed outlier: 6.727A  pdb=" N   VAL A 867 " --> pdb=" O   PRO A 856 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 858 " --> pdb=" O   TRP A 865 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE A 622 " --> pdb=" O   PRO A 936 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   HIS A 624 " --> pdb=" O   ASP A 934 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 553
      removed outlier: 3.633A  pdb=" N   GLY A 550 " --> pdb=" O   LEU A 942 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 560
    Processing sheet with id=AA9, first strand: chain 'A' and resid 875 through 879
      removed outlier: 3.715A  pdb=" N   VAL A 888 " --> pdb=" O   PHE A 878 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 907 through 913
      removed outlier: 5.778A  pdb=" N   ASP A 908 " --> pdb=" O   GLU A 926 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   GLU A 926 " --> pdb=" O   ASP A 908 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1037 through 1038
      removed outlier: 3.704A  pdb=" N   ARG A1037 " --> pdb=" O   CYS A1076 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   CYS A1076 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080

    435 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      23 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      20 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.43: 4234
        1.43 -     1.64: 5594
        1.64 -     1.85: 78
        1.85 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 9918
  Sorted by residual:
  bond pdb=" O4'  DC P  31 "
       pdb=" C1'  DC P  31 "
    ideal  model  delta    sigma   weight residual
    1.414  1.391  0.023 2.00e-02 2.50e+03 1.31e+00
  bond pdb=" C2'  DA T  16 "
       pdb=" C1'  DA T  16 "
    ideal  model  delta    sigma   weight residual
    1.525  1.504  0.021 2.00e-02 2.50e+03 1.05e+00
  bond pdb=" C   PHE A 675 "
       pdb=" N   MET A 676 "
    ideal  model  delta    sigma   weight residual
    1.340  1.399 -0.058 5.87e-02 2.90e+02 9.87e-01
  bond pdb=" C2'  DA P  22 "
       pdb=" C1'  DA P  22 "
    ideal  model  delta    sigma   weight residual
    1.525  1.505  0.020 2.00e-02 2.50e+03 9.58e-01
  bond pdb=" C3'  DA T  13 "
       pdb=" C2'  DA T  13 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 9.02e-01
  ... (remaining 9913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 12204
        1.01 -     2.02: 1016
        2.02 -     3.02: 211
        3.02 -     4.03: 69
        4.03 -     5.04: 16
  Bond angle restraints: 13516
  Sorted by residual:
  angle pdb=" N   TYR A 473 "
        pdb=" CA  TYR A 473 "
        pdb=" C   TYR A 473 "
      ideal   model   delta    sigma   weight residual
     111.40  115.70   -4.30 1.22e+00 6.72e-01 1.24e+01
  angle pdb=" C2'  DG P  20 "
        pdb=" C1'  DG P  20 "
        pdb=" N9   DG P  20 "
      ideal   model   delta    sigma   weight residual
     113.50  118.13   -4.63 1.50e+00 4.44e-01 9.55e+00
  angle pdb=" C2'  DA P  21 "
        pdb=" C1'  DA P  21 "
        pdb=" N9   DA P  21 "
      ideal   model   delta    sigma   weight residual
     113.50  118.08   -4.58 1.50e+00 4.44e-01 9.31e+00
  angle pdb=" N   PHE A 905 "
        pdb=" CA  PHE A 905 "
        pdb=" C   PHE A 905 "
      ideal   model   delta    sigma   weight residual
     111.69  115.33   -3.64 1.23e+00 6.61e-01 8.76e+00
  angle pdb=" C   LYS A1143 "
        pdb=" N   ILE A1144 "
        pdb=" CA  ILE A1144 "
      ideal   model   delta    sigma   weight residual
     123.16  120.09    3.07 1.06e+00 8.90e-01 8.41e+00
  ... (remaining 13511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5289
       17.94 -    35.88: 458
       35.88 -    53.82: 161
       53.82 -    71.76: 33
       71.76 -    89.70: 19
  Dihedral angle restraints: 5960
    sinusoidal: 2661
      harmonic: 3299
  Sorted by residual:
  dihedral pdb=" CA  PHE A 905 "
           pdb=" C   PHE A 905 "
           pdb=" N   THR A 906 "
           pdb=" CA  THR A 906 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.30  -29.70     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  ARG A  52 "
           pdb=" C   ARG A  52 "
           pdb=" N   LEU A  53 "
           pdb=" CA  LEU A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.30   28.70     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" CA  VAL A1069 "
           pdb=" C   VAL A1069 "
