Starting phenix.real_space_refine
on Wed Mar 12 20:11:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iuz_60916/03_2025/9iuz_60916.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iuz_60916/03_2025/9iuz_60916.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iuz_60916/03_2025/9iuz_60916.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iuz_60916/03_2025/9iuz_60916.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iuz_60916/03_2025/9iuz_60916.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iuz_60916/03_2025/9iuz_60916.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    5286      2.51       5
     N    1443      2.21       5
     O    1555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8349
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 4171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4171
          Classifications: {'peptide': 537}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 514}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 3708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3708
          Classifications: {'peptide': 478}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 457}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 384
          Classifications: {'peptide': 46}
          Link IDs: {'TRANS': 45}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'O6E': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'O6E': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.24, per 1000 atoms: 0.63
  Number of scatterers: 8349
  At special positions: 0
  Unit cell: (73.95, 120.7, 119, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      65     16.00
     O    1555      8.00
     N    1443      7.00
     C    5286      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 952.8 milliseconds
  

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      46.1% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'B' and resid 55 through 77
      removed outlier: 3.566A  pdb=" N   GLN B  59 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   THR B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL B  63 " --> pdb=" O   GLN B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 90
    Processing helix  chain 'B' and resid 97 through 110
      removed outlier: 3.649A  pdb=" N   ILE B 101 " --> pdb=" O   PRO B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 162 through 166
    Processing helix  chain 'B' and resid 168 through 180
    Processing helix  chain 'B' and resid 223 through 247
    Processing helix  chain 'B' and resid 253 through 269
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 309 through 319
    Processing helix  chain 'B' and resid 355 through 366
    Processing helix  chain 'B' and resid 411 through 458
      removed outlier: 4.099A  pdb=" N   ARG B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TYR B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 465
      removed outlier: 3.567A  pdb=" N   ILE B 463 " --> pdb=" O   PRO B 460 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL B 464 " --> pdb=" O   ALA B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 473
    Processing helix  chain 'B' and resid 495 through 510
    Processing helix  chain 'B' and resid 520 through 525
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.512A  pdb=" N   GLY B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 560
      removed outlier: 3.568A  pdb=" N   GLU B 560 " --> pdb=" O   THR B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 592
    Processing helix  chain 'B' and resid 600 through 621
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 3.626A  pdb=" N   MET A 140 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 168 through 181
    Processing helix  chain 'A' and resid 223 through 247
      removed outlier: 3.557A  pdb=" N   SER A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE A 228 " --> pdb=" O   PRO A 224 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A 229 " --> pdb=" O   ALA A 225 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLN A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 269
    Processing helix  chain 'A' and resid 304 through 308
    Processing helix  chain 'A' and resid 309 through 319
    Processing helix  chain 'A' and resid 355 through 366
    Processing helix  chain 'A' and resid 411 through 457
      removed outlier: 3.714A  pdb=" N   GLN A 423 " --> pdb=" O   GLU A 419 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA A 424 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 457 " --> pdb=" O   ASP A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 464
      removed outlier: 3.510A  pdb=" N   ILE A 463 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 464 " --> pdb=" O   ALA A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 495 through 510
    Processing helix  chain 'A' and resid 528 through 533
