Starting phenix.real_space_refine
on Fri Feb  6 18:23:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ogb_70460/02_2026/9ogb_70460_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ogb_70460/02_2026/9ogb_70460.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ogb_70460/02_2026/9ogb_70460.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ogb_70460/02_2026/9ogb_70460.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ogb_70460/02_2026/9ogb_70460_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ogb_70460/02_2026/9ogb_70460_trim.cif"
  }
  resolution = 3.25
  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=   0.008
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
     P       3      5.49       5
     Mg      1      5.21       5
     S      78      5.16       5
     C    8403      2.51       5
     N    2214      2.21       5
     O    2424      1.98       5
     F       6      1.80       5
     H   13165      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 26294
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 16785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1031, 16785
          Classifications: {'peptide': 1031}
          Link IDs: {'PTRANS': 35, 'TRANS': 995}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 2787
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 6, 'TRANS': 163}
    Chain: "C"
      Number of atoms: 3634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 3634
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 224}
    Chain: "E"
      Number of atoms: 1349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1349
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 1675
          Classifications: {'peptide': 106}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 96}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'V6A': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.22, per 1000 atoms: 0.20
  Number of scatterers: 26294
  At special positions: 0
  Unit cell: (94.242, 110.088, 182.646, 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)
     S      78     16.00
     P       3     15.00
     Mg      1     11.99
     F       6      9.00
     O    2424      8.00
     N    2214      7.00
     C    8403      6.00
     H   13165      1.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.01
  Conformation dependent library (CDL) restraints added in 868.5 milliseconds
  

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3114

  Finding SS restraints...
    Secondary structure from input PDB file:
      86 helices and 3 sheets defined
      73.1% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 14
    Processing helix  chain 'A' and resid 15 through 18
    Processing helix  chain 'A' and resid 24 through 37
      removed outlier: 3.623A  pdb=" N   TYR A  36 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 56
      removed outlier: 3.689A  pdb=" N   HIS A  56 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 70
      removed outlier: 3.950A  pdb=" N   ARG A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   GLU A  68 " --> pdb=" O   ASP A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.605A  pdb=" N   LYS A  76 " --> pdb=" O   ASN A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 94
    Processing helix  chain 'A' and resid 95 through 115
    Processing helix  chain 'A' and resid 123 through 146
      Proline residue:  A 143  - end of helix
    Processing helix  chain 'A' and resid 148 through 160
    Processing helix  chain 'A' and resid 160 through 180
      removed outlier: 4.464A  pdb=" N   ASN A 166 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 215
      removed outlier: 5.339A  pdb=" N   SER A 203 " --> pdb=" O   CYS A 199 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   GLN A 204 " --> pdb=" O   ASN A 200 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE A 205 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU A 208 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 233
    Processing helix  chain 'A' and resid 237 through 243
      removed outlier: 3.856A  pdb=" N   ILE A 241 " --> pdb=" O   PRO A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 255
      removed outlier: 3.609A  pdb=" N   LEU A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 274
      removed outlier: 4.458A  pdb=" N   ASN A 262 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   VAL A 263 " --> pdb=" O   MET A 259 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 298
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'A' and resid 312 through 340
      removed outlier: 6.675A  pdb=" N   GLN A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LEU A 336 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 337 " --> pdb=" O   HIS A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 359
    Processing helix  chain 'A' and resid 362 through 384
      removed outlier: 3.591A  pdb=" N   TYR A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 423
      Proline residue:  A 411  - end of helix
      removed outlier: 4.059A  pdb=" N   PHE A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   LYS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 485
      removed outlier: 7.612A  pdb=" N   VAL A 470 " --> pdb=" O   HIS A 466 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   ASP A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 504
