Starting phenix.real_space_refine
on Tue Jul 29 14:53:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zrj_14916/07_2025/7zrj_14916.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zrj_14916/07_2025/7zrj_14916.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2025/7zrj_14916.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2025/7zrj_14916.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2025/7zrj_14916.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2025/7zrj_14916.cif"
  }
  resolution = 3.7
  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=   0.001 sd=   0.005
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: 6
    Type Number    sf(0)   Gaussians
     K       7      8.98       5
     P       5      5.49       5
     S      62      5.16       5
     C    7120      2.51       5
     N    1821      2.21       5
     O    1994      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11009
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4155
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 25, 'TRANS': 531}
    Chain: "C"
      Number of atoms: 1431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1431
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 13, 'TRANS': 176}
    Chain: "D"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 200
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "B"
      Number of atoms: 5016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 5016
          Classifications: {'peptide': 675}
          Link IDs: {'PTRANS': 26, 'TRANS': 648}
    Chain: "A"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 206
          Unusual residues: {'  K': 6, 'CDL': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'  K': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.98, per 1000 atoms: 0.63
  Number of scatterers: 11009
  At special positions: 0
  Unit cell: (98.164, 112.332, 153.824, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       7     19.00
     S      62     16.00
     P       5     15.00
     O    1994      8.00
     N    1821      7.00
     C    7120      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.84
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2636

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 10 sheets defined
      62.8% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 32
      Proline residue:  A  22  - end of helix
      removed outlier: 3.624A  pdb=" N   SER A  25 " --> pdb=" O   ARG A  21 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLY A  26 " --> pdb=" O   PRO A  22 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ARG A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 51
      removed outlier: 3.898A  pdb=" N   ARG A  48 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ALA A  49 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 82
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 125 through 131
      removed outlier: 3.742A  pdb=" N   GLN A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 157
      removed outlier: 3.576A  pdb=" N   GLN A 136 " --> pdb=" O   GLY A 132 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ALA A 141 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 179 through 193
    Processing helix  chain 'A' and resid 218 through 228
      removed outlier: 3.791A  pdb=" N   GLN A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 274
      removed outlier: 4.606A  pdb=" N   ILE A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      Proline residue:  A 263  - end of helix
      removed outlier: 3.838A  pdb=" N   MET A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 305
      removed outlier: 4.023A  pdb=" N   LEU A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.914A  pdb=" N   ALA A 311 " --> pdb=" O   PRO A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.533A  pdb=" N   PHE A 354 " --> pdb=" O   HIS A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 368
      removed outlier: 3.788A  pdb=" N   VAL A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 377 through 399
      removed outlier: 3.688A  pdb=" N   TYR A 381 " --> pdb=" O   GLY A 377 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   MET A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   PHE A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 435
      removed outlier: 4.650A  pdb=" N   LEU A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.797A  pdb=" N   ARG A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
      removed outlier: 4.064A  pdb=" N   PHE A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 495
    Processing helix  chain 'A' and resid 496 through 510
      removed outlier: 4.020A  pdb=" N   SER A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LYS A 510 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 538
    Processing helix  chain 'A' and resid 543 through 549
      removed outlier: 4.165A  pdb=" N   LEU A 549 " --> pdb=" O   PRO A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 556
    Processing helix  chain 'C' and resid 3 through 19
    Processing helix  chain 'C' and resid 21 through 34
      removed outlier: 3.535A  pdb=" N   TRP C  32 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 39
    Processing helix  chain 'C' and resid 91 through 109
    Processing helix  chain 'C' and resid 133 through 140