           pdb=" N   LYS A1070 "
           pdb=" CA  LYS A1070 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.41  -27.59     0      5.00e+00 4.00e-02 3.04e+01
  ... (remaining 5957 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1196
       0.052 -    0.104: 213
       0.104 -    0.156: 44
       0.156 -    0.208: 2
       0.208 -    0.260: 1
  Chirality restraints: 1456
  Sorted by residual:
  chirality pdb=" C4'  DA T  13 "
            pdb=" C5'  DA T  13 "
            pdb=" O4'  DA T  13 "
            pdb=" C3'  DA T  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.27   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  ARG A 749 "
            pdb=" N   ARG A 749 "
            pdb=" C   ARG A 749 "
            pdb=" CB  ARG A 749 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.45e-01
  chirality pdb=" CA  PRO A1103 "
            pdb=" N   PRO A1103 "
            pdb=" C   PRO A1103 "
            pdb=" CB  PRO A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.52e-01
  ... (remaining 1453 not shown)

  Planarity restraints: 1655
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A1138 "   -0.018 2.00e-02 2.50e+03   3.50e-02 1.23e+01
        pdb=" C   GLY A1138 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLY A1138 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   SER A1139 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT P  26 "    0.022 2.00e-02 2.50e+03   2.11e-02 1.11e+01
        pdb=" N1   DT P  26 "   -0.055 2.00e-02 2.50e+03
        pdb=" C2   DT P  26 "    0.030 2.00e-02 2.50e+03
        pdb=" O2   DT P  26 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DT P  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DT P  26 "   -0.000 2.00e-02 2.50e+03
        pdb=" O4   DT P  26 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DT P  26 "    0.002 2.00e-02 2.50e+03
        pdb=" C7   DT P  26 "    0.006 2.00e-02 2.50e+03
        pdb=" C6   DT P  26 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 476 "   -0.016 2.00e-02 2.50e+03   3.25e-02 1.06e+01
        pdb=" C   PRO A 476 "    0.056 2.00e-02 2.50e+03
        pdb=" O   PRO A 476 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PHE A 477 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1652 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 217
        2.69 -     3.24: 9703
        3.24 -     3.80: 14215
        3.80 -     4.35: 18138
        4.35 -     4.90: 30515
  Nonbonded interactions: 72788
  Sorted by model distance:
  nonbonded pdb=" OP1  DC P  31 "
            pdb="CA    CA A1303 "
     model   vdw
     2.141 2.510
  nonbonded pdb=" OP1  DC P  31 "
            pdb="CA    CA A1302 "
     model   vdw
     2.151 2.510
  nonbonded pdb=" O5'  DC P  31 "
            pdb="CA    CA A1303 "
     model   vdw
     2.202 2.510
  nonbonded pdb=" OE2 GLU A 223 "
            pdb=" NH2 ARG A 231 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG1 THR A 528 "
            pdb=" OD1 ASP A 530 "
     model   vdw
     2.257 3.040
  ... (remaining 72783 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.300
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
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   0.058   9922  Z= 0.144
  Angle     :  0.831  26.651  13528  Z= 0.411
  Chirality :  0.042   0.260   1456
  Planarity :  0.009   0.084   1655
  Dihedral  : 16.408  89.702   3824
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.23), residues: 1114
  helix: -0.95 (0.20), residues: 452
  sheet:  0.49 (0.37), residues: 181
  loop : -0.70 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.003   ARG A 167 
 TYR   0.028   0.005   TYR A 726 
 PHE   0.023   0.004   PHE A 367 
 TRP   0.031   0.007   TRP A 865 
 HIS   0.007   0.002   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9918)
  covalent geometry    : angle       0.66618 (13516)
  hydrogen bonds       : bond        0.16312 (  458)
  hydrogen bonds       : angle       7.54394 ( 1288)
  metal coordination   : bond        0.03458 (    4)
  metal coordination   : angle      16.71321 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.8145 (m-30) cc_final: 0.7334 (p0)
REVERT: A  119 PHE cc_start: 0.8582 (t80) cc_final: 0.8381 (t80)
REVERT: A  447 MET cc_start: 0.9296 (mpp) cc_final: 0.8455 (mpp)
REVERT: A  818 TYR cc_start: 0.8472 (t80) cc_final: 0.8004 (t80)