      removed outlier: 3.731A  pdb=" N   ILE A 504 " --> pdb=" O   ALA A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 531
    Processing helix  chain 'A' and resid 533 through 550
    Processing helix  chain 'A' and resid 551 through 556
    Processing helix  chain 'A' and resid 558 through 573
    Processing helix  chain 'A' and resid 579 through 600
      removed outlier: 6.295A  pdb=" N   ARG A 597 " --> pdb=" O   GLN A 593 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   HIS A 598 " --> pdb=" O   LYS A 594 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE A 599 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   VAL A 600 " --> pdb=" O   ARG A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 622
      removed outlier: 3.914A  pdb=" N   GLU A 613 " --> pdb=" O   PRO A 609 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN A 619 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   THR A 620 " --> pdb=" O   ASN A 616 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ILE A 622 " --> pdb=" O   ILE A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 643
      removed outlier: 4.043A  pdb=" N   ALA A 643 " --> pdb=" O   TYR A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 675
      removed outlier: 4.551A  pdb=" N   LEU A 660 " --> pdb=" O   LYS A 656 " (cutoff:3.500A)
      Proline residue:  A 661  - end of helix
      removed outlier: 3.756A  pdb=" N   VAL A 664 " --> pdb=" O   LEU A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 680
    Processing helix  chain 'A' and resid 681 through 703
    Processing helix  chain 'A' and resid 706 through 712
      removed outlier: 3.642A  pdb=" N   ARG A 712 " --> pdb=" O   ILE A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 736
    Processing helix  chain 'A' and resid 737 through 741
    Processing helix  chain 'A' and resid 742 through 766
    Processing helix  chain 'A' and resid 768 through 776
    Processing helix  chain 'A' and resid 776 through 784
      removed outlier: 3.939A  pdb=" N   LEU A 780 " --> pdb=" O   PHE A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 791
    Processing helix  chain 'A' and resid 792 through 797
      removed outlier: 5.993A  pdb=" N   GLU A 797 " --> pdb=" O   ALA A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 812
      removed outlier: 4.050A  pdb=" N   SER A 802 " --> pdb=" O   PRO A 798 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   MET A 804 " --> pdb=" O   VAL A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 817
      removed outlier: 4.769A  pdb=" N   ALA A 817 " --> pdb=" O   HIS A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 835
      removed outlier: 5.188A  pdb=" N   GLU A 828 " --> pdb=" O   ASP A 824 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   CYS A 829 " --> pdb=" O   ALA A 825 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN A 832 " --> pdb=" O   GLU A 828 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   MET A 833 " --> pdb=" O   CYS A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 859
    Processing helix  chain 'A' and resid 859 through 866
      removed outlier: 4.005A  pdb=" N   PHE A 863 " --> pdb=" O   CYS A 859 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A 864 " --> pdb=" O   PHE A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 883
    Processing helix  chain 'A' and resid 886 through 905
    Processing helix  chain 'A' and resid 907 through 931
      removed outlier: 3.861A  pdb=" N   GLN A 912 " --> pdb=" O   GLU A 908 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   SER A 913 " --> pdb=" O   ALA A 909 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   CYS A 920 " --> pdb=" O   GLN A 916 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   ASP A 921 " --> pdb=" O   THR A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 937
      removed outlier: 3.807A  pdb=" N   HIS A 935 " --> pdb=" O   ASP A 932 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR A 936 " --> pdb=" O   THR A 933 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   ALA A 937 " --> pdb=" O   SER A 934 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 932 through 937'
    Processing helix  chain 'A' and resid 938 through 956
      removed outlier: 3.565A  pdb=" N   GLY A 956 " --> pdb=" O   LEU A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 986
      removed outlier: 4.056A  pdb=" N   GLN A 975 " --> pdb=" O   GLN A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 1004
    Processing helix  chain 'A' and resid 1007 through 1022
    Processing helix  chain 'A' and resid 1034 through 1051
    Processing helix  chain 'B' and resid 24 through 35
      removed outlier: 3.929A  pdb=" N   VAL B  29 " --> pdb=" O   LYS B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'B' and resid 96 through 102
      removed outlier: 3.807A  pdb=" N   TYR B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 112
    Processing helix  chain 'B' and resid 139 through 144
      removed outlier: 4.017A  pdb=" N   LYS B 143 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LYS B 144 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 139 through 144'
    Processing helix  chain 'B' and resid 160 through 172