      removed outlier: 3.910A  pdb=" N   GLN C 140 " --> pdb=" O   ALA C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 149
    Processing helix  chain 'C' and resid 151 through 162
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'D' and resid 5 through 25
    Processing helix  chain 'B' and resid 14 through 22
    Processing helix  chain 'B' and resid 26 through 30
    Processing helix  chain 'B' and resid 33 through 56
      removed outlier: 4.200A  pdb=" N   VAL B  39 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 99
      removed outlier: 4.108A  pdb=" N   GLY B  99 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 160
    Processing helix  chain 'B' and resid 198 through 210
    Processing helix  chain 'B' and resid 215 through 246
      removed outlier: 4.403A  pdb=" N   TRP B 240 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      Proline residue:  B 241  - end of helix
      removed outlier: 3.718A  pdb=" N   GLY B 246 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 263
    Processing helix  chain 'B' and resid 264 through 271
    Processing helix  chain 'B' and resid 272 through 285
      removed outlier: 5.977A  pdb=" N   GLY B 278 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 300
    Processing helix  chain 'B' and resid 307 through 311
      removed outlier: 3.578A  pdb=" N   GLY B 310 " --> pdb=" O   ASN B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 342
    Processing helix  chain 'B' and resid 346 through 360
    Processing helix  chain 'B' and resid 397 through 408
    Processing helix  chain 'B' and resid 413 through 427
      removed outlier: 4.143A  pdb=" N   ASP B 417 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 463
    Processing helix  chain 'B' and resid 474 through 484
    Processing helix  chain 'B' and resid 495 through 509
    Processing helix  chain 'B' and resid 522 through 529
    Processing helix  chain 'B' and resid 539 through 546
    Processing helix  chain 'B' and resid 554 through 556
      No H-bonds generated for 'chain 'B' and resid 554 through 556'
    Processing helix  chain 'B' and resid 557 through 582
      removed outlier: 3.621A  pdb=" N   LEU B 569 " --> pdb=" O   GLY B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 595
      Proline residue:  B 592  - end of helix
    Processing helix  chain 'B' and resid 599 through 605
      removed outlier: 4.135A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 637
      removed outlier: 3.782A  pdb=" N   ILE B 617 " --> pdb=" O   PRO B 613 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   LEU B 618 " --> pdb=" O   ASP B 614 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      Proline residue:  B 633  - end of helix
    Processing helix  chain 'B' and resid 645 through 661
      removed outlier: 4.372A  pdb=" N   LEU B 659 " --> pdb=" O   TRP B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 680
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205
    Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44
      removed outlier: 3.874A  pdb=" N   GLY C  51 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132
    Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 134
    Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139
    Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 155
      removed outlier: 6.103A  pdb=" N   VAL B 153 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ALA B 163 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU B 155 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLU B 161 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 289
    Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491
      removed outlier: 6.670A  pdb=" N   THR B 467 " --> pdb=" O   ASP B 489 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   LEU B 491 " --> pdb=" O   THR B 467 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   MET B 469 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 393 through 396
      removed outlier: 6.262A  pdb=" N   VAL B 433 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU B 435 " --> pdb=" O   ARG B 438 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ARG B 438 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)

    637 hydrogen bonds defined for protein.
    1869 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: 5.23

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1859
        1.32 -     1.45: 2669
        1.45 -     1.57: 6548
        1.57 -     1.69: 12
        1.69 -     1.82: 112
  Bond restraints: 11200
  Sorted by residual:
  bond pdb=" OA3 CDL A 607 "
       pdb=" PA1 CDL A 607 "
    ideal  model  delta    sigma   weight residual
    1.529  1.502  0.027 1.00e-02 1.00e+04 7.20e+00
  bond pdb=" OA3 CDL A 608 "
       pdb=" PA1 CDL A 608 "
    ideal  model  delta    sigma   weight residual
    1.529  1.503  0.026 1.00e-02 1.00e+04 6.95e+00
  bond pdb=" N   ASP C 111 "
       pdb=" CA  ASP C 111 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.034 1.31e-02 5.83e+03 6.86e+00
  bond pdb=" OB3 CDL A 608 "
       pdb=" PB2 CDL A 608 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.27e+00
  bond pdb=" OB3 CDL A 607 "
       pdb=" PB2 CDL A 607 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.11e+00
  ... (remaining 11195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 14796
        2.14 -     4.29: 313
        4.29 -     6.43: 63
        6.43 -     8.57: 19
