Starting phenix.real_space_refine
on Thu Jul  2 18:31:36 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7aap_11692/07_2026/7aap_11692.map"
  }
  resolution = 2.5
  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=   0.000 sd=   0.003
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: 8
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      26      5.49       5
     Mg      3      5.21       5
     S      66      5.16       5
     C    5919      2.51       5
     N    1581      2.21       5
     O    1848      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9446
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 7345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 911, 7345
          Classifications: {'peptide': 911}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 880}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 882
          Classifications: {'peptide': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
    Chain: "C"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 513
          Classifications: {'peptide': 67}
          Link IDs: {'TRANS': 66}
    Chain: "D"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 221
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "P"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 189
          Classifications: {'RNA': 9}
          Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5}
          Link IDs: {'rna3p': 8}
    Chain: "T"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 250
          Classifications: {'RNA': 12}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 13
          Unusual residues: {' MG': 2, ' ZN': 2, 'POP': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "T"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GE6': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2446  SG  CYS A 301      42.374  62.670  43.895  1.00 49.57           S
  ATOM   2487  SG  CYS A 306      42.428  61.687  40.192  1.00 46.12           S
  ATOM   2519  SG  CYS A 310      45.719  61.837  42.215  1.00 41.58           S
  ATOM   3927  SG  CYS A 487      24.274  58.627  52.787  1.00 52.25           S
  ATOM   5180  SG  CYS A 645      23.549  58.149  49.031  1.00 57.21           S
  ATOM   5186  SG  CYS A 646      26.332  60.537  50.194  1.00 55.39           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   POP A1005 " occ=0.50
      ... (7 atoms not shown)
      pdb=" P2  POP A1005 " occ=0.50
  Time building chain proxies: 1.81, per 1000 atoms: 0.19
  Number of scatterers: 9446
  At special positions: 0
  Unit cell: (102.7, 92.95, 117.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      2     29.99
     S      66     16.00
     P      26     15.00
     Mg      3     11.99
     F       1      9.00
     O    1848      8.00
     N    1581      7.00
     C    5919      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: 0.82
  Conformation dependent library (CDL) restraints added in 256.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 295 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 301 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 306 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 310 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" ND1 HIS A 642 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 646 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 645 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 487 "
      Number of angles added : 6


  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 10 sheets defined
      54.1% alpha, 18.9% beta
      5 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 13
    Processing helix  chain 'A' and resid 61 through 63
      No H-bonds generated for 'chain 'A' and resid 61 through 63'
    Processing helix  chain 'A' and resid 76 through 91
      removed outlier: 3.613A  pdb=" N   THR A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 133
      removed outlier: 3.523A  pdb=" N   LEU A 127 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 153 through 159
      removed outlier: 3.829A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LYS A 159 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 177
    Processing helix  chain 'A' and resid 178 through 199
    Processing helix  chain 'A' and resid 206 through 210
    Processing helix  chain 'A' and resid 234 through 248
      Proline residue:  A 243  - end of helix
      removed outlier: 3.969A  pdb=" N   THR A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.301A  pdb=" N   ALA A 253 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   VAL A 257 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   ASP A 258 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.656A  pdb=" N   PHE A 313 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   THR A 319 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 326
    Processing helix  chain 'A' and resid 367 through 377
    Processing helix  chain 'A' and resid 377 through 385
      removed outlier: 4.080A  pdb=" N   HIS A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A 384 " --> pdb=" O   MET A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 426
    Processing helix  chain 'A' and resid 447 through 454
    Processing helix  chain 'A' and resid 455 through 459
    Processing helix  chain 'A' and resid 465 through 480
      removed outlier: 3.878A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR A 479 " --> pdb=" O   VAL A 475 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE A 480 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 493
