Starting phenix.real_space_refine
on Wed Mar  4 03:50:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dd7_27335/03_2026/8dd7_27335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dd7_27335/03_2026/8dd7_27335.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dd7_27335/03_2026/8dd7_27335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dd7_27335/03_2026/8dd7_27335.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dd7_27335/03_2026/8dd7_27335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dd7_27335/03_2026/8dd7_27335.map"
  }
  resolution = 3.3
  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=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      66      5.16       5
     C    6633      2.51       5
     N    1780      2.21       5
     O    1889      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10370
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4192
          Classifications: {'peptide': 516}
          Link IDs: {'PTRANS': 26, 'TRANS': 489}
    Chain: "B"
      Number of atoms: 6125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 759, 6125
          Classifications: {'peptide': 759}
          Link IDs: {'PTRANS': 29, 'TRANS': 729}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   CYS A 296 " occ=0.75
      ... (4 atoms not shown)
      pdb=" SG  CYS A 296 " occ=0.75
  Time building chain proxies: 2.29, per 1000 atoms: 0.22
  Number of scatterers: 10370
  At special positions: 0
  Unit cell: (87.72, 99.072, 145.512, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      66     16.00
     P       2     15.00
     O    1889      8.00
     N    1780      7.00
     C    6633      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 547.6 milliseconds
  

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2416

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 2 sheets defined
      65.6% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 28
    Processing helix  chain 'A' and resid 53 through 75
    Processing helix  chain 'A' and resid 87 through 99
    Processing helix  chain 'A' and resid 111 through 113
      No H-bonds generated for 'chain 'A' and resid 111 through 113'
    Processing helix  chain 'A' and resid 114 through 128
    Processing helix  chain 'A' and resid 142 through 151
    Processing helix  chain 'A' and resid 157 through 169
    Processing helix  chain 'A' and resid 179 through 183
    Processing helix  chain 'A' and resid 189 through 196
    Processing helix  chain 'A' and resid 204 through 209
    Processing helix  chain 'A' and resid 213 through 219
      removed outlier: 3.675A  pdb=" N   GLY A 216 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE A 217 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A 218 " --> pdb=" O   MET A 215 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A 219 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 219'
    Processing helix  chain 'A' and resid 226 through 246
      removed outlier: 3.503A  pdb=" N   GLU A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
    Processing helix  chain 'A' and resid 267 through 272
    Processing helix  chain 'A' and resid 276 through 294
      removed outlier: 3.576A  pdb=" N   VAL A 284 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 321
      removed outlier: 3.531A  pdb=" N   ILE A 313 " --> pdb=" O   THR A 309 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TRP A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   MET A 321 " --> pdb=" O   TYR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 355
    Processing helix  chain 'A' and resid 360 through 373
    Processing helix  chain 'A' and resid 377 through 390
      removed outlier: 3.511A  pdb=" N   VAL A 384 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 408
      removed outlier: 4.001A  pdb=" N   GLY A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 424
    Processing helix  chain 'A' and resid 439 through 448
      removed outlier: 3.620A  pdb=" N   LYS A 445 " --> pdb=" O   VAL A 441 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG A 446 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 458
    Processing helix  chain 'A' and resid 471 through 475
    Processing helix  chain 'A' and resid 476 through 484
      removed outlier: 3.621A  pdb=" N   GLN A 482 " --> pdb=" O   GLU A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 517
      removed outlier: 3.708A  pdb=" N   ILE A 517 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 5
      No H-bonds generated for 'chain 'B' and resid 3 through 5'
    Processing helix  chain 'B' and resid 6 through 17
    Processing helix  chain 'B' and resid 30 through 44
    Processing helix  chain 'B' and resid 50 through 60
    Processing helix  chain 'B' and resid 60 through 73
      removed outlier: 3.845A  pdb=" N   SER B  64 " --> pdb=" O   GLN B  60 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ILE B  67 " --> pdb=" O   ARG B  63 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 75 through 90
    Processing helix  chain 'B' and resid 92 through 96
    Processing helix  chain 'B' and resid 98 through 103
      removed outlier: 4.432A  pdb=" N   MET B 102 " --> pdb=" O   SER B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 127
    Processing helix  chain 'B' and resid 128 through 144
      removed outlier: 4.084A  pdb=" N   THR B 132 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 170
    Processing helix  chain 'B' and resid 171 through 177
      removed outlier: 3.807A  pdb=" N   HIS B 176 " --> pdb=" O   GLU B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 202
      removed outlier: 4.125A  pdb=" N   SER B 190 " --> pdb=" O   PRO B 186 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   GLN B 192 " --> pdb=" O   GLY B 188 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASN B 193 " --> pdb=" O   ILE B 189 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 214
      removed outlier: 3.597A  pdb=" N   LEU B 207 " --> pdb=" O   SER B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 219
