Starting phenix.real_space_refine
on Wed Feb  4 01:56:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lvb_63418/02_2026/9lvb_63418.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lvb_63418/02_2026/9lvb_63418.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lvb_63418/02_2026/9lvb_63418.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lvb_63418/02_2026/9lvb_63418.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lvb_63418/02_2026/9lvb_63418.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lvb_63418/02_2026/9lvb_63418.cif"
  }
  resolution = 3.97
  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=   0.001 sd=   0.059
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: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5282      2.51       5
     N    1345      2.21       5
     O    1533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8192
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3987
          Classifications: {'peptide': 505}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 486}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1686
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1632
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201}
    Chain: "N"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 887
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 1.89, per 1000 atoms: 0.23
  Number of scatterers: 8192
  At special positions: 0
  Unit cell: (64.638, 96.957, 168.059, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1533      8.00
     N    1345      7.00
     C    5282      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 570 " - pdb=" SG  CYS A 573 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03

  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: 0.86
  Conformation dependent library (CDL) restraints added in 222.5 milliseconds
  

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 15 sheets defined
      42.8% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 75
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 75 through 112
    Processing helix  chain 'A' and resid 116 through 136
      removed outlier: 4.134A  pdb=" N   GLU A 120 " --> pdb=" O   LYS A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 158
      removed outlier: 4.024A  pdb=" N   VAL A 142 " --> pdb=" O   ASN A 138 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LYS A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 197
      removed outlier: 3.622A  pdb=" N   GLU A 197 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 222
      removed outlier: 4.392A  pdb=" N   LYS A 220 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 234
    Processing helix  chain 'A' and resid 237 through 268
      removed outlier: 3.907A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE A 247 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   CYS A 263 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 290
    Processing helix  chain 'A' and resid 299 through 323
      removed outlier: 3.711A  pdb=" N   PHE A 304 " --> pdb=" O   ARG A 300 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LEU A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY A 306 " --> pdb=" O   TRP A 302 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ALA A 314 " --> pdb=" O   THR A 310 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   SER A 321 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A 322 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 350
      removed outlier: 3.555A  pdb=" N   THR A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA A 345 " --> pdb=" O   TYR A 341 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A 347 " --> pdb=" O   THR A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 358
      removed outlier: 3.792A  pdb=" N   VAL A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 398
      Proline residue:  A 388  - end of helix
    Processing helix  chain 'A' and resid 399 through 402
      removed outlier: 3.584A  pdb=" N   LEU A 402 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 399 through 402'
    Processing helix  chain 'A' and resid 407 through 411
    Processing helix  chain 'A' and resid 414 through 448
      removed outlier: 3.877A  pdb=" N   ILE A 422 " --> pdb=" O   ASP A 418 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   THR A 437 " --> pdb=" O   GLY A 433 " (cutoff:3.500A)
      Proline residue:  A 438  - end of helix
    Processing helix  chain 'A' and resid 462 through 464
      No H-bonds generated for 'chain 'A' and resid 462 through 464'
    Processing helix  chain 'A' and resid 465 through 474
      removed outlier: 4.491A  pdb=" N   ILE A 469 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 490
    Processing helix  chain 'A' and resid 490 through 495
    Processing helix  chain 'A' and resid 496 through 507
      removed outlier: 3.797A  pdb=" N   SER A 500 " --> pdb=" O   TYR A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 509
      No H-bonds generated for 'chain 'A' and resid 508 through 509'
    Processing helix  chain 'A' and resid 510 through 515
      removed outlier: 3.719A  pdb=" N   ASN A 515 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 565
