Starting phenix.real_space_refine
on Sat Aug 23 07:17:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdi_37137/08_2025/8kdi_37137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdi_37137/08_2025/8kdi_37137.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdi_37137/08_2025/8kdi_37137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdi_37137/08_2025/8kdi_37137.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdi_37137/08_2025/8kdi_37137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdi_37137/08_2025/8kdi_37137.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
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      40      5.16       5
     C    6811      2.51       5
     N    1718      2.21       5
     O    1963      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10532
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3451
          Classifications: {'peptide': 447}
          Link IDs: {'PTRANS': 23, 'TRANS': 423}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1686
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 205}
    Chain: "H"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1689
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 2.27, per 1000 atoms: 0.22
  Number of scatterers: 10532
  At special positions: 0
  Unit cell: (81.3285, 141.174, 148.847, 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      40     16.00
     O    1963      8.00
     N    1718      7.00
     C    6811      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.12
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.12
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.11
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 202 " distance=2.07

  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
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 381 "
      " NAG A 702 " - " ASN A 506 "
      " NAG A 703 " - " ASN A 365 "
      " NAG A 704 " - " ASN A 424 "
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 409.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2502

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      47.4% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 5.341A  pdb=" N   LYS A 171 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 207
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 4.170A  pdb=" N   GLY A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 255
      removed outlier: 3.750A  pdb=" N   GLY A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG A 247 " --> pdb=" O   GLY A 243 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ASP A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   TYR A 250 " --> pdb=" O   GLY A 246 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 286 through 300
    Processing helix  chain 'A' and resid 322 through 341
      removed outlier: 3.641A  pdb=" N   VAL A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLU A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 355 through 371
    Processing helix  chain 'A' and resid 384 through 395
      removed outlier: 4.256A  pdb=" N   SER A 394 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ASN A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 407
      removed outlier: 4.270A  pdb=" N   ASP A 407 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 427
    Processing helix  chain 'A' and resid 440 through 444
    Processing helix  chain 'A' and resid 449 through 458
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 504 through 507
    Processing helix  chain 'A' and resid 508 through 514
      removed outlier: 4.039A  pdb=" N   GLU A 514 " --> pdb=" O   LYS A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 533
    Processing helix  chain 'A' and resid 533 through 539
    Processing helix  chain 'A' and resid 612 through 614
      No H-bonds generated for 'chain 'A' and resid 612 through 614'
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.508A  pdb=" N   ALA B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLY B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 71 through 80
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.585A  pdb=" N   ALA B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 124
      removed outlier: 3.853A  pdb=" N   TYR B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLU B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.599A  pdb=" N   PHE B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.757A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 222
      removed outlier: 4.267A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA B 201 " --> pdb=" O   GLN B 197 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ALA B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ALA B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 254
      removed outlier: 3.527A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 261
      removed outlier: 3.688A  pdb=" N   LEU B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASN B 261 " --> pdb=" O   TRP B 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 256 through 261'
    Processing helix  chain 'B' and resid 262 through 267
    Processing helix  chain 'B' and resid 272 through 298
      removed outlier: 3.746A  pdb=" N   LEU B 276 " --> pdb=" O   ARG B 272 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 3.711A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 325
    Processing helix  chain 'B' and resid 326 through 345
    Processing helix  chain 'B' and resid 346 through 356
      removed outlier: 3.914A  pdb=" N   PHE B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 373 through 387
      removed outlier: 3.869A  pdb=" N   TYR B 387 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 390
      No H-bonds generated for 'chain 'B' and resid 388 through 390'
    Processing helix  chain 'B' and resid 392 through 422
    Processing helix  chain 'B' and resid 435 through 454
      removed outlier: 4.332A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 467
      removed outlier: 3.770A  pdb=" N   CYS B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.304A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.917A  pdb=" N   LEU L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 129 through 133
    Processing helix  chain 'L' and resid 189 through 194
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.744A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.536A  pdb=" N   LYS H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 136 through 140
      removed outlier: 3.930A  pdb=" N   ASN H 140 " --> pdb=" O   ALA H 137 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 194 through 198
      removed outlier: 3.598A  pdb=" N   GLU H 198 " --> pdb=" O   TRP H 195 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401
      removed outlier: 3.649A  pdb=" N   LEU A 399 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   GLY A 379 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL A 347 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE A 466 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 540 through 544
      removed outlier: 4.042A  pdb=" N   SER A 552 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ARG A 625 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   LEU A 595 " --> pdb=" O   ARG A 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574
      removed outlier: 6.362A  pdb=" N   GLY A 573 " --> pdb=" O   ILE L 100 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 14
      removed outlier: 3.672A  pdb=" N   ALA L  90 " --> pdb=" O   LEU L 110 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 14
      removed outlier: 3.672A  pdb=" N   ALA L  90 " --> pdb=" O   LEU L 110 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   THR L 103 " --> pdb=" O   GLN L  96 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.620A  pdb=" N   VAL L 139 " --> pdb=" O   PHE L 124 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 159 through 161
      removed outlier: 4.430A  pdb=" N   TRP L 154 " --> pdb=" O   ARG L 161 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.477A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   MET H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.477A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 127 through 131
      removed outlier: 5.329A  pdb=" N   THR H 144 " --> pdb=" O   VAL H 190 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL H 190 " --> pdb=" O   THR H 144 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   GLY H 146 " --> pdb=" O   VAL H 188 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   VAL H 188 " --> pdb=" O   GLY H 146 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   LEU H 148 " --> pdb=" O   SER H 186 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   SER H 186 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   LYS H 150 " --> pdb=" O   LEU H 184 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU H 184 " --> pdb=" O   LYS H 150 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   SER H 185 " --> pdb=" O   PRO H 174 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   SER H 187 " --> pdb=" O   THR H 172 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   THR H 172 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   THR H 189 " --> pdb=" O   VAL H 170 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL H 170 " --> pdb=" O   THR H 189 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 201 through 205
      removed outlier: 3.584A  pdb=" N   LYS H 215 " --> pdb=" O   CYS H 202 " (cutoff:3.500A)

    546 hydrogen bonds defined for protein.
