Starting phenix.real_space_refine
on Sat May 10 22:15:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r11_14227/05_2025/7r11_14227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r11_14227/05_2025/7r11_14227.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r11_14227/05_2025/7r11_14227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r11_14227/05_2025/7r11_14227.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r11_14227/05_2025/7r11_14227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r11_14227/05_2025/7r11_14227.cif"
  }
  resolution = 3.5
  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=   0.002 sd=   0.057
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
     Zn      1      6.06       5
     S      39      5.16       5
     C    4392      2.51       5
     N    1131      2.21       5
     O    1307      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6870
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 4802
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 587, 4795
          Classifications: {'peptide': 587}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 587, 4795
          Classifications: {'peptide': 587}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4920
    Chain: "A"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1969
          Classifications: {'peptide': 250}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 235}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      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
  Time building chain proxies: 6.78, per 1000 atoms: 0.99
  Number of scatterers: 6870
  At special positions: 0
  Unit cell: (75.46, 95.942, 141.218, 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)
     Zn      1     29.99
     S      39     16.00
     O    1307      8.00
     N    1131      7.00
     C    4392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG A1302 " - " ASN A 331 "
      " NAG D 701 " - " ASN D 432 "
      " NAG D 703 " - " ASN D  53 "
      " NAG D 704 " - " ASN D 103 "
      " NAG D 705 " - " ASN D 546 "
      " NAG D 706 " - " ASN D  90 "
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 702 "
        pdb="ZN    ZN D 702 " - pdb=" NE2 HIS D 374 "


  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 7 sheets defined
      51.4% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.841A  pdb=" N   HIS D  34 " --> pdb=" O   ASP D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 81
      removed outlier: 3.535A  pdb=" N   MET D  62 " --> pdb=" O   ASN D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 101
    Processing helix  chain 'D' and resid 103 through 107
      removed outlier: 4.169A  pdb=" N   VAL D 107 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 146 through 155
      removed outlier: 3.562A  pdb=" N   ASN D 154 " --> pdb=" O   GLU D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 176
      removed outlier: 4.175A  pdb=" N   LYS D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 176 through 194
      removed outlier: 3.528A  pdb=" N   ASN D 194 " --> pdb=" O   MET D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 219 through 223
    Processing helix  chain 'D' and resid 226 through 233
      removed outlier: 3.676A  pdb=" N   GLU D 232 " --> pdb=" O   HIS D 228 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE D 233 " --> pdb=" O   THR D 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 252
    Processing helix  chain 'D' and resid 253 through 256
      removed outlier: 4.476A  pdb=" N   ILE D 256 " --> pdb=" O   PRO D 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 253 through 256'
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 280
      removed outlier: 4.162A  pdb=" N   SER D 280 " --> pdb=" O   ASN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 301
    Processing helix  chain 'D' and resid 305 through 319
    Processing helix  chain 'D' and resid 326 through 331
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.589A  pdb=" N   ALA D 384 " --> pdb=" O   GLN D 380 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 393
      removed outlier: 3.520A  pdb=" N   ARG D 393 " --> pdb=" O   PHE D 390 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 413
      removed outlier: 3.553A  pdb=" N   ALA D 403 " --> pdb=" O   GLY D 399 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL D 404 " --> pdb=" O   PHE D 400 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY D 405 " --> pdb=" O   HIS D 401 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.692A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 466
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 484
      removed outlier: 3.688A  pdb=" N   LYS D 476 " --> pdb=" O   GLN D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 499 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 3.631A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
      removed outlier: 3.609A  pdb=" N   LYS D 541 " --> pdb=" O   PRO D 538 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   CYS D 542 " --> pdb=" O   LEU D 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 538 through 542'
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.716A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 572
    Processing helix  chain 'D' and resid 581 through 588
      removed outlier: 3.621A  pdb=" N   PHE D 588 " --> pdb=" O   LEU D 584 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 588 through 600
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 4.102A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.460A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 3.989A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.277A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352
      removed outlier: 6.032A  pdb=" N   ASP D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 328
      removed outlier: 6.889A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 542 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY A 550 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL A 576 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.294A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.460A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474

