Starting phenix.real_space_refine
on Wed Sep 17 18:43:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kat_22783/09_2025/7kat_22783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kat_22783/09_2025/7kat_22783.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kat_22783/09_2025/7kat_22783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kat_22783/09_2025/7kat_22783.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kat_22783/09_2025/7kat_22783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kat_22783/09_2025/7kat_22783.cif"
  }
  resolution = 4.4
  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=   0.007 sd=   0.058
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      39      5.16       5
     C    6813      2.51       5
     N    1754      2.21       5
     O    1825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10431
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3358
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 20, 'TRANS': 419}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 64
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 435
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "B"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 229
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 3809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3809
          Classifications: {'peptide': 485}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 27, 'TRANS': 457}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 86
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1129
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "F"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1471
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 2.45, per 1000 atoms: 0.23
  Number of scatterers: 10431
  At special positions: 0
  Unit cell: (109.48, 126.14, 136.85, 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      39     16.00
     O    1825      8.00
     N    1754      7.00
     C    6813      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 324.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2526

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      68.4% alpha, 4.7% 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 28 through 47
    Processing helix  chain 'A' and resid 63 through 70
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 107 through 137
      removed outlier: 4.028A  pdb=" N   ARG A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.501A  pdb=" N   LEU A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 213 through 226
      removed outlier: 3.502A  pdb=" N   ARG A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LYS A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 3.678A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   TYR A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 260
      removed outlier: 3.618A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 314
      removed outlier: 4.189A  pdb=" N   ILE A 293 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 341 through 347
      removed outlier: 3.607A  pdb=" N   TYR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN A 347 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 341 through 347'
    Processing helix  chain 'A' and resid 351 through 358
    Processing helix  chain 'A' and resid 358 through 384
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.646A  pdb=" N   LYS A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 440
    Processing helix  chain 'A' and resid 444 through 466
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 4.276A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'B' and resid 53 through 82
    Processing helix  chain 'D' and resid 13 through 36
      removed outlier: 3.602A  pdb=" N   PHE D  17 " --> pdb=" O   THR D  13 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      Proline residue:  D  28  - end of helix
    Processing helix  chain 'D' and resid 58 through 67
      removed outlier: 4.430A  pdb=" N   LEU D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   GLU D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLU D  65 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR D  66 " --> pdb=" O   LEU D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 94 through 113
    Processing helix  chain 'D' and resid 212 through 217
    Processing helix  chain 'D' and resid 219 through 233
      removed outlier: 3.922A  pdb=" N   LEU D 223 " --> pdb=" O   ALA D 219 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   VAL D 224 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 249
      removed outlier: 3.772A  pdb=" N   TYR D 237 " --> pdb=" O   LEU D 233 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TYR D 249 " --> pdb=" O   ARG D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 268
    Processing helix  chain 'D' and resid 276 through 285
      removed outlier: 3.639A  pdb=" N   ILE D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 294
      removed outlier: 3.963A  pdb=" N   LYS D 291 " --> pdb=" O   ALA D 287 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN D 292 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE D 293 " --> pdb=" O   GLU D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 4.400A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 362
      removed outlier: 3.803A  pdb=" N   ALA D 349 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 3.991A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
      removed outlier: 3.537A  pdb=" N   LEU D 395 " --> pdb=" O   THR D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.507A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.315A  pdb=" N   GLU D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 466 through 470
      removed outlier: 3.528A  pdb=" N   LEU D 469 " --> pdb=" O   PRO D 466 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 480 through 486
    Processing helix  chain 'D' and resid 487 through 492
      removed outlier: 4.121A  pdb=" N   MET D 491 " --> pdb=" O   PRO D 487 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 541
    Processing helix  chain 'D' and resid 554 through 558
    Processing helix  chain 'E' and resid 71 through 86
      removed outlier: 3.667A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS E  86 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 124
      removed outlier: 3.661A  pdb=" N   LYS E  93 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 3.617A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 182
      removed outlier: 4.307A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 4.324A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.788A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG E 203 " --> pdb=" O   ASN E 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 199 through 203'
    Processing helix  chain 'F' and resid 21 through 41
      removed outlier: 3.516A  pdb=" N   GLY F  40 " --> pdb=" O   THR F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 52 through 71
      removed outlier: 3.848A  pdb=" N   ASN F  68 " --> pdb=" O   SER F  64 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU F  69 " --> pdb=" O   GLY F  65 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN F  70 " --> pdb=" O   MET F  66 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 91
      removed outlier: 3.689A  pdb=" N   LYS F  79 " --> pdb=" O   ASN F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 120
      Proline residue:  F 103  - end of helix
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.942A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 168
    Processing helix  chain 'F' and resid 174 through 192
      removed outlier: 3.612A  pdb=" N   ALA F 178 " --> pdb=" O   MET F 174 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211
    Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284
    Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 327
    Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434
      removed outlier: 6.694A  pdb=" N   LYS D 454 " --> pdb=" O   ILE D 431 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   ALA D 433 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   SER D 452 " --> pdb=" O   ALA D 433 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
      removed outlier: 3.803A  pdb=" N   CYS D 514 " --> pdb=" O   LYS D 593 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY D 584 " --> pdb=" O   VAL D 610 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE D 604 " --> pdb=" O   VAL D 590 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL D 592 " --> pdb=" O   LEU D 602 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU D 602 " --> pdb=" O   VAL D 592 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6

    652 hydrogen bonds defined for protein.