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 511 through 519
      removed outlier: 3.848A  pdb=" N   TYR A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 531
    Processing helix  chain 'A' and resid 561 through 581
      removed outlier: 3.538A  pdb=" N   THR A 567 " --> pdb=" O   CYS A 563 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN A 570 " --> pdb=" O   MET A 566 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   LYS A 574 " --> pdb=" O   GLN A 570 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   LEU A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 606
    Processing helix  chain 'A' and resid 621 through 626
      removed outlier: 3.598A  pdb=" N   MET A 626 " --> pdb=" O   CYS A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 640 through 642
      No H-bonds generated for 'chain 'A' and resid 640 through 642'
    Processing helix  chain 'A' and resid 647 through 660
    Processing helix  chain 'A' and resid 686 through 709
    Processing helix  chain 'A' and resid 717 through 733
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 768 through 773
    Processing helix  chain 'A' and resid 778 through 790
      removed outlier: 3.541A  pdb=" N   TYR A 788 " --> pdb=" O   SER A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 833 through 842
    Processing helix  chain 'A' and resid 847 through 850
    Processing helix  chain 'A' and resid 851 through 867
      removed outlier: 3.515A  pdb=" N   ILE A 856 " --> pdb=" O   GLY A 852 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLU A 857 " --> pdb=" O   THR A 853 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER A 861 " --> pdb=" O   GLU A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 874 through 894
      removed outlier: 3.813A  pdb=" N   VAL A 880 " --> pdb=" O   GLU A 876 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   PHE A 881 " --> pdb=" O   TYR A 877 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   HIS A 882 " --> pdb=" O   ALA A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 917
      removed outlier: 3.760A  pdb=" N   TYR A 915 " --> pdb=" O   THR A 912 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   GLU A 917 " --> pdb=" O   ARG A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 923
    Processing helix  chain 'B' and resid 79 through 93
      removed outlier: 3.631A  pdb=" N   VAL B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR B  84 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 110
      removed outlier: 3.567A  pdb=" N   ASN B 105 " --> pdb=" O   ASP B 101 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA B 110 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 125
      removed outlier: 3.521A  pdb=" N   ALA B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 142
      removed outlier: 3.703A  pdb=" N   ASN B 140 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'C' and resid 3 through 19
      removed outlier: 3.841A  pdb=" N   LYS C   7 " --> pdb=" O   MET C   3 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL C  12 " --> pdb=" O   CYS C   8 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU C  17 " --> pdb=" O   LEU C  13 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN C  18 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLN C  19 " --> pdb=" O   SER C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 42
      removed outlier: 3.545A  pdb=" N   GLN C  31 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU C  40 " --> pdb=" O   HIS C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 62
      removed outlier: 3.591A  pdb=" N   ALA C  48 " --> pdb=" O   ASP C  44 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   PHE C  49 " --> pdb=" O   THR C  45 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   GLU C  50 " --> pdb=" O   THR C  46 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS C  51 " --> pdb=" O   GLU C  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL C  58 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   MET C  62 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 66
    Processing helix  chain 'D' and resid 85 through 99
      removed outlier: 3.555A  pdb=" N   THR D  93 " --> pdb=" O   THR D  89 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP D  99 " --> pdb=" O   LEU D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 111
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21
      removed outlier: 3.963A  pdb=" N   ARG A  18 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   SER A  68 " --> pdb=" O   GLU A  58 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   VAL A  71 " --> pdb=" O   GLN A 117 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   GLN A 117 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL A 111 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 38
      removed outlier: 4.579A  pdb=" N   CYS A  53 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   THR A  51 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ARG A  33 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   LEU A  49 " --> pdb=" O   ARG A  33 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   PHE A  35 " --> pdb=" O   LYS A  47 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   LYS A  47 " --> pdb=" O   PHE A  35 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ILE A  37 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   PHE A  45 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224