    Processing helix  chain 'B' and resid 220 through 232
      removed outlier: 3.882A  pdb=" N   TYR B 232 " --> pdb=" O   ILE B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 248
      removed outlier: 3.721A  pdb=" N   LEU B 240 " --> pdb=" O   HIS B 236 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   PHE B 248 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 571
    Processing helix  chain 'B' and resid 577 through 609
      removed outlier: 4.224A  pdb=" N   ASP B 591 " --> pdb=" O   GLU B 587 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   TYR B 597 " --> pdb=" O   LEU B 593 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   SER B 598 " --> pdb=" O   LEU B 594 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TYR B 599 " --> pdb=" O   LYS B 595 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLU B 603 " --> pdb=" O   TYR B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 635
      removed outlier: 3.897A  pdb=" N   PHE B 621 " --> pdb=" O   ASP B 617 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LYS B 630 " --> pdb=" O   THR B 626 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   PHE B 631 " --> pdb=" O   TYR B 627 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU B 635 " --> pdb=" O   PHE B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 642
      removed outlier: 3.801A  pdb=" N   HIS B 641 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 669
      removed outlier: 3.820A  pdb=" N   LEU B 651 " --> pdb=" O   THR B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 676 through 703
    Processing helix  chain 'B' and resid 707 through 723
    Processing helix  chain 'B' and resid 729 through 737
    Processing helix  chain 'B' and resid 744 through 766
      removed outlier: 3.637A  pdb=" N   LEU B 748 " --> pdb=" O   SER B 744 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 780
    Processing helix  chain 'B' and resid 786 through 798
      removed outlier: 3.710A  pdb=" N   HIS B 790 " --> pdb=" O   LEU B 786 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   TYR B 791 " --> pdb=" O   GLU B 787 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B 795 " --> pdb=" O   TYR B 791 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LEU B 796 " --> pdb=" O   TYR B 792 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 798 through 803
      removed outlier: 3.558A  pdb=" N   GLY B 803 " --> pdb=" O   PHE B 799 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 806 through 819
      removed outlier: 3.688A  pdb=" N   PHE B 811 " --> pdb=" O   ASN B 807 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   THR B 812 " --> pdb=" O   ASP B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 829 through 843
      removed outlier: 4.142A  pdb=" N   LYS B 834 " --> pdb=" O   PRO B 830 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   THR B 835 " --> pdb=" O   ILE B 831 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 850 through 855
    Processing helix  chain 'B' and resid 858 through 863
    Processing helix  chain 'B' and resid 990 through 1002
      removed outlier: 3.519A  pdb=" N   ILE B 994 " --> pdb=" O   ASP B 990 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU B 998 " --> pdb=" O   ILE B 994 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE B1000 " --> pdb=" O   LEU B 996 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1005 through 1018
      removed outlier: 3.866A  pdb=" N   LEU B1009 " --> pdb=" O   ALA B1005 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B1011 " --> pdb=" O   HIS B1007 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ARG B1013 " --> pdb=" O   LEU B1009 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   ILE B1014 " --> pdb=" O   TRP B1010 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1019 through 1028
    Processing helix  chain 'B' and resid 1039 through 1047
      removed outlier: 4.325A  pdb=" N   HIS B1044 " --> pdb=" O   PRO B1040 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   CYS B1045 " --> pdb=" O   VAL B1041 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1058 through 1063
    Processing helix  chain 'B' and resid 1064 through 1066
      No H-bonds generated for 'chain 'B' and resid 1064 through 1066'
    Processing helix  chain 'B' and resid 1067 through 1077
      removed outlier: 4.334A  pdb=" N   LEU B1073 " --> pdb=" O   PRO B1069 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B1074 " --> pdb=" O   PHE B1070 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   LEU B1077 " --> pdb=" O   LEU B1073 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1102 through 1108
    Processing helix  chain 'B' and resid 1210 through 1219
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84
      removed outlier: 8.600A  pdb=" N   LEU A  82 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   PHE A  84 " --> pdb=" O   PRO A  38 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   PHE A  40 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ALA A   6 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   CYS A 105 " --> pdb=" O   ALA A   6 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL A   8 " --> pdb=" O   CYS A 105 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   GLU A 107 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   TRP A  10 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   HIS A 102 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   VAL A 133 " --> pdb=" O   HIS A 102 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   ILE A 104 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   LYS A 135 " --> pdb=" O   ILE A 104 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   ILE A 106 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 21
      removed outlier: 3.736A  pdb=" N   GLU B  21 " --> pdb=" O   THR B  24 " (cutoff:3.500A)

    516 hydrogen bonds defined for protein.