    1482 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: 1.31

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1698
        1.31 -     1.44: 3022
        1.44 -     1.58: 6015
        1.58 -     1.72: 4
        1.72 -     1.85: 58
  Bond restraints: 10797
  Sorted by residual:
  bond pdb=" CG  HIS L  97 "
       pdb=" CD2 HIS L  97 "
    ideal  model  delta    sigma   weight residual
    1.354  1.251  0.103 1.10e-02 8.26e+03 8.68e+01
  bond pdb=" CB  HIS L  97 "
       pdb=" CG  HIS L  97 "
    ideal  model  delta    sigma   weight residual
    1.497  1.412  0.085 1.40e-02 5.10e+03 3.68e+01
  bond pdb=" CB  HIS H  35 "
       pdb=" CG  HIS H  35 "
    ideal  model  delta    sigma   weight residual
    1.497  1.428  0.069 1.40e-02 5.10e+03 2.43e+01
  bond pdb=" C   GLY A 462 "
       pdb=" O   GLY A 462 "
    ideal  model  delta    sigma   weight residual
    1.229  1.190  0.040 8.20e-03 1.49e+04 2.33e+01
  bond pdb=" C   LEU A 213 "
       pdb=" N   PRO A 214 "
    ideal  model  delta    sigma   weight residual
    1.331  1.269  0.061 1.31e-02 5.83e+03 2.18e+01
  ... (remaining 10792 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.37: 14204
        4.37 -     8.74: 483
        8.74 -    13.11: 25
       13.11 -    17.48: 1
       17.48 -    21.85: 1
  Bond angle restraints: 14714
  Sorted by residual:
  angle pdb=" O   LEU A 213 "
        pdb=" C   LEU A 213 "
        pdb=" N   PRO A 214 "
      ideal   model   delta    sigma   weight residual
     121.42   99.57   21.85 1.06e+00 8.90e-01 4.25e+02
  angle pdb=" CA  LEU A 213 "
        pdb=" C   LEU A 213 "
        pdb=" O   LEU A 213 "
      ideal   model   delta    sigma   weight residual
     119.76  132.87  -13.11 8.90e-01 1.26e+00 2.17e+02
  angle pdb=" C   LEU A 213 "
        pdb=" N   PRO A 214 "
        pdb=" CA  PRO A 214 "
      ideal   model   delta    sigma   weight residual
     119.85  111.75    8.10 1.01e+00 9.80e-01 6.43e+01
  angle pdb=" N   PRO A 214 "
        pdb=" CA  PRO A 214 "
        pdb=" CB  PRO A 214 "
      ideal   model   delta    sigma   weight residual
     103.33   95.93    7.40 9.30e-01 1.16e+00 6.34e+01
  angle pdb=" CA  LEU A 213 "
        pdb=" C   LEU A 213 "
        pdb=" N   PRO A 214 "
      ideal   model   delta    sigma   weight residual
     118.75  126.47   -7.72 9.70e-01 1.06e+00 6.33e+01
  ... (remaining 14709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 5867
       17.57 -    35.14: 434
       35.14 -    52.72: 87
       52.72 -    70.29: 13
       70.29 -    87.86: 11
  Dihedral angle restraints: 6412
    sinusoidal: 2513
      harmonic: 3899
  Sorted by residual:
  dihedral pdb=" CA  SER A 410 "
           pdb=" C   SER A 410 "
           pdb=" N   THR A 411 "
           pdb=" CA  THR A 411 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  136.43   43.57     0      5.00e+00 4.00e-02 7.59e+01
  dihedral pdb=" CA  TRP A 557 "
           pdb=" C   TRP A 557 "
           pdb=" N   ASP A 558 "
           pdb=" CA  ASP A 558 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.80  -31.20     0      5.00e+00 4.00e-02 3.89e+01
  dihedral pdb=" CA  GLY A 412 "
           pdb=" C   GLY A 412 "
           pdb=" N   GLU A 413 "
           pdb=" CA  GLU A 413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.09  -30.91     0      5.00e+00 4.00e-02 3.82e+01
  ... (remaining 6409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 1368
       0.117 -    0.233: 312
       0.233 -    0.349: 16
       0.349 -    0.466: 3
       0.466 -    0.582: 1
  Chirality restraints: 1700
  Sorted by residual:
  chirality pdb=" CA  PRO A 548 "
            pdb=" N   PRO A 548 "
            pdb=" C   PRO A 548 "
            pdb=" CB  PRO A 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.14    0.58 2.00e-01 2.50e+01 8.47e+00
  chirality pdb=" CA  HIS L  97 "
            pdb=" N   HIS L  97 "
            pdb=" C   HIS L  97 "
            pdb=" CB  HIS L  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.05e+00
  chirality pdb=" CA  TYR H 103 "
            pdb=" N   TYR H 103 "
            pdb=" C   TYR H 103 "
            pdb=" CB  TYR H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.93e+00
  ... (remaining 1697 not shown)

  Planarity restraints: 1845
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.088 2.00e-02 2.50e+03   7.34e-02 6.74e+01
        pdb=" C7  NAG A 702 "    0.026 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.067 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.118 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H 100 "   -0.509 9.50e-02 1.11e+02   2.28e-01 3.21e+01
        pdb=" NE  ARG H 100 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG H 100 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG H 100 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG H 100 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 525 "    0.387 9.50e-02 1.11e+02   1.73e-01 1.86e+01
        pdb=" NE  ARG A 525 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 525 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 525 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 525 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1842 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 20