    302 hydrogen bonds defined for protein.
    855 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: 1.90

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2188
        1.34 -     1.46: 1733
        1.46 -     1.58: 3074
        1.58 -     1.70: 0
        1.70 -     1.81: 60
  Bond restraints: 7055
  Sorted by residual:
  bond pdb=" N   ARG D 582 "
       pdb=" CA  ARG D 582 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 9.20e-03 1.18e+04 1.21e+01
  bond pdb=" N   ASN D 580 "
       pdb=" CA  ASN D 580 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.038 1.26e-02 6.30e+03 9.32e+00
  bond pdb=" N   VAL A 539 "
       pdb=" CA  VAL A 539 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.14e-02 7.69e+03 9.14e+00
  bond pdb=" N   ILE D  54 "
       pdb=" CA  ILE D  54 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.13e+00
  bond pdb=" N   VAL D 581 "
       pdb=" CA  VAL D 581 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.041 1.37e-02 5.33e+03 8.74e+00
  ... (remaining 7050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 9206
        1.23 -     2.45: 281
        2.45 -     3.68: 85
        3.68 -     4.90: 10
        4.90 -     6.13: 6
  Bond angle restraints: 9588
  Sorted by residual:
  angle pdb=" CA  THR D  55 "
        pdb=" C   THR D  55 "
        pdb=" O   THR D  55 "
      ideal   model   delta    sigma   weight residual
     121.60  117.83    3.77 1.21e+00 6.83e-01 9.70e+00
  angle pdb=" N   GLN D 524 "
        pdb=" CA  GLN D 524 "
        pdb=" C   GLN D 524 "
      ideal   model   delta    sigma   weight residual
     111.07  107.92    3.15 1.07e+00 8.73e-01 8.69e+00
  angle pdb=" CA  ASN D  53 "
        pdb=" CB  ASN D  53 "
        pdb=" CG  ASN D  53 "
      ideal   model   delta    sigma   weight residual
     112.60  115.44   -2.84 1.00e+00 1.00e+00 8.08e+00
  angle pdb=" N   ARG D 245 "
        pdb=" CA  ARG D 245 "
        pdb=" C   ARG D 245 "
      ideal   model   delta    sigma   weight residual
     111.07  108.07    3.00 1.07e+00 8.73e-01 7.85e+00
  angle pdb=" CA  ASN D 580 "
        pdb=" C   ASN D 580 "
        pdb=" O   ASN D 580 "
      ideal   model   delta    sigma   weight residual
     121.06  117.85    3.21 1.16e+00 7.43e-01 7.68e+00
  ... (remaining 9583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 3918
       17.22 -    34.44: 280
       34.44 -    51.66: 47
       51.66 -    68.89: 14
       68.89 -    86.11: 1
  Dihedral angle restraints: 4260
    sinusoidal: 1805
      harmonic: 2455
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.76  -32.76     1      1.00e+01 1.00e-02 1.53e+01
  dihedral pdb=" CA  ILE D 223 "
           pdb=" C   ILE D 223 "
           pdb=" N   GLU D 224 "
           pdb=" CA  GLU D 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.77   17.23     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" N   VAL D 581 "
           pdb=" CA  VAL D 581 "
           pdb=" CB  VAL D 581 "
           pdb=" CG1 VAL D 581 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.06   55.06     3      1.50e+01 4.44e-03 9.32e+00
  ... (remaining 4257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 858
       0.056 -    0.112: 152
       0.112 -    0.167: 20
       0.167 -    0.223: 5
       0.223 -    0.279: 1
  Chirality restraints: 1036
  Sorted by residual:
  chirality pdb=" CA  VAL A 551 "
            pdb=" N   VAL A 551 "
            pdb=" C   VAL A 551 "
            pdb=" CB  VAL A 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.72   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  ASN D  53 "
            pdb=" N   ASN D  53 "
            pdb=" C   ASN D  53 "
            pdb=" CB  ASN D  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  VAL A 539 "
            pdb=" CA  VAL A 539 "
            pdb=" CG1 VAL A 539 "
            pdb=" CG2 VAL A 539 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.36e-01
  ... (remaining 1033 not shown)