REVERT: A  878 PHE cc_start: 0.7505 (m-80) cc_final: 0.6673 (m-10)
REVERT: A  896 MET cc_start: 0.8941 (tmm) cc_final: 0.8626 (tmm)
REVERT: A  952 LEU cc_start: 0.9080 (mt) cc_final: 0.8745 (mp)
REVERT: A  974 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6761 (tptt)
REVERT: A 1087 SER cc_start: 0.8774 (m) cc_final: 0.8541 (p)
REVERT: A 1135 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8169 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1306
  time to fit residues: 27.3114
Evaluate side-chains
  77 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.0970
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A 342 HIS
A 511 HIS
A 772 HIS
A1067 GLN
A1163 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.110661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.083180 restraints weight = 22771.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.085549 restraints weight = 13471.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.087156 restraints weight = 9516.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.088241 restraints weight = 7576.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.088763 restraints weight = 6523.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9922  Z= 0.146
  Angle     :  0.646  13.642  13528  Z= 0.336
  Chirality :  0.042   0.158   1456
  Planarity :  0.005   0.037   1655
  Dihedral  : 15.793  82.175   1509
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.97 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1114
  helix:  0.86 (0.23), residues: 466
  sheet:  0.61 (0.39), residues: 180
  loop : -0.28 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 114 
 TYR   0.016   0.001   TYR A 827 
 PHE   0.019   0.002   PHE A 596 
 TRP   0.015   0.001   TRP A 671 
 HIS   0.003   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9918)
  covalent geometry    : angle       0.61539 (13516)
  hydrogen bonds       : bond        0.05011 (  458)
  hydrogen bonds       : angle       5.32333 ( 1288)
  metal coordination   : bond        0.00463 (    4)
  metal coordination   : angle       6.57558 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ARG cc_start: 0.8066 (mmp-170) cc_final: 0.7758 (mmp-170)
REVERT: A   83 ASP cc_start: 0.8011 (m-30) cc_final: 0.7483 (p0)
REVERT: A  285 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6676 (t80)
REVERT: A  383 MET cc_start: 0.8757 (tpp) cc_final: 0.8269 (ttm)
REVERT: A  405 MET cc_start: 0.9268 (tpp) cc_final: 0.8944 (mmm)
REVERT: A  447 MET cc_start: 0.9394 (mpp) cc_final: 0.8814 (mpp)
REVERT: A  471 MET cc_start: 0.8567 (tpp) cc_final: 0.8205 (tpp)
REVERT: A  630 MET cc_start: 0.8437 (ttp) cc_final: 0.8184 (ttp)
REVERT: A  896 MET cc_start: 0.9031 (tmm) cc_final: 0.8626 (tmm)
REVERT: A  952 LEU cc_start: 0.9070 (mt) cc_final: 0.8612 (mp)
REVERT: A  953 LYS cc_start: 0.8711 (mppt) cc_final: 0.8355 (mppt)
REVERT: A  974 LYS cc_start: 0.6879 (mmtt) cc_final: 0.6632 (tptt)
REVERT: A  979 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7272 (pt)
REVERT: A  983 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8317 (mttm)
REVERT: A 1024 MET cc_start: 0.7841 (ttm) cc_final: 0.7344 (ttm)
  outliers start: 20
  outliers final: 11
  residues processed: 100
  average time/residue: 0.1166
  time to fit residues: 16.3014
Evaluate side-chains
  83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 104 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 108 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.109946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.082200 restraints weight = 23063.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.084469 restraints weight = 13868.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.086024 restraints weight = 9942.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.087058 restraints weight = 8003.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.087654 restraints weight = 6951.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9922  Z= 0.129
  Angle     :  0.582  13.556  13528  Z= 0.302
  Chirality :  0.041   0.169   1456
  Planarity :  0.005   0.042   1655
  Dihedral  : 15.410  77.998   1509
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 10.38 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.26), residues: 1114
  helix:  1.47 (0.24), residues: 469
  sheet:  0.64 (0.39), residues: 193