      removed outlier: 3.840A  pdb=" N   LEU A 532 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 528 through 533'
    Processing helix  chain 'A' and resid 580 through 592
    Processing helix  chain 'A' and resid 600 through 621
    Processing helix  chain 'C' and resid 45 through 54
    Processing sheet with id=AA1, first strand: chain 'B' and resid 113 through 114
      removed outlier: 4.007A  pdb=" N   TYR B 133 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ALA B 122 " --> pdb=" O   ILE B 131 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   TYR B 133 " --> pdb=" O   MET B 120 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   MET B 120 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 302 through 303
      removed outlier: 3.670A  pdb=" N   TYR B 303 " --> pdb=" O   GLY B 284 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY B 284 " --> pdb=" O   TYR B 303 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   VAL B 275 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   GLU B 289 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 273 " --> pdb=" O   GLU B 289 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   MET B 394 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   GLY B 379 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   LEU B 396 " --> pdb=" O   ILE B 377 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ILE B 377 " --> pdb=" O   LEU B 396 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLY B 398 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 486 through 491
      removed outlier: 3.742A  pdb=" N   PHE B 481 " --> pdb=" O   TYR B 488 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY B 478 " --> pdb=" O   PHE B 553 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE B 549 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   MET B 539 " --> pdb=" O   THR B 518 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114
      removed outlier: 3.513A  pdb=" N   TYR A 133 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   MET A 120 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   HIS A 206 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE A 192 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303
      removed outlier: 3.626A  pdb=" N   TYR A 303 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   VAL A 275 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLU A 289 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL A 273 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   TRP A 397 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL A 375 " --> pdb=" O   TRP A 397 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LEU A 399 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   MET A 373 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   VAL A 401 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU A 371 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   HIS A 403 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ALA A 369 " --> pdb=" O   HIS A 403 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 491
      removed outlier: 3.602A  pdb=" N   GLY A 478 " --> pdb=" O   PHE A 553 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG A 554 " --> pdb=" O   GLY A 538 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 23

    451 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1957
        1.33 -     1.45: 1713
        1.45 -     1.57: 4736
        1.57 -     1.69: 0
        1.69 -     1.81: 107
  Bond restraints: 8513
  Sorted by residual:
  bond pdb=" N   ILE B 499 "
       pdb=" CA  ILE B 499 "
    ideal  model  delta    sigma   weight residual
    1.460  1.489 -0.029 1.21e-02 6.83e+03 5.81e+00
  bond pdb=" CAC O6E B1001 "
       pdb=" CAH O6E B1001 "
    ideal  model  delta    sigma   weight residual
    1.522  1.561 -0.039 2.00e-02 2.50e+03 3.81e+00
  bond pdb=" N   LEU B  87 "
       pdb=" CA  LEU B  87 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.21e-02 6.83e+03 3.51e+00
  bond pdb=" N   MET B 439 "
       pdb=" CA  MET B 439 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.21e-02 6.83e+03 3.18e+00
  bond pdb=" N   MET B 431 "
       pdb=" CA  MET B 431 "
    ideal  model  delta    sigma   weight residual
    1.459  1.479 -0.020 1.19e-02 7.06e+03 2.75e+00
  ... (remaining 8508 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 11390
        2.25 -     4.51: 113
        4.51 -     6.76: 10
        6.76 -     9.01: 3
        9.01 -    11.27: 2
  Bond angle restraints: 11518
  Sorted by residual:
  angle pdb=" CAH O6E B1001 "
        pdb=" CAC O6E B1001 "
        pdb=" CBJ O6E B1001 "
      ideal   model   delta    sigma   weight residual
     112.38  101.11   11.27 3.00e+00 1.11e-01 1.41e+01
  angle pdb=" C   GLN B 498 "
        pdb=" N   ILE B 499 "
        pdb=" CA  ILE B 499 "
      ideal   model   delta    sigma   weight residual
     120.42  115.98    4.44 1.42e+00 4.96e-01 9.76e+00