        8.57 -    10.72: 6
  Bond angle restraints: 15197
  Sorted by residual:
  angle pdb=" C   GLY A  83 "
        pdb=" N   GLN A  84 "
        pdb=" CA  GLN A  84 "
      ideal   model   delta    sigma   weight residual
     121.54  130.84   -9.30 1.91e+00 2.74e-01 2.37e+01
  angle pdb=" N   GLU B 544 "
        pdb=" CA  GLU B 544 "
        pdb=" CB  GLU B 544 "
      ideal   model   delta    sigma   weight residual
     110.28  117.15   -6.87 1.55e+00 4.16e-01 1.96e+01
  angle pdb=" CA  GLU B 544 "
        pdb=" CB  GLU B 544 "
        pdb=" CG  GLU B 544 "
      ideal   model   delta    sigma   weight residual
     114.10  122.69   -8.59 2.00e+00 2.50e-01 1.84e+01
  angle pdb=" CB  MET A 227 "
        pdb=" CG  MET A 227 "
        pdb=" SD  MET A 227 "
      ideal   model   delta    sigma   weight residual
     112.70  123.42  -10.72 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" CA  TYR A 381 "
        pdb=" CB  TYR A 381 "
        pdb=" CG  TYR A 381 "
      ideal   model   delta    sigma   weight residual
     113.90  120.24   -6.34 1.80e+00 3.09e-01 1.24e+01
  ... (remaining 15192 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 5880
       17.26 -    34.51: 636
       34.51 -    51.77: 156
       51.77 -    69.02: 45
       69.02 -    86.28: 15
  Dihedral angle restraints: 6732
    sinusoidal: 2629
      harmonic: 4103
  Sorted by residual:
  dihedral pdb=" CA  ALA A 470 "
           pdb=" C   ALA A 470 "
           pdb=" N   PHE A 471 "
           pdb=" CA  PHE A 471 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.28   28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  PHE A 373 "
           pdb=" C   PHE A 373 "
           pdb=" N   GLY A 374 "
           pdb=" CA  GLY A 374 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.42  -20.58     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  ILE B 656 "
           pdb=" C   ILE B 656 "
           pdb=" N   TYR B 657 "
           pdb=" CA  TYR B 657 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.57  -19.43     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 6729 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1433
       0.058 -    0.116: 332
       0.116 -    0.174: 39
       0.174 -    0.233: 3
       0.233 -    0.291: 3
  Chirality restraints: 1810
  Sorted by residual:
  chirality pdb=" CG  LEU A 170 "
            pdb=" CB  LEU A 170 "
            pdb=" CD1 LEU A 170 "
            pdb=" CD2 LEU A 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CB  ILE B 386 "
            pdb=" CA  ILE B 386 "
            pdb=" CG1 ILE B 386 "
            pdb=" CG2 ILE B 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CB  VAL C 175 "
            pdb=" CA  VAL C 175 "
            pdb=" CG1 VAL C 175 "
            pdb=" CG2 VAL C 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1807 not shown)

  Planarity restraints: 1908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 153 "    0.011 2.00e-02 2.50e+03   2.33e-02 5.45e+00
        pdb=" CD  GLU C 153 "   -0.040 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 153 "    0.015 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 153 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 116 "    0.037 5.00e-02 4.00e+02   5.68e-02 5.16e+00
        pdb=" N   PRO C 117 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 117 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 117 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 133 "   -0.036 5.00e-02 4.00e+02   5.51e-02 4.85e+00
        pdb=" N   PRO C 134 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C 134 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 134 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1905 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.77: 2044
        2.77 -     3.36: 12829
        3.36 -     3.96: 21825
        3.96 -     4.55: 30073
        4.55 -     5.14: 44847
  Nonbonded interactions: 111618
  Sorted by model distance:
  nonbonded pdb=" O   ASP C 111 "
            pdb=" OD1 ASP C 111 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   LEU A 541 "
            pdb=" OH  TYR B 587 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   THR A 248 "
            pdb=" OG1 THR A 251 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   SER A 119 "
            pdb=" OG1 THR A 123 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   PRO C  23 "
            pdb=" OG1 THR C  27 "
     model   vdw
     2.296 3.040
  ... (remaining 111613 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     29.740
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
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   0.043  11200  Z= 0.199
  Angle     :  0.804  10.716  15197  Z= 0.406
  Chirality :  0.049   0.291   1810
  Planarity :  0.005   0.057   1908
  Dihedral  : 16.082  86.276   4096
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.20), residues: 1438
  helix: -0.15 (0.17), residues: 859
  sheet: -1.55 (0.79), residues: 35
  loop : -1.80 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 115 
 HIS   0.002   0.001   HIS B 563 
 PHE   0.030   0.002   PHE C  34 
 TYR   0.029   0.002   TYR A 381 
 ARG   0.009   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10175 (  637)
  hydrogen bonds       : angle       5.27452 ( 1869)
  covalent geometry    : bond        0.00391 (11200)