      removed outlier: 3.828A  pdb=" N   PHE A 536 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL A 538 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL A 539 " --> pdb=" O   ALA A 535 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A 542 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE A 548 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   GLY A 550 " --> pdb=" O   PHE A 546 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   TRP A 551 " --> pdb=" O   GLY A 547 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 65 through 68
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.661A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 112
    Processing helix  chain 'H' and resid 199 through 203
      removed outlier: 3.674A  pdb=" N   LEU H 203 " --> pdb=" O   SER H 200 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.745A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 123 through 130
      removed outlier: 3.969A  pdb=" N   LYS L 128 " --> pdb=" O   ASP L 124 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER L 129 " --> pdb=" O   SER L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 186 through 190
    Processing helix  chain 'N' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'H' and resid 8 through 10
      removed outlier: 3.775A  pdb=" N   SER H  10 " --> pdb=" O   SER H  24 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER H  24 " --> pdb=" O   SER H  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   CYS H  25 " --> pdb=" O   ALA H  82 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA H  82 " --> pdb=" O   CYS H  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15
    Processing sheet with id=AA3, first strand: chain 'H' and resid 20 through 22
      removed outlier: 3.721A  pdb=" N   LEU H  21 " --> pdb=" O   MET H  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 63
      removed outlier: 3.670A  pdb=" N   SER H  62 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR H  53 " --> pdb=" O   SER H  62 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   HIS H  38 " --> pdb=" O   ALA H 100 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA H 100 " --> pdb=" O   HIS H  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 138
      removed outlier: 3.565A  pdb=" N   SER H 134 " --> pdb=" O   LYS H 157 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS H 157 " --> pdb=" O   SER H 134 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLY H 153 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 134 through 138
      removed outlier: 3.565A  pdb=" N   SER H 134 " --> pdb=" O   LYS H 157 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS H 157 " --> pdb=" O   SER H 134 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLY H 153 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 164 through 168
      removed outlier: 3.755A  pdb=" N   THR H 165 " --> pdb=" O   ASN H 213 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   TYR H 208 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'L' and resid 47 through 50
      removed outlier: 6.625A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120
      removed outlier: 3.787A  pdb=" N   SER L 116 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ASN L 139 " --> pdb=" O   SER L 116 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA L 132 " --> pdb=" O   LEU L 183 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU L 183 " --> pdb=" O   ALA L 132 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 148
    Processing sheet with id=AB3, first strand: chain 'L' and resid 151 through 152
      removed outlier: 3.645A  pdb=" N   ALA L 195 " --> pdb=" O   LYS L 151 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 5 through 7
      removed outlier: 3.926A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA N  23 " --> pdb=" O   GLN N   5 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   SER N   7 " --> pdb=" O   SER N  21 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR N  69 " --> pdb=" O   GLN N  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 46 through 51
      removed outlier: 3.947A  pdb=" N   VAL N  48 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   VAL N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   MET N  34 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE N  98 " --> pdb=" O   TYR N 110 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   TYR N 110 " --> pdb=" O   ILE N  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'N' and resid 46 through 51
      removed outlier: 3.947A  pdb=" N   VAL N  48 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   VAL N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   MET N  34 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1116 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: 1.20

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1840
        1.33 -     1.45: 2018
        1.45 -     1.57: 4505
        1.57 -     1.70: 0
        1.70 -     1.82: 46
  Bond restraints: 8409
  Sorted by residual:
  bond pdb=" CA  PHE A 283 "
       pdb=" CB  PHE A 283 "
    ideal  model  delta    sigma   weight residual
    1.528  1.463  0.065 1.59e-02 3.96e+03 1.68e+01
  bond pdb=" N   PHE A 283 "
       pdb=" CA  PHE A 283 "
    ideal  model  delta    sigma   weight residual
    1.459  1.418  0.041 1.23e-02 6.61e+03 1.10e+01
  bond pdb=" C   PHE A 283 "