  angle pdb=" N   LYS A 546 "
        pdb=" CA  LYS A 546 "
        pdb=" C   LYS A 546 "
      ideal   model   delta    sigma   weight residual
     114.75  110.83    3.92 1.26e+00 6.30e-01 9.70e+00
  angle pdb=" CB  MET B 422 "
        pdb=" CG  MET B 422 "
        pdb=" SD  MET B 422 "
      ideal   model   delta    sigma   weight residual
     112.70  121.85   -9.15 3.00e+00 1.11e-01 9.31e+00
  angle pdb=" C   ASN B 430 "
        pdb=" N   MET B 431 "
        pdb=" CA  MET B 431 "
      ideal   model   delta    sigma   weight residual
     120.44  116.56    3.88 1.30e+00 5.92e-01 8.93e+00
  ... (remaining 11513 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4360
       18.00 -    36.00: 604
       36.00 -    53.99: 163
       53.99 -    71.99: 27
       71.99 -    89.99: 16
  Dihedral angle restraints: 5170
    sinusoidal: 2104
      harmonic: 3066
  Sorted by residual:
  dihedral pdb=" CA  LEU A 550 "
           pdb=" C   LEU A 550 "
           pdb=" N   PHE A 551 "
           pdb=" CA  PHE A 551 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.05  -18.95     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CB  GLU B  72 "
           pdb=" CG  GLU B  72 "
           pdb=" CD  GLU B  72 "
           pdb=" OE1 GLU B  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.38   87.38     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU A 504 "
           pdb=" CG  GLU A 504 "
           pdb=" CD  GLU A 504 "
           pdb=" OE1 GLU A 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.30   87.30     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 5167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 942
       0.037 -    0.075: 248
       0.075 -    0.112: 79
       0.112 -    0.150: 20
       0.150 -    0.187: 1
  Chirality restraints: 1290
  Sorted by residual:
  chirality pdb=" CG  LEU A 507 "
            pdb=" CB  LEU A 507 "
            pdb=" CD1 LEU A 507 "
            pdb=" CD2 LEU A 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" CA  ASP A 209 "
            pdb=" N   ASP A 209 "
            pdb=" C   ASP A 209 "
            pdb=" CB  ASP A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE A 377 "
            pdb=" N   ILE A 377 "
            pdb=" C   ILE A 377 "
            pdb=" CB  ILE A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1287 not shown)

  Planarity restraints: 1477
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 580 "    0.039 5.00e-02 4.00e+02   6.00e-02 5.76e+00
        pdb=" N   PRO A 581 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 505 "    0.014 2.00e-02 2.50e+03   1.44e-02 5.18e+00
        pdb=" CG  TRP A 505 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 505 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 505 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 505 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 505 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 505 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 505 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 505 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 505 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 580 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO B 581 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 581 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 581 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1474 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1306
        2.76 -     3.30: 7834
        3.30 -     3.83: 13394
        3.83 -     4.37: 14410
        4.37 -     4.90: 26089
  Nonbonded interactions: 63033
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 264 "
            pdb=" OG1 THR A 268 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   ASP B  82 "
            pdb=" OG  SER B  86 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG  SER C  45 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   LEU A 614 "
            pdb=" OG  SER A 617 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER A 495 "
            pdb=" OE1 GLN A 498 "
     model   vdw
     2.259 3.040
  ... (remaining 63028 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 111 through 144 or resid 156 through 565 or resid 577 thro \ 
ugh 621 or resid 1001))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.540
  Find NCS groups from input model:        0.290
  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:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8513  Z= 0.170
  Angle     :  0.562  11.268  11518  Z= 0.297
  Chirality :  0.039   0.187   1290
  Planarity :  0.004   0.060   1477
  Dihedral  : 18.043  89.989   3186
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 30.60 %
    Favored  : 68.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.40 (0.27), residues: 1039
  helix:  2.89 (0.25), residues: 418
  sheet:  0.13 (0.38), residues: 188