    1926 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: 1.56

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3281
        1.35 -     1.46: 2359
        1.46 -     1.58: 4938
        1.58 -     1.70: 0
        1.70 -     1.81: 61
  Bond restraints: 10639
  Sorted by residual:
  bond pdb=" C   THR D 595 "
       pdb=" N   ASP D 596 "
    ideal  model  delta    sigma   weight residual
    1.332  1.319  0.013 1.40e-02 5.10e+03 9.23e-01
  bond pdb=" N   LEU D 235 "
       pdb=" CA  LEU D 235 "
    ideal  model  delta    sigma   weight residual
    1.462  1.454  0.008 8.50e-03 1.38e+04 8.92e-01
  bond pdb=" CA  LEU F 102 "
       pdb=" C   LEU F 102 "
    ideal  model  delta    sigma   weight residual
    1.521  1.530 -0.009 1.14e-02 7.69e+03 6.10e-01
  bond pdb=" C   TRP D  14 "
       pdb=" N   PRO D  15 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.30e-02 5.92e+03 5.75e-01
  bond pdb=" C   VAL D 215 "
       pdb=" O   VAL D 215 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.19e-02 7.06e+03 5.71e-01
  ... (remaining 10634 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 14200
        1.52 -     3.05: 174
        3.05 -     4.57: 28
        4.57 -     6.10: 15
        6.10 -     7.62: 5
  Bond angle restraints: 14422
  Sorted by residual:
  angle pdb=" N   ILE E 126 "
        pdb=" CA  ILE E 126 "
        pdb=" C   ILE E 126 "
      ideal   model   delta    sigma   weight residual
     113.71  109.71    4.00 9.50e-01 1.11e+00 1.77e+01
  angle pdb=" C   GLU A 266 "
        pdb=" N   LEU A 267 "
        pdb=" CA  LEU A 267 "
      ideal   model   delta    sigma   weight residual
     122.38  114.76    7.62 2.90e+00 1.19e-01 6.91e+00
  angle pdb=" C   LYS A 416 "
        pdb=" N   ILE A 417 "
        pdb=" CA  ILE A 417 "
      ideal   model   delta    sigma   weight residual
     123.16  120.70    2.46 1.06e+00 8.90e-01 5.41e+00
  angle pdb=" CA  ILE E 126 "
        pdb=" C   ILE E 126 "
        pdb=" N   GLY E 127 "
      ideal   model   delta    sigma   weight residual
     119.87  116.76    3.11 1.34e+00 5.57e-01 5.37e+00
  angle pdb=" CA  VAL D 215 "
        pdb=" C   VAL D 215 "
        pdb=" N   ASP D 216 "
      ideal   model   delta    sigma   weight residual
     116.60  119.92   -3.32 1.45e+00 4.76e-01 5.24e+00
  ... (remaining 14417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6007
       17.91 -    35.82: 348
       35.82 -    53.73: 40
       53.73 -    71.65: 5
       71.65 -    89.56: 6
  Dihedral angle restraints: 6406
    sinusoidal: 2514
      harmonic: 3892
  Sorted by residual:
  dihedral pdb=" CB  GLU E 142 "
           pdb=" CG  GLU E 142 "
           pdb=" CD  GLU E 142 "
           pdb=" OE1 GLU E 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.56  -89.56     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A 382 "
           pdb=" CG  GLU A 382 "
           pdb=" CD  GLU A 382 "
           pdb=" OE1 GLU A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.22   85.22     1      3.00e+01 1.11e-03 9.78e+00
  dihedral pdb=" CB  GLU E 128 "
           pdb=" CG  GLU E 128 "
           pdb=" CD  GLU E 128 "
           pdb=" OE1 GLU E 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.63   82.63     1      3.00e+01 1.11e-03 9.30e+00
  ... (remaining 6403 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1258
       0.035 -    0.071: 329
       0.071 -    0.106: 108
       0.106 -    0.142: 15
       0.142 -    0.177: 2
  Chirality restraints: 1712
  Sorted by residual:
  chirality pdb=" CB  VAL A  82 "
            pdb=" CA  VAL A  82 "
            pdb=" CG1 VAL A  82 "
            pdb=" CG2 VAL A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.85e-01
  chirality pdb=" CA  THR A 291 "
            pdb=" N   THR A 291 "
            pdb=" C   THR A 291 "
            pdb=" CB  THR A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  ILE D 470 "
            pdb=" N   ILE D 470 "
            pdb=" C   ILE D 470 "
            pdb=" CB  ILE D 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 1709 not shown)

  Planarity restraints: 1791
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO F  48 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D  27 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO D  28 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO D  28 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D  28 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 462 "   -0.016 5.00e-02 4.00e+02   2.39e-02 9.17e-01
        pdb=" N   PRO D 463 "    0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO D 463 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO D 463 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 1788 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 552