       pdb=" O   PHE A 283 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.028 1.19e-02 7.06e+03 5.61e+00
  bond pdb=" N   LEU A 119 "
       pdb=" CA  LEU A 119 "
    ideal  model  delta    sigma   weight residual
    1.459  1.434  0.025 1.19e-02 7.06e+03 4.45e+00
  bond pdb=" CG  MET A 149 "
       pdb=" SD  MET A 149 "
    ideal  model  delta    sigma   weight residual
    1.803  1.755  0.048 2.50e-02 1.60e+03 3.74e+00
  ... (remaining 8404 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 11024
        1.29 -     2.58: 324
        2.58 -     3.87: 75
        3.87 -     5.16: 14
        5.16 -     6.45: 12
  Bond angle restraints: 11449
  Sorted by residual:
  angle pdb=" C   PRO N  14 "
        pdb=" N   GLY N  15 "
        pdb=" CA  GLY N  15 "
      ideal   model   delta    sigma   weight residual
     122.86  116.41    6.45 1.46e+00 4.69e-01 1.95e+01
  angle pdb=" N   LYS A 337 "
        pdb=" CA  LYS A 337 "
        pdb=" C   LYS A 337 "
      ideal   model   delta    sigma   weight residual
     112.38  107.55    4.83 1.22e+00 6.72e-01 1.57e+01
  angle pdb=" N   ARG N  45 "
        pdb=" CA  ARG N  45 "
        pdb=" C   ARG N  45 "
      ideal   model   delta    sigma   weight residual
     111.17  116.57   -5.40 1.41e+00 5.03e-01 1.47e+01
  angle pdb=" N   MET A 149 "
        pdb=" CA  MET A 149 "
        pdb=" CB  MET A 149 "
      ideal   model   delta    sigma   weight residual
     110.39  116.43   -6.04 1.66e+00 3.63e-01 1.32e+01
  angle pdb=" N   GLY H 103 "
        pdb=" CA  GLY H 103 "
        pdb=" C   GLY H 103 "
      ideal   model   delta    sigma   weight residual
     111.36  107.31    4.05 1.17e+00 7.31e-01 1.20e+01
  ... (remaining 11444 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 4194
       16.90 -    33.80: 497
       33.80 -    50.70: 165
       50.70 -    67.60: 28
       67.60 -    84.50: 9
  Dihedral angle restraints: 4893
    sinusoidal: 1823
      harmonic: 3070
  Sorted by residual:
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.68   69.68     1      1.00e+01 1.00e-02 6.27e+01
  dihedral pdb=" CA  TRP H 105 "
           pdb=" C   TRP H 105 "
           pdb=" N   PRO H 106 "
           pdb=" CA  PRO H 106 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -28.88   28.88     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CA  CYS L 136 "
           pdb=" C   CYS L 136 "
           pdb=" N   LEU L 137 "
           pdb=" CA  LEU L 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.44  -25.56     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 4890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 842
       0.032 -    0.063: 315
       0.063 -    0.095: 66
       0.095 -    0.127: 49
       0.127 -    0.158: 4
  Chirality restraints: 1276
  Sorted by residual:
  chirality pdb=" CA  PHE A 283 "
            pdb=" N   PHE A 283 "
            pdb=" C   PHE A 283 "
            pdb=" CB  PHE A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  VAL N 117 "
            pdb=" N   VAL N 117 "
            pdb=" C   VAL N 117 "
            pdb=" CB  VAL N 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  ILE H  54 "
            pdb=" N   ILE H  54 "
            pdb=" C   ILE H  54 "
            pdb=" CB  ILE H  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1273 not shown)

  Planarity restraints: 1439
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 145 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.13e+00
        pdb=" C   ALA A 145 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ALA A 145 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 146 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 283 "   -0.013 2.00e-02 2.50e+03   1.14e-02 2.29e+00
        pdb=" CG  PHE A 283 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 283 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 283 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 283 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 283 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 283 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 545 "   -0.007 2.00e-02 2.50e+03   1.33e-02 1.78e+00
        pdb=" C   GLY A 545 "    0.023 2.00e-02 2.50e+03
        pdb=" O   GLY A 545 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   PHE A 546 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1436 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 132
        2.62 -     3.19: 7908
        3.19 -     3.76: 12599
        3.76 -     4.33: 16365
        4.33 -     4.90: 26355
  Nonbonded interactions: 63359
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  78 "
            pdb=" OE1 GLN L  80 "
     model   vdw
     2.055 3.040
  nonbonded pdb=" O   LYS A 276 "
            pdb=" OG1 THR A 280 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" NE2 GLN A  62 "
            pdb=" OE1 GLN A 259 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   ALA A 488 "
            pdb=" OG  SER A 492 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OD2 ASP H  76 "
            pdb=" OH  TYR H  83 "
     model   vdw
     2.220 3.040
  ... (remaining 63354 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.050
  Find NCS groups from input model:        0.030
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8415  Z= 0.168
  Angle     :  0.594   6.445  11461  Z= 0.339
  Chirality :  0.038   0.158   1276