  loop : -0.70 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 505 
 HIS   0.003   0.001   HIS B 206 
 PHE   0.009   0.001   PHE C  58 
 TYR   0.019   0.001   TYR B 487 
 ARG   0.007   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 MET cc_start: 0.8585 (ttp) cc_final: 0.8323 (ttp)
REVERT: B  595 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6591 (ttp-170)
REVERT: A  159 MET cc_start: 0.7503 (mmt) cc_final: 0.7229 (tpt)
REVERT: A  266 ASP cc_start: 0.8861 (t0) cc_final: 0.8568 (t0)
REVERT: A  594 SER cc_start: 0.8005 (m) cc_final: 0.7728 (p)
REVERT: C   30 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8411 (pttm)
  outliers start: 5
  outliers final: 3
  residues processed: 135
  average time/residue: 0.1921
  time to fit residues: 36.0372
Evaluate side-chains
  124 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  514 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0040
   chunk 60 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   overall best weight:    1.9998

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 HIS
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 GLN
A 318 GLN
A 336 GLN
A 358 HIS
A 403 HIS
** C  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.137700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.102911 restraints weight = 13666.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 3.84
r_work: 0.3371 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8513  Z= 0.262
  Angle     :  0.574   7.802  11518  Z= 0.295
  Chirality :  0.041   0.144   1290
  Planarity :  0.004   0.058   1477
  Dihedral  :  5.438  70.729   1232
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 26.39 %
    Favored  : 70.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.19 (0.27), residues: 1039
  helix:  2.70 (0.25), residues: 426
  sheet: -0.12 (0.38), residues: 192
  loop : -0.79 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 505 
 HIS   0.004   0.001   HIS B 302 
 PHE   0.008   0.002   PHE B 314 
 TYR   0.017   0.002   TYR B 487 
 ARG   0.004   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 MET cc_start: 0.8634 (ttp) cc_final: 0.8233 (ttp)
REVERT: B  595 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6535 (ttp-170)
REVERT: A  266 ASP cc_start: 0.9329 (t0) cc_final: 0.8987 (t0)
REVERT: A  368 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8010 (mm)
REVERT: A  416 TYR cc_start: 0.8005 (m-80) cc_final: 0.7792 (m-80)
REVERT: A  594 SER cc_start: 0.8547 (m) cc_final: 0.8046 (p)
REVERT: A  604 MET cc_start: 0.9072 (mmt) cc_final: 0.8867 (mmt)
REVERT: A  605 ASP cc_start: 0.9248 (m-30) cc_final: 0.9040 (m-30)
REVERT: C   30 LYS cc_start: 0.8313 (ttpt) cc_final: 0.8036 (ttpt)
REVERT: C   32 GLN cc_start: 0.8304 (tt0) cc_final: 0.8047 (tp40)
  outliers start: 31
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1973
  time to fit residues: 40.9922
Evaluate side-chains
  133 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  584 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
A 188 ASN
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.140157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105922 restraints weight = 13667.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.79
r_work: 0.3412 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8513  Z= 0.157
  Angle     :  0.516   7.856  11518  Z= 0.263
  Chirality :  0.039   0.147   1290
  Planarity :  0.004   0.057   1477
  Dihedral  :  4.915  70.305   1226
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 26.83 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.39 (0.27), residues: 1039
  helix:  2.92 (0.25), residues: 425
  sheet:  0.05 (0.38), residues: 188
  loop : -0.78 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.006   0.001   PHE B 117 
 TYR   0.014   0.001   TYR B 487 
 ARG   0.005   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 MET cc_start: 0.8544 (ttp) cc_final: 0.8274 (ttp)
REVERT: B  595 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.6406 (ttp-170)
REVERT: A  303 TYR cc_start: 0.8953 (p90) cc_final: 0.8552 (p90)
REVERT: A  368 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7970 (mm)
REVERT: A  594 SER cc_start: 0.8467 (m) cc_final: 0.7963 (p)
REVERT: A  605 ASP cc_start: 0.9255 (m-30) cc_final: 0.8982 (m-30)
REVERT: A  618 PHE cc_start: 0.6866 (m-80) cc_final: 0.6659 (m-80)
REVERT: C   30 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7990 (ttpt)
REVERT: C   32 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7951 (tp40)
  outliers start: 24
  outliers final: 11
  residues processed: 143
  average time/residue: 0.2669
  time to fit residues: 53.5550
Evaluate side-chains
  131 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  258 ASP
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  584 SER
Chi-restraints excluded: chain C residue   32 GLN