  Planarity restraints: 1237
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 145 "   -0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO D 146 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO D 146 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 146 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 262 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.45e+00
        pdb=" N   PRO D 263 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 263 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 263 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D  32 "   -0.008 2.00e-02 2.50e+03   1.53e-02 2.33e+00
        pdb=" C   PHE D  32 "    0.026 2.00e-02 2.50e+03
        pdb=" O   PHE D  32 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN D  33 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1234 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1596
        2.79 -     3.32: 6369
        3.32 -     3.84: 10763
        3.84 -     4.37: 12074
        4.37 -     4.90: 21571
  Nonbonded interactions: 52373
  Sorted by model distance:
  nonbonded pdb=" O   PHE D 327 "
            pdb=" OG  SER D 331 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   ASP D 431 "
            pdb=" OG1 THR D 434 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   THR A 393 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.333 3.040
  ... (remaining 52368 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=0.50 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:             11.980
  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:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.890
  Find NCS groups from input model:        0.080
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
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      :  0.004   0.041   7071  Z= 0.202
  Angle     :  0.563   6.131   9625  Z= 0.309
  Chirality :  0.046   0.279   1036
  Planarity :  0.004   0.058   1230
  Dihedral  : 11.822  86.106   2660
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  7.05 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.29), residues: 830
  helix:  1.00 (0.27), residues: 385
  sheet: -0.19 (0.63), residues: 57
  loop : -0.73 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 436 
 HIS   0.003   0.000   HIS D 374 
 PHE   0.010   0.001   PHE D 369 
 TYR   0.015   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 514 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00471 (    7)
  link_NAG-ASN         : angle       1.80383 (   21)
  hydrogen bonds       : bond        0.14029 (  302)
  hydrogen bonds       : angle       5.23148 (  855)
  metal coordination   : bond        0.00116 (    1)
  SS BOND              : bond        0.00192 (    8)
  SS BOND              : angle       0.64488 (   16)
  covalent geometry    : bond        0.00358 ( 7055)
  covalent geometry    : angle       0.55752 ( 9588)

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.763 
Fit side-chains
REVERT: D  168 TRP cc_start: 0.7965 (t-100) cc_final: 0.7462 (t-100)
REVERT: D  223 ILE cc_start: 0.7665 (mt) cc_final: 0.6864 (mt)
REVERT: D  300 GLN cc_start: 0.6498 (mm110) cc_final: 0.6021 (tm-30)
REVERT: D  547 SER cc_start: 0.7753 (t) cc_final: 0.7487 (t)
REVERT: A  428 ASP cc_start: 0.5576 (p0) cc_final: 0.5333 (p0)
REVERT: A  578 ASP cc_start: 0.6644 (t0) cc_final: 0.6176 (t70)
  outliers start: 4
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2160
  time to fit residues: 37.1934
Evaluate side-chains
  88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0000
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 345 HIS
** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.193414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.162793 restraints weight = 8787.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.160612 restraints weight = 14968.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.163041 restraints weight = 12600.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7071  Z= 0.180
  Angle     :  0.629  12.615   9625  Z= 0.313
  Chirality :  0.044   0.192   1036
  Planarity :  0.005   0.053   1230
  Dihedral  :  6.401  59.250   1055
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.70 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.29), residues: 830
  helix:  0.83 (0.26), residues: 392
  sheet: -0.02 (0.62), residues: 58
  loop : -0.72 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 436 
 HIS   0.003   0.001   HIS D 401 
 PHE   0.019   0.002   PHE D 327 
 TYR   0.023   0.002   TYR D 385 
 ARG   0.005   0.001   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00424 (    7)
  link_NAG-ASN         : angle       1.77642 (   21)
  hydrogen bonds       : bond        0.05338 (  302)
  hydrogen bonds       : angle       4.56533 (  855)
  metal coordination   : bond        0.00165 (    1)
  SS BOND              : bond        0.00354 (    8)
  SS BOND              : angle       1.28065 (   16)
  covalent geometry    : bond        0.00422 ( 7055)
  covalent geometry    : angle       0.62219 ( 9588)