    Processing helix  chain 'C' and resid 55 through 64
    Processing helix  chain 'C' and resid 65 through 73
    Processing helix  chain 'C' and resid 74 through 79
      removed outlier: 5.441A  pdb=" N   ALA C  77 " --> pdb=" O   GLU C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 97
      removed outlier: 3.693A  pdb=" N   TYR C  92 " --> pdb=" O   THR C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 107
      removed outlier: 3.614A  pdb=" N   VAL C 101 " --> pdb=" O   ASP C  97 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR C 107 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 128
      removed outlier: 3.672A  pdb=" N   TRP C 124 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 140
    Processing helix  chain 'C' and resid 153 through 161
      removed outlier: 3.506A  pdb=" N   LYS C 161 " --> pdb=" O   TRP C 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 173
      removed outlier: 3.514A  pdb=" N   VAL C 167 " --> pdb=" O   ASN C 163 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 197
    Processing helix  chain 'C' and resid 201 through 216
      removed outlier: 3.669A  pdb=" N   GLY C 216 " --> pdb=" O   HIS C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 225
    Processing helix  chain 'C' and resid 227 through 232
      removed outlier: 3.582A  pdb=" N   ARG C 232 " --> pdb=" O   ARG C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 246
      removed outlier: 4.423A  pdb=" N   LYS C 239 " --> pdb=" O   GLN C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 263
    Processing helix  chain 'C' and resid 266 through 272
      removed outlier: 3.733A  pdb=" N   LYS C 272 " --> pdb=" O   PRO C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 285
    Processing helix  chain 'E' and resid 32 through 37
    Processing helix  chain 'E' and resid 39 through 46
    Processing helix  chain 'E' and resid 66 through 84
      removed outlier: 3.759A  pdb=" N   LYS E  72 " --> pdb=" O   HIS E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 98
      No H-bonds generated for 'chain 'E' and resid 96 through 98'
    Processing helix  chain 'E' and resid 99 through 111
    Processing helix  chain 'F' and resid 23 through 35
      removed outlier: 3.978A  pdb=" N   ILE F  34 " --> pdb=" O   ILE F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 104
    Processing sheet with id=AA1, first strand: chain 'A' and resid 430 through 435
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 56
      removed outlier: 3.645A  pdb=" N   GLU B  48 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   PHE B  13 " --> pdb=" O   ASP B  64 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   TRP B  66 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   LEU B  15 " --> pdb=" O   TRP B  66 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   THR B  68 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LEU B  17 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LYS B  14 " --> pdb=" O   CYS B  87 " (cutoff:3.500A)
      removed outlier: 8.286A  pdb=" N   ILE B  89 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   MET B  91 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL B  18 " --> pdb=" O   MET B  91 " (cutoff:3.500A)
      removed outlier: 8.853A  pdb=" N   ASP B  93 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ALA B  88 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   CYS B 122 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ILE B  90 " --> pdb=" O   CYS B 122 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   ASN B 124 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   PHE B  92 " --> pdb=" O   ASN B 124 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLN B 147 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 59 through 61
      removed outlier: 3.818A  pdb=" N   ALA F  73 " --> pdb=" O   PHE F   4 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   LEU F  44 " --> pdb=" O   LEU F  51 " (cutoff:3.500A)

    821 hydrogen bonds defined for protein.
    2388 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.44

  Time building geometry restraints manager: 3.92 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 13132
        1.03 -     1.23: 37
        1.23 -     1.42: 5502
        1.42 -     1.62: 7772
        1.62 -     1.81: 122
  Bond restraints: 26565
  Sorted by residual:
  bond pdb=" N   MET F   1 "
       pdb=" H1  MET F   1 "
    ideal  model  delta    sigma   weight residual
    0.960  0.860  0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" C13 V6A A1101 "
       pdb=" N04 V6A A1101 "
    ideal  model  delta    sigma   weight residual
    1.356  1.452 -0.096 2.00e-02 2.50e+03 2.32e+01
  bond pdb=" C14 V6A A1101 "
       pdb=" N05 V6A A1101 "
    ideal  model  delta    sigma   weight residual
    1.372  1.453 -0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" C05 V6A A1101 "
       pdb=" C09 V6A A1101 "
    ideal  model  delta    sigma   weight residual
    1.462  1.519 -0.057 2.00e-02 2.50e+03 8.20e+00
  bond pdb=" N04 V6A A1101 "
       pdb=" N05 V6A A1101 "
    ideal  model  delta    sigma   weight residual
    1.360  1.407 -0.047 2.00e-02 2.50e+03 5.54e+00
  ... (remaining 26560 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 47460