        2.73 -     3.27: 11272
        3.27 -     3.81: 17200
        3.81 -     4.36: 18541
        4.36 -     4.90: 32319
  Nonbonded interactions: 79884
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 386 "
            pdb=" OD1 ASP D 388 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG1 THR A 201 "
            pdb=" OE1 GLU A 212 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   PHE A 198 "
            pdb=" OH  TYR C  66 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   HIS D 282 "
            pdb=" OG  SER D 285 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   TRP A 380 "
            pdb=" OG  SER A 384 "
     model   vdw
     2.273 3.040
  ... (remaining 79879 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:             1.510
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.280
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
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      :  0.002   0.024  10639  Z= 0.122
  Angle     :  0.513   7.624  14422  Z= 0.291
  Chirality :  0.037   0.177   1712
  Planarity :  0.003   0.041   1791
  Dihedral  : 11.321  89.557   3880
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.22), residues: 1316
  helix:  0.62 (0.18), residues: 816
  sheet: -1.99 (0.51), residues: 84
  loop : -2.11 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 185 
 TYR   0.008   0.001   TYR F 190 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.010   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10639)
  covalent geometry    : angle       0.51271 (14422)
  hydrogen bonds       : bond        0.13979 (  652)
  hydrogen bonds       : angle       4.57385 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.9450 (mtp) cc_final: 0.9149 (mmm)
REVERT: A  400 MET cc_start: 0.9512 (mmm) cc_final: 0.9285 (mmm)
REVERT: D   24 MET cc_start: 0.9260 (mmp) cc_final: 0.9027 (mmm)
REVERT: D   29 MET cc_start: 0.8550 (mmt) cc_final: 0.8317 (tmm)
REVERT: D  608 MET cc_start: 0.8604 (ptm) cc_final: 0.8386 (ppp)
REVERT: F  108 MET cc_start: 0.9642 (mtm) cc_final: 0.9263 (ttt)
REVERT: F  128 ASP cc_start: 0.9433 (m-30) cc_final: 0.9213 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0898
  time to fit residues: 10.9570
Evaluate side-chains
  46 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A 188 ASN
D 113 ASN
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 424 HIS
D 427 ASN
D 494 GLN
D 558 HIS
E  88 HIS
E 123 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 GLN
F  68 ASN
F  71 GLN
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.036212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.026399 restraints weight = 123475.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.027059 restraints weight = 74170.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.027502 restraints weight = 52016.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.027837 restraints weight = 40822.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.028053 restraints weight = 34261.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10639  Z= 0.201
  Angle     :  0.572   7.188  14422  Z= 0.289
  Chirality :  0.039   0.144   1712
  Planarity :  0.003   0.042   1791
  Dihedral  :  3.419  16.528   1421
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.23), residues: 1316
  helix:  1.71 (0.18), residues: 826
  sheet: -1.12 (0.54), residues: 86
  loop : -1.48 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 510 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.014   0.001   PHE D 343 
 TRP   0.014   0.001   TRP D 513 
 HIS   0.004   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10639)
  covalent geometry    : angle       0.57229 (14422)
  hydrogen bonds       : bond        0.03585 (  652)
  hydrogen bonds       : angle       3.79233 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9400 (mtm) cc_final: 0.8858 (mtp)
REVERT: A  158 MET cc_start: 0.9529 (mtp) cc_final: 0.9141 (mmm)
REVERT: D   29 MET cc_start: 0.8711 (mmt) cc_final: 0.8425 (tmm)
REVERT: D  608 MET cc_start: 0.8490 (ptm) cc_final: 0.8263 (ppp)
REVERT: F  108 MET cc_start: 0.9482 (mtm) cc_final: 0.9061 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0710
  time to fit residues: 6.5946
Evaluate side-chains
  44 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 45 optimal weight:    0.4980