Chi-restraints excluded: chain C residue   45 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 11 optimal weight:    0.4980
   chunk 77 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.138370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.103588 restraints weight = 13699.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 3.85
r_work: 0.3373 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8513  Z= 0.207
  Angle     :  0.540   7.951  11518  Z= 0.270
  Chirality :  0.039   0.174   1290
  Planarity :  0.004   0.056   1477
  Dihedral  :  5.098  72.307   1226
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 26.16 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.38 (0.27), residues: 1039
  helix:  2.89 (0.25), residues: 426
  sheet: -0.06 (0.38), residues: 196
  loop : -0.73 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.009   0.001   PHE A 551 
 TYR   0.021   0.001   TYR B 487 
 ARG   0.006   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 MET cc_start: 0.7824 (mtt) cc_final: 0.7525 (ttm)
REVERT: B  365 MET cc_start: 0.8582 (ttp) cc_final: 0.8276 (ttp)
REVERT: B  498 GLN cc_start: 0.9270 (mt0) cc_final: 0.9061 (mt0)
REVERT: B  499 ILE cc_start: 0.9149 (mm) cc_final: 0.8942 (mm)
REVERT: B  595 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.6396 (ttp-170)
REVERT: A  303 TYR cc_start: 0.8971 (p90) cc_final: 0.8472 (p90)
REVERT: A  368 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7984 (mm)
REVERT: A  471 MET cc_start: 0.8291 (mtp) cc_final: 0.8071 (mtp)
REVERT: A  594 SER cc_start: 0.8489 (m) cc_final: 0.7997 (p)
REVERT: A  605 ASP cc_start: 0.9275 (m-30) cc_final: 0.8990 (m-30)
REVERT: C   30 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7899 (ttpt)
REVERT: C   32 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8000 (tp40)
  outliers start: 29
  outliers final: 17
  residues processed: 148
  average time/residue: 0.1958
  time to fit residues: 40.5160
Evaluate side-chains
  142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  342 GLN
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  584 SER
Chi-restraints excluded: chain C residue   32 GLN
Chi-restraints excluded: chain C residue   45 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
C  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.139562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.105095 restraints weight = 13566.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 3.79
r_work: 0.3399 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8513  Z= 0.162
  Angle     :  0.535   8.755  11518  Z= 0.266
  Chirality :  0.039   0.182   1290
  Planarity :  0.004   0.056   1477
  Dihedral  :  5.057  73.663   1226
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 26.72 %
    Favored  : 70.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.48 (0.28), residues: 1039
  helix:  2.95 (0.25), residues: 426
  sheet: -0.05 (0.37), residues: 205
  loop : -0.62 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.007   0.001   PHE A 551 
 TYR   0.020   0.001   TYR B 487 
 ARG   0.006   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 MET cc_start: 0.7870 (mtt) cc_final: 0.7543 (ttm)
REVERT: B  365 MET cc_start: 0.8586 (ttp) cc_final: 0.8354 (ttp)
REVERT: B  498 GLN cc_start: 0.9274 (mt0) cc_final: 0.9043 (mt0)
REVERT: B  499 ILE cc_start: 0.9307 (mm) cc_final: 0.9059 (mm)
REVERT: B  595 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6479 (ttp-170)
REVERT: A  303 TYR cc_start: 0.8950 (p90) cc_final: 0.8476 (p90)
REVERT: A  368 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7957 (mm)
REVERT: A  594 SER cc_start: 0.8506 (m) cc_final: 0.8019 (p)
REVERT: A  605 ASP cc_start: 0.9273 (m-30) cc_final: 0.9023 (m-30)
REVERT: A  618 PHE cc_start: 0.6764 (m-80) cc_final: 0.6546 (m-80)
REVERT: C   30 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7933 (ttpp)
  outliers start: 29
  outliers final: 17
  residues processed: 145
  average time/residue: 0.1961
  time to fit residues: 40.3311
Evaluate side-chains
  140 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  342 GLN
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  584 SER
Chi-restraints excluded: chain C residue   45 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 82 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 115 GLN
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.138729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.104022 restraints weight = 13767.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 3.80
r_work: 0.3402 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8513  Z= 0.193
  Angle     :  0.543   8.452  11518  Z= 0.270
  Chirality :  0.039   0.160   1290
  Planarity :  0.004   0.054   1477
  Dihedral  :  5.193  73.654   1226
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 27.49 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.45 (0.27), residues: 1039
  helix:  2.93 (0.25), residues: 426