  Planarity :  0.003   0.031   1439
  Dihedral  : 16.708  84.496   2911
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 29.08 %
    Favored  : 68.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.96 (0.27), residues: 1048
  helix:  0.77 (0.28), residues: 366
  sheet: -1.18 (0.39), residues: 200
  loop : -1.49 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 144 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.026   0.001   PHE A 283 
 TRP   0.008   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8409)
  covalent geometry    : angle       0.59429 (11449)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       0.72563 (   12)
  hydrogen bonds       : bond        0.20814 (  378)
  hydrogen bonds       : angle       8.74032 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.7146 (p0) cc_final: 0.6012 (t70)
REVERT: A  101 TYR cc_start: 0.7157 (t80) cc_final: 0.6793 (t80)
REVERT: A  123 TRP cc_start: 0.8225 (m100) cc_final: 0.7079 (m100)
REVERT: A  226 ILE cc_start: 0.8399 (mm) cc_final: 0.8072 (mp)
REVERT: A  245 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6046 (mm)
REVERT: A  427 HIS cc_start: 0.8012 (t-90) cc_final: 0.7717 (t-90)
REVERT: H  190 TYR cc_start: 0.7851 (m-80) cc_final: 0.7570 (m-10)
REVERT: L  107 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6811 (tp30)
REVERT: L  153 ASP cc_start: 0.8297 (t0) cc_final: 0.7810 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 170
  average time/residue: 0.0773
  time to fit residues: 17.8548
Evaluate side-chains
  123 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  129 SER
Chi-restraints excluded: chain L residue  156 LEU
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   93 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0870
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 187 GLN
A 266 ASN
** A 556 ASN ** 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 = 0.4022 r_free = 0.4022 target = 0.135047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.119420 restraints weight = 23332.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.120799 restraints weight = 17348.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.121880 restraints weight = 14056.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.122561 restraints weight = 11977.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.122865 restraints weight = 10640.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8415  Z= 0.140
  Angle     :  0.622   8.111  11461  Z= 0.322
  Chirality :  0.042   0.208   1276
  Planarity :  0.004   0.037   1439
  Dihedral  :  6.144  52.800   1164
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.59 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.73 (0.27), residues: 1048
  helix:  0.76 (0.27), residues: 388
  sheet: -0.95 (0.38), residues: 193
  loop : -1.31 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 213 
 TYR   0.018   0.001   TYR A 350 
 PHE   0.021   0.001   PHE N  47 
 TRP   0.011   0.001   TRP A 527 
 HIS   0.005   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8409)
  covalent geometry    : angle       0.62093 (11449)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       1.30283 (   12)
  hydrogen bonds       : bond        0.04827 (  378)
  hydrogen bonds       : angle       5.92738 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.6742 (p0) cc_final: 0.5853 (t70)
REVERT: A  101 TYR cc_start: 0.6634 (t80) cc_final: 0.6379 (t80)
REVERT: A  226 ILE cc_start: 0.8187 (mm) cc_final: 0.7762 (mp)
REVERT: A  245 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6255 (mm)
REVERT: H   93 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7611 (t0)
REVERT: H  190 TYR cc_start: 0.7353 (m-80) cc_final: 0.7131 (m-10)
REVERT: L  153 ASP cc_start: 0.8055 (t0) cc_final: 0.7439 (t0)
REVERT: N   32 TYR cc_start: 0.5461 (OUTLIER) cc_final: 0.4959 (m-80)
  outliers start: 40
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0502
  time to fit residues: 11.5328
Evaluate side-chains
  131 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0030
   chunk 20 optimal weight:    0.8980
   chunk 74 optimal weight:    9.9990
   chunk 62 optimal weight:    0.0070
   overall best weight:    0.5408

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN
A 347 ASN
** A 556 ASN ** 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 = 0.4015 r_free = 0.4015 target = 0.135117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.119221 restraints weight = 22920.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.120774 restraints weight = 16538.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121956 restraints weight = 13029.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.122773 restraints weight = 10840.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.123197 restraints weight = 9502.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8415  Z= 0.126
  Angle     :  0.603  10.417  11461  Z= 0.305
  Chirality :  0.041   0.178   1276
  Planarity :  0.004   0.041   1439
  Dihedral  :  5.466  53.790   1146
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.08 %
    Favored  : 66.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.64 (0.27), residues: 1048
  helix:  0.77 (0.27), residues: 392
  sheet: -0.86 (0.39), residues: 178
  loop : -1.22 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  31 