        2.60 -     3.17: 8927
        3.17 -     3.75: 15713
        3.75 -     4.32: 22987
        4.32 -     4.90: 37298
  Nonbonded interactions: 84945
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 213 "
            pdb=" CA  PRO A 214 "
     model   vdw
     2.022 2.776
  nonbonded pdb=" CB  LYS A 532 "
            pdb=" OE1 GLU B 303 "
     model   vdw
     2.074 3.440
  nonbonded pdb=" OH  TYR A 250 "
            pdb=" OE2 GLU A 471 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   LEU A 213 "
            pdb=" C   PRO A 214 "
     model   vdw
     2.334 3.270
  nonbonded pdb=" CB  GLN L  96 "
            pdb=" OE1 GLN L  96 "
     model   vdw
     2.497 2.752
  ... (remaining 84940 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:             0.120
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.990
  Find NCS groups from input model:        0.040
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
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      :  0.013   0.103  10806  Z= 0.822
  Angle     :  1.930  21.854  14736  Z= 1.271
  Chirality :  0.092   0.582   1700
  Planarity :  0.012   0.228   1841
  Dihedral  : 13.638  87.859   3895
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.54 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  5.11 %
    Favored  : 93.42 %
  Cbeta Deviations :  0.72 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.92 (0.20), residues: 1343
  helix: -1.68 (0.18), residues: 509
  sheet: -0.34 (0.30), residues: 270
  loop : -1.16 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG A 562 
 TYR   0.029   0.005   TYR A 250 
 PHE   0.029   0.005   PHE L  56 
 TRP   0.046   0.007   TRP H 110 
 HIS   0.010   0.003   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.01297 (10797)
  covalent geometry    : angle       1.92294 (14714)
  SS BOND              : bond        0.06864 (    5)
  SS BOND              : angle       4.60584 (   10)
  hydrogen bonds       : bond        0.18393 (  535)
  hydrogen bonds       : angle       8.28512 ( 1482)
  link_NAG-ASN         : bond        0.01216 (    4)
  link_NAG-ASN         : angle       4.84201 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 290
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.4716 (mtm110) cc_final: 0.4188 (mtm180)
REVERT: A  211 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.6396 (ttt180)
REVERT: A  212 GLU cc_start: 0.8021 (pm20) cc_final: 0.7666 (tt0)
REVERT: A  234 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7198 (mt0)
REVERT: A  236 HIS cc_start: 0.6447 (m-70) cc_final: 0.5955 (m90)
REVERT: A  252 SER cc_start: 0.8897 (t) cc_final: 0.8662 (p)
REVERT: A  290 PHE cc_start: 0.8210 (t80) cc_final: 0.7911 (t80)
REVERT: A  442 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (p)
REVERT: A  457 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8735 (mt)
REVERT: A  475 ASP cc_start: 0.8306 (t0) cc_final: 0.7896 (p0)
REVERT: A  484 MET cc_start: 0.8558 (mtm) cc_final: 0.8055 (tpt)
REVERT: A  535 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.7879 (t)
REVERT: A  604 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8181 (pm20)
REVERT: A  612 GLU cc_start: 0.8156 (tt0) cc_final: 0.7838 (tp30)
REVERT: A  625 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7879 (ttp80)
REVERT: B   81 SER cc_start: 0.8610 (t) cc_final: 0.8350 (p)
REVERT: B  265 GLU cc_start: 0.5906 (tm-30) cc_final: 0.5617 (tp30)
REVERT: B  268 ILE cc_start: 0.5238 (mm) cc_final: 0.4827 (tt)
REVERT: B  296 TYR cc_start: 0.7016 (m-80) cc_final: 0.6718 (m-10)
REVERT: B  349 LEU cc_start: 0.8726 (tp) cc_final: 0.8477 (tt)
REVERT: B  365 MET cc_start: 0.8348 (mtt) cc_final: 0.7948 (mmm)
REVERT: B  387 TYR cc_start: 0.7809 (m-80) cc_final: 0.7481 (m-80)
REVERT: B  444 LEU cc_start: 0.8718 (mt) cc_final: 0.8494 (tp)
REVERT: B  454 THR cc_start: 0.8275 (p) cc_final: 0.7898 (t)
REVERT: L    1 ASP cc_start: 0.7532 (m-30) cc_final: 0.6981 (p0)
REVERT: L   21 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7257 (mmt)
REVERT: L   66 ASP cc_start: 0.8502 (m-30) cc_final: 0.8131 (t0)
REVERT: L  111 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7598 (mm-30)
REVERT: L  124 PHE cc_start: 0.8587 (m-80) cc_final: 0.8157 (m-80)
REVERT: L  130 GLN cc_start: 0.9009 (tt0) cc_final: 0.8559 (tm-30)
REVERT: L  154 TRP cc_start: 0.8374 (m100) cc_final: 0.7891 (m100)
REVERT: L  190 ASP cc_start: 0.8772 (m-30) cc_final: 0.8571 (p0)
REVERT: H    6 GLN cc_start: 0.8811 (mt0) cc_final: 0.8501 (mt0)
REVERT: H   10 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: H  112 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7994 (pm20)
REVERT: H  178 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6804 (pt0)
REVERT: H  180 ASP cc_start: 0.8655 (m-30) cc_final: 0.8294 (p0)
  outliers start: 17
  outliers final: 3
  residues processed: 302
  average time/residue: 0.1039
  time to fit residues: 42.7021
Evaluate side-chains
  185 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 178
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain H residue   83 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.0010
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.7592

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 339 GLN
