Starting phenix.real_space_refine
on Fri Dec  8 05:55:09 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/12_2023/6irs_9721_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/12_2023/6irs_9721.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/12_2023/6irs_9721.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/12_2023/6irs_9721.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/12_2023/6irs_9721_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/12_2023/6irs_9721_updated.pdb"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    4807      2.51       5
     N    1172      2.21       5
     O    1329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  181": "NH1" <-> "NH2"
    Residue "A ARG  183": "NH1" <-> "NH2"
    Residue "A ARG  212": "NH1" <-> "NH2"
    Residue "A ARG  535": "NH1" <-> "NH2"
    Residue "B PHE  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  421": "NH1" <-> "NH2"
    Residue "B ARG  427": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7337
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3479
          Classifications: {'peptide': 457}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 24, 'TRANS': 432}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 96
          Unusual residues: {'3PH': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.60, per 1000 atoms: 0.63
  Number of scatterers: 7337
  At special positions: 0
  Unit cell: (82.916, 84.007, 124.374, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O    1329      8.00
     N    1172      7.00
     C    4807      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 2.67
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      51.1% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 168 through 174
    Processing helix  chain 'A' and resid 179 through 206
      removed outlier: 3.677A  pdb=" N   LEU A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   TRP A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU A 192 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   MET A 197 " --> pdb=" O   GLY A 193 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ILE A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 222
      removed outlier: 3.863A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 219 through 222'
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 242 through 252
      removed outlier: 3.985A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ARG A 248 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   ASP A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   TYR A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 300
      removed outlier: 3.631A  pdb=" N   LYS A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 341
      removed outlier: 4.212A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 353
      No H-bonds generated for 'chain 'A' and resid 351 through 353'
    Processing helix  chain 'A' and resid 357 through 371
      removed outlier: 3.717A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 392
      removed outlier: 3.837A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 386 through 392'
    Processing helix  chain 'A' and resid 413 through 427
      removed outlier: 3.530A  pdb=" N   THR A 427 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 459
      removed outlier: 3.921A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   MET A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 513
      No H-bonds generated for 'chain 'A' and resid 510 through 513'
    Processing helix  chain 'A' and resid 520 through 533
      removed outlier: 3.619A  pdb=" N   ARG A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 539
    Processing helix  chain 'B' and resid 54 through 63
      removed outlier: 3.908A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B  63 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 69
      removed outlier: 3.554A  pdb=" N   PHE B  69 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 66 through 69'
    Processing helix  chain 'B' and resid 72 through 79
      removed outlier: 3.760A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 109
      removed outlier: 3.553A  pdb=" N   PHE B  95 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER B  96 " --> pdb=" O   CYS B  92 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 123
      removed outlier: 3.638A  pdb=" N   TYR B 119 " --> pdb=" O   ASP B 116 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU B 122 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 136
      removed outlier: 3.542A  pdb=" N   GLU B 136 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 154
      removed outlier: 3.860A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 187
      removed outlier: 4.036A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 220
      removed outlier: 3.848A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA B 199 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA B 201 " --> pdb=" O   GLN B 197 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ILE B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
      removed outlier: 3.721A  pdb=" N   SER B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 266