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: D  300 GLN cc_start: 0.6172 (mm110) cc_final: 0.5867 (tm-30)
REVERT: A  584 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.6269 (tt)
  outliers start: 15
  outliers final: 2
  residues processed: 104
  average time/residue: 0.2071
  time to fit residues: 29.1013
Evaluate side-chains
  86 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain A residue  584 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0050
   chunk 8 optimal weight:    0.0980
   chunk 66 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0970
   chunk 69 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 43 optimal weight:    0.3980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.2392

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

Flipped N/Q/H residues before XYZ refinement:
** D  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 345 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.200094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.170092 restraints weight = 10991.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.171199 restraints weight = 20640.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.172687 restraints weight = 13374.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3925 r_free = 0.3925    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3925 r_free = 0.3925    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7071  Z= 0.115
  Angle     :  0.553   9.125   9625  Z= 0.276
  Chirality :  0.041   0.177   1036
  Planarity :  0.004   0.050   1230
  Dihedral  :  5.587  55.613   1055
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.28 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.29), residues: 830
  helix:  1.09 (0.27), residues: 391
  sheet: -0.16 (0.61), residues: 63
  loop : -0.61 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.002   0.001   HIS D 374 
 PHE   0.022   0.001   PHE A 486 
 TYR   0.012   0.001   TYR D 385 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00424 (    7)
  link_NAG-ASN         : angle       1.33020 (   21)
  hydrogen bonds       : bond        0.04338 (  302)
  hydrogen bonds       : angle       4.23396 (  855)
  metal coordination   : bond        0.00092 (    1)
  SS BOND              : bond        0.00245 (    8)
  SS BOND              : angle       1.73523 (   16)
  covalent geometry    : bond        0.00250 ( 7055)
  covalent geometry    : angle       0.54589 ( 9588)

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A  370 ASN cc_start: 0.6083 (OUTLIER) cc_final: 0.5767 (p0)
REVERT: A  584 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6304 (tt)
  outliers start: 9
  outliers final: 2
  residues processed: 100
  average time/residue: 0.1882
  time to fit residues: 26.0759
Evaluate side-chains
  87 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  584 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0570
   chunk 17 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0470
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0040
   overall best weight:    0.2008

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

Flipped N/Q/H residues before XYZ refinement:
D  24 GLN
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.198727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.175434 restraints weight = 17162.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.174721 restraints weight = 26365.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.173846 restraints weight = 9527.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7071  Z= 0.109
  Angle     :  0.534   8.311   9625  Z= 0.265
  Chirality :  0.041   0.171   1036
  Planarity :  0.004   0.049   1230
  Dihedral  :  5.162  55.615   1055
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.55 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.29), residues: 830
  helix:  1.18 (0.27), residues: 393
  sheet:  0.40 (0.67), residues: 48
  loop : -0.64 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP D 168 
 HIS   0.002   0.001   HIS D 345 
 PHE   0.018   0.001   PHE D 504 
 TYR   0.011   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00394 (    7)
  link_NAG-ASN         : angle       1.29356 (   21)
  hydrogen bonds       : bond        0.04062 (  302)
  hydrogen bonds       : angle       4.07886 (  855)
  metal coordination   : bond        0.00087 (    1)
  SS BOND              : bond        0.00179 (    8)
  SS BOND              : angle       0.67398 (   16)
  covalent geometry    : bond        0.00237 ( 7055)
  covalent geometry    : angle       0.53116 ( 9588)