  covalent geometry    : angle       0.80405 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.513 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7393 (m100) cc_final: 0.7135 (m100)
REVERT: A  412 ARG cc_start: 0.6980 (mmt180) cc_final: 0.6656 (mmt180)
REVERT: B  303 VAL cc_start: 0.8514 (t) cc_final: 0.8105 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2514
  time to fit residues: 61.4378
Evaluate side-chains
  129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    9.9990
   chunk 108 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 112 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 129 optimal weight:    7.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
A 466 ASN
A 467 ASN
A 513 GLN
** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.118799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.089153 restraints weight = 21126.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.089212 restraints weight = 12294.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.090405 restraints weight = 10468.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  11200  Z= 0.203
  Angle     :  0.633  10.018  15197  Z= 0.321
  Chirality :  0.043   0.142   1810
  Planarity :  0.004   0.044   1908
  Dihedral  : 11.021  86.914   1714
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.25 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.22), residues: 1438
  helix:  0.65 (0.18), residues: 866
  sheet: -1.52 (0.71), residues: 49
  loop : -1.60 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 655 
 HIS   0.004   0.001   HIS A 451 
 PHE   0.020   0.002   PHE A 373 
 TYR   0.021   0.002   TYR B 657 
 ARG   0.004   0.000   ARG B 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04170 (  637)
  hydrogen bonds       : angle       4.61086 ( 1869)
  covalent geometry    : bond        0.00475 (11200)
  covalent geometry    : angle       0.63273 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 1.837 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7602 (m100) cc_final: 0.7329 (m100)
REVERT: B  469 MET cc_start: 0.7586 (ttt) cc_final: 0.7152 (mtp)
  outliers start: 16
  outliers final: 11
  residues processed: 140
  average time/residue: 0.2585
  time to fit residues: 54.3755
Evaluate side-chains
  133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  629 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 119 optimal weight:   30.0000
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0980
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 107 optimal weight:    7.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C 157 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.121272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.092005 restraints weight = 21382.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.093054 restraints weight = 11592.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.093693 restraints weight = 8675.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11200  Z= 0.117
  Angle     :  0.552   7.880  15197  Z= 0.277
  Chirality :  0.041   0.224   1810
  Planarity :  0.004   0.044   1908
  Dihedral  : 10.420  86.650   1714
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.16 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.22), residues: 1438
  helix:  1.04 (0.18), residues: 866
  sheet: -1.27 (0.71), residues: 51
  loop : -1.49 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 115 
 HIS   0.004   0.001   HIS A 451 
 PHE   0.013   0.001   PHE B 173 
 TYR   0.021   0.002   TYR A 381 
 ARG   0.004   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (  637)
  hydrogen bonds       : angle       4.30548 ( 1869)
  covalent geometry    : bond        0.00260 (11200)
  covalent geometry    : angle       0.55232 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 1.941 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7525 (m100) cc_final: 0.7280 (m100)
REVERT: A  445 MET cc_start: 0.7704 (mmt) cc_final: 0.7117 (mmt)
REVERT: C   93 GLU cc_start: 0.8237 (tp30) cc_final: 0.8002 (tp30)
REVERT: B  469 MET cc_start: 0.7555 (ttt) cc_final: 0.7182 (mtp)
  outliers start: 15
  outliers final: 6
  residues processed: 144
  average time/residue: 0.2304
  time to fit residues: 50.0494
Evaluate side-chains
  127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  526 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 131 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 106 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 112 optimal weight:    0.6980
   chunk 126 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   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 447 ASN
C 157 GLN
B 603 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.121676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.092663 restraints weight = 21114.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.093539 restraints weight = 12359.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.093732 restraints weight = 9595.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11200  Z= 0.109
  Angle     :  0.544  10.442  15197  Z= 0.271
  Chirality :  0.040   0.143   1810
  Planarity :  0.004   0.044   1908
  Dihedral  :  9.933  86.343   1714
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.10 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.23), residues: 1438
  helix:  1.17 (0.18), residues: 866
  sheet: -0.94 (0.71), residues: 49