        1.61 -     3.22: 587
        3.22 -     4.83: 64
        4.83 -     6.44: 9
        6.44 -     8.05: 1
  Bond angle restraints: 48121
  Sorted by residual:
  angle pdb=" CB  ARG F  29 "
        pdb=" CG  ARG F  29 "
        pdb=" CD  ARG F  29 "
      ideal   model   delta    sigma   weight residual
     111.30  119.35   -8.05 2.30e+00 1.89e-01 1.23e+01
  angle pdb=" N   ARG F  29 "
        pdb=" CA  ARG F  29 "
        pdb=" CB  ARG F  29 "
      ideal   model   delta    sigma   weight residual
     110.12  115.04   -4.92 1.47e+00 4.63e-01 1.12e+01
  angle pdb=" N   ILE C 183 "
        pdb=" CA  ILE C 183 "
        pdb=" C   ILE C 183 "
      ideal   model   delta    sigma   weight residual
     113.00  109.39    3.61 1.30e+00 5.92e-01 7.71e+00
  angle pdb=" C   GLY B  75 "
        pdb=" N   GLY B  76 "
        pdb=" CA  GLY B  76 "
      ideal   model   delta    sigma   weight residual
     121.86  119.53    2.33 8.50e-01 1.38e+00 7.51e+00
  angle pdb=" C   VAL A 777 "
        pdb=" CA  VAL A 777 "
        pdb=" CB  VAL A 777 "
      ideal   model   delta    sigma   weight residual
     114.00  110.76    3.24 1.31e+00 5.83e-01 6.13e+00
  ... (remaining 48116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.25: 12080
       31.25 -    62.49: 328
       62.49 -    93.74: 33
       93.74 -   124.98: 0
      124.98 -   156.23: 1
  Dihedral angle restraints: 12442
    sinusoidal: 6816
      harmonic: 5626
  Sorted by residual:
  dihedral pdb=" C8  GTP B 201 "
           pdb=" C1' GTP B 201 "
           pdb=" N9  GTP B 201 "
           pdb=" O4' GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -51.64  156.23     1      2.00e+01 2.50e-03 4.60e+01
  dihedral pdb=" C4' GTP B 201 "
           pdb=" C5' GTP B 201 "
           pdb=" O5' GTP B 201 "
           pdb=" PA  GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  178.00   82.87     1      2.00e+01 2.50e-03 2.10e+01
  dihedral pdb=" CA  TYR B  82 "
           pdb=" C   TYR B  82 "
           pdb=" N   ILE B  83 "
           pdb=" CA  ILE B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.47  -20.53     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 12439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1339
       0.028 -    0.056: 461
       0.056 -    0.083: 174
       0.083 -    0.111: 78
       0.111 -    0.139: 19
  Chirality restraints: 2071
  Sorted by residual:
  chirality pdb=" CA  VAL A 792 "
            pdb=" N   VAL A 792 "
            pdb=" C   VAL A 792 "
            pdb=" CB  VAL A 792 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  ILE A 236 "
            pdb=" N   ILE A 236 "
            pdb=" C   ILE A 236 "
            pdb=" CB  ILE A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE B 119 "
            pdb=" N   ILE B 119 "
            pdb=" C   ILE B 119 "
            pdb=" CB  ILE B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 2068 not shown)

  Planarity restraints: 3867
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 116 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO A 117 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 117 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 117 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C  75 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.93e+00
        pdb=" C   LYS C  75 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LYS C  75 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY C  76 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  29 "    0.073 9.50e-02 1.11e+02   2.58e-02 2.37e+00
        pdb=" NE  ARG F  29 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  29 "    0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  29 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG F  29 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG F  29 "   -0.004 2.00e-02 2.50e+03
        pdb="HH21 ARG F  29 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG F  29 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 3864 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 1086
        2.15 -     2.77: 52573
        2.77 -     3.38: 78725
        3.38 -     3.99: 96902
        3.99 -     4.60: 154004
  Nonbonded interactions: 383290
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 797 "
            pdb=" H   GLU A 799 "
     model   vdw
     1.543 2.450
  nonbonded pdb=" O   LEU B  15 "
            pdb=" H   TRP B  66 "
     model   vdw
     1.546 2.450
  nonbonded pdb=" O   GLU F  20 "
            pdb=" H   GLY F  58 "
     model   vdw
     1.562 2.450
  nonbonded pdb=" O   GLN A 437 "
            pdb=" HE  ARG A 746 "
     model   vdw
     1.564 2.450
  nonbonded pdb="HD22 ASN A 951 "
            pdb=" OE1 GLN A1006 "
     model   vdw
     1.566 2.450
  ... (remaining 383285 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.170
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.110
  Set scattering table:                    0.110
  Process input model:                     27.610
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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      :  0.004   0.096  13401  Z= 0.182
  Angle     :  0.549   8.051  18163  Z= 0.298
  Chirality :  0.037   0.139   2071
  Planarity :  0.003   0.057   2312
  Dihedral  : 14.483 156.228   4999