      removed outlier: 7.041A  pdb=" N   VAL A 233 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   GLY A 203 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355
      removed outlier: 6.539A  pdb=" N   VAL A 335 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   VAL A 341 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ILE A 333 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   SER A 343 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 9.767A  pdb=" N   SER A 363 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   PHE A 334 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355
      removed outlier: 6.539A  pdb=" N   VAL A 335 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   VAL A 341 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ILE A 333 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   SER A 343 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 555 through 559
      removed outlier: 4.505A  pdb=" N   ARG A 555 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   THR A 540 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA A 399 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL A 675 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B 158 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU B 189 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ILE B 156 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 555 through 559
      removed outlier: 4.505A  pdb=" N   ARG A 555 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   THR A 540 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA A 399 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL A 675 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B 158 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU B 189 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ILE B 156 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415
    Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 757
      removed outlier: 4.508A  pdb=" N   ALA A 762 " --> pdb=" O   TRP A 617 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   TRP A 617 " --> pdb=" O   ALA A 762 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822
      removed outlier: 3.611A  pdb=" N   MET A 818 " --> pdb=" O   LEU A 829 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASP A 825 " --> pdb=" O   GLN A 822 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      10 hydrogen bonds
      20 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2844
        1.34 -     1.45: 1619
        1.45 -     1.57: 5083
        1.57 -     1.69: 47
        1.69 -     1.81: 99
  Bond restraints: 9692
  Sorted by residual:
  bond pdb=" O10 GE6 T1601 "
       pdb=" P03 GE6 T1601 "
    ideal  model  delta    sigma   weight residual
    1.764  1.614  0.150 2.00e-02 2.50e+03 5.61e+01
  bond pdb=" C08 GE6 T1601 "
       pdb=" C10 GE6 T1601 "
    ideal  model  delta    sigma   weight residual
    1.454  1.387  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" O07 GE6 T1601 "
       pdb=" P02 GE6 T1601 "
    ideal  model  delta    sigma   weight residual
    1.657  1.599  0.058 2.00e-02 2.50e+03 8.52e+00
  bond pdb=" O06 GE6 T1601 "
       pdb=" P01 GE6 T1601 "
    ideal  model  delta    sigma   weight residual
    1.652  1.596  0.056 2.00e-02 2.50e+03 7.91e+00
  bond pdb=" N   ARG A 553 "
       pdb=" CA  ARG A 553 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.031 1.22e-02 6.72e+03 6.30e+00
  ... (remaining 9687 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 12973
        1.37 -     2.73: 192
        2.73 -     4.10: 65
        4.10 -     5.46: 13
        5.46 -     6.83: 7
  Bond angle restraints: 13250
  Sorted by residual:
  angle pdb=" N   ASN A 552 "
        pdb=" CA  ASN A 552 "
        pdb=" C   ASN A 552 "
      ideal   model   delta    sigma   weight residual
     113.20  109.15    4.05 1.21e+00 6.83e-01 1.12e+01
  angle pdb=" CA  GLU A 917 "
        pdb=" CB  GLU A 917 "
        pdb=" CG  GLU A 917 "
      ideal   model   delta    sigma   weight residual
     114.10  120.54   -6.44 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" CA  ALA A 554 "
        pdb=" C   ALA A 554 "
        pdb=" O   ALA A 554 "
      ideal   model   delta    sigma   weight residual
     121.05  117.58    3.47 1.14e+00 7.69e-01 9.26e+00
  angle pdb=" C4'   A P  19 "
        pdb=" C3'   A P  19 "
        pdb=" O3'   A P  19 "
      ideal   model   delta    sigma   weight residual
     113.00  108.60    4.40 1.50e+00 4.44e-01 8.62e+00
  angle pdb=" CA  GLU C  50 "
        pdb=" CB  GLU C  50 "
        pdb=" CG  GLU C  50 "
      ideal   model   delta    sigma   weight residual
     114.10  119.80   -5.70 2.00e+00 2.50e-01 8.12e+00
  ... (remaining 13245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.36: 5555
       26.36 -    52.73: 178
       52.73 -    79.09: 15
       79.09 -   105.45: 7
      105.45 -   131.82: 2
  Dihedral angle restraints: 5757
    sinusoidal: 2436
      harmonic: 3321
  Sorted by residual:
  dihedral pdb=" O4  POP A1005 "
           pdb=" O   POP A1005 "
           pdb=" P2  POP A1005 "
           pdb=" P1  POP A1005 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.41   70.19 -127.61     1      2.00e+01 2.50e-03 3.86e+01
  dihedral pdb=" O2  POP A1005 "
           pdb=" O   POP A1005 "
           pdb=" P1  POP A1005 "
