Starting phenix.real_space_refine
on Fri Feb 14 18:04:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kat_22783/02_2025/7kat_22783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kat_22783/02_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_22783/02_2025/7kat_22783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kat_22783/02_2025/7kat_22783.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kat_22783/02_2025/7kat_22783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kat_22783/02_2025/7kat_22783.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG: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: {'PHE:plan': 1, 'ASP: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: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8}
          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: {'GLN:plan1': 1, 'GLU:plan': 3, '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: 5.82, per 1000 atoms: 0.56
  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: 2.67
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.95
  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: 2.96

  Time building geometry restraints manager: 3.02 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:             0.840
  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:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     24.090
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.560
-------------------------------------------------------------------------------
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= 0.147
  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 : 6.90
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.010   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 334 
 PHE   0.009   0.001   PHE A  92 
 TYR   0.008   0.001   TYR F 190 
 ARG   0.002   0.000   ARG F 185 

*********************** 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  : 1.234 
Fit side-chains
   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: 0.9040 (mmm)
REVERT: D  608 MET cc_start: 0.8604 (ptm) cc_final: 0.8386 (ppp)
REVERT: E   81 MET cc_start: 0.9058 (ttm) cc_final: 0.8829 (ptp)
REVERT: F  108 MET cc_start: 0.9642 (mtm) cc_final: 0.9264 (ttt)
REVERT: F  128 ASP cc_start: 0.9433 (m-30) cc_final: 0.9212 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2117
  time to fit residues: 25.9458
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  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   chunk 103 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 119 optimal weight:    9.9990
   overall best weight:    4.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
D 113 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.036082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.026322 restraints weight = 123229.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.026977 restraints weight = 73273.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.027419 restraints weight = 51336.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10639  Z= 0.279
  Angle     :  0.584   7.291  14422  Z= 0.295
  Chirality :  0.039   0.145   1712
  Planarity :  0.004   0.043   1791
  Dihedral  :  3.471  16.709   1421
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.23), residues: 1316
  helix:  1.69 (0.18), residues: 826
  sheet: -1.11 (0.55), residues: 86
  loop : -1.47 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 513 
 HIS   0.004   0.001   HIS D 334 
 PHE   0.015   0.001   PHE D 343 
 TYR   0.011   0.001   TYR F 190 
 ARG   0.004   0.001   ARG D 510 

*********************** 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
  54 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9406 (mtm) cc_final: 0.8859 (mtp)
REVERT: A  158 MET cc_start: 0.9533 (mtp) cc_final: 0.9158 (mmm)
REVERT: D  608 MET cc_start: 0.8506 (ptm) cc_final: 0.8260 (ppp)
REVERT: F  108 MET cc_start: 0.9448 (mtm) cc_final: 0.9032 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1748
  time to fit residues: 16.0040
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  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 131 optimal weight:    1.9990
   chunk 112 optimal weight:    0.5980
   chunk 60 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 41 optimal weight:    0.6980
   chunk 88 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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  68 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 = 0.3020 r_free = 0.3020 target = 0.036787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.026954 restraints weight = 122653.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.027609 restraints weight = 72305.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.028102 restraints weight = 50843.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10639  Z= 0.155
  Angle     :  0.506  10.814  14422  Z= 0.248
  Chirality :  0.038   0.148   1712
  Planarity :  0.003   0.046   1791
  Dihedral  :  3.307  16.762   1421
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.24), residues: 1316
  helix:  2.11 (0.18), residues: 841
  sheet: -0.91 (0.54), residues: 88
  loop : -1.30 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 513 
 HIS   0.002   0.001   HIS D 309 
 PHE   0.012   0.001   PHE A  92 
 TYR   0.009   0.001   TYR A 456 
 ARG   0.002   0.000   ARG D 510 