A 352 ASN
B 242 ASN
B 358 HIS
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN
L 172 GLN
H 140 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.155383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114280 restraints weight = 14961.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.104442 restraints weight = 22043.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.102272 restraints weight = 22353.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.101681 restraints weight = 21808.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.101674 restraints weight = 20269.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10806  Z= 0.187
  Angle     :  0.758   9.473  14736  Z= 0.386
  Chirality :  0.047   0.186   1700
  Planarity :  0.005   0.036   1841
  Dihedral  :  7.247  53.766   1536
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.29 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.04 (0.22), residues: 1343
  helix:  0.65 (0.22), residues: 516
  sheet:  0.13 (0.31), residues: 272
  loop : -0.50 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 211 
 TYR   0.035   0.002   TYR H 103 
 PHE   0.024   0.002   PHE B 445 
 TRP   0.023   0.002   TRP H  47 
 HIS   0.006   0.002   HIS A 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (10797)
  covalent geometry    : angle       0.75297 (14714)
  SS BOND              : bond        0.00442 (    5)
  SS BOND              : angle       1.77446 (   10)
  hydrogen bonds       : bond        0.05044 (  535)
  hydrogen bonds       : angle       5.29405 ( 1482)
  link_NAG-ASN         : bond        0.00254 (    4)
  link_NAG-ASN         : angle       2.68890 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  396 LYS cc_start: 0.7734 (mmmm) cc_final: 0.7465 (mtpp)
REVERT: A  457 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9013 (mt)
REVERT: A  528 ASP cc_start: 0.7664 (t0) cc_final: 0.7432 (t0)
REVERT: A  594 ASP cc_start: 0.7124 (m-30) cc_final: 0.6882 (m-30)
REVERT: B  294 LEU cc_start: 0.8082 (tp) cc_final: 0.7697 (tp)
REVERT: B  387 TYR cc_start: 0.8750 (m-80) cc_final: 0.8516 (m-80)
REVERT: B  391 LYS cc_start: 0.7972 (mmpt) cc_final: 0.7287 (ptpp)
REVERT: B  454 THR cc_start: 0.6639 (p) cc_final: 0.6220 (t)
REVERT: L  154 TRP cc_start: 0.8595 (m100) cc_final: 0.8313 (m100)
REVERT: H  198 GLU cc_start: 0.7571 (mp0) cc_final: 0.7298 (mp0)
  outliers start: 32
  outliers final: 18
  residues processed: 212
  average time/residue: 0.0903
  time to fit residues: 26.9388
Evaluate side-chains
  158 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  450 SER
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  159 SER
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 126 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   chunk 129 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  19 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.161367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129190 restraints weight = 14928.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.119394 restraints weight = 21224.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.117068 restraints weight = 26831.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.117159 restraints weight = 25634.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.117080 restraints weight = 21798.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10806  Z= 0.159
  Angle     :  0.680   9.427  14736  Z= 0.343
  Chirality :  0.044   0.201   1700
  Planarity :  0.004   0.039   1841
  Dihedral  :  6.288  55.505   1529
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.46 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.56 (0.23), residues: 1343
  helix:  1.19 (0.22), residues: 523
  sheet:  0.42 (0.31), residues: 272
  loop : -0.37 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 114 
 TYR   0.033   0.002   TYR H 103 
 PHE   0.027   0.002   PHE B  95 
 TRP   0.019   0.001   TRP H  47 
 HIS   0.011   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10797)
  covalent geometry    : angle       0.67704 (14714)
  SS BOND              : bond        0.00397 (    5)
  SS BOND              : angle       1.36818 (   10)
  hydrogen bonds       : bond        0.04370 (  535)
  hydrogen bonds       : angle       4.85017 ( 1482)
  link_NAG-ASN         : bond        0.00335 (    4)
  link_NAG-ASN         : angle       2.16958 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.8346 (t) cc_final: 0.8059 (p)
REVERT: A  457 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8791 (mt)
REVERT: A  475 ASP cc_start: 0.7752 (t0) cc_final: 0.7461 (t0)
REVERT: A  594 ASP cc_start: 0.7104 (m-30) cc_final: 0.6897 (m-30)
REVERT: B  294 LEU cc_start: 0.7929 (tp) cc_final: 0.7585 (tp)
REVERT: B  387 TYR cc_start: 0.8830 (m-80) cc_final: 0.8488 (m-80)
REVERT: B  391 LYS cc_start: 0.7687 (mmpt) cc_final: 0.7069 (ptpp)
REVERT: B  454 THR cc_start: 0.6911 (p) cc_final: 0.6536 (t)
REVERT: L  129 GLU cc_start: 0.7901 (pt0) cc_final: 0.7689 (pt0)
REVERT: H   73 ASP cc_start: 0.7206 (t0) cc_final: 0.6861 (t70)
  outliers start: 32
  outliers final: 16
  residues processed: 181
  average time/residue: 0.0968
  time to fit residues: 24.8900
Evaluate side-chains