           pdb=" P2  POP A1005 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -88.77 -176.80   88.04     1      2.00e+01 2.50e-03 2.32e+01
  dihedral pdb=" O10 GE6 T1601 "
           pdb=" O07 GE6 T1601 "
           pdb=" P02 GE6 T1601 "
           pdb=" P01 GE6 T1601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     198.44   66.62  131.82     1      3.00e+01 1.11e-03 1.78e+01
  ... (remaining 5754 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1119
       0.038 -    0.076: 273
       0.076 -    0.115: 93
       0.115 -    0.153: 9
       0.153 -    0.191: 7
  Chirality restraints: 1501
  Sorted by residual:
  chirality pdb=" C3'   A T  18 "
            pdb=" C4'   A T  18 "
            pdb=" O3'   A T  18 "
            pdb=" C2'   A T  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.67    0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" C2'   U P  20 "
            pdb=" C3'   U P  20 "
            pdb=" O2'   U P  20 "
            pdb=" C1'   U P  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.57   -0.19 2.00e-01 2.50e+01 8.62e-01
  chirality pdb=" C2'   A T  18 "
            pdb=" C3'   A T  18 "
            pdb=" O2'   A T  18 "
            pdb=" C1'   A T  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.57   -0.18 2.00e-01 2.50e+01 8.36e-01
  ... (remaining 1498 not shown)

  Planarity restraints: 1614
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 926 "    0.035 5.00e-02 4.00e+02   5.41e-02 4.69e+00
        pdb=" N   PRO A 927 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 927 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 927 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A P  19 "   -0.021 2.00e-02 2.50e+03   9.33e-03 2.39e+00
        pdb=" N9    A P  19 "    0.005 2.00e-02 2.50e+03
        pdb=" C8    A P  19 "    0.013 2.00e-02 2.50e+03
        pdb=" N7    A P  19 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A P  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    A P  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" N6    A P  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A P  19 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A P  19 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    A P  19 "    0.008 2.00e-02 2.50e+03
        pdb=" C4    A P  19 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C  50 "    0.007 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" CD  GLU C  50 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU C  50 "    0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU C  50 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1611 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 119
        2.66 -     3.22: 8743
        3.22 -     3.78: 14756
        3.78 -     4.34: 21626
        4.34 -     4.90: 33690
  Nonbonded interactions: 78934
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 209 "
            pdb="MG    MG A1004 "
     model   vdw
     2.097 2.170
  nonbonded pdb="MG    MG A1004 "
            pdb=" O3  POP A1005 "
     model   vdw
     2.159 2.170
  nonbonded pdb="MG    MG A1004 "
            pdb=" O5  POP A1005 "
     model   vdw
     2.216 2.170
  nonbonded pdb=" OG1 THR A 120 "
            pdb=" OD1 ASP A 211 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER B 173 "
            pdb=" OD1 ASP B 175 "
     model   vdw
     2.250 3.040
  ... (remaining 78929 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.080
  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:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.740
  Find NCS groups from input model:        0.130
  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:7.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
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   0.150   9700  Z= 0.164
  Angle     :  0.492   6.827  13256  Z= 0.268
  Chirality :  0.040   0.191   1501
  Planarity :  0.002   0.054   1614
  Dihedral  : 12.871 131.817   3611
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.10 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.59 (0.25), residues: 1110
  helix:  0.54 (0.23), residues: 504
  sheet:  0.89 (0.48), residues: 112
  loop :  0.31 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  80 
 TYR   0.014   0.001   TYR A  80 
 PHE   0.007   0.001   PHE A 741 
 TRP   0.013   0.001   TRP A 916 
 HIS   0.006   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.16 ( 9692)
  covalent geometry    : angle       0.49160 /  0.27 (13250)
  hydrogen bonds       : bond        0.24964 / 16.79 (  429)
  hydrogen bonds       : angle       7.29375 /  5.28 ( 1226)
  metal coordination   : bond        0.00384 /  0.26 (    8)
  metal coordination   : angle       0.65128 /  0.38 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 175
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 HIS cc_start: 0.8674 (t70) cc_final: 0.8472 (t-90)
REVERT: A   98 LYS cc_start: 0.8405 (tttt) cc_final: 0.8101 (tttm)
REVERT: A  196 MET cc_start: 0.8759 (mtp) cc_final: 0.8448 (mtp)
REVERT: A  806 THR cc_start: 0.8299 (p) cc_final: 0.7425 (p)
REVERT: A  855 MET cc_start: 0.7963 (mtm) cc_final: 0.7677 (mtt)
REVERT: A  875 GLN cc_start: 0.8955 (tp40) cc_final: 0.8628 (tp40)
REVERT: C   28 LEU cc_start: 0.8239 (mm) cc_final: 0.7726 (mt)
REVERT: D   94 MET cc_start: 0.6740 (mtt) cc_final: 0.6086 (mpt)
  outliers start: 2
  outliers final: 0
  residues processed: 175
  average time/residue: 0.5218
  time to fit residues: 97.8745
Evaluate side-chains
  124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    1.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