   chunk 106 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 126 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** 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 = 0.3032 r_free = 0.3032 target = 0.037121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.027235 restraints weight = 120473.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.027945 restraints weight = 71154.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.028419 restraints weight = 49525.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.028786 restraints weight = 38357.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.028958 restraints weight = 32028.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10639  Z= 0.096
  Angle     :  0.497  10.845  14422  Z= 0.241
  Chirality :  0.038   0.150   1712
  Planarity :  0.003   0.045   1791
  Dihedral  :  3.225  16.301   1421
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.24), residues: 1316
  helix:  2.19 (0.18), residues: 837
  sheet: -0.90 (0.54), residues: 88
  loop : -1.29 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  92 
 TYR   0.009   0.001   TYR F 190 
 PHE   0.011   0.001   PHE A  92 
 TRP   0.010   0.001   TRP D 513 
 HIS   0.003   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (10639)
  covalent geometry    : angle       0.49750 (14422)
  hydrogen bonds       : bond        0.03088 (  652)
  hydrogen bonds       : angle       3.40456 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9370 (mtm) cc_final: 0.8885 (mtp)
REVERT: A  158 MET cc_start: 0.9521 (mtp) cc_final: 0.9159 (tpt)
REVERT: A  165 MET cc_start: 0.9385 (mmp) cc_final: 0.9174 (mmm)
REVERT: C   68 ILE cc_start: 0.9942 (mm) cc_final: 0.9681 (tt)
REVERT: D  606 MET cc_start: 0.8502 (ptm) cc_final: 0.8294 (ptm)
REVERT: D  608 MET cc_start: 0.8485 (ptm) cc_final: 0.8265 (ppp)
REVERT: F   87 MET cc_start: 0.9308 (ppp) cc_final: 0.9095 (ppp)
REVERT: F  108 MET cc_start: 0.9476 (mtm) cc_final: 0.9082 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0729
  time to fit residues: 7.4200
Evaluate side-chains
  47 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0970
   chunk 61 optimal weight:    5.9990
   chunk 97 optimal weight:   40.0000
   chunk 48 optimal weight:    5.9990
   chunk 41 optimal weight:   20.0000
   chunk 77 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 117 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   overall best weight:    3.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  71 GLN
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 106 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.036141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.026360 restraints weight = 123521.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.027027 restraints weight = 72970.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.027497 restraints weight = 51207.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.027824 restraints weight = 39727.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.028042 restraints weight = 33305.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10639  Z= 0.167
  Angle     :  0.544   7.775  14422  Z= 0.272
  Chirality :  0.038   0.144   1712
  Planarity :  0.003   0.046   1791
  Dihedral  :  3.415  18.247   1421
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.24), residues: 1316
  helix:  2.26 (0.18), residues: 836
  sheet: -0.71 (0.54), residues: 88
  loop : -1.00 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 510 
 TYR   0.011   0.001   TYR A 456 
 PHE   0.016   0.001   PHE D 343 
 TRP   0.015   0.001   TRP D 513 
 HIS   0.003   0.001   HIS D 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10639)
  covalent geometry    : angle       0.54418 (14422)
  hydrogen bonds       : bond        0.03336 (  652)
  hydrogen bonds       : angle       3.56892 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9386 (mtm) cc_final: 0.8873 (mtt)
REVERT: A  158 MET cc_start: 0.9507 (mtp) cc_final: 0.9110 (mmm)
REVERT: A  165 MET cc_start: 0.9422 (mmp) cc_final: 0.9203 (mmm)
REVERT: A  400 MET cc_start: 0.9198 (mmp) cc_final: 0.8148 (tpp)
REVERT: F   87 MET cc_start: 0.9323 (ppp) cc_final: 0.9098 (ppp)
REVERT: F  108 MET cc_start: 0.9458 (mtm) cc_final: 0.9097 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0781
  time to fit residues: 6.8702
Evaluate side-chains
  43 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 0 optimal weight:   40.0000
   chunk 13 optimal weight:   10.0000
   chunk 117 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 334 HIS
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  71 GLN