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.21), residues: 1613
  helix:  1.38 (0.16), residues: 1010
  sheet:  0.05 (0.54), residues: 97
  loop : -0.28 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.000   ARG F  29 
 TYR   0.012   0.001   TYR A 454 
 PHE   0.021   0.001   PHE A 882 
 TRP   0.015   0.001   TRP A 762 
 HIS   0.006   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (13400)
  covalent geometry    : angle       0.54874 (18163)
  hydrogen bonds       : bond        0.15217 (  821)
  hydrogen bonds       : angle       6.11219 ( 2388)
  Misc. bond           : bond        0.00057 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.8349 (ttp) cc_final: 0.7960 (ttp)
REVERT: C   97 ASP cc_start: 0.8437 (t0) cc_final: 0.8120 (t70)
REVERT: E   74 CYS cc_start: 0.9116 (m) cc_final: 0.8866 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2939
  time to fit residues: 66.3186
Evaluate side-chains
  137 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 145 ASN
F  49 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.074754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.057913 restraints weight = 155915.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.43
r_work: 0.3138 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.0945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13401  Z= 0.144
  Angle     :  0.559   5.953  18163  Z= 0.302
  Chirality :  0.038   0.156   2071
  Planarity :  0.004   0.059   2312
  Dihedral  :  6.863 152.928   1772
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.72 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.24 (0.21), residues: 1613
  helix:  1.42 (0.16), residues: 1046
  sheet: -0.17 (0.54), residues: 95
  loop : -0.18 (0.31), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  43 
 TYR   0.011   0.001   TYR A 372 
 PHE   0.018   0.001   PHE A 882 
 TRP   0.017   0.001   TRP A 762 
 HIS   0.008   0.001   HIS E  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13400)
  covalent geometry    : angle       0.55860 (18163)
  hydrogen bonds       : bond        0.05064 (  821)
  hydrogen bonds       : angle       5.15866 ( 2388)
  Misc. bond           : bond        0.00006 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 156
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.4095 (tpp) cc_final: 0.3877 (ttp)
REVERT: A  213 MET cc_start: 0.8316 (ttp) cc_final: 0.7856 (ttp)
REVERT: A  771 MET cc_start: 0.8940 (tmm) cc_final: 0.8516 (tmm)
REVERT: C   97 ASP cc_start: 0.8549 (t0) cc_final: 0.8168 (t70)
  outliers start: 6
  outliers final: 5
  residues processed: 158
  average time/residue: 0.2601
  time to fit residues: 61.3425
Evaluate side-chains
  152 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 147
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   chunk 154 optimal weight:    0.6980
   chunk 2 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 149 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 130 optimal weight:    0.4980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 321 ASN
A 791 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.074757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.057897 restraints weight = 155891.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 4.43
r_work: 0.3141 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13401  Z= 0.138
  Angle     :  0.528   5.889  18163  Z= 0.283
  Chirality :  0.038   0.146   2071
  Planarity :  0.004   0.058   2312
  Dihedral  :  6.716 149.592   1772
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.82 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.25 (0.21), residues: 1613
  helix:  1.48 (0.16), residues: 1052
  sheet: -0.18 (0.53), residues: 93
  loop : -0.31 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 423 
 TYR   0.012   0.001   TYR A 372 
 PHE   0.018   0.001   PHE A 882 
 TRP   0.015   0.001   TRP A 762 
 HIS   0.004   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (13400)
  covalent geometry    : angle       0.52805 (18163)
  hydrogen bonds       : bond        0.04420 (  821)
  hydrogen bonds       : angle       4.90710 ( 2388)
  Misc. bond           : bond        0.00013 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 162
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.8346 (ttp) cc_final: 0.7950 (ttp)
REVERT: A  771 MET cc_start: 0.8931 (tmm) cc_final: 0.8485 (tmm)
REVERT: C   97 ASP cc_start: 0.8513 (t0) cc_final: 0.8133 (t70)
REVERT: F    6 MET cc_start: 0.8593 (ttt) cc_final: 0.8240 (ttp)
  outliers start: 5
  outliers final: 5
  residues processed: 163
  average time/residue: 0.2720
  time to fit residues: 65.2535
Evaluate side-chains
  160 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 155
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 129 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 152 optimal weight:    8.9990
   chunk 131 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 133 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 156 optimal weight:    9.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
A 791 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.073505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.056712 restraints weight = 157092.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 4.39