    1512 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: 1.55

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3108
        1.34 -     1.46: 2250
        1.46 -     1.58: 5148
        1.58 -     1.70: 4
        1.70 -     1.83: 106
  Bond restraints: 10616
  Sorted by residual:
  bond pdb=" C4A FAD A 602 "
       pdb=" C5A FAD A 602 "
    ideal  model  delta    sigma   weight residual
    1.386  1.471 -0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C5X FAD A 602 "
       pdb=" C9A FAD A 602 "
    ideal  model  delta    sigma   weight residual
    1.412  1.492 -0.080 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" C5A FAD A 602 "
       pdb=" C6A FAD A 602 "
    ideal  model  delta    sigma   weight residual
    1.407  1.482 -0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" CA  GLN B 573 "
       pdb=" CB  GLN B 573 "
    ideal  model  delta    sigma   weight residual
    1.529  1.581 -0.052 1.38e-02 5.25e+03 1.40e+01
  bond pdb=" C7  FAD A 602 "
       pdb=" C8  FAD A 602 "
    ideal  model  delta    sigma   weight residual
    1.420  1.488 -0.068 2.00e-02 2.50e+03 1.16e+01
  ... (remaining 10611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 14062
        2.67 -     5.34: 274
        5.34 -     8.01: 50
        8.01 -    10.69: 15
       10.69 -    13.36: 4
  Bond angle restraints: 14405
  Sorted by residual:
  angle pdb=" N   TRP B   3 "
        pdb=" CA  TRP B   3 "
        pdb=" C   TRP B   3 "
      ideal   model   delta    sigma   weight residual
     113.89  103.07   10.82 1.58e+00 4.01e-01 4.69e+01
  angle pdb=" N   LEU B 998 "
        pdb=" CA  LEU B 998 "
        pdb=" C   LEU B 998 "
      ideal   model   delta    sigma   weight residual
     111.36  104.85    6.51 1.09e+00 8.42e-01 3.57e+01
  angle pdb=" N   LEU B1211 "
        pdb=" CA  LEU B1211 "
        pdb=" C   LEU B1211 "
      ideal   model   delta    sigma   weight residual
     111.71  105.25    6.46 1.15e+00 7.56e-01 3.16e+01
  angle pdb=" CA  LYS B1117 "
        pdb=" CB  LYS B1117 "
        pdb=" CG  LYS B1117 "
      ideal   model   delta    sigma   weight residual
     114.10  123.86   -9.76 2.00e+00 2.50e-01 2.38e+01
  angle pdb=" CA  TRP B1210 "
        pdb=" CB  TRP B1210 "
        pdb=" CG  TRP B1210 "
      ideal   model   delta    sigma   weight residual
     113.60  122.15   -8.55 1.90e+00 2.77e-01 2.03e+01
  ... (remaining 14400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 5403
       17.85 -    35.70: 722
       35.70 -    53.55: 197
       53.55 -    71.40: 37
       71.40 -    89.25: 16
  Dihedral angle restraints: 6375
    sinusoidal: 2648
      harmonic: 3727
  Sorted by residual:
  dihedral pdb=" CD  ARG B1216 "
           pdb=" NE  ARG B1216 "
           pdb=" CZ  ARG B1216 "
           pdb=" NH1 ARG B1216 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   52.13  -52.13     1      1.00e+01 1.00e-02 3.71e+01
  dihedral pdb=" CA  HIS B1036 "
           pdb=" C   HIS B1036 "
           pdb=" N   ILE B1037 "
           pdb=" CA  ILE B1037 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.22  -25.78     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  MET B1065 "
           pdb=" C   MET B1065 "
           pdb=" N   LEU B1066 "
           pdb=" CA  LEU B1066 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.66   24.34     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 6372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1371
       0.068 -    0.136: 202
       0.136 -    0.204: 29
       0.204 -    0.273: 2
       0.273 -    0.341: 1
  Chirality restraints: 1605
  Sorted by residual:
  chirality pdb=" CA  MET B1038 "
            pdb=" N   MET B1038 "
            pdb=" C   MET B1038 "
            pdb=" CB  MET B1038 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CB  THR B 626 "
            pdb=" CA  THR B 626 "
            pdb=" OG1 THR B 626 "
            pdb=" CG2 THR B 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  ILE B 642 "
            pdb=" CA  ILE B 642 "
            pdb=" CG1 ILE B 642 "
            pdb=" CG2 ILE B 642 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1602 not shown)

  Planarity restraints: 1827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B1216 "   -0.864 9.50e-02 1.11e+02   3.87e-01 9.11e+01
        pdb=" NE  ARG B1216 "    0.051 2.00e-02 2.50e+03
        pdb=" CZ  ARG B1216 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B1216 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B1216 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B1210 "    0.031 2.00e-02 2.50e+03   1.90e-02 9.00e+00
        pdb=" CG  TRP B1210 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP B1210 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP B1210 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B1210 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B1210 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B1210 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B1210 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B1210 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B1210 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 850 "    0.018 2.00e-02 2.50e+03   1.80e-02 8.12e+00