  loop : -0.17 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 114 
 TYR   0.011   0.001   TYR A 827 
 PHE   0.029   0.002   PHE A 119 
 TRP   0.018   0.002   TRP A 865 
 HIS   0.004   0.001   HIS A 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9918)
  covalent geometry    : angle       0.56838 (13516)
  hydrogen bonds       : bond        0.04389 (  458)
  hydrogen bonds       : angle       4.81477 ( 1288)
  metal coordination   : bond        0.00505 (    4)
  metal coordination   : angle       4.26522 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7921 (m-30) cc_final: 0.7587 (p0)
REVERT: A  285 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6668 (t80)
REVERT: A  383 MET cc_start: 0.8668 (tpp) cc_final: 0.8305 (ttm)
REVERT: A  444 MET cc_start: 0.8521 (mmm) cc_final: 0.7977 (mmm)
REVERT: A  447 MET cc_start: 0.9323 (mpp) cc_final: 0.8517 (mpp)
REVERT: A  471 MET cc_start: 0.8842 (tpp) cc_final: 0.8150 (tpp)
REVERT: A  561 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7467 (mtt-85)
REVERT: A  630 MET cc_start: 0.8407 (ttp) cc_final: 0.8195 (ttp)
REVERT: A  645 MET cc_start: 0.8681 (mpt) cc_final: 0.8289 (mpp)
REVERT: A  676 MET cc_start: 0.7059 (mmm) cc_final: 0.6858 (mmm)
REVERT: A  896 MET cc_start: 0.9032 (tmm) cc_final: 0.8689 (tmm)
REVERT: A  974 LYS cc_start: 0.6942 (mmtt) cc_final: 0.6661 (tptt)
REVERT: A  979 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7173 (pt)
REVERT: A  983 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8297 (mttm)
REVERT: A 1024 MET cc_start: 0.7890 (ttm) cc_final: 0.7390 (ttm)
REVERT: A 1107 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8339 (mmtm)
  outliers start: 18
  outliers final: 9
  residues processed: 96
  average time/residue: 0.1224
  time to fit residues: 16.3387
Evaluate side-chains
  80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0030
   chunk 83 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.6994

-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.108358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.081204 restraints weight = 23321.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.083401 restraints weight = 14053.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.084898 restraints weight = 10094.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.085881 restraints weight = 8127.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.086455 restraints weight = 7085.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9922  Z= 0.157
  Angle     :  0.578  13.530  13528  Z= 0.304
  Chirality :  0.041   0.153   1456
  Planarity :  0.005   0.042   1655
  Dihedral  : 15.396  79.662   1509
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.38 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1114
  helix:  1.70 (0.24), residues: 468
  sheet:  0.71 (0.38), residues: 203
  loop : -0.22 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 114 
 TYR   0.016   0.001   TYR A 910 
 PHE   0.025   0.002   PHE A 119 
 TRP   0.012   0.001   TRP A 671 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9918)
  covalent geometry    : angle       0.56685 (13516)
  hydrogen bonds       : bond        0.04600 (  458)
  hydrogen bonds       : angle       4.71995 ( 1288)
  metal coordination   : bond        0.00932 (    4)
  metal coordination   : angle       3.79142 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.8029 (m-30) cc_final: 0.7678 (p0)
REVERT: A  285 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6648 (t80)
REVERT: A  383 MET cc_start: 0.8668 (tpp) cc_final: 0.8265 (ttm)
REVERT: A  460 VAL cc_start: 0.9195 (t) cc_final: 0.8983 (p)
REVERT: A  471 MET cc_start: 0.8971 (tpp) cc_final: 0.8282 (tpp)
REVERT: A  582 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9097 (mm)
REVERT: A  896 MET cc_start: 0.9045 (tmm) cc_final: 0.8680 (tmm)
REVERT: A  974 LYS cc_start: 0.6917 (mmtt) cc_final: 0.6658 (tptt)
REVERT: A  979 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7419 (pt)
REVERT: A  983 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8384 (mttm)
REVERT: A 1039 MET cc_start: 0.7709 (tpt) cc_final: 0.7132 (tpt)
REVERT: A 1107 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8271 (mmtm)
  outliers start: 23
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1199
  time to fit residues: 15.8940
Evaluate side-chains