r_work: 0.3110 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13401  Z= 0.220
  Angle     :  0.567   7.355  18163  Z= 0.308
  Chirality :  0.038   0.135   2071
  Planarity :  0.004   0.057   2312
  Dihedral  :  6.777 148.342   1772
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  6.74 %
    Favored  : 92.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.02 (0.21), residues: 1613
  helix:  1.31 (0.16), residues: 1048
  sheet: -0.37 (0.52), residues: 93
  loop : -0.39 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 423 
 TYR   0.012   0.001   TYR E  79 
 PHE   0.017   0.001   PHE A 882 
 TRP   0.014   0.001   TRP A 762 
 HIS   0.004   0.001   HIS E  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (13400)
  covalent geometry    : angle       0.56707 (18163)
  hydrogen bonds       : bond        0.04350 (  821)
  hydrogen bonds       : angle       4.96624 ( 2388)
  Misc. bond           : bond        0.00002 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 156
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.4134 (tpp) cc_final: 0.3853 (ttm)
REVERT: A  213 MET cc_start: 0.8390 (ttp) cc_final: 0.8007 (ttp)
REVERT: A  583 MET cc_start: 0.9338 (tpp) cc_final: 0.9064 (tpt)
REVERT: A  771 MET cc_start: 0.8957 (tmm) cc_final: 0.8504 (tmm)
REVERT: A  799 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9106 (mt-10)
REVERT: C   97 ASP cc_start: 0.8540 (t0) cc_final: 0.8168 (t70)
REVERT: F    6 MET cc_start: 0.8655 (ttt) cc_final: 0.8286 (ttp)
  outliers start: 6
  outliers final: 5
  residues processed: 156
  average time/residue: 0.2651
  time to fit residues: 60.7101
Evaluate side-chains
  153 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain E residue   21 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 154 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
A 791 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.074147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.057308 restraints weight = 156088.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 4.42
r_work: 0.3123 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13401  Z= 0.152
  Angle     :  0.535   6.093  18163  Z= 0.287
  Chirality :  0.038   0.143   2071
  Planarity :  0.004   0.057   2312
  Dihedral  :  6.734 146.288   1772
  Min Nonbonded Distance : 1.773

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  7.43 %
    Favored  : 92.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.21), residues: 1613
  helix:  1.44 (0.16), residues: 1051
  sheet: -0.59 (0.52), residues: 95
  loop : -0.41 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 417 
 TYR   0.012   0.001   TYR A 372 
 PHE   0.017   0.001   PHE A 882 
 TRP   0.016   0.001   TRP A 762 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13400)
  covalent geometry    : angle       0.53474 (18163)
  hydrogen bonds       : bond        0.04112 (  821)
  hydrogen bonds       : angle       4.77813 ( 2388)
  Misc. bond           : bond        0.00013 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 162
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.8364 (ttp) cc_final: 0.7992 (ttp)
REVERT: A  583 MET cc_start: 0.9328 (tpp) cc_final: 0.8963 (tpt)
REVERT: A  771 MET cc_start: 0.8930 (tmm) cc_final: 0.8476 (tmm)
REVERT: A  799 GLU cc_start: 0.9334 (mt-10) cc_final: 0.9078 (mt-10)
REVERT: C   97 ASP cc_start: 0.8546 (t0) cc_final: 0.8158 (t70)
REVERT: F    6 MET cc_start: 0.8631 (ttt) cc_final: 0.8304 (ttp)
  outliers start: 5
  outliers final: 5
  residues processed: 163
  average time/residue: 0.2744
  time to fit residues: 65.2221
Evaluate side-chains
  160 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 155
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 147 optimal weight:    6.9990
   chunk 117 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 125 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
E  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.075008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.058142 restraints weight = 154420.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 4.40
r_work: 0.3142 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13401  Z= 0.133
  Angle     :  0.529   6.208  18163  Z= 0.281
  Chirality :  0.037   0.146   2071
  Planarity :  0.004   0.055   2312
  Dihedral  :  6.676 144.326   1772
  Min Nonbonded Distance : 1.789

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  8.12 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.24 (0.21), residues: 1613
  helix:  1.54 (0.16), residues: 1050
  sheet: -0.66 (0.51), residues: 95
  loop : -0.38 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 423 
 TYR   0.013   0.001   TYR A 372 
 PHE   0.017   0.001   PHE A 882 
 TRP   0.016   0.001   TRP A 762 
 HIS   0.005   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13400)
  covalent geometry    : angle       0.52866 (18163)
  hydrogen bonds       : bond        0.03919 (  821)
  hydrogen bonds       : angle       4.65319 ( 2388)
  Misc. bond           : bond        0.00012 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 162
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.9078 (m-80) cc_final: 0.8872 (m-80)
REVERT: A   73 MET cc_start: 0.4156 (tpp) cc_final: 0.3870 (ttm)
REVERT: A  213 MET cc_start: 0.8360 (ttp) cc_final: 0.7971 (ttp)