        pdb=" CG  TRP B 850 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 850 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 850 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 850 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 850 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 850 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 850 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 850 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 850 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1824 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2731
        2.80 -     3.32: 10040
        3.32 -     3.85: 17587
        3.85 -     4.37: 20295
        4.37 -     4.90: 33540
  Nonbonded interactions: 84193
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 577 "
            pdb=" OD1 ASP B 579 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   LEU B 209 "
            pdb=" OG1 THR B 213 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   SER B 777 "
            pdb=" OG1 THR B 781 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" ND2 ASN B 701 "
            pdb=" OE1 GLN B 718 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   SER B1130 "
            pdb=" OG  SER B1130 "
     model   vdw
     2.296 3.040
  ... (remaining 84188 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.75 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.880
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
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      :  0.005   0.085  10616  Z= 0.263
  Angle     :  0.944  13.358  14405  Z= 0.513
  Chirality :  0.051   0.341   1605
  Planarity :  0.011   0.387   1827
  Dihedral  : 17.626  89.249   3959
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 24.80 %
    Favored  : 74.76 %
  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: -2.46 (0.22), residues: 1263
  helix: -1.53 (0.16), residues: 749
  sheet: -0.48 (1.04), residues: 35
  loop : -1.65 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 294 
 TYR   0.020   0.001   TYR B1095 
 PHE   0.034   0.002   PHE B 811 
 TRP   0.050   0.002   TRP B1210 
 HIS   0.006   0.001   HIS B1075 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (10616)
  covalent geometry    : angle       0.94380 (14405)
  hydrogen bonds       : bond        0.22333 (  516)
  hydrogen bonds       : angle       7.75510 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 LEU cc_start: 0.8624 (tp) cc_final: 0.8383 (tp)
REVERT: A  270 LEU cc_start: 0.8667 (tt) cc_final: 0.8181 (mp)
REVERT: B  179 MET cc_start: 0.4315 (ptt) cc_final: 0.4045 (ptt)
REVERT: B  185 MET cc_start: 0.6852 (mmm) cc_final: 0.6338 (mmm)
REVERT: B  211 LEU cc_start: 0.8697 (tp) cc_final: 0.8384 (mt)
REVERT: B  789 MET cc_start: 0.5516 (mmt) cc_final: 0.4917 (mmm)
REVERT: B  813 MET cc_start: 0.6151 (tmm) cc_final: 0.5623 (tmm)
REVERT: B  814 MET cc_start: 0.7873 (mmt) cc_final: 0.7356 (mmp)
REVERT: B 1075 HIS cc_start: 0.8218 (p90) cc_final: 0.7939 (p-80)
  outliers start: 5
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0875
  time to fit residues: 14.4674
Evaluate side-chains
  90 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 285 HIS
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1007 HIS
B1036 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.122142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.086917 restraints weight = 25406.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 4.23
r_work: 0.3175 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10616  Z= 0.192
  Angle     :  0.672   7.735  14405  Z= 0.342
  Chirality :  0.043   0.165   1605
  Planarity :  0.005   0.050   1827
  Dihedral  :  6.805  71.650   1426
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.48 %
    Favored  : 75.02 %
  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 (0.23), residues: 1263
  helix: -0.29 (0.18), residues: 771
  sheet: -0.36 (1.11), residues: 35
  loop : -1.41 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.019   0.002   TYR B1043 
 PHE   0.030   0.002   PHE B 811 
 TRP   0.023   0.002   TRP B1210 
 HIS   0.005   0.001   HIS B1075 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (10616)
  covalent geometry    : angle       0.67169 (14405)
  hydrogen bonds       : bond        0.04840 (  516)
  hydrogen bonds       : angle       5.07918 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 88
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8637 (tpp-160)
REVERT: A   90 TYR cc_start: 0.8853 (t80) cc_final: 0.8647 (t80)
REVERT: B  179 MET cc_start: 0.4721 (ptt) cc_final: 0.4475 (ptt)
REVERT: B  814 MET cc_start: 0.8040 (mmt) cc_final: 0.7728 (mmp)
REVERT: B 1038 MET cc_start: 0.5825 (ttm) cc_final: 0.5176 (tpt)
  outliers start: 40
  outliers final: 17
  residues processed: 122
  average time/residue: 0.1058
  time to fit residues: 18.5543
Evaluate side-chains
  95 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  611 ASN
Chi-restraints excluded: chain B residue  709 ASP
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue 1073 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   chunk 37 optimal weight:    0.4980
   chunk 69 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1012 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.123792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.087131 restraints weight = 25333.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 3.44
r_work: 0.3184 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10616  Z= 0.149
  Angle     :  0.601   7.870  14405  Z= 0.307
  Chirality :  0.041   0.212   1605
  Planarity :  0.004   0.061   1827
  Dihedral  :  6.497  75.972   1426
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.45 %