  81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 108 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 112 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 980 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.112217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.084080 restraints weight = 23427.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.086431 restraints weight = 13839.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.088027 restraints weight = 9880.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.088946 restraints weight = 7954.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.089684 restraints weight = 7017.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9922  Z= 0.161
  Angle     :  0.579  12.954  13528  Z= 0.303
  Chirality :  0.041   0.152   1456
  Planarity :  0.005   0.048   1655
  Dihedral  : 15.442  81.329   1509
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.60 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.26), residues: 1114
  helix:  1.85 (0.24), residues: 467
  sheet:  0.69 (0.38), residues: 207
  loop : -0.33 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1077 
 TYR   0.016   0.001   TYR A 910 
 PHE   0.024   0.002   PHE A 119 
 TRP   0.014   0.002   TRP A 369 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9918)
  covalent geometry    : angle       0.56690 (13516)
  hydrogen bonds       : bond        0.04627 (  458)
  hydrogen bonds       : angle       4.67475 ( 1288)
  metal coordination   : bond        0.00942 (    4)
  metal coordination   : angle       4.01203 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7856 (m-30) cc_final: 0.7626 (p0)
REVERT: A  285 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6815 (t80)
REVERT: A  383 MET cc_start: 0.8738 (tpp) cc_final: 0.8328 (ttm)
REVERT: A  447 MET cc_start: 0.9131 (mpp) cc_final: 0.8265 (mtp)
REVERT: A  460 VAL cc_start: 0.9153 (t) cc_final: 0.8941 (p)
REVERT: A  471 MET cc_start: 0.8894 (tpp) cc_final: 0.8233 (tpp)
REVERT: A  582 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9178 (mm)
REVERT: A  896 MET cc_start: 0.9002 (tmm) cc_final: 0.8658 (tmm)
REVERT: A  940 MET cc_start: 0.8371 (ttp) cc_final: 0.8128 (ttp)
REVERT: A  974 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6699 (tptt)
REVERT: A  979 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7540 (pt)
REVERT: A  983 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8429 (mttm)
REVERT: A 1039 MET cc_start: 0.7330 (tpt) cc_final: 0.7034 (tpt)
REVERT: A 1107 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8338 (mmtm)
  outliers start: 18
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1080
  time to fit residues: 13.0401
Evaluate side-chains
  78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 112 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
A 980 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.113802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.085096 restraints weight = 23312.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.087524 restraints weight = 13870.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.089142 restraints weight = 9898.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090171 restraints weight = 8014.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.090767 restraints weight = 7012.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9922  Z= 0.114
  Angle     :  0.541  12.567  13528  Z= 0.278
  Chirality :  0.040   0.143   1456
  Planarity :  0.004   0.045   1655
  Dihedral  : 15.339  79.329   1509
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.71 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.26), residues: 1114
  helix:  2.07 (0.24), residues: 467
  sheet:  0.64 (0.38), residues: 207
  loop : -0.33 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1077 
 TYR   0.011   0.001   TYR A 827 
 PHE   0.026   0.001   PHE A 119 
 TRP   0.010   0.001   TRP A 369 
 HIS   0.002   0.001   HIS A 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9918)
  covalent geometry    : angle       0.53033 (13516)
  hydrogen bonds       : bond        0.03911 (  458)
  hydrogen bonds       : angle       4.37390 ( 1288)
  metal coordination   : bond        0.00302 (    4)
  metal coordination   : angle       3.57598 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A  285 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6642 (t80)