 TYR   0.030   0.001   TYR A 350 
 PHE   0.015   0.001   PHE A 229 
 TRP   0.009   0.001   TRP A 527 
 HIS   0.004   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8409)
  covalent geometry    : angle       0.60181 (11449)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       1.43905 (   12)
  hydrogen bonds       : bond        0.04350 (  378)
  hydrogen bonds       : angle       5.47364 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 119
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8110 (m100) cc_final: 0.7043 (m100)
REVERT: A  245 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6373 (mm)
REVERT: A  424 MET cc_start: 0.7166 (tpp) cc_final: 0.6966 (mmm)
REVERT: H   93 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7518 (t0)
REVERT: L  153 ASP cc_start: 0.8054 (t0) cc_final: 0.7391 (t0)
REVERT: N    1 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6571 (pp30)
REVERT: N   32 TYR cc_start: 0.5765 (OUTLIER) cc_final: 0.4555 (m-80)
  outliers start: 40
  outliers final: 23
  residues processed: 148
  average time/residue: 0.0610
  time to fit residues: 13.4347
Evaluate side-chains
  135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 93 optimal weight:    0.1980
   chunk 94 optimal weight:    0.0020
   chunk 63 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.136321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.120580 restraints weight = 23400.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.122083 restraints weight = 19262.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.122954 restraints weight = 15182.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.123393 restraints weight = 12721.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.123758 restraints weight = 11449.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8415  Z= 0.124
  Angle     :  0.593   9.001  11461  Z= 0.300
  Chirality :  0.040   0.152   1276
  Planarity :  0.004   0.043   1439
  Dihedral  :  5.215  54.390   1144
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.73 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.60 (0.27), residues: 1048
  helix:  0.82 (0.27), residues: 395
  sheet: -0.91 (0.40), residues: 173
  loop : -1.20 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  31 
 TYR   0.017   0.001   TYR N  80 
 PHE   0.015   0.001   PHE A 115 
 TRP   0.009   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8409)
  covalent geometry    : angle       0.59164 (11449)
  SS BOND              : bond        0.00307 (    6)
  SS BOND              : angle       1.43259 (   12)
  hydrogen bonds       : bond        0.04043 (  378)
  hydrogen bonds       : angle       5.20461 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 114
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8241 (m100) cc_final: 0.7182 (m100)
REVERT: A  279 TRP cc_start: 0.2159 (m-10) cc_final: 0.1463 (m100)
REVERT: H   93 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7508 (t0)
REVERT: L  153 ASP cc_start: 0.8144 (t0) cc_final: 0.7504 (t0)
REVERT: N    1 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6517 (pp30)
REVERT: N   32 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.4441 (m-80)
  outliers start: 40
  outliers final: 27
  residues processed: 145
  average time/residue: 0.0706
  time to fit residues: 15.3182
Evaluate side-chains
  139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.1980
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 556 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.136143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.119807 restraints weight = 23523.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.121069 restraints weight = 18452.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.122044 restraints weight = 14538.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.122965 restraints weight = 12029.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.123077 restraints weight = 10771.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8415  Z= 0.133
  Angle     :  0.599   8.756  11461  Z= 0.303
  Chirality :  0.040   0.148   1276
  Planarity :  0.004   0.046   1439
  Dihedral  :  5.252  54.686   1144
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 29.30 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.61 (0.27), residues: 1048
  helix:  0.82 (0.27), residues: 397
  sheet: -0.82 (0.39), residues: 180
  loop : -1.27 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 150 
 TYR   0.015   0.001   TYR L  50 
 PHE   0.017   0.001   PHE A 229 
 TRP   0.007   0.001   TRP A 527 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8409)
  covalent geometry    : angle       0.59813 (11449)
  SS BOND              : bond        0.00322 (    6)
  SS BOND              : angle       1.32288 (   12)
  hydrogen bonds       : bond        0.03955 (  378)
  hydrogen bonds       : angle       5.13036 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8354 (m100) cc_final: 0.7301 (m100)
REVERT: A  411 MET cc_start: 0.6802 (mmm) cc_final: 0.6587 (mmm)
REVERT: H   93 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7525 (t0)
REVERT: L  107 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6512 (mm-30)
REVERT: L  153 ASP cc_start: 0.8224 (t0) cc_final: 0.7568 (t0)
REVERT: N   32 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.4571 (m-80)