  152 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  199 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 57 optimal weight:    0.0570
   chunk 2 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 95 optimal weight:    0.3980
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.0902

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

Flipped N/Q/H residues before XYZ refinement:
A 295 GLN
B 304 GLN
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  43 GLN
H  43 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.161600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.125436 restraints weight = 14836.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124852 restraints weight = 23692.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.123573 restraints weight = 21752.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.121413 restraints weight = 20134.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.120947 restraints weight = 21431.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10806  Z= 0.137
  Angle     :  0.639   7.173  14736  Z= 0.321
  Chirality :  0.043   0.209   1700
  Planarity :  0.004   0.047   1841
  Dihedral  :  5.776  55.565   1527
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.41 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.79 (0.23), residues: 1343
  helix:  1.50 (0.23), residues: 523
  sheet:  0.44 (0.30), residues: 281
  loop : -0.32 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  60 
 TYR   0.031   0.001   TYR H 103 
 PHE   0.032   0.002   PHE B 445 
 TRP   0.015   0.001   TRP L 169 
 HIS   0.005   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10797)
  covalent geometry    : angle       0.63712 (14714)
  SS BOND              : bond        0.00333 (    5)
  SS BOND              : angle       1.09842 (   10)
  hydrogen bonds       : bond        0.03946 (  535)
  hydrogen bonds       : angle       4.61874 ( 1482)
  link_NAG-ASN         : bond        0.00212 (    4)
  link_NAG-ASN         : angle       1.67716 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9002 (p)
REVERT: A  457 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8943 (mt)
REVERT: A  475 ASP cc_start: 0.7646 (t0) cc_final: 0.7402 (t0)
REVERT: B  369 GLN cc_start: 0.6490 (tp40) cc_final: 0.5931 (tm-30)
REVERT: B  391 LYS cc_start: 0.7882 (mmpt) cc_final: 0.7178 (ptpp)
REVERT: H   73 ASP cc_start: 0.7085 (t0) cc_final: 0.6834 (t70)
  outliers start: 32
  outliers final: 17
  residues processed: 178
  average time/residue: 0.0871
  time to fit residues: 22.2149
Evaluate side-chains
  147 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0980
   chunk 31 optimal weight:    0.5980
   chunk 48 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 71 optimal weight:    9.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
** B 501 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 = 0.3880 r_free = 0.3880 target = 0.161186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.125863 restraints weight = 14811.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116920 restraints weight = 23696.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.114669 restraints weight = 23903.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.115618 restraints weight = 24255.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.115843 restraints weight = 19747.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.4123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10806  Z= 0.151
  Angle     :  0.644  11.987  14736  Z= 0.321
  Chirality :  0.043   0.190   1700
  Planarity :  0.004   0.040   1841
  Dihedral  :  5.568  56.263   1525
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.41 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.90 (0.23), residues: 1343
  helix:  1.63 (0.23), residues: 522
  sheet:  0.53 (0.31), residues: 281
  loop : -0.31 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  38 
 TYR   0.029   0.002   TYR H 129 
 PHE   0.020   0.002   PHE A 541 
 TRP   0.021   0.001   TRP L 169 
 HIS   0.006   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (10797)
  covalent geometry    : angle       0.63865 (14714)
  SS BOND              : bond        0.00344 (    5)
  SS BOND              : angle       2.89518 (   10)
  hydrogen bonds       : bond        0.03789 (  535)
  hydrogen bonds       : angle       4.58060 ( 1482)
  link_NAG-ASN         : bond        0.00195 (    4)
  link_NAG-ASN         : angle       1.50202 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 134
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  252 SER cc_start: 0.8497 (p) cc_final: 0.8247 (t)
REVERT: A  457 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8792 (mt)
REVERT: A  475 ASP cc_start: 0.7865 (t0) cc_final: 0.7549 (t0)
REVERT: A  507 MET cc_start: 0.8384 (mtm) cc_final: 0.7918 (ttm)
REVERT: B  369 GLN cc_start: 0.7516 (tp40) cc_final: 0.7158 (tp40)
REVERT: B  386 LEU cc_start: 0.8960 (mt) cc_final: 0.8690 (mt)
REVERT: B  391 LYS cc_start: 0.7983 (mmpt) cc_final: 0.7087 (ptpp)
REVERT: B  483 LYS cc_start: 0.6732 (mmpt) cc_final: 0.6471 (mmmt)
REVERT: H   73 ASP cc_start: 0.7160 (t0) cc_final: 0.6807 (t70)
REVERT: H  166 LEU cc_start: 0.7889 (mt) cc_final: 0.7635 (mp)