*********************** 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
  60 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9396 (mtm) cc_final: 0.8925 (mtp)
REVERT: A  158 MET cc_start: 0.9503 (mtp) cc_final: 0.9136 (tpt)
REVERT: A  400 MET cc_start: 0.9245 (mmp) cc_final: 0.8128 (tpp)
REVERT: C   68 ILE cc_start: 0.9941 (mm) cc_final: 0.9685 (tt)
REVERT: D  608 MET cc_start: 0.8466 (ptm) cc_final: 0.8251 (ppp)
REVERT: F  108 MET cc_start: 0.9504 (mtm) cc_final: 0.9101 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1758
  time to fit residues: 17.4715
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  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 80 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 102 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 330 HIS
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 106 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.035908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.026188 restraints weight = 123244.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.026831 restraints weight = 73598.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.027293 restraints weight = 51942.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2384

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= 0.254
  Angle     :  0.566   8.136  14422  Z= 0.284
  Chirality :  0.039   0.143   1712
  Planarity :  0.003   0.047   1791
  Dihedral  :  3.521  18.775   1421
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.24), residues: 1316
  helix:  2.22 (0.18), residues: 830
  sheet: -0.79 (0.53), residues: 88
  loop : -1.00 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 513 
 HIS   0.003   0.001   HIS D 390 
 PHE   0.033   0.001   PHE A 245 
 TYR   0.012   0.001   TYR A 456 
 ARG   0.003   0.000   ARG D 510 

*********************** 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  : 1.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9385 (mtm) cc_final: 0.8850 (mtt)
REVERT: A  158 MET cc_start: 0.9516 (mtp) cc_final: 0.9127 (mmm)
REVERT: D  608 MET cc_start: 0.8457 (ptm) cc_final: 0.8213 (ppp)
REVERT: F  108 MET cc_start: 0.9454 (mtm) cc_final: 0.9102 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1902
  time to fit residues: 16.7301
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  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 71 optimal weight:    0.0010
   chunk 81 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   chunk 110 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    2.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 HIS ** 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  68 ASN ** 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 = 0.3001 r_free = 0.3001 target = 0.036035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.026467 restraints weight = 122451.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.027143 restraints weight = 73460.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.027592 restraints weight = 51178.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10639  Z= 0.168
  Angle     :  0.512   9.045  14422  Z= 0.252
  Chirality :  0.038   0.146   1712
  Planarity :  0.003   0.049   1791
  Dihedral  :  3.406  17.816   1421
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.24), residues: 1316
  helix:  2.37 (0.18), residues: 844
  sheet: -0.66 (0.54), residues: 88
  loop : -0.85 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 513 
 HIS   0.005   0.001   HIS D 330 
 PHE   0.009   0.001   PHE D 343 
 TYR   0.010   0.001   TYR A 456 
 ARG   0.002   0.000   ARG D 509 

*********************** 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
  54 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9405 (mtm) cc_final: 0.8869 (mtt)
REVERT: A  158 MET cc_start: 0.9499 (mtp) cc_final: 0.9092 (mmm)
REVERT: A  400 MET cc_start: 0.9243 (mmp) cc_final: 0.8165 (tpp)
REVERT: C   68 ILE cc_start: 0.9941 (mm) cc_final: 0.9721 (tt)
REVERT: F  108 MET cc_start: 0.9430 (mtm) cc_final: 0.9059 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1759
  time to fit residues: 16.0210
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  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 83 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 108 optimal weight:   10.0000
   chunk 123 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 ** 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  68 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 = 0.2975 r_free = 0.2975 target = 0.035493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.026046 restraints weight = 125437.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.026678 restraints weight = 75157.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.027115 restraints weight = 53197.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10639  Z= 0.272
  Angle     :  0.590   8.552  14422  Z= 0.295
  Chirality :  0.040   0.167   1712
  Planarity :  0.003   0.049   1791
  Dihedral  :  3.671  19.581   1421
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.24), residues: 1316
  helix:  2.23 (0.18), residues: 835
  sheet: -0.44 (0.54), residues: 86
  loop : -0.78 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 513 
 HIS   0.005   0.001   HIS D 334 
 PHE   0.018   0.001   PHE D 343 
 TYR   0.014   0.001   TYR A 456 
 ARG   0.003   0.000   ARG D 510 