  outliers start: 36
  outliers final: 27
  residues processed: 142
  average time/residue: 0.0658
  time to fit residues: 13.9989
Evaluate side-chains
  136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  141 SER
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  136 CYS
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0470
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 556 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.135958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.119687 restraints weight = 22973.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.121241 restraints weight = 16831.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.122294 restraints weight = 13368.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.123135 restraints weight = 11370.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.123584 restraints weight = 10029.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8415  Z= 0.126
  Angle     :  0.596   9.088  11461  Z= 0.301
  Chirality :  0.041   0.163   1276
  Planarity :  0.004   0.049   1439
  Dihedral  :  5.066  55.111   1142
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 29.30 %
    Favored  : 66.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.45 (0.27), residues: 1048
  helix:  0.94 (0.27), residues: 396
  sheet: -0.69 (0.40), residues: 175
  loop : -1.19 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 213 
 TYR   0.015   0.001   TYR L  50 
 PHE   0.020   0.001   PHE A 115 
 TRP   0.007   0.001   TRP A 527 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8409)
  covalent geometry    : angle       0.59463 (11449)
  SS BOND              : bond        0.00296 (    6)
  SS BOND              : angle       1.32585 (   12)
  hydrogen bonds       : bond        0.03848 (  378)
  hydrogen bonds       : angle       5.01918 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 110
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8228 (m100) cc_final: 0.7197 (m100)
REVERT: H   93 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7539 (t0)
REVERT: L  107 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6512 (mm-30)
REVERT: L  153 ASP cc_start: 0.8085 (t0) cc_final: 0.7443 (t0)
REVERT: L  169 ASP cc_start: 0.7744 (p0) cc_final: 0.7479 (p0)
REVERT: L  171 LYS cc_start: 0.8444 (mmtm) cc_final: 0.7604 (pttp)
REVERT: N    1 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6931 (pp30)
REVERT: N   32 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.4617 (m-80)
  outliers start: 38
  outliers final: 26
  residues processed: 139
  average time/residue: 0.0625
  time to fit residues: 13.1478
Evaluate side-chains
  137 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  141 SER
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue  129 SER
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 22 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0370
   chunk 79 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   overall best weight:    1.0662

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN
A 483 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.134611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.118004 restraints weight = 23462.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.119566 restraints weight = 17238.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.120700 restraints weight = 13698.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.121369 restraints weight = 11601.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.122073 restraints weight = 10293.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8415  Z= 0.153
  Angle     :  0.626   9.560  11461  Z= 0.319
  Chirality :  0.042   0.192   1276
  Planarity :  0.004   0.049   1439
  Dihedral  :  4.875  46.300   1141
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.53 %
    Favored  : 65.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.54 (0.27), residues: 1048
  helix:  0.86 (0.26), residues: 398
  sheet: -0.63 (0.41), residues: 172
  loop : -1.28 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 213 
 TYR   0.021   0.001   TYR A 350 
 PHE   0.018   0.001   PHE A 352 
 TRP   0.008   0.001   TRP A 540 
 HIS   0.004   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8409)
  covalent geometry    : angle       0.61978 (11449)
  SS BOND              : bond        0.00413 (    6)
  SS BOND              : angle       2.74887 (   12)
  hydrogen bonds       : bond        0.04024 (  378)
  hydrogen bonds       : angle       5.05063 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8295 (m100) cc_final: 0.7271 (m100)
REVERT: A  196 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8204 (t0)
REVERT: A  376 LEU cc_start: 0.2767 (OUTLIER) cc_final: 0.2389 (tp)
REVERT: H   93 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7602 (t0)
REVERT: L  153 ASP cc_start: 0.8119 (t0) cc_final: 0.7593 (t0)
REVERT: L  169 ASP cc_start: 0.7882 (p0) cc_final: 0.7381 (p0)
REVERT: L  171 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7527 (pttm)
REVERT: N    1 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6585 (pp30)
REVERT: N   32 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.4509 (m-80)
  outliers start: 40
  outliers final: 31
  residues processed: 139
  average time/residue: 0.0652
  time to fit residues: 13.7619
Evaluate side-chains