  sheet: -0.04 (0.37), residues: 205
  loop : -0.67 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.008   0.001   PHE A 551 
 TYR   0.022   0.001   TYR B 487 
 ARG   0.007   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 MET cc_start: 0.7900 (mtt) cc_final: 0.7577 (ttm)
REVERT: B  365 MET cc_start: 0.8605 (ttp) cc_final: 0.8356 (ttp)
REVERT: B  498 GLN cc_start: 0.9268 (mt0) cc_final: 0.9035 (mt0)
REVERT: B  595 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.6452 (ttp-170)
REVERT: A  303 TYR cc_start: 0.8970 (p90) cc_final: 0.8588 (p90)
REVERT: A  368 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7955 (mm)
REVERT: A  594 SER cc_start: 0.8549 (m) cc_final: 0.8066 (p)
REVERT: A  605 ASP cc_start: 0.9285 (m-30) cc_final: 0.8940 (m-30)
REVERT: C   28 LEU cc_start: 0.7686 (mp) cc_final: 0.7462 (mp)
REVERT: C   30 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7894 (ttpt)
  outliers start: 30
  outliers final: 19
  residues processed: 148
  average time/residue: 0.1945
  time to fit residues: 40.5591
Evaluate side-chains
  142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  342 GLN
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  402 CYS
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain B residue  614 LEU
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  584 SER
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   45 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0050
   chunk 92 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
C  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.140461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.106309 restraints weight = 13714.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 3.79
r_work: 0.3432 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8513  Z= 0.153
  Angle     :  0.533   8.541  11518  Z= 0.266
  Chirality :  0.039   0.154   1290
  Planarity :  0.004   0.055   1477
  Dihedral  :  5.124  74.618   1226
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 29.05 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.27), residues: 1039
  helix:  2.99 (0.25), residues: 426
  sheet:  0.01 (0.37), residues: 205
  loop : -0.64 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.011   0.001   PHE A 551 
 TYR   0.021   0.001   TYR B 487 
 ARG   0.006   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 MET cc_start: 0.8625 (ttp) cc_final: 0.8387 (ttp)
REVERT: B  498 GLN cc_start: 0.9234 (mt0) cc_final: 0.8919 (mp10)
REVERT: B  595 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.6527 (ttp-170)
REVERT: A  303 TYR cc_start: 0.8925 (p90) cc_final: 0.8549 (p90)
REVERT: A  594 SER cc_start: 0.8516 (m) cc_final: 0.8019 (p)
REVERT: A  605 ASP cc_start: 0.9258 (m-30) cc_final: 0.8904 (m-30)
REVERT: C   30 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8006 (ttpt)
  outliers start: 26
  outliers final: 15
  residues processed: 140
  average time/residue: 0.2115
  time to fit residues: 41.7952
Evaluate side-chains
  135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  402 CYS
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain C residue   27 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 95 optimal weight:    0.4980
   chunk 47 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.140822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.106456 restraints weight = 13823.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 3.81
r_work: 0.3436 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8513  Z= 0.153
  Angle     :  0.543   8.705  11518  Z= 0.268
  Chirality :  0.040   0.297   1290
  Planarity :  0.004   0.054   1477
  Dihedral  :  5.179  75.036   1226
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 29.16 %
    Favored  : 68.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.58 (0.28), residues: 1039
  helix:  3.05 (0.25), residues: 426
  sheet: -0.00 (0.37), residues: 205
  loop : -0.58 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.013   0.001   PHE A 551 
 TYR   0.023   0.001   TYR B 487 
 ARG   0.007   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 MET cc_start: 0.8668 (ttp) cc_final: 0.8424 (ttp)
REVERT: B  466 GLN cc_start: 0.8003 (pt0) cc_final: 0.7491 (pm20)
REVERT: B  498 GLN cc_start: 0.9238 (mt0) cc_final: 0.8925 (mp10)
REVERT: B  595 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.6494 (ttp-170)
REVERT: A  303 TYR cc_start: 0.8887 (p90) cc_final: 0.8583 (p90)
REVERT: A  594 SER cc_start: 0.8438 (m) cc_final: 0.7934 (p)
REVERT: A  605 ASP cc_start: 0.9249 (m-30) cc_final: 0.8887 (m-30)
REVERT: C   28 LEU cc_start: 0.7691 (mp) cc_final: 0.7458 (mp)
REVERT: C   30 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8010 (ttpt)
  outliers start: 22
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1869
  time to fit residues: 35.9347
Evaluate side-chains
  137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  402 CYS