A 414 ASN
A 416 ASN
A 713 ASN
B 179 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.129939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.084229 restraints weight = 13263.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 2.28
r_work: 0.2906 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2767
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2767 r_free = 0.2767    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2767 r_free = 0.2767    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2767
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9020
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9700  Z= 0.190
  Angle     :  0.554   6.317  13256  Z= 0.302
  Chirality :  0.043   0.160   1501
  Planarity :  0.004   0.038   1614
  Dihedral  :  7.836 129.963   1527
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.17 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.90 (0.25), residues: 1110
  helix:  1.03 (0.23), residues: 509
  sheet:  0.46 (0.45), residues: 122
  loop :  0.33 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 914 
 TYR   0.017   0.002   TYR B 135 
 PHE   0.021   0.001   PHE A 652 
 TRP   0.017   0.002   TRP A 916 
 HIS   0.008   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.19 ( 9692)
  covalent geometry    : angle       0.55217 /  0.30 (13250)
  hydrogen bonds       : bond        0.05058 /  3.48 (  429)
  hydrogen bonds       : angle       4.86815 /  3.51 ( 1226)
  metal coordination   : bond        0.00521 /  0.34 (    8)
  metal coordination   : angle       1.94206 /  1.14 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8591 (tttt) cc_final: 0.8207 (tttm)
REVERT: A  855 MET cc_start: 0.8317 (mtm) cc_final: 0.7947 (mtt)
REVERT: A  875 GLN cc_start: 0.8874 (tp40) cc_final: 0.8263 (tp-100)
REVERT: A  879 ASP cc_start: 0.8844 (m-30) cc_final: 0.8419 (m-30)
REVERT: A  889 ARG cc_start: 0.8064 (mpt-90) cc_final: 0.7509 (mpt-90)
REVERT: B  168 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8070 (mm110)
REVERT: B  171 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7772 (mt-10)
REVERT: C   26 SER cc_start: 0.8002 (t) cc_final: 0.7673 (p)
  outliers start: 18
  outliers final: 5
  residues processed: 143
  average time/residue: 0.5243
  time to fit residues: 80.7367
Evaluate side-chains
  124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 119
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  892 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0170
   chunk 50 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.4026

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.130001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.084504 restraints weight = 13384.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.27
r_work: 0.2904 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.2768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9017
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9700  Z= 0.142
  Angle     :  0.490   6.191  13256  Z= 0.266
  Chirality :  0.041   0.156   1501
  Planarity :  0.003   0.042   1614
  Dihedral  :  7.351 123.430   1527
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.10 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.97 (0.26), residues: 1110
  helix:  1.23 (0.24), residues: 510
  sheet:  0.15 (0.43), residues: 132
  loop :  0.29 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 914 
 TYR   0.012   0.001   TYR A 515 
 PHE   0.018   0.001   PHE A 652 
 TRP   0.020   0.002   TRP A 916 
 HIS   0.006   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 9692)
  covalent geometry    : angle       0.48879 /  0.27 (13250)
  hydrogen bonds       : bond        0.04216 /  2.92 (  429)
  hydrogen bonds       : angle       4.41296 /  3.19 ( 1226)
  metal coordination   : bond        0.00603 /  0.41 (    8)
  metal coordination   : angle       1.55742 /  0.93 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8567 (tttt) cc_final: 0.8178 (tttm)
REVERT: A  404 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8055 (p0)
REVERT: A  414 ASN cc_start: 0.8343 (m110) cc_final: 0.8124 (m-40)
REVERT: A  541 GLN cc_start: 0.8583 (tt0) cc_final: 0.8292 (tt0)
REVERT: A  736 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8445 (p0)
REVERT: A  796 GLU cc_start: 0.8027 (tt0) cc_final: 0.7526 (tm-30)
REVERT: A  855 MET cc_start: 0.8330 (mtm) cc_final: 0.8013 (ttm)
REVERT: A  889 ARG cc_start: 0.8258 (mpt-90) cc_final: 0.8036 (mtm-85)
REVERT: B  163 ASP cc_start: 0.8436 (m-30) cc_final: 0.8205 (m-30)
REVERT: C   26 SER cc_start: 0.7907 (t) cc_final: 0.7682 (p)
REVERT: D   94 MET cc_start: 0.6053 (mtp) cc_final: 0.5442 (mpt)
  outliers start: 15
  outliers final: 8
  residues processed: 136
  average time/residue: 0.4531
  time to fit residues: 66.7183
Evaluate side-chains
  128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  736 ASP
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain A residue  892 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 108 ASN
B 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.082270 restraints weight = 13515.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.24
r_work: 0.2867 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9053
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9700  Z= 0.211
  Angle     :  0.544   6.272  13256  Z= 0.295
  Chirality :  0.043   0.156   1501
  Planarity :  0.003   0.029   1614
  Dihedral  :  7.268 121.512   1527