  loop : -1.41 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.003   0.000   HIS A 451 
 PHE   0.012   0.001   PHE B 173 
 TYR   0.020   0.001   TYR A 381 
 ARG   0.004   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03453 (  637)
  hydrogen bonds       : angle       4.20269 ( 1869)
  covalent geometry    : bond        0.00241 (11200)
  covalent geometry    : angle       0.54368 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7539 (m100) cc_final: 0.7302 (m100)
REVERT: A  183 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8357 (mm)
REVERT: A  187 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8827 (mm)
REVERT: A  445 MET cc_start: 0.7772 (mmt) cc_final: 0.7146 (mmt)
REVERT: B  469 MET cc_start: 0.7447 (ttt) cc_final: 0.7195 (mtp)
REVERT: B  518 ASP cc_start: 0.6269 (p0) cc_final: 0.6031 (p0)
  outliers start: 22
  outliers final: 9
  residues processed: 143
  average time/residue: 0.1949
  time to fit residues: 42.3863
Evaluate side-chains
  136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  603 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 107 optimal weight:   20.0000
   chunk 104 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 138 optimal weight:    0.5980
   chunk 137 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 141 optimal weight:    3.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 603 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.120276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.092037 restraints weight = 21105.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.092344 restraints weight = 12921.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.092392 restraints weight = 10912.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11200  Z= 0.140
  Angle     :  0.571  13.728  15197  Z= 0.285
  Chirality :  0.041   0.149   1810
  Planarity :  0.004   0.043   1908
  Dihedral  :  9.674  84.220   1714
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.15 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.23), residues: 1438
  helix:  1.21 (0.18), residues: 862
  sheet: -0.73 (0.73), residues: 49
  loop : -1.35 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 115 
 HIS   0.002   0.001   HIS A 451 
 PHE   0.013   0.001   PHE B 173 
 TYR   0.019   0.002   TYR A 381 
 ARG   0.004   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03580 (  637)
  hydrogen bonds       : angle       4.25459 ( 1869)
  covalent geometry    : bond        0.00325 (11200)
  covalent geometry    : angle       0.57109 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 2.923 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7551 (m100) cc_final: 0.7334 (m100)
REVERT: A  187 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8869 (mm)
REVERT: A  445 MET cc_start: 0.8074 (mmt) cc_final: 0.7277 (mmt)
REVERT: C   93 GLU cc_start: 0.8134 (tp30) cc_final: 0.7891 (tp30)
REVERT: C  128 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8943 (pp)
REVERT: B  518 ASP cc_start: 0.6258 (p0) cc_final: 0.6014 (p0)
  outliers start: 26
  outliers final: 12
  residues processed: 147
  average time/residue: 0.2315
  time to fit residues: 51.7343
Evaluate side-chains
  136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  549 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 136 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0270
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 121 optimal weight:    3.9990
   chunk 90 optimal weight:   20.0000
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   chunk 119 optimal weight:   40.0000
   chunk 134 optimal weight:    0.0040
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.4850

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

Flipped N/Q/H residues before XYZ refinement:
C 157 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.122705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.093868 restraints weight = 21142.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.094217 restraints weight = 12374.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.095225 restraints weight = 9559.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11200  Z= 0.101
  Angle     :  0.551  14.115  15197  Z= 0.271
  Chirality :  0.040   0.147   1810
  Planarity :  0.004   0.043   1908
  Dihedral  :  9.146  85.144   1714
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.77 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.23), residues: 1438
  helix:  1.30 (0.18), residues: 864
  sheet: -0.56 (0.74), residues: 49
  loop : -1.33 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.002   0.000   HIS A 451 
 PHE   0.012   0.001   PHE B 173 
 TYR   0.021   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03301 (  637)
  hydrogen bonds       : angle       4.12674 ( 1869)
  covalent geometry    : bond        0.00217 (11200)
  covalent geometry    : angle       0.55087 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.608 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7517 (m100) cc_final: 0.7294 (m100)
REVERT: A  187 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8790 (mm)
REVERT: A  445 MET cc_start: 0.7953 (mmt) cc_final: 0.7264 (mmt)
REVERT: C   93 GLU cc_start: 0.8189 (tp30) cc_final: 0.7903 (tp30)
REVERT: C  128 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8875 (pp)
REVERT: B  383 MET cc_start: 0.6391 (ttt) cc_final: 0.5188 (tmm)