REVERT: H  216 LYS cc_start: 0.7939 (tptp) cc_final: 0.7643 (tptp)
  outliers start: 38
  outliers final: 26
  residues processed: 163
  average time/residue: 0.0909
  time to fit residues: 21.1145
Evaluate side-chains
  151 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 127 optimal weight:    0.8980
   chunk 114 optimal weight:    0.8980
   chunk 126 optimal weight:    0.7980
   chunk 52 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 115 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 145 GLN
B 304 GLN
** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  17 GLN
L 172 GLN
H 206 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.162261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.130567 restraints weight = 14849.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.130041 restraints weight = 21445.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.129446 restraints weight = 19822.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.126144 restraints weight = 18328.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.124573 restraints weight = 24702.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10806  Z= 0.118
  Angle     :  0.619  12.504  14736  Z= 0.304
  Chirality :  0.042   0.187   1700
  Planarity :  0.004   0.040   1841
  Dihedral  :  5.390  56.455   1525
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.19 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.06 (0.23), residues: 1343
  helix:  1.81 (0.23), residues: 522
  sheet:  0.65 (0.31), residues: 284
  loop : -0.32 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  38 
 TYR   0.028   0.001   TYR L 146 
 PHE   0.024   0.001   PHE B 445 
 TRP   0.018   0.001   TRP L 169 
 HIS   0.004   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10797)
  covalent geometry    : angle       0.61513 (14714)
  SS BOND              : bond        0.00327 (    5)
  SS BOND              : angle       1.60742 (   10)
  hydrogen bonds       : bond        0.03510 (  535)
  hydrogen bonds       : angle       4.45366 ( 1482)
  link_NAG-ASN         : bond        0.00571 (    4)
  link_NAG-ASN         : angle       2.05028 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.8193 (p) cc_final: 0.7805 (t)
REVERT: A  457 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9034 (mt)
REVERT: A  475 ASP cc_start: 0.7605 (t0) cc_final: 0.7402 (t0)
REVERT: A  507 MET cc_start: 0.7926 (mtm) cc_final: 0.7497 (ttm)
REVERT: B  305 MET cc_start: 0.7445 (mtp) cc_final: 0.7245 (mtm)
REVERT: B  314 ASP cc_start: 0.7616 (m-30) cc_final: 0.7274 (m-30)
REVERT: B  391 LYS cc_start: 0.7768 (mmpt) cc_final: 0.7097 (ptpp)
REVERT: H   73 ASP cc_start: 0.7066 (t0) cc_final: 0.6846 (t70)
REVERT: H  115 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8769 (tt)
  outliers start: 35
  outliers final: 18
  residues processed: 161
  average time/residue: 0.0884
  time to fit residues: 20.0077
Evaluate side-chains
  145 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 100 optimal weight:    0.3980
   chunk 70 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 103 optimal weight:    0.3980
   chunk 32 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0270
   chunk 116 optimal weight:    0.5980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  17 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.163243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.130675 restraints weight = 14786.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.122938 restraints weight = 21145.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.120819 restraints weight = 27038.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.121141 restraints weight = 24749.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.121258 restraints weight = 20006.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10806  Z= 0.108
  Angle     :  0.612   9.753  14736  Z= 0.299
  Chirality :  0.042   0.226   1700
  Planarity :  0.004   0.040   1841
  Dihedral  :  5.309  55.827   1525
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 16.36 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.12 (0.23), residues: 1343
  helix:  1.84 (0.23), residues: 523
  sheet:  0.74 (0.32), residues: 284
  loop : -0.30 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  40 
 TYR   0.030   0.001   TYR L 146 
 PHE   0.019   0.001   PHE B 445 
 TRP   0.022   0.001   TRP L 169 
 HIS   0.003   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10797)
  covalent geometry    : angle       0.60988 (14714)
  SS BOND              : bond        0.00277 (    5)
  SS BOND              : angle       1.26597 (   10)
  hydrogen bonds       : bond        0.03356 (  535)
  hydrogen bonds       : angle       4.37784 ( 1482)
  link_NAG-ASN         : bond        0.00234 (    4)
  link_NAG-ASN         : angle       1.62099 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 140
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 ASP cc_start: 0.7577 (t0) cc_final: 0.7331 (t0)
REVERT: A  507 MET cc_start: 0.8007 (mtm) cc_final: 0.7649 (ttm)
REVERT: A  609 LEU cc_start: 0.8647 (mt) cc_final: 0.8183 (mt)
REVERT: B  145 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8044 (mp10)