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.02 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.78 (0.25), residues: 1110
  helix:  1.16 (0.23), residues: 516
  sheet:  0.01 (0.44), residues: 133
  loop :  0.09 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 735 
 TYR   0.016   0.002   TYR A 515 
 PHE   0.021   0.002   PHE A 652 
 TRP   0.020   0.002   TRP A 916 
 HIS   0.004   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00489 /  0.21 ( 9692)
  covalent geometry    : angle       0.54193 /  0.29 (13250)
  hydrogen bonds       : bond        0.04715 /  3.28 (  429)
  hydrogen bonds       : angle       4.47167 /  3.24 ( 1226)
  metal coordination   : bond        0.00782 /  0.49 (    8)
  metal coordination   : angle       2.04544 /  1.22 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8551 (tttt) cc_final: 0.8201 (tttm)
REVERT: A  404 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8184 (p0)
REVERT: A  541 GLN cc_start: 0.8654 (tt0) cc_final: 0.8368 (tt0)
REVERT: A  796 GLU cc_start: 0.7916 (tt0) cc_final: 0.7457 (tm-30)
REVERT: A  855 MET cc_start: 0.8406 (mtm) cc_final: 0.8023 (ttm)
REVERT: B  163 ASP cc_start: 0.8357 (m-30) cc_final: 0.7870 (m-30)
REVERT: B  171 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8098 (mt-10)
REVERT: C   26 SER cc_start: 0.7935 (t) cc_final: 0.7701 (p)
REVERT: D   94 MET cc_start: 0.6477 (mtp) cc_final: 0.5721 (mpt)
  outliers start: 15
  outliers final: 6
  residues processed: 135
  average time/residue: 0.4993
  time to fit residues: 72.8167
Evaluate side-chains
  125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain A residue  892 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0980
   chunk 14 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 93 optimal weight:    7.9990
   chunk 109 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0470
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.8080

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.130445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.085489 restraints weight = 13473.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 2.24
r_work: 0.2920 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9008
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9700  Z= 0.106
  Angle     :  0.464   6.003  13256  Z= 0.253
  Chirality :  0.039   0.156   1501
  Planarity :  0.003   0.034   1614
  Dihedral  :  6.943 123.429   1527
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.62 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.94 (0.26), residues: 1110
  helix:  1.35 (0.24), residues: 518
  sheet:  0.01 (0.43), residues: 132
  loop :  0.11 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 914 
 TYR   0.012   0.001   TYR A 515 
 PHE   0.016   0.001   PHE A 652 
 TRP   0.019   0.001   TRP A 916 
 HIS   0.004   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.11 ( 9692)
  covalent geometry    : angle       0.46354 /  0.25 (13250)
  hydrogen bonds       : bond        0.03528 /  2.44 (  429)
  hydrogen bonds       : angle       4.19892 /  3.05 ( 1226)
  metal coordination   : bond        0.00560 /  0.38 (    8)
  metal coordination   : angle       1.46547 /  0.91 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8534 (tttt) cc_final: 0.8148 (tttm)
REVERT: A  541 GLN cc_start: 0.8585 (tt0) cc_final: 0.8299 (tt0)
REVERT: A  736 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8583 (p0)
REVERT: A  796 GLU cc_start: 0.7874 (tt0) cc_final: 0.7383 (tm-30)
REVERT: A  855 MET cc_start: 0.8426 (mtm) cc_final: 0.8080 (ttm)
REVERT: B  163 ASP cc_start: 0.8203 (m-30) cc_final: 0.7786 (m-30)
REVERT: D   94 MET cc_start: 0.6444 (mtp) cc_final: 0.5724 (mpt)
  outliers start: 13
  outliers final: 6
  residues processed: 127
  average time/residue: 0.5150
  time to fit residues: 70.6561
Evaluate side-chains
  122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  736 ASP
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain B residue   88 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    0.0000
   chunk 4 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 99 optimal weight:    9.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 108 ASN
B 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.128865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.083575 restraints weight = 13400.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.23
r_work: 0.2890 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9036
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9700  Z= 0.149
  Angle     :  0.486   6.103  13256  Z= 0.264
  Chirality :  0.041   0.153   1501
  Planarity :  0.003   0.028   1614
  Dihedral  :  6.959 123.880   1527
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.03 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.95 (0.26), residues: 1110
  helix:  1.39 (0.24), residues: 516
  sheet:  0.01 (0.44), residues: 132
  loop :  0.08 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 914 
 TYR   0.020   0.001   TYR B 135 
 PHE   0.018   0.001   PHE A 652 
 TRP   0.019   0.002   TRP A 916 
 HIS   0.003   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 9692)
  covalent geometry    : angle       0.48462 /  0.26 (13250)
  hydrogen bonds       : bond        0.04006 /  2.79 (  429)
  hydrogen bonds       : angle       4.24399 /  3.08 ( 1226)
  metal coordination   : bond        0.00530 /  0.34 (    8)
  metal coordination   : angle       1.57371 /  0.95 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 VAL cc_start: 0.8289 (t) cc_final: 0.7940 (p)