REVERT: B  518 ASP cc_start: 0.6275 (p0) cc_final: 0.6046 (p0)
  outliers start: 17
  outliers final: 9
  residues processed: 141
  average time/residue: 0.2914
  time to fit residues: 62.6606
Evaluate side-chains
  134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  549 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 124 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 117 optimal weight:   20.0000
   chunk 55 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.121387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.094281 restraints weight = 21444.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.094065 restraints weight = 13520.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.094168 restraints weight = 12269.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11200  Z= 0.124
  Angle     :  0.566  14.270  15197  Z= 0.279
  Chirality :  0.040   0.146   1810
  Planarity :  0.004   0.043   1908
  Dihedral  :  8.983  83.407   1714
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.77 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.23), residues: 1438
  helix:  1.30 (0.18), residues: 864
  sheet: -0.48 (0.73), residues: 49
  loop : -1.31 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 115 
 HIS   0.002   0.000   HIS A 451 
 PHE   0.013   0.001   PHE B 173 
 TYR   0.018   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  637)
  hydrogen bonds       : angle       4.16400 ( 1869)
  covalent geometry    : bond        0.00284 (11200)
  covalent geometry    : angle       0.56591 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 2.016 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7556 (m100) cc_final: 0.7309 (m100)
REVERT: A  187 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8789 (mm)
REVERT: A  445 MET cc_start: 0.8021 (mmt) cc_final: 0.7399 (mmt)
REVERT: C   93 GLU cc_start: 0.8230 (tp30) cc_final: 0.7950 (tp30)
REVERT: C  128 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8925 (pp)
REVERT: B  392 MET cc_start: 0.5289 (tmm) cc_final: 0.5043 (tmm)
REVERT: B  518 ASP cc_start: 0.6263 (p0) cc_final: 0.5982 (p0)
  outliers start: 21
  outliers final: 13
  residues processed: 143
  average time/residue: 0.2493
  time to fit residues: 54.5561
Evaluate side-chains
  139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  484 GLU
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  549 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 92 optimal weight:    0.0060
   chunk 29 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 129 optimal weight:    5.9990
   chunk 98 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9990
   chunk 123 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 157 GLN
B 603 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.121748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.094758 restraints weight = 21119.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.094257 restraints weight = 13659.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.094878 restraints weight = 11976.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11200  Z= 0.109
  Angle     :  0.571  15.036  15197  Z= 0.276
  Chirality :  0.040   0.143   1810
  Planarity :  0.004   0.043   1908
  Dihedral  :  8.788  83.170   1714
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.95 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.23), residues: 1438
  helix:  1.33 (0.18), residues: 864
  sheet: -0.42 (0.73), residues: 49
  loop : -1.28 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 115 
 HIS   0.002   0.000   HIS A 451 
 PHE   0.012   0.001   PHE B 173 
 TYR   0.020   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (  637)
  hydrogen bonds       : angle       4.10837 ( 1869)
  covalent geometry    : bond        0.00244 (11200)
  covalent geometry    : angle       0.57082 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 1.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7527 (m100) cc_final: 0.7289 (m100)
REVERT: A  187 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8738 (mm)
REVERT: A  445 MET cc_start: 0.8022 (mmt) cc_final: 0.7376 (mmt)
REVERT: C   93 GLU cc_start: 0.8236 (tp30) cc_final: 0.7896 (tp30)
REVERT: B  383 MET cc_start: 0.6173 (ttt) cc_final: 0.4998 (tmm)
REVERT: B  392 MET cc_start: 0.5259 (tmm) cc_final: 0.4995 (tmm)
REVERT: B  518 ASP cc_start: 0.6213 (p0) cc_final: 0.5954 (p0)
  outliers start: 23
  outliers final: 15
  residues processed: 149
  average time/residue: 0.2605
  time to fit residues: 59.7576
Evaluate side-chains
  141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 1.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  484 GLU
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  587 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 112 optimal weight:   30.0000
   chunk 102 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 138 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 61 optimal weight:    0.2980
   chunk 121 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 465 ASN
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.122102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.095998 restraints weight = 21152.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.095151 restraints weight = 15603.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.095540 restraints weight = 13943.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11200  Z= 0.111