REVERT: A  294 MET cc_start: 0.8000 (mtp) cc_final: 0.7628 (mpp)
REVERT: A  383 MET cc_start: 0.8718 (tpp) cc_final: 0.8508 (ttp)
REVERT: A  447 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8258 (mtt)
REVERT: A  471 MET cc_start: 0.8884 (tpp) cc_final: 0.8154 (tpp)
REVERT: A  582 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9089 (mm)
REVERT: A  645 MET cc_start: 0.8798 (mpt) cc_final: 0.8516 (mpp)
REVERT: A  896 MET cc_start: 0.8986 (tmm) cc_final: 0.8651 (tmm)
REVERT: A  940 MET cc_start: 0.8256 (ttp) cc_final: 0.7884 (ttm)
REVERT: A  974 LYS cc_start: 0.7124 (mmtt) cc_final: 0.6290 (tmtt)
REVERT: A  979 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7466 (pt)
REVERT: A  983 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8357 (tttm)
REVERT: A 1107 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8334 (mmtm)
  outliers start: 17
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1092
  time to fit residues: 14.0947
Evaluate side-chains
  85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  447 MET
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0980
   chunk 8 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 980 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.114776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.087083 restraints weight = 23213.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.089445 restraints weight = 13758.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.091031 restraints weight = 9842.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.092112 restraints weight = 7947.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.092585 restraints weight = 6913.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9922  Z= 0.104
  Angle     :  0.527  12.823  13528  Z= 0.269
  Chirality :  0.039   0.139   1456
  Planarity :  0.004   0.045   1655
  Dihedral  : 15.126  77.120   1509
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.42 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.26), residues: 1114
  helix:  2.26 (0.24), residues: 467
  sheet:  0.59 (0.36), residues: 215
  loop : -0.34 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 114 
 TYR   0.011   0.001   TYR A 298 
 PHE   0.025   0.001   PHE A 119 
 TRP   0.015   0.001   TRP A 369 
 HIS   0.002   0.000   HIS A 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 9918)
  covalent geometry    : angle       0.51705 (13516)
  hydrogen bonds       : bond        0.03476 (  458)
  hydrogen bonds       : angle       4.17115 ( 1288)
  metal coordination   : bond        0.00212 (    4)
  metal coordination   : angle       3.45020 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A  285 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6727 (t80)
REVERT: A  383 MET cc_start: 0.8694 (tpp) cc_final: 0.8491 (ttp)
REVERT: A  447 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8227 (mtt)
REVERT: A  471 MET cc_start: 0.8835 (tpp) cc_final: 0.8107 (tpp)
REVERT: A  582 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9028 (mm)
REVERT: A  645 MET cc_start: 0.8778 (mpt) cc_final: 0.8487 (mpp)
REVERT: A  722 ARG cc_start: 0.5863 (mtt-85) cc_final: 0.5650 (mtt-85)
REVERT: A  896 MET cc_start: 0.8923 (tmm) cc_final: 0.8591 (tmm)
REVERT: A  940 MET cc_start: 0.8157 (ttp) cc_final: 0.7774 (ttm)
REVERT: A 1107 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8333 (mmtm)
  outliers start: 19
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1039
  time to fit residues: 14.7907
Evaluate side-chains
  89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  447 MET
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 83 optimal weight:    0.4980
   chunk 84 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
A 911 GLN
A 980 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.112510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.084404 restraints weight = 23439.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.086806 restraints weight = 13601.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.088419 restraints weight = 9615.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.089417 restraints weight = 7742.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.089898 restraints weight = 6771.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9922  Z= 0.154