    Favored  : 74.06 %
  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: -0.50 (0.24), residues: 1263
  helix:  0.27 (0.18), residues: 776
  sheet: -0.58 (1.06), residues: 35
  loop : -1.25 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1091 
 TYR   0.018   0.001   TYR B 597 
 PHE   0.033   0.001   PHE B 811 
 TRP   0.018   0.002   TRP B1210 
 HIS   0.006   0.001   HIS B1075 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10616)
  covalent geometry    : angle       0.60079 (14405)
  hydrogen bonds       : bond        0.04057 (  516)
  hydrogen bonds       : angle       4.74984 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 82
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8611 (tpp-160)
REVERT: A   90 TYR cc_start: 0.8921 (t80) cc_final: 0.8698 (t80)
REVERT: A  410 ASP cc_start: 0.8760 (p0) cc_final: 0.8500 (p0)
REVERT: B  179 MET cc_start: 0.4669 (ptt) cc_final: 0.4461 (ptt)
REVERT: B  724 MET cc_start: 0.7579 (tpp) cc_final: 0.7173 (tpp)
REVERT: B  734 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6859 (mm)
REVERT: B  814 MET cc_start: 0.8153 (mmt) cc_final: 0.7792 (mmp)
REVERT: B  850 TRP cc_start: 0.5724 (p90) cc_final: 0.5289 (m-90)
REVERT: B 1102 TYR cc_start: 0.4759 (OUTLIER) cc_final: 0.4222 (p90)
  outliers start: 40
  outliers final: 21
  residues processed: 119
  average time/residue: 0.0923
  time to fit residues: 16.0508
Evaluate side-chains
  101 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  709 ASP
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1041 VAL
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1102 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 123 optimal weight:   20.0000
   chunk 98 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 104 optimal weight:    9.9990
   chunk 106 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 125 optimal weight:    8.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 254 GLN
B 241 GLN
** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 782 GLN
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.119919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.083975 restraints weight = 25775.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 3.57
r_work: 0.3094 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  10616  Z= 0.261
  Angle     :  0.687   8.498  14405  Z= 0.347
  Chirality :  0.045   0.319   1605
  Planarity :  0.005   0.056   1827
  Dihedral  :  6.582  75.681   1426
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.49 %
    Favored  : 72.49 %
  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: -0.56 (0.24), residues: 1263
  helix:  0.25 (0.18), residues: 770
  sheet: -1.05 (1.00), residues: 35
  loop : -1.27 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 278 
 TYR   0.025   0.002   TYR B 597 
 PHE   0.033   0.002   PHE B 811 
 TRP   0.016   0.002   TRP B1210 
 HIS   0.005   0.001   HIS B1036 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 (10616)
  covalent geometry    : angle       0.68708 (14405)
  hydrogen bonds       : bond        0.04255 (  516)
  hydrogen bonds       : angle       4.82016 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 74
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8538 (tpp-160)
REVERT: B  714 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7908 (mp)
REVERT: B  734 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6974 (mm)
REVERT: B  814 MET cc_start: 0.8106 (mmt) cc_final: 0.7798 (mmp)
REVERT: B  850 TRP cc_start: 0.5744 (p90) cc_final: 0.5340 (m-90)
REVERT: B 1079 ILE cc_start: 0.4246 (OUTLIER) cc_final: 0.3931 (mt)
REVERT: B 1102 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.4236 (p90)
  outliers start: 46
  outliers final: 26
  residues processed: 116
  average time/residue: 0.0951
  time to fit residues: 15.9310
Evaluate side-chains
  100 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 69
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  611 ASN
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain B residue  709 ASP
Chi-restraints excluded: chain B residue  714 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1031 VAL
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1079 ILE
Chi-restraints excluded: chain B residue 1102 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 105 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 117 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 69 optimal weight:    7.9990
   chunk 107 optimal weight:   30.0000
   chunk 0 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.117717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.082140 restraints weight = 25342.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.96
r_work: 0.3086 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10616  Z= 0.226
  Angle     :  0.646   8.840  14405  Z= 0.326
  Chirality :  0.044   0.294   1605
  Planarity :  0.005   0.049   1827
  Dihedral  :  6.571  76.406   1426
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 23.06 %
    Favored  : 72.40 %
  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: -0.46 (0.24), residues: 1263
  helix:  0.33 (0.18), residues: 773
  sheet: -1.19 (0.98), residues: 35
  loop : -1.22 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 278 
 TYR   0.024   0.002   TYR B 597 
 PHE   0.029   0.002   PHE B 811 
 TRP   0.016   0.002   TRP B1096 
 HIS   0.003   0.001   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (10616)