  Angle     :  0.581  15.149  15197  Z= 0.282
  Chirality :  0.041   0.149   1810
  Planarity :  0.004   0.043   1908
  Dihedral  :  8.683  82.500   1714
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 16.12 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.23), residues: 1438
  helix:  1.30 (0.18), residues: 865
  sheet: -0.31 (0.74), residues: 49
  loop : -1.29 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 115 
 HIS   0.002   0.000   HIS C  66 
 PHE   0.012   0.001   PHE B 173 
 TYR   0.020   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03361 (  637)
  hydrogen bonds       : angle       4.14056 ( 1869)
  covalent geometry    : bond        0.00250 (11200)
  covalent geometry    : angle       0.58144 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7498 (m100) cc_final: 0.7256 (m100)
REVERT: A  187 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8743 (mm)
REVERT: A  445 MET cc_start: 0.8059 (mmt) cc_final: 0.7384 (mmt)
REVERT: C   93 GLU cc_start: 0.8247 (tp30) cc_final: 0.8040 (tp30)
REVERT: B  383 MET cc_start: 0.5976 (ttt) cc_final: 0.4918 (tmm)
REVERT: B  392 MET cc_start: 0.5376 (tmm) cc_final: 0.5104 (tmm)
REVERT: B  518 ASP cc_start: 0.6091 (p0) cc_final: 0.5826 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 143
  average time/residue: 0.2334
  time to fit residues: 51.1657
Evaluate side-chains
  142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  484 GLU
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  587 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 122 optimal weight:    0.0670
   chunk 64 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0970
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9920

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

Flipped N/Q/H residues before XYZ refinement:
** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.121555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.095527 restraints weight = 21269.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.094404 restraints weight = 16760.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.094631 restraints weight = 15196.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11200  Z= 0.119
  Angle     :  0.585  15.169  15197  Z= 0.283
  Chirality :  0.041   0.146   1810
  Planarity :  0.004   0.043   1908
  Dihedral  :  8.627  81.068   1714
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.48 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.23), residues: 1438
  helix:  1.26 (0.18), residues: 864
  sheet: -0.32 (0.75), residues: 49
  loop : -1.27 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.002   0.000   HIS C  66 
 PHE   0.014   0.001   PHE C  34 
 TYR   0.020   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  637)
  hydrogen bonds       : angle       4.14977 ( 1869)
  covalent geometry    : bond        0.00272 (11200)
  covalent geometry    : angle       0.58520 (15197)

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

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

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2876 Ramachandran restraints generated.
    1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 2.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7511 (m100) cc_final: 0.7272 (m100)
REVERT: A  187 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8738 (mm)
REVERT: A  445 MET cc_start: 0.8200 (mmt) cc_final: 0.7428 (mmt)
REVERT: C   93 GLU cc_start: 0.8142 (tp30) cc_final: 0.7779 (tp30)
REVERT: B  383 MET cc_start: 0.5954 (ttt) cc_final: 0.4933 (tmm)
REVERT: B  392 MET cc_start: 0.5293 (tmm) cc_final: 0.5005 (tmm)
REVERT: B  518 ASP cc_start: 0.6082 (p0) cc_final: 0.5832 (p0)
  outliers start: 17
  outliers final: 15
  residues processed: 141
  average time/residue: 0.2751
  time to fit residues: 59.6234
Evaluate side-chains
  141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 2.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  484 GLU
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  587 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 74 optimal weight:   20.0000
   chunk 72 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.121561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.093712 restraints weight = 21095.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.093498 restraints weight = 13625.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.094328 restraints weight = 11497.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11200  Z= 0.124
  Angle     :  0.587  15.141  15197  Z= 0.285
  Chirality :  0.041   0.149   1810
  Planarity :  0.004   0.043   1908
  Dihedral  :  8.611  80.065   1714
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.39 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.23), residues: 1438
  helix:  1.23 (0.18), residues: 864
  sheet: -0.30 (0.74), residues: 49
  loop : -1.28 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.002   0.000   HIS C  66 
 PHE   0.018   0.001   PHE B  78 
 TYR   0.020   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  637)
  hydrogen bonds       : angle       4.16649 ( 1869)
  covalent geometry    : bond        0.00284 (11200)
  covalent geometry    : angle       0.58745 (15197)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3779.13 seconds
wall clock time: 73 minutes 8.50 seconds (4388.50 seconds total)