REVERT: A  771 MET cc_start: 0.8955 (tmm) cc_final: 0.8506 (tmm)
REVERT: A  799 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9062 (mt-10)
REVERT: C   97 ASP cc_start: 0.8522 (t0) cc_final: 0.8141 (t70)
REVERT: F    6 MET cc_start: 0.8614 (ttt) cc_final: 0.8312 (ttp)
  outliers start: 6
  outliers final: 6
  residues processed: 163
  average time/residue: 0.2687
  time to fit residues: 63.2008
Evaluate side-chains
  164 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain F residue   84 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 134 optimal weight:    0.3980
   chunk 70 optimal weight:    4.9990
   chunk 145 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 138 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 617 ASN
E  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.074396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.057631 restraints weight = 155426.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 4.39
r_work: 0.3128 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13401  Z= 0.174
  Angle     :  0.545   6.029  18163  Z= 0.292
  Chirality :  0.038   0.141   2071
  Planarity :  0.004   0.054   2312
  Dihedral  :  6.714 143.473   1772
  Min Nonbonded Distance : 1.757

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.81 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.19 (0.21), residues: 1613
  helix:  1.50 (0.16), residues: 1047
  sheet: -0.69 (0.51), residues: 95
  loop : -0.39 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 423 
 TYR   0.011   0.001   TYR E  79 
 PHE   0.017   0.001   PHE A 882 
 TRP   0.014   0.001   TRP A 762 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (13400)
  covalent geometry    : angle       0.54523 (18163)
  hydrogen bonds       : bond        0.03931 (  821)
  hydrogen bonds       : angle       4.68164 ( 2388)
  Misc. bond           : bond        0.00003 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.9072 (m-80) cc_final: 0.8854 (m-80)
REVERT: A   73 MET cc_start: 0.4054 (tpp) cc_final: 0.3854 (ttm)
REVERT: A  213 MET cc_start: 0.8389 (ttp) cc_final: 0.8012 (ttp)
REVERT: A  771 MET cc_start: 0.8959 (tmm) cc_final: 0.8508 (tmm)
REVERT: A  799 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9073 (mt-10)
REVERT: C   97 ASP cc_start: 0.8547 (t0) cc_final: 0.8185 (t70)
  outliers start: 7
  outliers final: 7
  residues processed: 160
  average time/residue: 0.2784
  time to fit residues: 65.0380
Evaluate side-chains
  162 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain F residue   84 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 77 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 125 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 574 HIS
A 870 GLN
E  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.074321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.057521 restraints weight = 155209.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 4.39
r_work: 0.3126 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13401  Z= 0.170
  Angle     :  0.548   6.266  18163  Z= 0.293
  Chirality :  0.038   0.155   2071
  Planarity :  0.004   0.054   2312
  Dihedral  :  6.697 141.811   1772
  Min Nonbonded Distance : 1.758

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.95 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.18 (0.21), residues: 1613
  helix:  1.51 (0.16), residues: 1047
  sheet: -1.23 (0.52), residues: 83
  loop : -0.35 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 190 
 TYR   0.017   0.001   TYR C 173 
 PHE   0.017   0.001   PHE A 882 
 TRP   0.015   0.001   TRP A 762 
 HIS   0.005   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13400)
  covalent geometry    : angle       0.54773 (18163)
  hydrogen bonds       : bond        0.03889 (  821)
  hydrogen bonds       : angle       4.63778 ( 2388)
  Misc. bond           : bond        0.00008 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 156
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.9062 (m-80) cc_final: 0.8833 (m-80)
REVERT: A   73 MET cc_start: 0.4035 (tpp) cc_final: 0.3809 (ttm)
REVERT: A  213 MET cc_start: 0.8409 (ttp) cc_final: 0.7683 (ttp)
REVERT: A  771 MET cc_start: 0.8986 (tmm) cc_final: 0.8527 (tmm)
REVERT: A  799 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9054 (mt-10)
REVERT: C   97 ASP cc_start: 0.8562 (t0) cc_final: 0.8197 (t70)
REVERT: C  172 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8610 (t70)
REVERT: E  102 GLU cc_start: 0.8919 (pm20) cc_final: 0.8673 (pm20)
REVERT: F   15 PHE cc_start: 0.8153 (m-80) cc_final: 0.7893 (m-80)
  outliers start: 7
  outliers final: 6
  residues processed: 159
  average time/residue: 0.2870
  time to fit residues: 66.3160
Evaluate side-chains
  159 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue  172 ASP
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   31 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 160 optimal weight:    0.0000
   chunk 85 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 146 optimal weight:    8.9990
   overall best weight:    0.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 574 HIS
E  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.075145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.058220 restraints weight = 155021.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 4.42