** F 101 GLN ** 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 = 0.2989 r_free = 0.2989 target = 0.035894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2576 r_free = 0.2576 target = 0.026177 restraints weight = 124449.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.026836 restraints weight = 73895.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.027292 restraints weight = 51697.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.027583 restraints weight = 40257.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.027811 restraints weight = 33988.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10639  Z= 0.178
  Angle     :  0.554   8.788  14422  Z= 0.276
  Chirality :  0.039   0.154   1712
  Planarity :  0.003   0.049   1791
  Dihedral  :  3.540  18.690   1421
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.24), residues: 1316
  helix:  2.29 (0.18), residues: 835
  sheet: -0.48 (0.54), residues: 86
  loop : -0.88 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 510 
 TYR   0.011   0.001   TYR A 456 
 PHE   0.013   0.001   PHE D 343 
 TRP   0.014   0.001   TRP D 513 
 HIS   0.003   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10639)
  covalent geometry    : angle       0.55446 (14422)
  hydrogen bonds       : bond        0.03287 (  652)
  hydrogen bonds       : angle       3.60767 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9415 (mtm) cc_final: 0.8889 (mtt)
REVERT: A  158 MET cc_start: 0.9507 (mtp) cc_final: 0.9128 (mmm)
REVERT: D  606 MET cc_start: 0.8491 (ptm) cc_final: 0.8179 (ptt)
REVERT: D  608 MET cc_start: 0.8035 (ppp) cc_final: 0.7466 (ppp)
REVERT: F   57 MET cc_start: 0.9343 (tpt) cc_final: 0.9124 (tpp)
REVERT: F   87 MET cc_start: 0.9342 (ppp) cc_final: 0.9106 (ppp)
REVERT: F  108 MET cc_start: 0.9451 (mtm) cc_final: 0.9094 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0750
  time to fit residues: 6.3800
Evaluate side-chains
  44 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 103 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 84 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 126 optimal weight:    3.9990
   chunk 25 optimal weight:   40.0000
   chunk 75 optimal weight:    1.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 HIS
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** 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 = 0.2988 r_free = 0.2988 target = 0.035749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.026316 restraints weight = 125868.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.026967 restraints weight = 74740.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.027419 restraints weight = 52409.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.027729 restraints weight = 40941.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.027944 restraints weight = 34355.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10639  Z= 0.171
  Angle     :  0.552   9.018  14422  Z= 0.274
  Chirality :  0.039   0.140   1712
  Planarity :  0.003   0.050   1791
  Dihedral  :  3.561  18.936   1421
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.24), residues: 1316
  helix:  2.25 (0.18), residues: 851
  sheet: -0.38 (0.54), residues: 86
  loop : -0.89 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 510 
 TYR   0.012   0.001   TYR A 456 
 PHE   0.014   0.001   PHE D 343 
 TRP   0.015   0.001   TRP D 513 
 HIS   0.003   0.001   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10639)
  covalent geometry    : angle       0.55169 (14422)
  hydrogen bonds       : bond        0.03285 (  652)
  hydrogen bonds       : angle       3.60384 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9434 (mtm) cc_final: 0.8868 (mtt)
REVERT: A  158 MET cc_start: 0.9519 (mtp) cc_final: 0.9172 (mmm)
REVERT: A  165 MET cc_start: 0.9527 (mmp) cc_final: 0.9326 (mmm)
REVERT: D  608 MET cc_start: 0.8267 (ppp) cc_final: 0.7624 (ppp)
REVERT: F   57 MET cc_start: 0.9338 (tpt) cc_final: 0.9120 (tpp)
REVERT: F  108 MET cc_start: 0.9412 (mtm) cc_final: 0.9057 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0743
  time to fit residues: 6.4330
Evaluate side-chains
  45 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 67 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** 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 = 0.2980 r_free = 0.2980 target = 0.035501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.026061 restraints weight = 124929.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.026692 restraints weight = 77149.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.027136 restraints weight = 53768.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.027462 restraints weight = 41650.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.027648 restraints weight = 34852.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10639  Z= 0.178