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.717 
Fit side-chains
REVERT: D  323 MET cc_start: 0.7713 (mmt) cc_final: 0.7482 (mpp)
REVERT: A  370 ASN cc_start: 0.5863 (OUTLIER) cc_final: 0.5648 (p0)
REVERT: A  584 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6249 (tt)
  outliers start: 12
  outliers final: 3
  residues processed: 95
  average time/residue: 0.1708
  time to fit residues: 22.4384
Evaluate side-chains
  88 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  584 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2108 > 50:
  distance: 69 - 75:  33.848
  distance: 76 - 77:  39.747
  distance: 76 - 79:  40.310
  distance: 77 - 78:  40.193
  distance: 79 - 80:  38.690
  distance: 80 - 81:  38.812
  distance: 80 - 82:  40.348
  distance: 84 - 85:  57.656
  distance: 84 - 87:  55.870
  distance: 85 - 86:  39.350
  distance: 85 - 91:   7.000
  distance: 87 - 88:  39.464
  distance: 88 - 90:  39.853
  distance: 91 - 92:  35.251
  distance: 92 - 93:  40.524
  distance: 93 - 94:  30.743
  distance: 93 - 95:  41.875
  distance: 95 - 96:  40.531
  distance: 96 - 97:  69.089
  distance: 96 - 99:  13.025
  distance: 97 - 103:  56.322
  distance: 99 - 100:  15.257
  distance: 100 - 101:  60.176
  distance: 100 - 102:  44.428
  distance: 103 - 104:  39.478
  distance: 104 - 105:  39.066
  distance: 104 - 107:  40.932
  distance: 107 - 108:  40.916
  distance: 108 - 109:  56.594
  distance: 109 - 110:  39.633
  distance: 111 - 112:  29.676
  distance: 112 - 113:   8.292
  distance: 112 - 115:  64.029
  distance: 113 - 114:  39.976
  distance: 115 - 116:  39.990
  distance: 116 - 117:  26.862
  distance: 117 - 119:  58.080
  distance: 118 - 120:  63.513
  distance: 119 - 120:  11.891
  distance: 120 - 122:  13.107
  distance: 121 - 123:   4.582
  distance: 122 - 124:   8.818
  distance: 123 - 124:  62.020
  distance: 125 - 126:  40.199
  distance: 127 - 128:  57.200
  distance: 127 - 129:  40.561
  distance: 130 - 131:  16.926
  distance: 131 - 132:  18.116
  distance: 131 - 140:   8.352
  distance: 133 - 134:  43.638
  distance: 134 - 135:  15.865
  distance: 135 - 136:  14.214
  distance: 136 - 137:  25.231
  distance: 137 - 138:   3.795
  distance: 137 - 139:   6.646
  distance: 140 - 141:  10.923
  distance: 141 - 142:   8.021
  distance: 141 - 144:  65.082
  distance: 142 - 143:  18.673
  distance: 142 - 151:  21.478
  distance: 145 - 146:  40.057
  distance: 145 - 147:  27.897
  distance: 146 - 148:  17.939
  distance: 147 - 149:  32.142
  distance: 148 - 150:  39.297
  distance: 149 - 150:  25.567
  distance: 151 - 152:  10.826
  distance: 152 - 153:  10.613
  distance: 152 - 155:  38.368
  distance: 153 - 154:   6.952
  distance: 153 - 165:  29.102
  distance: 154 - 179:  26.144
  distance: 155 - 156:  41.734
  distance: 156 - 157:  47.902
  distance: 156 - 158:  33.135
  distance: 157 - 159:  23.761
  distance: 158 - 160:  15.412
  distance: 158 - 161:   6.288
  distance: 159 - 160:   3.769
  distance: 160 - 162:  20.622
  distance: 161 - 163:  29.329
  distance: 162 - 164:  22.899
  distance: 163 - 164:  35.629