  Angle     :  0.579  12.361  13528  Z= 0.296
  Chirality :  0.041   0.144   1456
  Planarity :  0.004   0.044   1655
  Dihedral  : 15.149  78.355   1509
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.82 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1114
  helix:  2.17 (0.24), residues: 470
  sheet:  0.56 (0.36), residues: 212
  loop : -0.37 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1077 
 TYR   0.016   0.001   TYR A 910 
 PHE   0.013   0.001   PHE A 104 
 TRP   0.010   0.001   TRP A 671 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9918)
  covalent geometry    : angle       0.56704 (13516)
  hydrogen bonds       : bond        0.04265 (  458)
  hydrogen bonds       : angle       4.38731 ( 1288)
  metal coordination   : bond        0.00930 (    4)
  metal coordination   : angle       3.95858 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  285 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6849 (t80)
REVERT: A  383 MET cc_start: 0.8754 (tpp) cc_final: 0.8518 (ttp)
REVERT: A  447 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8434 (mtt)
REVERT: A  471 MET cc_start: 0.8860 (tpp) cc_final: 0.8091 (tpp)
REVERT: A  582 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9078 (mm)
REVERT: A  645 MET cc_start: 0.8895 (mpt) cc_final: 0.8623 (mpp)
REVERT: A  896 MET cc_start: 0.8999 (tmm) cc_final: 0.8645 (tmm)
REVERT: A  940 MET cc_start: 0.8375 (ttp) cc_final: 0.7995 (ttm)
REVERT: A 1107 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8334 (mmtm)
  outliers start: 19
  outliers final: 14
  residues processed: 84
  average time/residue: 0.1064
  time to fit residues: 13.4505
Evaluate side-chains
  86 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  447 MET
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  815 PHE
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 98 optimal weight:    0.2980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 980 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.113983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.086216 restraints weight = 23336.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.088616 restraints weight = 13677.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090084 restraints weight = 9721.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.091194 restraints weight = 7913.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.091902 restraints weight = 6898.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9922  Z= 0.114
  Angle     :  0.551  13.020  13528  Z= 0.279
  Chirality :  0.040   0.219   1456
  Planarity :  0.004   0.044   1655
  Dihedral  : 15.120  77.311   1509
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.12 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.26), residues: 1114
  helix:  2.23 (0.24), residues: 469
  sheet:  0.55 (0.36), residues: 214
  loop : -0.34 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1077 
 TYR   0.011   0.001   TYR A 298 
 PHE   0.015   0.001   PHE A 119 
 TRP   0.010   0.001   TRP A 369 
 HIS   0.002   0.000   HIS A 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9918)
  covalent geometry    : angle       0.54057 (13516)
  hydrogen bonds       : bond        0.03736 (  458)
  hydrogen bonds       : angle       4.22804 ( 1288)
  metal coordination   : bond        0.00329 (    4)
  metal coordination   : angle       3.62126 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ARG cc_start: 0.8213 (mmp-170) cc_final: 0.7868 (mmp-170)
REVERT: A  285 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6811 (t80)
REVERT: A  383 MET cc_start: 0.8733 (tpp) cc_final: 0.8495 (ttp)
REVERT: A  447 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8207 (mtt)
REVERT: A  471 MET cc_start: 0.8872 (tpp) cc_final: 0.8106 (tpp)
REVERT: A  582 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9027 (mm)
REVERT: A  645 MET cc_start: 0.8758 (mpt) cc_final: 0.8471 (mpp)
REVERT: A  896 MET cc_start: 0.8943 (tmm) cc_final: 0.8600 (tmm)
REVERT: A  940 MET cc_start: 0.8238 (ttp) cc_final: 0.7840 (ttm)
REVERT: A 1107 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8331 (mmtm)
  outliers start: 20
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0980
  time to fit residues: 12.3551
Evaluate side-chains
  83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  447 MET