  137 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 101
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  196 ASN
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  141 SER
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue  129 SER
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 97 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.135557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.119776 restraints weight = 23039.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.121129 restraints weight = 17627.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.122009 restraints weight = 14325.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.122774 restraints weight = 12431.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.123084 restraints weight = 11014.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8415  Z= 0.132
  Angle     :  0.640  14.421  11461  Z= 0.321
  Chirality :  0.041   0.165   1276
  Planarity :  0.004   0.050   1439
  Dihedral  :  4.813  47.301   1141
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 29.53 %
    Favored  : 66.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 (0.27), residues: 1048
  helix:  0.98 (0.27), residues: 395
  sheet: -0.65 (0.39), residues: 182
  loop : -1.25 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 213 
 TYR   0.023   0.001   TYR L  50 
 PHE   0.012   0.001   PHE A 115 
 TRP   0.010   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8409)
  covalent geometry    : angle       0.63729 (11449)
  SS BOND              : bond        0.00300 (    6)
  SS BOND              : angle       1.87869 (   12)
  hydrogen bonds       : bond        0.03965 (  378)
  hydrogen bonds       : angle       5.00828 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8341 (m100) cc_final: 0.7371 (m100)
REVERT: A  196 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8207 (t0)
REVERT: A  376 LEU cc_start: 0.3060 (OUTLIER) cc_final: 0.2676 (tp)
REVERT: H   93 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7518 (t0)
REVERT: L  107 GLU cc_start: 0.6451 (mm-30) cc_final: 0.5837 (mm-30)
REVERT: L  153 ASP cc_start: 0.8143 (t0) cc_final: 0.7605 (t0)
REVERT: L  169 ASP cc_start: 0.7797 (p0) cc_final: 0.7584 (p0)
REVERT: L  171 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7544 (pttp)
REVERT: N    1 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6998 (pp30)
REVERT: N   32 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.4507 (m-80)
  outliers start: 39
  outliers final: 31
  residues processed: 138
  average time/residue: 0.0678
  time to fit residues: 13.9996
Evaluate side-chains
  141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 105
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  196 ASN
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  141 SER
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  129 SER
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 80 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 93 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN
A 248 ASN
N  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.134894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.118993 restraints weight = 23232.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.120312 restraints weight = 17785.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.121205 restraints weight = 14501.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.121646 restraints weight = 12568.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.122337 restraints weight = 11482.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8415  Z= 0.143
  Angle     :  0.650  14.974  11461  Z= 0.326
  Chirality :  0.042   0.175   1276
  Planarity :  0.004   0.049   1439
  Dihedral  :  4.832  47.153   1141
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 29.19 %
    Favored  : 66.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.51 (0.27), residues: 1048
  helix:  0.92 (0.27), residues: 398
  sheet: -0.64 (0.39), residues: 182
  loop : -1.30 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 213 
 TYR   0.016   0.001   TYR L  50 
 PHE   0.012   0.001   PHE N  47 
 TRP   0.010   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8409)
  covalent geometry    : angle       0.64823 (11449)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       1.79045 (   12)
  hydrogen bonds       : bond        0.03937 (  378)
  hydrogen bonds       : angle       5.02156 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 108
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8311 (m100) cc_final: 0.7394 (m100)
REVERT: A  376 LEU cc_start: 0.2931 (OUTLIER) cc_final: 0.2572 (tp)
REVERT: H   93 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7532 (t0)
REVERT: L  107 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6083 (mm-30)
REVERT: L  153 ASP cc_start: 0.8034 (t0) cc_final: 0.7511 (t0)
REVERT: L  171 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7552 (pttp)
REVERT: N    1 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7027 (pp30)
REVERT: N   32 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.4558 (m-80)
REVERT: N   80 TYR cc_start: 0.6654 (m-10) cc_final: 0.6401 (m-10)
  outliers start: 39
  outliers final: 34
  residues processed: 137
  average time/residue: 0.0566
  time to fit residues: 11.7960