  covalent geometry    : angle       0.64620 (14405)
  hydrogen bonds       : bond        0.04075 (  516)
  hydrogen bonds       : angle       4.76362 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 74
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8583 (tpp-160)
REVERT: A  357 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8010 (mp10)
REVERT: B  734 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6998 (mm)
REVERT: B  814 MET cc_start: 0.8059 (mmt) cc_final: 0.7742 (mmp)
REVERT: B  850 TRP cc_start: 0.6001 (p90) cc_final: 0.5334 (m-90)
REVERT: B 1102 TYR cc_start: 0.4835 (OUTLIER) cc_final: 0.4224 (p90)
  outliers start: 52
  outliers final: 31
  residues processed: 120
  average time/residue: 0.1056
  time to fit residues: 18.2068
Evaluate side-chains
  104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 69
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  357 GLN
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  611 ASN
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain B residue  709 ASP
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1039 GLU
Chi-restraints excluded: chain B residue 1041 VAL
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1102 TYR
Chi-restraints excluded: chain B residue 1118 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0770
   chunk 102 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 55 optimal weight:    0.3980
   chunk 107 optimal weight:   20.0000
   chunk 108 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 701 ASN
B 718 GLN
** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 782 GLN
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.120266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.085376 restraints weight = 25307.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 4.79
r_work: 0.3134 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10616  Z= 0.120
  Angle     :  0.607  17.027  14405  Z= 0.299
  Chirality :  0.041   0.248   1605
  Planarity :  0.004   0.064   1827
  Dihedral  :  6.166  81.517   1426
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 23.67 %
    Favored  : 72.49 %
  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: -0.07 (0.24), residues: 1263
  helix:  0.63 (0.19), residues: 775
  sheet: -1.01 (1.00), residues: 35
  loop : -1.06 (0.32), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  56 
 TYR   0.018   0.001   TYR B1095 
 PHE   0.038   0.001   PHE B 811 
 TRP   0.028   0.001   TRP B1096 
 HIS   0.005   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10616)
  covalent geometry    : angle       0.60651 (14405)
  hydrogen bonds       : bond        0.03610 (  516)
  hydrogen bonds       : angle       4.56246 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 78
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8326 (mp)
REVERT: A  357 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8047 (mp10)
REVERT: A  410 ASP cc_start: 0.8676 (p0) cc_final: 0.8354 (p0)
REVERT: B   80 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8644 (pt0)
REVERT: B  182 MET cc_start: 0.6445 (mmp) cc_final: 0.6230 (pmm)
REVERT: B  734 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6930 (mm)
REVERT: B  814 MET cc_start: 0.8061 (mmt) cc_final: 0.7664 (mmm)
REVERT: B  850 TRP cc_start: 0.5886 (p90) cc_final: 0.5232 (m-90)
REVERT: B 1075 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7985 (p-80)
REVERT: B 1102 TYR cc_start: 0.4979 (OUTLIER) cc_final: 0.4385 (p90)
  outliers start: 44
  outliers final: 29
  residues processed: 116
  average time/residue: 0.0937
  time to fit residues: 16.1245
Evaluate side-chains
  109 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 74
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  357 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain B residue  709 ASP
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1039 GLU
Chi-restraints excluded: chain B residue 1041 VAL
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1075 HIS
Chi-restraints excluded: chain B residue 1102 TYR
Chi-restraints excluded: chain B residue 1118 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 119 optimal weight:    0.0010
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0870
   chunk 110 optimal weight:    0.0020
   chunk 33 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    0.3372

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

Flipped N/Q/H residues before XYZ refinement:
A 285 HIS
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 720 GLN
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.120209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.081677 restraints weight = 25095.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.86
r_work: 0.3181 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10616  Z= 0.113
  Angle     :  0.584  10.189  14405  Z= 0.290
  Chirality :  0.041   0.238   1605
  Planarity :  0.004   0.056   1827
  Dihedral  :  5.910  82.932   1426
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 24.37 %
    Favored  : 72.23 %
  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:  0.09 (0.25), residues: 1263
  helix:  0.78 (0.19), residues: 775
  sheet: -0.92 (1.00), residues: 35
  loop : -1.02 (0.32), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 130 
 TYR   0.016   0.001   TYR B1095 
 PHE   0.033   0.001   PHE B 811 
 TRP   0.029   0.001   TRP B1096 
 HIS   0.003   0.000   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (10616)