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain C residue   27 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.2980
   chunk 16 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 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 = 0.4015 r_free = 0.4015 target = 0.137827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.103290 restraints weight = 13846.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.79
r_work: 0.3388 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8513  Z= 0.224
  Angle     :  0.578   9.401  11518  Z= 0.285
  Chirality :  0.041   0.273   1290
  Planarity :  0.004   0.055   1477
  Dihedral  :  5.279  74.259   1226
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 28.94 %
    Favored  : 68.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.27), residues: 1039
  helix:  2.90 (0.25), residues: 426
  sheet: -0.09 (0.37), residues: 205
  loop : -0.64 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.012   0.002   PHE A 551 
 TYR   0.023   0.001   TYR B 487 
 ARG   0.008   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 MET cc_start: 0.8608 (ttp) cc_final: 0.8372 (ttp)
REVERT: B  466 GLN cc_start: 0.8099 (pt0) cc_final: 0.7652 (pm20)
REVERT: B  498 GLN cc_start: 0.9247 (mt0) cc_final: 0.8984 (mt0)
REVERT: B  595 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.6524 (ttp-170)
REVERT: A  303 TYR cc_start: 0.8962 (p90) cc_final: 0.8576 (p90)
REVERT: A  594 SER cc_start: 0.8456 (m) cc_final: 0.7980 (p)
REVERT: A  605 ASP cc_start: 0.9262 (m-30) cc_final: 0.9006 (m-30)
REVERT: C   28 LEU cc_start: 0.7713 (mp) cc_final: 0.7473 (mp)
REVERT: C   30 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7978 (ttpt)
  outliers start: 21
  outliers final: 16
  residues processed: 137
  average time/residue: 0.1962
  time to fit residues: 37.9589
Evaluate side-chains
  137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain C residue   27 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 90 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  32 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 = 0.4019 r_free = 0.4019 target = 0.138262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.103835 restraints weight = 13733.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 3.77
r_work: 0.3393 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8513  Z= 0.209
  Angle     :  0.576   9.284  11518  Z= 0.283
  Chirality :  0.040   0.257   1290
  Planarity :  0.004   0.055   1477
  Dihedral  :  5.176  74.330   1226
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 29.38 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.36 (0.27), residues: 1039
  helix:  2.85 (0.24), residues: 426
  sheet: -0.15 (0.37), residues: 206
  loop : -0.66 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.012   0.001   PHE A 551 
 TYR   0.023   0.001   TYR B 487 
 ARG   0.008   0.000   ARG B 547 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 MET cc_start: 0.8617 (ttp) cc_final: 0.8366 (ttp)
REVERT: B  466 GLN cc_start: 0.8128 (pt0) cc_final: 0.7596 (pm20)
REVERT: B  498 GLN cc_start: 0.9248 (mt0) cc_final: 0.8936 (mp10)
REVERT: B  595 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.6526 (ttp-170)
REVERT: A  164 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8589 (mtt90)
REVERT: A  303 TYR cc_start: 0.8959 (p90) cc_final: 0.8490 (p90)
REVERT: A  594 SER cc_start: 0.8463 (m) cc_final: 0.7976 (p)
REVERT: A  605 ASP cc_start: 0.9249 (m-30) cc_final: 0.8991 (m-30)
REVERT: C   28 LEU cc_start: 0.7709 (mp) cc_final: 0.7465 (mp)
REVERT: C   30 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8003 (ttpt)
  outliers start: 19
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1967
  time to fit residues: 37.8843
Evaluate side-chains
  141 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  357 CYS
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  518 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   59 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.141068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.107815 restraints weight = 13733.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 3.78
r_work: 0.3498 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8513  Z= 0.170
  Angle     :  0.568  10.282  11518  Z= 0.277
  Chirality :  0.041   0.301   1290
  Planarity :  0.004   0.055   1477
  Dihedral  :  5.040  74.848   1226
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 29.16 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.45 (0.27), residues: 1039
  helix:  2.91 (0.25), residues: 426
  sheet: -0.06 (0.37), residues: 206
  loop : -0.63 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 206 
 PHE   0.010   0.001   PHE A 551 
 TYR   0.023   0.001   TYR B 487 
 ARG   0.008   0.000   ARG B 547 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4612.78 seconds
wall clock time: 80 minutes 31.92 seconds (4831.92 seconds total)