REVERT: B  243 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6275 (tp)
REVERT: B  314 ASP cc_start: 0.7982 (m-30) cc_final: 0.7756 (m-30)
REVERT: B  391 LYS cc_start: 0.7813 (mmpt) cc_final: 0.7083 (ptpp)
REVERT: B  500 MET cc_start: 0.5503 (mtp) cc_final: 0.5150 (mtt)
REVERT: H   73 ASP cc_start: 0.7022 (t0) cc_final: 0.6808 (t70)
REVERT: H  115 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8738 (tt)
  outliers start: 42
  outliers final: 26
  residues processed: 168
  average time/residue: 0.0896
  time to fit residues: 21.5292
Evaluate side-chains
  155 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0020
   chunk 72 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 35 optimal weight:    0.1980
   chunk 57 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.2394

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
B 501 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.162247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136651 restraints weight = 14747.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134875 restraints weight = 21842.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.133717 restraints weight = 19518.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.132711 restraints weight = 19996.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.131845 restraints weight = 21637.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10806  Z= 0.134
  Angle     :  0.630   8.611  14736  Z= 0.308
  Chirality :  0.042   0.185   1700
  Planarity :  0.004   0.040   1841
  Dihedral  :  5.087  54.682   1523
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.66 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.11 (0.23), residues: 1343
  helix:  1.84 (0.23), residues: 521
  sheet:  0.77 (0.31), residues: 285
  loop : -0.33 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  60 
 TYR   0.036   0.001   TYR L 146 
 PHE   0.020   0.002   PHE B 402 
 TRP   0.065   0.002   TRP L 169 
 HIS   0.005   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10797)
  covalent geometry    : angle       0.62810 (14714)
  SS BOND              : bond        0.00290 (    5)
  SS BOND              : angle       1.09329 (   10)
  hydrogen bonds       : bond        0.03405 (  535)
  hydrogen bonds       : angle       4.41547 ( 1482)
  link_NAG-ASN         : bond        0.00214 (    4)
  link_NAG-ASN         : angle       1.49527 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  475 ASP cc_start: 0.7875 (t0) cc_final: 0.7627 (t0)
REVERT: A  507 MET cc_start: 0.8108 (mtm) cc_final: 0.7680 (ttm)
REVERT: A  609 LEU cc_start: 0.8609 (mt) cc_final: 0.8174 (mt)
REVERT: B  314 ASP cc_start: 0.8009 (m-30) cc_final: 0.7734 (m-30)
REVERT: B  391 LYS cc_start: 0.7776 (mmpt) cc_final: 0.7177 (ptpp)
REVERT: B  421 ARG cc_start: 0.6340 (tpp80) cc_final: 0.6097 (mmp80)
REVERT: H   73 ASP cc_start: 0.7201 (t0) cc_final: 0.6872 (t70)
REVERT: H  115 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8706 (tt)
  outliers start: 26
  outliers final: 23
  residues processed: 148
  average time/residue: 0.0832
  time to fit residues: 17.6121
Evaluate side-chains
  145 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 127 optimal weight:    0.3980
   chunk 83 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 60 optimal weight:    0.1980
   chunk 126 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 414 HIS
H 178 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.162661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136417 restraints weight = 14750.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.135862 restraints weight = 24723.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.132844 restraints weight = 21915.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.129799 restraints weight = 26737.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.128577 restraints weight = 25496.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10806  Z= 0.116
  Angle     :  0.642  12.749  14736  Z= 0.310
  Chirality :  0.042   0.186   1700
  Planarity :  0.004   0.041   1841
  Dihedral  :  5.051  54.205   1523
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.35 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.09 (0.23), residues: 1343
  helix:  1.79 (0.23), residues: 521
  sheet:  0.82 (0.31), residues: 285
  loop : -0.35 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  40 
 TYR   0.032   0.001   TYR L 146 
 PHE   0.022   0.001   PHE B 402 
 TRP   0.062   0.002   TRP L 169 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10797)
  covalent geometry    : angle       0.64103 (14714)
  SS BOND              : bond        0.00253 (    5)
  SS BOND              : angle       0.86363 (   10)
  hydrogen bonds       : bond        0.03304 (  535)
  hydrogen bonds       : angle       4.39487 ( 1482)
  link_NAG-ASN         : bond        0.00234 (    4)
  link_NAG-ASN         : angle       1.40038 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  211 ARG cc_start: 0.7512 (ttp80) cc_final: 0.7088 (mtm110)
REVERT: A  475 ASP cc_start: 0.7727 (t0) cc_final: 0.7481 (t0)
REVERT: A  507 MET cc_start: 0.8140 (mtm) cc_final: 0.7720 (ttm)
REVERT: A  609 LEU cc_start: 0.8575 (mt) cc_final: 0.8108 (mt)