REVERT: A   98 LYS cc_start: 0.8526 (tttt) cc_final: 0.8244 (tttm)
REVERT: A  648 LEU cc_start: 0.9024 (mm) cc_final: 0.8767 (tp)
REVERT: A  796 GLU cc_start: 0.7881 (tt0) cc_final: 0.7388 (tm-30)
REVERT: A  855 MET cc_start: 0.8470 (mtm) cc_final: 0.8133 (ttm)
REVERT: A  875 GLN cc_start: 0.8620 (tp40) cc_final: 0.8149 (tp-100)
REVERT: D   94 MET cc_start: 0.6432 (mtp) cc_final: 0.5730 (mpt)
  outliers start: 17
  outliers final: 8
  residues processed: 128
  average time/residue: 0.4722
  time to fit residues: 65.0946
Evaluate side-chains
  126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain A residue  892 HIS
Chi-restraints excluded: chain B residue   88 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 104 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.126963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.081444 restraints weight = 13330.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.23
r_work: 0.2843 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (12 function evaluations)
r_final: 0.2714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9060
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9700  Z= 0.255
  Angle     :  0.564   8.401  13256  Z= 0.306
  Chirality :  0.044   0.154   1501
  Planarity :  0.004   0.031   1614
  Dihedral  :  7.284 118.393   1527
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.43 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.80 (0.25), residues: 1110
  helix:  1.27 (0.23), residues: 514
  sheet: -0.06 (0.43), residues: 133
  loop : -0.00 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 914 
 TYR   0.017   0.002   TYR A 149 
 PHE   0.022   0.002   PHE A 652 
 TRP   0.024   0.002   TRP B 182 
 HIS   0.004   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00595 /  0.25 ( 9692)
  covalent geometry    : angle       0.56215 /  0.31 (13250)
  hydrogen bonds       : bond        0.04823 /  3.36 (  429)
  hydrogen bonds       : angle       4.45771 /  3.23 ( 1226)
  metal coordination   : bond        0.00866 /  0.53 (    8)
  metal coordination   : angle       2.06029 /  1.23 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 VAL cc_start: 0.8410 (t) cc_final: 0.8077 (p)
REVERT: A   98 LYS cc_start: 0.8588 (tttt) cc_final: 0.8246 (tttm)
REVERT: A  648 LEU cc_start: 0.9040 (mm) cc_final: 0.8786 (tp)
REVERT: A  796 GLU cc_start: 0.7898 (tt0) cc_final: 0.7433 (tm-30)
REVERT: A  855 MET cc_start: 0.8534 (mtm) cc_final: 0.8157 (ttm)
REVERT: A  875 GLN cc_start: 0.8581 (tp40) cc_final: 0.8145 (tp-100)
  outliers start: 15
  outliers final: 9
  residues processed: 126
  average time/residue: 0.5039
  time to fit residues: 68.3505
Evaluate side-chains
  122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain A residue  892 HIS
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain C residue   16 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0020
   chunk 8 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.6588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.130248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.085255 restraints weight = 13394.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.25
r_work: 0.2916 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9011
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9700  Z= 0.099
  Angle     :  0.470  10.365  13256  Z= 0.252
  Chirality :  0.039   0.161   1501
  Planarity :  0.003   0.026   1614
  Dihedral  :  6.925 122.577   1527
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 14.73 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  1.03 (0.26), residues: 1110
  helix:  1.41 (0.24), residues: 516
  sheet:  0.31 (0.47), residues: 112
  loop :  0.09 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 914 
 TYR   0.012   0.001   TYR A 788 
 PHE   0.016   0.001   PHE A 652 
 TRP   0.025   0.002   TRP A 916 
 HIS   0.003   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.10 ( 9692)
  covalent geometry    : angle       0.46892 /  0.25 (13250)
  hydrogen bonds       : bond        0.03425 /  2.36 (  429)
  hydrogen bonds       : angle       4.17215 /  3.03 ( 1226)
  metal coordination   : bond        0.00458 /  0.31 (    8)
  metal coordination   : angle       1.38218 /  0.85 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 VAL cc_start: 0.8244 (t) cc_final: 0.7936 (p)
REVERT: A   98 LYS cc_start: 0.8526 (tttt) cc_final: 0.8251 (tttm)
REVERT: A  796 GLU cc_start: 0.7862 (tt0) cc_final: 0.7363 (tm-30)
REVERT: A  855 MET cc_start: 0.8469 (mtm) cc_final: 0.8117 (ttm)
REVERT: A  875 GLN cc_start: 0.8594 (tp40) cc_final: 0.8147 (tp-100)
REVERT: C   27 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7797 (tptt)
  outliers start: 12
  outliers final: 8
  residues processed: 127
  average time/residue: 0.4907
  time to fit residues: 66.9259
Evaluate side-chains
  126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain C residue   16 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 45 optimal weight:    0.0020
   chunk 42 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 100 optimal weight:    0.2980
   chunk 88 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.2594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 176 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.129253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.083919 restraints weight = 13288.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.24
r_work: 0.2894 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9030