*********************** 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
  51 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9430 (mtm) cc_final: 0.8913 (mtt)
REVERT: A  158 MET cc_start: 0.9513 (mtp) cc_final: 0.9132 (mmm)
REVERT: A  165 MET cc_start: 0.9562 (mmp) cc_final: 0.9356 (mmm)
REVERT: D  608 MET cc_start: 0.8046 (ppp) cc_final: 0.7523 (ppp)
REVERT: F  108 MET cc_start: 0.9419 (mtm) cc_final: 0.9083 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1712
  time to fit residues: 14.5739
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  : 1.157 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 107 optimal weight:    9.9990
   chunk 123 optimal weight:    4.9990
   chunk 44 optimal weight:   20.0000
   chunk 56 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 125 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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
D 381 HIS
E  77 GLN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.035099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.025735 restraints weight = 127019.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.026354 restraints weight = 76946.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.026811 restraints weight = 54534.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10639  Z= 0.304
  Angle     :  0.613   9.288  14422  Z= 0.309
  Chirality :  0.040   0.159   1712
  Planarity :  0.004   0.051   1791
  Dihedral  :  3.847  19.930   1421
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.24), residues: 1316
  helix:  2.02 (0.18), residues: 842
  sheet: -0.45 (0.54), residues: 86
  loop : -0.86 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 283 
 HIS   0.005   0.002   HIS D 334 
 PHE   0.015   0.001   PHE D 343 
 TYR   0.014   0.002   TYR A 456 
 ARG   0.003   0.000   ARG D 510 

*********************** 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
  49 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 1.199 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9401 (mtm) cc_final: 0.8866 (mtt)
REVERT: A  158 MET cc_start: 0.9519 (mtp) cc_final: 0.9159 (mmm)
REVERT: D  608 MET cc_start: 0.8078 (ppp) cc_final: 0.7515 (ppp)
REVERT: F  108 MET cc_start: 0.9433 (mtm) cc_final: 0.9100 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1654
  time to fit residues: 14.0342
Evaluate side-chains
  41 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 76 optimal weight:    0.3980
   chunk 77 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 127 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 101 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 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 = 0.2998 r_free = 0.2998 target = 0.035970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.026556 restraints weight = 122748.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.027237 restraints weight = 72685.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.027711 restraints weight = 50255.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.3198

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= 0.155
  Angle     :  0.518   9.629  14422  Z= 0.254
  Chirality :  0.038   0.176   1712
  Planarity :  0.003   0.052   1791
  Dihedral  :  3.529  18.267   1421
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.24), residues: 1316
  helix:  2.39 (0.18), residues: 843
  sheet: -0.23 (0.54), residues: 86
  loop : -0.68 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 513 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.022   0.001   PHE A  92 
 TYR   0.012   0.001   TYR D 237 
 ARG   0.001   0.000   ARG E  99 