REVERT: B  243 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6336 (tp)
REVERT: B  314 ASP cc_start: 0.8187 (m-30) cc_final: 0.7904 (m-30)
REVERT: B  359 LEU cc_start: 0.7645 (mt) cc_final: 0.7409 (mt)
REVERT: B  391 LYS cc_start: 0.7785 (mmpt) cc_final: 0.7181 (ptpp)
REVERT: B  421 ARG cc_start: 0.6379 (tpp80) cc_final: 0.6105 (mmp80)
REVERT: B  500 MET cc_start: 0.5388 (mtp) cc_final: 0.5043 (mtt)
REVERT: H   73 ASP cc_start: 0.7127 (t0) cc_final: 0.6837 (t70)
REVERT: H  115 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8674 (tt)
  outliers start: 27
  outliers final: 16
  residues processed: 153
  average time/residue: 0.1118
  time to fit residues: 24.1258
Evaluate side-chains
  141 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 128 optimal weight:    0.9990
   chunk 63 optimal weight:   20.0000
   chunk 69 optimal weight:    0.7980
   chunk 98 optimal weight:   20.0000
   chunk 87 optimal weight:    8.9990
   chunk 118 optimal weight:    2.9990
   chunk 105 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
** B 497 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 = 0.3859 r_free = 0.3859 target = 0.158906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.125452 restraints weight = 14793.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120283 restraints weight = 23289.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.117798 restraints weight = 25840.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.117195 restraints weight = 23705.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.116691 restraints weight = 21213.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  10806  Z= 0.235
  Angle     :  0.718  12.027  14736  Z= 0.350
  Chirality :  0.045   0.173   1700
  Planarity :  0.005   0.047   1841
  Dihedral  :  5.332  56.046   1523
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.18 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.86 (0.23), residues: 1343
  helix:  1.52 (0.23), residues: 522
  sheet:  0.74 (0.31), residues: 287
  loop : -0.43 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 211 
 TYR   0.031   0.002   TYR H 103 
 PHE   0.022   0.002   PHE A 541 
 TRP   0.057   0.002   TRP L 169 
 HIS   0.010   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (10797)
  covalent geometry    : angle       0.71588 (14714)
  SS BOND              : bond        0.00371 (    5)
  SS BOND              : angle       1.39540 (   10)
  hydrogen bonds       : bond        0.03713 (  535)
  hydrogen bonds       : angle       4.57552 ( 1482)
  link_NAG-ASN         : bond        0.00198 (    4)
  link_NAG-ASN         : angle       1.50608 (   12)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7288 (ptp-170) cc_final: 0.6907 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8084 (t0) cc_final: 0.7811 (t0)
REVERT: A  572 VAL cc_start: 0.9492 (t) cc_final: 0.9277 (m)
REVERT: A  609 LEU cc_start: 0.8763 (mt) cc_final: 0.8369 (mt)
REVERT: B  145 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8108 (mp10)
REVERT: B  314 ASP cc_start: 0.8306 (m-30) cc_final: 0.8064 (m-30)
REVERT: B  391 LYS cc_start: 0.7877 (mmpt) cc_final: 0.7176 (ptpp)
REVERT: B  421 ARG cc_start: 0.6448 (tpp80) cc_final: 0.6103 (mmp80)
REVERT: H   73 ASP cc_start: 0.7267 (t0) cc_final: 0.6912 (t70)
REVERT: H  115 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8815 (tt)
  outliers start: 29
  outliers final: 25
  residues processed: 152
  average time/residue: 0.1166
  time to fit residues: 24.8031
Evaluate side-chains
  149 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
B 304 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.160809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.126633 restraints weight = 14886.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.125956 restraints weight = 21782.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.123002 restraints weight = 19960.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118453 restraints weight = 22717.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118472 restraints weight = 27129.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10806  Z= 0.144
  Angle     :  0.671  12.093  14736  Z= 0.324
  Chirality :  0.043   0.194   1700
  Planarity :  0.004   0.043   1841
  Dihedral  :  5.235  54.873   1523
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.87 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.89 (0.23), residues: 1343
  helix:  1.57 (0.23), residues: 524
  sheet:  0.77 (0.31), residues: 287
  loop : -0.44 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  60 
 TYR   0.030   0.001   TYR L 146 
 PHE   0.027   0.002   PHE B 379 
 TRP   0.052   0.002   TRP L 169 
 HIS   0.006   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10797)
  covalent geometry    : angle       0.66966 (14714)
  SS BOND              : bond        0.00285 (    5)
  SS BOND              : angle       1.05459 (   10)
  hydrogen bonds       : bond        0.03432 (  535)
  hydrogen bonds       : angle       4.49906 ( 1482)
  link_NAG-ASN         : bond        0.00200 (    4)
  link_NAG-ASN         : angle       1.42162 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1689.55 seconds
wall clock time: 29 minutes 59.89 seconds (1799.89 seconds total)