    Processing helix  chain 'B' and resid 274 through 299
      removed outlier: 3.698A  pdb=" N   ILE B 279 " --> pdb=" O   PRO B 275 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER B 281 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 4.205A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   THR B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 307
      removed outlier: 3.817A  pdb=" N   LEU B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 319
    Processing helix  chain 'B' and resid 327 through 338
      removed outlier: 3.855A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 344
      No H-bonds generated for 'chain 'B' and resid 341 through 344'
    Processing helix  chain 'B' and resid 347 through 355
      removed outlier: 3.563A  pdb=" N   PHE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL B 352 " --> pdb=" O   ARG B 348 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 389
      removed outlier: 3.510A  pdb=" N   MET B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR B 387 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ALA B 388 " --> pdb=" O   THR B 384 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 420
      removed outlier: 3.619A  pdb=" N   ASN B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   PHE B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA B 409 " --> pdb=" O   TRP B 405 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   MET B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 452
      removed outlier: 3.841A  pdb=" N   VAL B 437 " --> pdb=" O   LEU B 433 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE B 445 " --> pdb=" O   LEU B 441 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL B 449 " --> pdb=" O   PHE B 445 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   TRP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 463
    Processing helix  chain 'B' and resid 467 through 473
      removed outlier: 4.007A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 500
      removed outlier: 3.656A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS B 496 " --> pdb=" O   THR B 492 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 225 through 227
    Processing sheet with id=  B, first strand: chain 'A' and resid 259 through 262
      removed outlier: 6.928A  pdb=" N   ARG A 304 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LEU A 262 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   ILE A 306 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'A' and resid 346 through 348
    Processing sheet with id=  D, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.514A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   ARG A 626 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   LEU A 596 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 266 through 268
      removed outlier: 6.986A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    762 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: 1.99

  Time building geometry restraints manager: 2.96 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1456
        1.33 -     1.45: 1777
        1.45 -     1.57: 4235
        1.57 -     1.69: 4
        1.69 -     1.81: 40
  Bond restraints: 7512
  Sorted by residual:
  bond pdb=" C31 3PH B 601 "
       pdb=" O31 3PH B 601 "
    ideal  model  delta    sigma   weight residual
    1.325  1.454 -0.129 2.00e-02 2.50e+03 4.18e+01
  bond pdb=" C31 3PH B 602 "
       pdb=" O31 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.325  1.452 -0.127 2.00e-02 2.50e+03 4.04e+01
  bond pdb=" C21 3PH B 602 "
       pdb=" O21 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.328  1.455 -0.127 2.00e-02 2.50e+03 4.02e+01
  bond pdb=" C21 3PH B 601 "
       pdb=" O21 3PH B 601 "
    ideal  model  delta    sigma   weight residual
    1.328  1.455 -0.127 2.00e-02 2.50e+03 4.00e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" C2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.532  1.632 -0.100 2.00e-02 2.50e+03 2.50e+01
  ... (remaining 7507 not shown)

  Histogram of bond angle deviations from ideal:
       95.75 -   103.53: 108
      103.53 -   111.31: 3194
      111.31 -   119.09: 3000
      119.09 -   126.86: 3780
      126.86 -   134.64: 128
  Bond angle restraints: 10210
  Sorted by residual:
  angle pdb=" C   SER A 176 "
        pdb=" N   PRO A 177 "
        pdb=" CA  PRO A 177 "
      ideal   model   delta    sigma   weight residual
     119.84  129.79   -9.95 1.25e+00 6.40e-01 6.34e+01
  angle pdb=" N   MET A 490 "
        pdb=" CA  MET A 490 "
        pdb=" C   MET A 490 "
      ideal   model   delta    sigma   weight residual
     109.15   97.87   11.28 1.44e+00 4.82e-01 6.14e+01
  angle pdb=" N   MET A 508 "
        pdb=" CA  MET A 508 "
        pdb=" C   MET A 508 "
      ideal   model   delta    sigma   weight residual
     111.28  118.86   -7.58 1.09e+00 8.42e-01 4.84e+01
  angle pdb=" N   HIS B 319 "
        pdb=" CA  HIS B 319 "
        pdb=" C   HIS B 319 "
      ideal   model   delta    sigma   weight residual
     111.28  117.70   -6.42 1.09e+00 8.42e-01 3.47e+01
  angle pdb=" C   PHE B 161 "