  Angle     :  0.564   9.280  14422  Z= 0.281
  Chirality :  0.039   0.165   1712
  Planarity :  0.003   0.050   1791
  Dihedral  :  3.621  19.003   1421
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.24), residues: 1316
  helix:  2.29 (0.18), residues: 843
  sheet: -0.30 (0.54), residues: 86
  loop : -0.72 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 510 
 TYR   0.013   0.001   TYR A 456 
 PHE   0.014   0.001   PHE D 343 
 TRP   0.015   0.001   TRP D 513 
 HIS   0.002   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10639)
  covalent geometry    : angle       0.56354 (14422)
  hydrogen bonds       : bond        0.03330 (  652)
  hydrogen bonds       : angle       3.64030 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9429 (mtm) cc_final: 0.8891 (mtt)
REVERT: A  135 MET cc_start: 0.8725 (mmm) cc_final: 0.8491 (mmm)
REVERT: A  158 MET cc_start: 0.9515 (mtp) cc_final: 0.9173 (mmm)
REVERT: D  608 MET cc_start: 0.8302 (ppp) cc_final: 0.7574 (ppp)
REVERT: F  108 MET cc_start: 0.9406 (mtm) cc_final: 0.9057 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0703
  time to fit residues: 6.2330
Evaluate side-chains
  44 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 101 optimal weight:    0.2980
   chunk 24 optimal weight:    8.9990
   chunk 91 optimal weight:    0.3980
   chunk 8 optimal weight:    8.9990
   chunk 121 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 125 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  71 GLN
** F 101 GLN ** 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 = 0.3004 r_free = 0.3004 target = 0.036169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.026702 restraints weight = 122800.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.027360 restraints weight = 73166.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.027833 restraints weight = 51087.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.028153 restraints weight = 38926.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.028319 restraints weight = 32477.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10639  Z= 0.106
  Angle     :  0.511   9.802  14422  Z= 0.248
  Chirality :  0.038   0.173   1712
  Planarity :  0.003   0.050   1791
  Dihedral  :  3.433  17.675   1421
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.24), residues: 1316
  helix:  2.47 (0.18), residues: 844
  sheet: -0.11 (0.55), residues: 86
  loop : -0.62 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 510 
 TYR   0.012   0.001   TYR D 237 
 PHE   0.013   0.001   PHE A  92 
 TRP   0.011   0.001   TRP D 513 
 HIS   0.002   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (10639)
  covalent geometry    : angle       0.51083 (14422)
  hydrogen bonds       : bond        0.03053 (  652)
  hydrogen bonds       : angle       3.37355 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9451 (mtm) cc_final: 0.8901 (mtt)
REVERT: A  158 MET cc_start: 0.9508 (mtp) cc_final: 0.9170 (mmm)
REVERT: A  165 MET cc_start: 0.9547 (mmp) cc_final: 0.9312 (mmm)
REVERT: A  400 MET cc_start: 0.9223 (mmp) cc_final: 0.8317 (tpp)
REVERT: C   68 ILE cc_start: 0.9942 (mm) cc_final: 0.9717 (tt)
REVERT: D  608 MET cc_start: 0.8256 (ppp) cc_final: 0.7571 (ppp)
REVERT: F  108 MET cc_start: 0.9423 (mtm) cc_final: 0.9032 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0721
  time to fit residues: 6.7857
Evaluate side-chains
  47 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 113 optimal weight:    9.9990
   chunk 86 optimal weight:    8.9990
   chunk 128 optimal weight:    0.9990
   chunk 131 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 111 optimal weight:    0.0980
   chunk 42 optimal weight:   10.0000
   overall best weight:    4.0188

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** 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 = 0.2980 r_free = 0.2980 target = 0.035460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.026115 restraints weight = 123922.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.026725 restraints weight = 73542.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.027067 restraints weight = 51969.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.027415 restraints weight = 41998.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.027637 restraints weight = 34856.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10639  Z= 0.172
  Angle     :  0.559   9.327  14422  Z= 0.276
  Chirality :  0.039   0.143   1712
  Planarity :  0.003   0.049   1791
  Dihedral  :  3.608  18.785   1421
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.24), residues: 1316
  helix:  2.34 (0.18), residues: 849