r_work: 0.3143 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13401  Z= 0.128
  Angle     :  0.533   6.350  18163  Z= 0.283
  Chirality :  0.038   0.151   2071
  Planarity :  0.004   0.053   2312
  Dihedral  :  6.600 139.971   1772
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  8.95 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.33 (0.21), residues: 1613
  helix:  1.62 (0.16), residues: 1050
  sheet: -1.02 (0.53), residues: 81
  loop : -0.30 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  29 
 TYR   0.014   0.001   TYR A 372 
 PHE   0.017   0.001   PHE A 882 
 TRP   0.017   0.001   TRP A 762 
 HIS   0.005   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (13400)
  covalent geometry    : angle       0.53342 (18163)
  hydrogen bonds       : bond        0.03715 (  821)
  hydrogen bonds       : angle       4.52721 ( 2388)
  Misc. bond           : bond        0.00011 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 161
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.9060 (m-80) cc_final: 0.8821 (m-80)
REVERT: A  213 MET cc_start: 0.8367 (ttp) cc_final: 0.7617 (ttp)
REVERT: A  771 MET cc_start: 0.8965 (tmm) cc_final: 0.8502 (tmm)
REVERT: A  799 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9032 (mt-10)
REVERT: C   97 ASP cc_start: 0.8543 (t0) cc_final: 0.8178 (t70)
REVERT: E  102 GLU cc_start: 0.8914 (pm20) cc_final: 0.8706 (pm20)
REVERT: F   15 PHE cc_start: 0.8119 (m-80) cc_final: 0.7861 (m-80)
  outliers start: 8
  outliers final: 8
  residues processed: 163
  average time/residue: 0.2863
  time to fit residues: 67.6475
Evaluate side-chains
  166 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain F residue   84 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 139 optimal weight:    0.8980
   chunk 137 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 125 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
E  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.075189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.058341 restraints weight = 153998.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 4.41
r_work: 0.3148 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13401  Z= 0.125
  Angle     :  0.531   6.570  18163  Z= 0.280
  Chirality :  0.037   0.149   2071
  Planarity :  0.004   0.052   2312
  Dihedral  :  6.541 138.271   1772
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  9.36 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.40 (0.21), residues: 1613
  helix:  1.67 (0.16), residues: 1050
  sheet: -0.98 (0.53), residues: 81
  loop : -0.29 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  78 
 TYR   0.014   0.001   TYR C 173 
 PHE   0.018   0.001   PHE A 882 
 TRP   0.017   0.001   TRP A 762 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (13400)
  covalent geometry    : angle       0.53050 (18163)
  hydrogen bonds       : bond        0.03636 (  821)
  hydrogen bonds       : angle       4.49199 ( 2388)
  Misc. bond           : bond        0.00005 (    1)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 162
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.9047 (m-80) cc_final: 0.8808 (m-80)
REVERT: A  213 MET cc_start: 0.8363 (ttp) cc_final: 0.7592 (ttp)
REVERT: A  771 MET cc_start: 0.8965 (tmm) cc_final: 0.8506 (tmm)
REVERT: A  799 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9027 (mt-10)
REVERT: C   97 ASP cc_start: 0.8540 (t0) cc_final: 0.8186 (t70)
REVERT: C  172 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (t0)
REVERT: F    6 MET cc_start: 0.9063 (ttp) cc_final: 0.8754 (ttp)
  outliers start: 6
  outliers final: 4
  residues processed: 164
  average time/residue: 0.2802
  time to fit residues: 66.6232
Evaluate side-chains
  164 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 159
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain C residue  172 ASP
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   31 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 146 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 137 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.073665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.056789 restraints weight = 156391.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 4.44
r_work: 0.3107 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13401  Z= 0.237
  Angle     :  0.592   6.973  18163  Z= 0.320
  Chirality :  0.039   0.148   2071
  Planarity :  0.004   0.051   2312
  Dihedral  :  6.679 138.808   1772
  Min Nonbonded Distance : 1.730

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.43 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.21), residues: 1613
  helix:  1.38 (0.16), residues: 1050
  sheet: -1.08 (0.51), residues: 88
  loop : -0.43 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 259 
 TYR   0.015   0.001   TYR A 657 
 PHE   0.017   0.002   PHE A 882 
 TRP   0.012   0.001   TRP A 762 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (13400)
  covalent geometry    : angle       0.59182 (18163)
  hydrogen bonds       : bond        0.03931 (  821)
  hydrogen bonds       : angle       4.72571 ( 2388)
  Misc. bond           : bond        0.00006 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6682.99 seconds
wall clock time: 114 minutes 17.93 seconds (6857.93 seconds total)