Evaluate side-chains
  144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 106
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  141 SER
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue  129 SER
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 88 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0000
   chunk 93 optimal weight:    4.9990
   chunk 90 optimal weight:    0.4980
   chunk 73 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 72 optimal weight:    8.9990
   chunk 15 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
N  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.135088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.119238 restraints weight = 23054.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.120555 restraints weight = 17584.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.121382 restraints weight = 14412.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.122108 restraints weight = 12533.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.122434 restraints weight = 11235.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   8415  Z= 0.152
  Angle     :  0.958  59.181  11461  Z= 0.539
  Chirality :  0.042   0.391   1276
  Planarity :  0.004   0.049   1439
  Dihedral  :  4.865  47.159   1141
  Min Nonbonded Distance : 1.812

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 29.08 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.51 (0.27), residues: 1048
  helix:  0.93 (0.27), residues: 398
  sheet: -0.63 (0.39), residues: 182
  loop : -1.30 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 213 
 TYR   0.015   0.001   TYR L  50 
 PHE   0.012   0.001   PHE N  47 
 TRP   0.009   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8409)
  covalent geometry    : angle       0.95710 (11449)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       1.69287 (   12)
  hydrogen bonds       : bond        0.03931 (  378)
  hydrogen bonds       : angle       5.01908 ( 1116)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 106
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TRP cc_start: 0.8388 (m100) cc_final: 0.7458 (m100)
REVERT: A  376 LEU cc_start: 0.2916 (OUTLIER) cc_final: 0.2584 (tp)
REVERT: H   93 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7537 (t0)
REVERT: L  107 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6080 (mm-30)
REVERT: L  153 ASP cc_start: 0.8101 (t0) cc_final: 0.7564 (t0)
REVERT: L  171 LYS cc_start: 0.8564 (mmtm) cc_final: 0.7566 (pttm)
REVERT: N    1 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.7011 (pp30)
REVERT: N   32 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.4578 (m-80)
REVERT: N   80 TYR cc_start: 0.6674 (m-10) cc_final: 0.6412 (m-10)
  outliers start: 38
  outliers final: 32
  residues processed: 135
  average time/residue: 0.0621
  time to fit residues: 12.7019
Evaluate side-chains
  141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 105
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  263 CYS
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  573 CYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  141 SER
Chi-restraints excluded: chain H residue  154 CYS
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue  129 SER
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain N residue   29 ILE
Chi-restraints excluded: chain N residue   32 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 86 optimal weight:    0.2980
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0970
   chunk 79 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0980
   chunk 32 optimal weight:    0.0050
   chunk 92 optimal weight:    0.3980
   overall best weight:    0.1792

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 248 ASN
** N  84 ASN ** 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 = 0.4011 r_free = 0.4011 target = 0.135088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.119249 restraints weight = 23197.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.120474 restraints weight = 17600.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.121480 restraints weight = 14582.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.122198 restraints weight = 12486.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.122461 restraints weight = 11146.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   8415  Z= 0.152
  Angle     :  0.959  59.181  11461  Z= 0.540
  Chirality :  0.042   0.391   1276
  Planarity :  0.004   0.049   1439
  Dihedral  :  4.865  47.159   1141
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 29.19 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.51 (0.27), residues: 1048
  helix:  0.93 (0.27), residues: 398
  sheet: -0.63 (0.39), residues: 182
  loop : -1.30 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 213 
 TYR   0.015   0.001   TYR L  50 
 PHE   0.012   0.001   PHE N  47 
 TRP   0.009   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8409)
  covalent geometry    : angle       0.95711 (11449)
  SS BOND              : bond        0.01237 (    6)
  SS BOND              : angle       2.08280 (   12)
  hydrogen bonds       : bond        0.03931 (  378)
  hydrogen bonds       : angle       5.01908 ( 1116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1223.75 seconds
wall clock time: 21 minutes 57.46 seconds (1317.46 seconds total)