*********************** 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
  52 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 1.229 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9432 (mtm) cc_final: 0.8893 (mtt)
REVERT: A  158 MET cc_start: 0.9522 (mtp) cc_final: 0.9124 (mmm)
REVERT: A  165 MET cc_start: 0.9556 (mmp) cc_final: 0.9349 (mmm)
REVERT: A  400 MET cc_start: 0.9243 (mmp) cc_final: 0.8319 (tpp)
REVERT: C   68 ILE cc_start: 0.9940 (mm) cc_final: 0.9708 (tt)
REVERT: D  608 MET cc_start: 0.8007 (ppp) cc_final: 0.7401 (ppp)
REVERT: F  108 MET cc_start: 0.9441 (mtm) cc_final: 0.9044 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1652
  time to fit residues: 14.9927
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  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 131 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 109 optimal weight:    9.9990
   chunk 127 optimal weight:    6.9990
   chunk 87 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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  68 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 = 0.2971 r_free = 0.2971 target = 0.035259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.025971 restraints weight = 125834.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.026586 restraints weight = 74553.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.027030 restraints weight = 52386.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10639  Z= 0.253
  Angle     :  0.575   9.078  14422  Z= 0.287
  Chirality :  0.039   0.139   1712
  Planarity :  0.003   0.050   1791
  Dihedral  :  3.756  19.510   1421
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.24), residues: 1316
  helix:  2.16 (0.18), residues: 857
  sheet: -0.30 (0.54), residues: 86
  loop : -0.78 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 513 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.024   0.001   PHE A 245 
 TYR   0.013   0.001   TYR A 456 
 ARG   0.003   0.000   ARG D 510 

*********************** 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  : 1.267 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9422 (mtm) cc_final: 0.8902 (mtt)
REVERT: A  158 MET cc_start: 0.9542 (mtp) cc_final: 0.9142 (mmm)
REVERT: A  165 MET cc_start: 0.9564 (mmp) cc_final: 0.9358 (mmm)
REVERT: D  608 MET cc_start: 0.8046 (ppp) cc_final: 0.7436 (ppp)
REVERT: F  108 MET cc_start: 0.9445 (mtm) cc_final: 0.9085 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1654
  time to fit residues: 15.0973
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  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 113 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0030
   chunk 91 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 130 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
D 494 GLN
D 520 GLN
E  77 GLN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.036201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.026781 restraints weight = 122667.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.027469 restraints weight = 72482.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.027925 restraints weight = 50070.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.3374

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= 0.123
  Angle     :  0.516   9.907  14422  Z= 0.249
  Chirality :  0.038   0.143   1712
  Planarity :  0.003   0.052   1791
  Dihedral  :  3.420  17.694   1421
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.24), residues: 1316
  helix:  2.46 (0.18), residues: 845
  sheet: -0.25 (0.53), residues: 90
  loop : -0.48 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 513 
 HIS   0.002   0.001   HIS F 122 
 PHE   0.023   0.001   PHE A 245 
 TYR   0.013   0.001   TYR D 237 
 ARG   0.002   0.000   ARG E  99 

********************** 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
  58 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9418 (mtm) cc_final: 0.8878 (mtt)
REVERT: A  158 MET cc_start: 0.9525 (mtp) cc_final: 0.9138 (tpt)
REVERT: C   68 ILE cc_start: 0.9944 (mm) cc_final: 0.9724 (tt)
REVERT: D  608 MET cc_start: 0.8240 (ppp) cc_final: 0.7619 (ppp)
REVERT: F  108 MET cc_start: 0.9473 (mtm) cc_final: 0.9031 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1706
  time to fit residues: 16.4919
Evaluate side-chains
  48 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:   20.0000
   chunk 85 optimal weight:    0.0770
   chunk 127 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    4.0146

-------------------------------------------------------------------------------
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  68 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 = 0.2979 r_free = 0.2979 target = 0.035447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.026121 restraints weight = 123468.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.026757 restraints weight = 74651.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.027117 restraints weight = 51983.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10639  Z= 0.233
  Angle     :  0.575  11.279  14422  Z= 0.284
  Chirality :  0.039   0.155   1712
  Planarity :  0.003   0.051   1791
  Dihedral  :  3.560  18.346   1421
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.24), residues: 1316
  helix:  2.34 (0.18), residues: 850
  sheet: -0.18 (0.54), residues: 86
  loop : -0.59 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 513 
 HIS   0.006   0.001   HIS C  72 
 PHE   0.021   0.001   PHE A 245 
 TYR   0.012   0.001   TYR A 456 
 ARG   0.002   0.000   ARG D 510 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2548.11 seconds
wall clock time: 47 minutes 4.43 seconds (2824.43 seconds total)