  sheet: -0.12 (0.55), residues: 86
  loop : -0.65 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 510 
 TYR   0.012   0.001   TYR A 456 
 PHE   0.017   0.001   PHE A  92 
 TRP   0.013   0.001   TRP D 513 
 HIS   0.003   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10639)
  covalent geometry    : angle       0.55856 (14422)
  hydrogen bonds       : bond        0.03308 (  652)
  hydrogen bonds       : angle       3.54909 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9418 (mtm) cc_final: 0.8889 (mtt)
REVERT: A  158 MET cc_start: 0.9522 (mtp) cc_final: 0.9222 (tpt)
REVERT: A  400 MET cc_start: 0.9217 (mmp) cc_final: 0.8315 (tpp)
REVERT: D  608 MET cc_start: 0.8316 (ppp) cc_final: 0.7623 (ppp)
REVERT: F  108 MET cc_start: 0.9416 (mtm) cc_final: 0.9061 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0657
  time to fit residues: 6.0380
Evaluate side-chains
  43 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0980
   chunk 118 optimal weight:    8.9990
   chunk 95 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  71 GLN
** F 101 GLN ** 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 = 0.3015 r_free = 0.3015 target = 0.036457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.026922 restraints weight = 121207.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.027615 restraints weight = 71290.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.028079 restraints weight = 49645.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.028412 restraints weight = 38512.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.028553 restraints weight = 32255.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10639  Z= 0.091
  Angle     :  0.514   9.981  14422  Z= 0.246
  Chirality :  0.038   0.145   1712
  Planarity :  0.003   0.050   1791
  Dihedral  :  3.345  16.312   1421
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.24), residues: 1316
  helix:  2.52 (0.18), residues: 844
  sheet:  0.06 (0.55), residues: 86
  loop : -0.59 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 179 
 TYR   0.013   0.001   TYR D 237 
 PHE   0.014   0.001   PHE A  92 
 TRP   0.011   0.001   TRP D 513 
 HIS   0.007   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 (10639)
  covalent geometry    : angle       0.51440 (14422)
  hydrogen bonds       : bond        0.02928 (  652)
  hydrogen bonds       : angle       3.21925 ( 1926)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9430 (mtm) cc_final: 0.8882 (mtt)
REVERT: A  158 MET cc_start: 0.9515 (mtp) cc_final: 0.9136 (tpt)
REVERT: C   68 ILE cc_start: 0.9902 (mm) cc_final: 0.9621 (tt)
REVERT: D  608 MET cc_start: 0.8279 (ppp) cc_final: 0.7572 (ppp)
REVERT: F  108 MET cc_start: 0.9442 (mtm) cc_final: 0.9102 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0721
  time to fit residues: 6.9676
Evaluate side-chains
  49 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 97 optimal weight:    0.0070
   chunk 116 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0670
   chunk 46 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 18 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    3.4142

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  71 GLN
** F 101 GLN ** 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 = 0.2987 r_free = 0.2987 target = 0.035700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.026229 restraints weight = 124416.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.026874 restraints weight = 73222.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.027356 restraints weight = 51449.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.027643 restraints weight = 39907.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.027865 restraints weight = 33679.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10639  Z= 0.149
  Angle     :  0.543   9.398  14422  Z= 0.265
  Chirality :  0.038   0.148   1712
  Planarity :  0.003   0.049   1791
  Dihedral  :  3.455  17.862   1421
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.24), residues: 1316
  helix:  2.48 (0.18), residues: 850
  sheet:  0.04 (0.55), residues: 86
  loop : -0.56 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 510 
 TYR   0.011   0.001   TYR A 456 
 PHE   0.014   0.001   PHE A  92 
 TRP   0.012   0.001   TRP D 513 
 HIS   0.003   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10639)
  covalent geometry    : angle       0.54326 (14422)
  hydrogen bonds       : bond        0.03096 (  652)
  hydrogen bonds       : angle       3.37782 ( 1926)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1523.17 seconds
wall clock time: 27 minutes 14.21 seconds (1634.21 seconds total)