        pdb=" N   PRO B 162 "
        pdb=" CA  PRO B 162 "
      ideal   model   delta    sigma   weight residual
     119.84  127.10   -7.26 1.25e+00 6.40e-01 3.38e+01
  ... (remaining 10205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.15: 4267
       21.15 -    42.29: 213
       42.29 -    63.44: 36
       63.44 -    84.59: 13
       84.59 -   105.74: 7
  Dihedral angle restraints: 4536
    sinusoidal: 1883
      harmonic: 2653
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 164 "
           pdb=" CB  CYS B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.35  -88.65     1      1.00e+01 1.00e-02 9.37e+01
  dihedral pdb=" CA  PRO B 360 "
           pdb=" C   PRO B 360 "
           pdb=" N   SER B 361 "
           pdb=" CA  SER B 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.14  -24.86     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  HIS A 221 "
           pdb=" C   HIS A 221 "
           pdb=" N   THR A 222 "
           pdb=" CA  THR A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.73  -24.27     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 4533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 983
       0.081 -    0.162: 184
       0.162 -    0.242: 23
       0.242 -    0.323: 6
       0.323 -    0.404: 4
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.31   -0.09 2.00e-02 2.50e+03 2.17e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.32   -0.08 2.00e-02 2.50e+03 1.58e+01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-01 2.50e+01 4.07e+00
  ... (remaining 1197 not shown)

  Planarity restraints: 1258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.337 2.00e-02 2.50e+03   2.87e-01 1.03e+03
        pdb=" C7  NAG D   2 "   -0.085 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.177 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.503 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.321 2.00e-02 2.50e+03   2.77e-01 9.60e+02
        pdb=" C7  NAG D   1 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.021 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.481 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.210 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 507 "   -0.090 2.00e-02 2.50e+03   1.14e-01 1.62e+02
        pdb=" CG  ASN A 507 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 507 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 507 "    0.196 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.133 2.00e-02 2.50e+03
  ... (remaining 1255 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 403
        2.70 -     3.25: 7108
        3.25 -     3.80: 11590
        3.80 -     4.35: 14642
        4.35 -     4.90: 23870
  Nonbonded interactions: 57613
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS B 367 "
            pdb=" CD  PRO B 368 "
     model   vdw
     2.150 3.520
  nonbonded pdb=" O   GLY B 107 "
            pdb=" OG  SER B 111 "
     model   vdw
     2.199 2.440
  nonbonded pdb=" C   TRP A 492 "
            pdb=" CG2 THR A 509 "
     model   vdw
     2.221 3.690
  nonbonded pdb=" CD1 ILE A 228 "
            pdb=" CZ  PHE A 234 "
     model   vdw
     2.250 3.760
  nonbonded pdb=" O   CYS B  92 "
            pdb=" OH  TYR B 254 "
     model   vdw
     2.277 2.440
  ... (remaining 57608 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  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:          3.940
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     23.890
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
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      :  0.011   0.129   7512  Z= 0.710
  Angle     :  1.357  12.491  10210  Z= 0.743
  Chirality :  0.069   0.404   1200
  Planarity :  0.014   0.287   1254
  Dihedral  : 14.191 105.736   2829
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  8.79 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  :  6.81 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.69 (0.19), residues: 922
  helix: -4.10 (0.12), residues: 475
  sheet: -1.86 (0.67), residues: 51
  loop : -3.48 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.035   0.005   TRP A 558 
   HIS   0.012   0.003   HIS A 221 
   PHE   0.034   0.004   PHE A 552 
   TYR   0.050   0.004   TYR A 454 
   ARG   0.015   0.002   ARG A 227 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 7
  residues processed: 238
  average time/residue: 0.2129
  time to fit residues: 65.5746
Evaluate side-chains
  139 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.836 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0748
  time to fit residues: 2.0091
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0470
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0770
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0070
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.2654

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 620 HIS
B 145 GLN
B 186 ASN
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7512  Z= 0.195
  Angle     :  0.788  12.559  10210  Z= 0.377
  Chirality :  0.046   0.218   1200
  Planarity :  0.006   0.057   1254
  Dihedral  : 12.090  88.575   1236