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9700  Z= 0.132
  Angle     :  0.487   6.135  13256  Z= 0.264
  Chirality :  0.040   0.153   1501
  Planarity :  0.003   0.026   1614
  Dihedral  :  6.917 124.086   1527
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.34 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  1.00 (0.26), residues: 1110
  helix:  1.43 (0.24), residues: 516
  sheet:  0.15 (0.45), residues: 122
  loop :  0.07 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 914 
 TYR   0.013   0.001   TYR A 149 
 PHE   0.017   0.001   PHE A 652 
 TRP   0.029   0.002   TRP B 182 
 HIS   0.003   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 9692)
  covalent geometry    : angle       0.48631 /  0.26 (13250)
  hydrogen bonds       : bond        0.03783 /  2.62 (  429)
  hydrogen bonds       : angle       4.18625 /  3.04 ( 1226)
  metal coordination   : bond        0.00479 /  0.32 (    8)
  metal coordination   : angle       1.47165 /  0.90 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 VAL cc_start: 0.8250 (t) cc_final: 0.7946 (p)
REVERT: A   98 LYS cc_start: 0.8510 (tttt) cc_final: 0.8242 (tttm)
REVERT: A  796 GLU cc_start: 0.7869 (tt0) cc_final: 0.7373 (tm-30)
REVERT: A  855 MET cc_start: 0.8494 (mtm) cc_final: 0.8161 (ttm)
REVERT: A  875 GLN cc_start: 0.8577 (tp40) cc_final: 0.8136 (tp-100)
REVERT: C   27 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7813 (tptt)
  outliers start: 13
  outliers final: 8
  residues processed: 123
  average time/residue: 0.5118
  time to fit residues: 67.6585
Evaluate side-chains
  123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain C residue   16 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 84 optimal weight:    0.4980
   chunk 81 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0570
   chunk 40 optimal weight:    0.1980
   overall best weight:    0.6700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.131060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.085985 restraints weight = 13284.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 2.24
r_work: 0.2930 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9002
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9700  Z= 0.099
  Angle     :  0.472  11.623  13256  Z= 0.252
  Chirality :  0.039   0.155   1501
  Planarity :  0.003   0.027   1614
  Dihedral  :  6.772 126.939   1527
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.54 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  1.06 (0.26), residues: 1110
  helix:  1.52 (0.24), residues: 507
  sheet:  0.06 (0.49), residues: 102
  loop :  0.10 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 889 
 TYR   0.012   0.001   TYR A 788 
 PHE   0.015   0.001   PHE A 652 
 TRP   0.023   0.002   TRP B 182 
 HIS   0.004   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 9692)
  covalent geometry    : angle       0.47113 /  0.25 (13250)
  hydrogen bonds       : bond        0.03264 /  2.25 (  429)
  hydrogen bonds       : angle       4.07165 /  2.96 ( 1226)
  metal coordination   : bond        0.00424 /  0.29 (    8)
  metal coordination   : angle       1.30561 /  0.81 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8495 (tptp)
REVERT: A   42 VAL cc_start: 0.8159 (t) cc_final: 0.7892 (p)
REVERT: A   98 LYS cc_start: 0.8481 (tttt) cc_final: 0.8196 (tttm)
REVERT: A  796 GLU cc_start: 0.7862 (tt0) cc_final: 0.7344 (tm-30)
REVERT: A  855 MET cc_start: 0.8473 (mtm) cc_final: 0.8158 (ttm)
REVERT: A  875 GLN cc_start: 0.8613 (tp40) cc_final: 0.8218 (tp-100)
REVERT: C   27 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7769 (tptt)
  outliers start: 10
  outliers final: 9
  residues processed: 129
  average time/residue: 0.5568
  time to fit residues: 77.3299
Evaluate side-chains
  130 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  879 ASP
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain C residue   16 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    0.2980
   chunk 48 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 ASN
B 176 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.129202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.083874 restraints weight = 13218.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 2.24
r_work: 0.2885 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9030
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9700  Z= 0.141
  Angle     :  0.497  10.875  13256  Z= 0.267
  Chirality :  0.040   0.150   1501
  Planarity :  0.003   0.026   1614
  Dihedral  :  6.853 125.582   1527
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.54 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 are not related in a simple way.
  whole:  0.99 (0.26), residues: 1110
  helix:  1.50 (0.24), residues: 507
  sheet: -0.03 (0.43), residues: 132
  loop :  0.04 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 889 
 TYR   0.025   0.001   TYR B 135 
 PHE   0.018   0.001   PHE A 652 
 TRP   0.034   0.002   TRP B 182 
 HIS   0.003   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 9692)
  covalent geometry    : angle       0.49598 /  0.27 (13250)
  hydrogen bonds       : bond        0.03839 /  2.66 (  429)
  hydrogen bonds       : angle       4.16865 /  3.03 ( 1226)
  metal coordination   : bond        0.00510 /  0.33 (    8)
  metal coordination   : angle       1.51855 /  0.93 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4080.17 seconds
wall clock time: 70 minutes 3.39 seconds (4203.39 seconds total)