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 63 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
A 980 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.113757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.085788 restraints weight = 23408.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.088241 restraints weight = 13518.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.089861 restraints weight = 9531.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.090851 restraints weight = 7670.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.091589 restraints weight = 6721.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9922  Z= 0.120
  Angle     :  0.560  12.985  13528  Z= 0.283
  Chirality :  0.040   0.231   1456
  Planarity :  0.004   0.044   1655
  Dihedral  : 15.076  76.644   1509
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.73 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.26), residues: 1114
  helix:  2.28 (0.24), residues: 469
  sheet:  0.52 (0.36), residues: 214
  loop : -0.32 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1077 
 TYR   0.011   0.001   TYR A 910 
 PHE   0.011   0.001   PHE A 596 
 TRP   0.009   0.001   TRP A  40 
 HIS   0.003   0.001   HIS A 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9918)
  covalent geometry    : angle       0.54902 (13516)
  hydrogen bonds       : bond        0.03808 (  458)
  hydrogen bonds       : angle       4.22040 ( 1288)
  metal coordination   : bond        0.00446 (    4)
  metal coordination   : angle       3.66562 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ARG cc_start: 0.8229 (mmp-170) cc_final: 0.7879 (mmp-170)
REVERT: A  285 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6823 (t80)
REVERT: A  383 MET cc_start: 0.8727 (tpp) cc_final: 0.8490 (ttp)
REVERT: A  447 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8272 (mtt)
REVERT: A  471 MET cc_start: 0.8848 (tpp) cc_final: 0.8050 (tpp)
REVERT: A  582 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9003 (mm)
REVERT: A  645 MET cc_start: 0.8795 (mpt) cc_final: 0.8506 (mpp)
REVERT: A  896 MET cc_start: 0.8964 (tmm) cc_final: 0.8610 (tmm)
REVERT: A  940 MET cc_start: 0.8280 (ttp) cc_final: 0.7910 (ttm)
REVERT: A 1107 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8041 (mmtm)
  outliers start: 16
  outliers final: 12
  residues processed: 78
  average time/residue: 0.0952
  time to fit residues: 11.1713
Evaluate side-chains
  84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  447 MET
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 32 optimal weight:    0.1980
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 73 optimal weight:    0.0270
   chunk 15 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 70 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A 980 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.115922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.088074 restraints weight = 23454.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.090519 restraints weight = 13623.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.092111 restraints weight = 9657.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093206 restraints weight = 7769.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.093895 restraints weight = 6772.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9922  Z= 0.100
  Angle     :  0.535  13.551  13528  Z= 0.268
  Chirality :  0.039   0.218   1456
  Planarity :  0.004   0.044   1655
  Dihedral  : 14.964  76.499   1509
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.93 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.26), residues: 1114
  helix:  2.39 (0.24), residues: 468
  sheet:  0.55 (0.36), residues: 215
  loop : -0.28 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1077 
 TYR   0.011   0.001   TYR A 298 
 PHE   0.010   0.001   PHE A 699 
 TRP   0.009   0.001   TRP A 369 
 HIS   0.003   0.000   HIS A 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 9918)
  covalent geometry    : angle       0.52531 (13516)
  hydrogen bonds       : bond        0.03211 (  458)
  hydrogen bonds       : angle       4.01475 ( 1288)
  metal coordination   : bond        0.00190 (    4)
  metal coordination   : angle       3.52369 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1579.45 seconds
wall clock time: 28 minutes 9.21 seconds (1689.21 seconds total)