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.29 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.05 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.22), residues: 922
  helix: -2.50 (0.18), residues: 503
  sheet: -1.15 (0.71), residues: 50
  loop : -3.05 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP A 558 
   HIS   0.007   0.002   HIS A 539 
   PHE   0.024   0.002   PHE B 474 
   TYR   0.014   0.002   TYR B 472 
   ARG   0.005   0.001   ARG A 614 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 11
  residues processed: 177
  average time/residue: 0.2027
  time to fit residues: 48.0504
Evaluate side-chains
  130 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.847 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0785
  time to fit residues: 2.6202
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 25 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 56 optimal weight:    0.3980
   chunk 22 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0010
   chunk 28 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 GLN
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 398 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7512  Z= 0.180
  Angle     :  0.715   9.998  10210  Z= 0.339
  Chirality :  0.044   0.209   1200
  Planarity :  0.005   0.043   1254
  Dihedral  : 11.184  86.233   1236
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.16 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.72 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.25), residues: 922
  helix: -1.40 (0.20), residues: 505
  sheet: -0.85 (0.76), residues: 46
  loop : -2.82 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 405 
   HIS   0.007   0.001   HIS B 319 
   PHE   0.019   0.002   PHE B 474 
   TYR   0.021   0.002   TYR A 629 
   ARG   0.006   0.001   ARG A 614 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 10
  residues processed: 137
  average time/residue: 0.2150
  time to fit residues: 38.9977
Evaluate side-chains
  120 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.855 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0698
  time to fit residues: 2.3771
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0570
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 78 optimal weight:    0.0070
   chunk 23 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.3516

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 273 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7512  Z= 0.166
  Angle     :  0.675  10.159  10210  Z= 0.319
  Chirality :  0.043   0.222   1200
  Planarity :  0.005   0.042   1254
  Dihedral  : 10.497  83.659   1236
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.62 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 20.03 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.26), residues: 922
  helix: -0.73 (0.22), residues: 501
  sheet: -0.51 (0.77), residues: 46
  loop : -2.70 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 405 
   HIS   0.007   0.001   HIS B 319 
   PHE   0.013   0.001   PHE B 451 
   TYR   0.016   0.002   TYR A 469 
   ARG   0.015   0.001   ARG B 272 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.853 
Fit side-chains
  outliers start: 14
  outliers final: 1
  residues processed: 141
  average time/residue: 0.2105
  time to fit residues: 39.3665
Evaluate side-chains
  106 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.844 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0971
  time to fit residues: 1.1414
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN
B 367 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7512  Z= 0.186
  Angle     :  0.676  10.850  10210  Z= 0.318
  Chirality :  0.043   0.229   1200
  Planarity :  0.004   0.043   1254
  Dihedral  :  9.932  82.199   1236
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.94 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 21.99 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.26), residues: 922
  helix: -0.33 (0.22), residues: 494
  sheet: -0.16 (0.78), residues: 47
  loop : -2.47 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B 405 
   HIS   0.006   0.001   HIS B 319 
   PHE   0.014   0.001   PHE B 451 
   TYR   0.018   0.002   TYR A 629 
   ARG   0.003   0.000   ARG A 614 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 6
  residues processed: 127
  average time/residue: 0.2346
  time to fit residues: 41.4663
Evaluate side-chains
  111 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 1.088 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1106
  time to fit residues: 2.9593
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    0.0470
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7512  Z= 0.190
  Angle     :  0.673  11.166  10210  Z= 0.316
  Chirality :  0.044   0.247   1200
  Planarity :  0.004   0.044   1254
  Dihedral  :  9.615  80.011   1236
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.05 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 23.04 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.27), residues: 922
  helix: -0.00 (0.23), residues: 489
  sheet:  0.01 (0.74), residues: 52
  loop : -2.51 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 405 