  covalent geometry    : angle       0.58397 (14405)
  hydrogen bonds       : bond        0.03456 (  516)
  hydrogen bonds       : angle       4.50332 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 79
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8406 (mp)
REVERT: A   58 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8515 (tpp-160)
REVERT: A  270 LEU cc_start: 0.8718 (tt) cc_final: 0.8426 (mp)
REVERT: A  357 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8050 (mp10)
REVERT: A  410 ASP cc_start: 0.8522 (p0) cc_final: 0.8236 (p0)
REVERT: B  730 LEU cc_start: 0.7902 (tp) cc_final: 0.7663 (tp)
REVERT: B  814 MET cc_start: 0.8092 (mmt) cc_final: 0.7702 (mmm)
REVERT: B  850 TRP cc_start: 0.5863 (p90) cc_final: 0.5201 (m-90)
REVERT: B 1075 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.8086 (p-80)
REVERT: B 1102 TYR cc_start: 0.4721 (OUTLIER) cc_final: 0.4178 (p90)
  outliers start: 39
  outliers final: 24
  residues processed: 113
  average time/residue: 0.1077
  time to fit residues: 17.2388
Evaluate side-chains
  103 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  315 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  357 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue 1039 GLU
Chi-restraints excluded: chain B residue 1041 VAL
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1075 HIS
Chi-restraints excluded: chain B residue 1088 ILE
Chi-restraints excluded: chain B residue 1102 TYR
Chi-restraints excluded: chain B residue 1118 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.118700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.079965 restraints weight = 25113.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.91
r_work: 0.3136 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10616  Z= 0.163
  Angle     :  0.613  14.221  14405  Z= 0.302
  Chirality :  0.043   0.274   1605
  Planarity :  0.004   0.054   1827
  Dihedral  :  5.942  85.536   1426
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.28 %
    Favored  : 72.23 %
  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:  0.02 (0.25), residues: 1263
  helix:  0.72 (0.19), residues: 778
  sheet: -0.92 (1.01), residues: 35
  loop : -1.06 (0.32), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 278 
 TYR   0.016   0.001   TYR B 597 
 PHE   0.032   0.001   PHE B 811 
 TRP   0.027   0.002   TRP B1096 
 HIS   0.014   0.001   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10616)
  covalent geometry    : angle       0.61308 (14405)
  hydrogen bonds       : bond        0.03649 (  516)
  hydrogen bonds       : angle       4.51236 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 76
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8397 (mp)
REVERT: A   58 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8529 (tpp-160)
REVERT: A  357 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8015 (mp10)
REVERT: A  410 ASP cc_start: 0.8661 (p0) cc_final: 0.8407 (p0)
REVERT: B  795 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8608 (mm)
REVERT: B  814 MET cc_start: 0.8105 (mmt) cc_final: 0.7746 (mmm)
REVERT: B  850 TRP cc_start: 0.5821 (p90) cc_final: 0.5083 (m-90)
REVERT: B 1075 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.8057 (p-80)
REVERT: B 1102 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.4378 (p90)
  outliers start: 40
  outliers final: 26
  residues processed: 112
  average time/residue: 0.1016
  time to fit residues: 16.5001
Evaluate side-chains
  106 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 74
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  315 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  357 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  795 LEU
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue 1039 GLU
Chi-restraints excluded: chain B residue 1041 VAL
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1075 HIS
Chi-restraints excluded: chain B residue 1102 TYR
Chi-restraints excluded: chain B residue 1118 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    0.4980
   chunk 56 optimal weight:    0.0570
   chunk 110 optimal weight:    0.0770
   chunk 55 optimal weight:    0.0980
   chunk 94 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0470
   overall best weight:    0.1554

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

Flipped N/Q/H residues before XYZ refinement:
A 285 HIS
B 226 GLN
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 701 ASN
B 718 GLN
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.121264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.083090 restraints weight = 25097.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.90
r_work: 0.3204 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10616  Z= 0.110
  Angle     :  0.596  12.811  14405  Z= 0.292
  Chirality :  0.041   0.208   1605
  Planarity :  0.004   0.053   1827
  Dihedral  :  5.783  85.270   1426
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.98 %
    Favored  : 72.14 %
  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:  0.23 (0.25), residues: 1263
  helix:  0.89 (0.19), residues: 774
  sheet: -0.80 (1.00), residues: 35
  loop : -0.98 (0.32), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  56 
 TYR   0.015   0.001   TYR B1095 
 PHE   0.032   0.001   PHE B 811 
 TRP   0.036   0.001   TRP B1096 
 HIS   0.007   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (10616)
  covalent geometry    : angle       0.59575 (14405)