   HIS   0.006   0.001   HIS B 367 
   PHE   0.014   0.001   PHE B 439 
   TYR   0.015   0.001   TYR B 103 
   ARG   0.003   0.000   ARG A 375 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 4
  residues processed: 122
  average time/residue: 0.2115
  time to fit residues: 34.4351
Evaluate side-chains
  109 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.859 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0797
  time to fit residues: 1.7181
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 64 optimal weight:   20.0000
   chunk 49 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0060
   chunk 87 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 398 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7512  Z= 0.167
  Angle     :  0.664  10.403  10210  Z= 0.310
  Chirality :  0.043   0.266   1200
  Planarity :  0.004   0.041   1254
  Dihedral  :  9.305  77.251   1236
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.62 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 23.04 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.27), residues: 922
  helix:  0.27 (0.23), residues: 489
  sheet:  0.17 (0.73), residues: 52
  loop : -2.49 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B 405 
   HIS   0.009   0.001   HIS B 367 
   PHE   0.018   0.001   PHE B 439 
   TYR   0.015   0.001   TYR B 103 
   ARG   0.007   0.001   ARG A 212 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 113
  average time/residue: 0.2144
  time to fit residues: 32.3781
Evaluate side-chains
  107 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.907 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0745
  time to fit residues: 1.8255
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0030
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7512  Z= 0.179
  Angle     :  0.671  10.137  10210  Z= 0.315
  Chirality :  0.043   0.277   1200
  Planarity :  0.004   0.041   1254
  Dihedral  :  9.141  75.193   1236
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.05 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 24.08 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.27), residues: 922
  helix:  0.50 (0.24), residues: 488
  sheet:  0.27 (0.74), residues: 52
  loop : -2.46 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 405 
   HIS   0.014   0.002   HIS B 367 
   PHE   0.027   0.001   PHE B 474 
   TYR   0.015   0.001   TYR B 103 
   ARG   0.005   0.000   ARG B 355 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 107
  average time/residue: 0.2237
  time to fit residues: 31.8328
Evaluate side-chains
  101 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.911 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0853
  time to fit residues: 1.3363
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6307 > 50:
  distance: 30 - 36:   7.629
  distance: 36 - 37:  16.707
  distance: 36 - 42:  23.019
  distance: 37 - 38:  15.684
  distance: 37 - 40:  22.849
  distance: 38 - 39:  31.313
  distance: 38 - 43:  19.273
  distance: 40 - 41:  14.881
  distance: 41 - 42:   9.457
  distance: 43 - 44:   6.428
  distance: 44 - 45:  21.453
  distance: 44 - 47:  12.546
  distance: 45 - 46:  49.813
  distance: 45 - 49:  37.327
  distance: 47 - 48:   6.656
  distance: 49 - 50:  14.620
  distance: 50 - 51:  22.051
  distance: 50 - 53:  20.855
  distance: 51 - 52:  21.380
  distance: 51 - 57:  28.366
  distance: 53 - 54:  45.488
  distance: 53 - 55:  27.441
  distance: 54 - 56:  19.710
  distance: 57 - 58:  17.214
  distance: 58 - 59:  17.025
  distance: 58 - 61:  18.959
  distance: 59 - 60:  13.842
  distance: 59 - 65:   7.992
  distance: 61 - 62:  14.622
  distance: 62 - 63:   9.521
  distance: 62 - 64:  13.400
  distance: 65 - 66:  12.396
  distance: 66 - 67:   6.260
  distance: 66 - 69:  20.542
  distance: 67 - 68:   4.833
  distance: 67 - 71:  11.553
  distance: 69 - 70:  15.089
  distance: 71 - 72:   7.720
  distance: 72 - 73:  12.180
  distance: 72 - 75:   5.454
  distance: 73 - 74:  26.360
  distance: 73 - 79:   9.536
  distance: 75 - 76:  14.409
  distance: 76 - 77:   9.826
  distance: 77 - 78:  19.026
  distance: 79 - 80:  11.885
  distance: 80 - 81:  38.955
  distance: 80 - 83:   4.102
  distance: 81 - 82:  41.180
  distance: 81 - 87:  16.715
  distance: 83 - 84:  35.008
  distance: 83 - 85:  24.205
  distance: 84 - 86:  10.254
  distance: 87 - 88:   6.352
  distance: 88 - 89:  21.686
  distance: 88 - 91:  27.142
  distance: 89 - 90:  18.125
  distance: 89 - 97:  15.901
  distance: 91 - 92:  37.045
  distance: 92 - 93:  23.788
  distance: 92 - 94:  31.470
  distance: 93 - 95:  20.892
  distance: 94 - 96:  18.808
  distance: 95 - 96:  20.039
  distance: 97 - 98:   9.420
  distance: 97 - 103:  38.722
  distance: 98 - 99:  23.742
  distance: 98 - 101:   3.430
  distance: 99 - 100:  25.132
  distance: 99 - 104:  23.529
  distance: 101 - 102:  44.229
  distance: 102 - 103:  14.247
  distance: 104 - 105:   7.743
  distance: 105 - 106:  17.748
  distance: 105 - 108:  23.620
  distance: 106 - 107:  14.985
  distance: 106 - 113:  10.997
  distance: 108 - 109:  13.675
  distance: 109 - 110:   6.944
  distance: 110 - 111:  11.949
  distance: 110 - 112:  27.790