  hydrogen bonds       : bond        0.03383 (  516)
  hydrogen bonds       : angle       4.43153 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8335 (mp)
REVERT: A  270 LEU cc_start: 0.8698 (tt) cc_final: 0.8472 (mp)
REVERT: A  357 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8080 (mp10)
REVERT: B  568 MET cc_start: 0.5212 (mpp) cc_final: 0.4478 (mtt)
REVERT: B  795 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8679 (mm)
REVERT: B  814 MET cc_start: 0.8073 (mmt) cc_final: 0.7668 (mmm)
REVERT: B  850 TRP cc_start: 0.5960 (p90) cc_final: 0.5230 (m-90)
REVERT: B 1075 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.8126 (p-80)
REVERT: B 1102 TYR cc_start: 0.4748 (OUTLIER) cc_final: 0.4193 (p90)
  outliers start: 33
  outliers final: 20
  residues processed: 107
  average time/residue: 0.0962
  time to fit residues: 14.6722
Evaluate side-chains
  100 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain A residue  315 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  357 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue  795 LEU
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1075 HIS
Chi-restraints excluded: chain B residue 1102 TYR
Chi-restraints excluded: chain B residue 1118 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 105 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0670
   chunk 69 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 91 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.0520

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

Flipped N/Q/H residues before XYZ refinement:
B 226 GLN
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.118973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.080534 restraints weight = 25043.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.88
r_work: 0.3146 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10616  Z= 0.158
  Angle     :  0.628  12.048  14405  Z= 0.309
  Chirality :  0.043   0.270   1605
  Planarity :  0.004   0.052   1827
  Dihedral  :  5.845  88.558   1426
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 25.59 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.25), residues: 1263
  helix:  0.80 (0.19), residues: 776
  sheet: -0.81 (1.01), residues: 35
  loop : -1.03 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 194 
 TYR   0.015   0.001   TYR B 597 
 PHE   0.033   0.001   PHE B 811 
 TRP   0.033   0.002   TRP B1096 
 HIS   0.005   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10616)
  covalent geometry    : angle       0.62829 (14405)
  hydrogen bonds       : bond        0.03628 (  516)
  hydrogen bonds       : angle       4.43793 ( 1512)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8371 (mp)
REVERT: A   58 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8527 (tpp-160)
REVERT: A  266 MET cc_start: 0.8020 (mmt) cc_final: 0.7532 (mmt)
REVERT: A  270 LEU cc_start: 0.8747 (tt) cc_final: 0.8380 (mp)
REVERT: A  357 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8573 (mm-40)
REVERT: B  182 MET cc_start: 0.6879 (tpt) cc_final: 0.6623 (pmm)
REVERT: B  814 MET cc_start: 0.8083 (mmt) cc_final: 0.7688 (mmm)
REVERT: B  850 TRP cc_start: 0.5921 (p90) cc_final: 0.5190 (m-10)
REVERT: B 1075 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8125 (p-80)
REVERT: B 1102 TYR cc_start: 0.4865 (OUTLIER) cc_final: 0.4261 (p90)
  outliers start: 24
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1069
  time to fit residues: 14.6347
Evaluate side-chains
  96 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  357 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  779 HIS
Chi-restraints excluded: chain B residue 1073 LEU
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1075 HIS
Chi-restraints excluded: chain B residue 1088 ILE
Chi-restraints excluded: chain B residue 1102 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 121 optimal weight:   20.0000
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 116 optimal weight:    0.0270
   chunk 96 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 7 optimal weight:    0.7980
   chunk 113 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.4242

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

Flipped N/Q/H residues before XYZ refinement:
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.117580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.078663 restraints weight = 25313.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.90
r_work: 0.3108 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10616  Z= 0.190
  Angle     :  0.659  12.021  14405  Z= 0.323
  Chirality :  0.044   0.312   1605
  Planarity :  0.004   0.050   1827
  Dihedral  :  5.936  81.988   1426
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 25.07 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.24), residues: 1263
  helix:  0.73 (0.19), residues: 774
  sheet: -1.08 (0.97), residues: 35
  loop : -1.06 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 278 
 TYR   0.019   0.002   TYR B 597 
 PHE   0.035   0.002   PHE B 811 
 TRP   0.032   0.002   TRP B1096 
 HIS   0.005   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (10616)
  covalent geometry    : angle       0.65946 (14405)
  hydrogen bonds       : bond        0.03794 (  516)
  hydrogen bonds       : angle       4.53143 ( 1512)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2776.23 seconds
wall clock time: 48 minutes 13.21 seconds (2893.21 seconds total)