Starting phenix.real_space_refine
on Sun Jul 27 05:33:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iol_60744/07_2025/9iol_60744.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iol_60744/07_2025/9iol_60744.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2025/9iol_60744.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2025/9iol_60744.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2025/9iol_60744.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2025/9iol_60744.cif"
  }
  resolution = 3.46
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      46      5.49       5
     S      40      5.16       5
     C    5631      2.51       5
     N    1530      2.21       5
     O    1789      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 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: 9036
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4104
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 23, 'TRANS': 488}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3970
          Classifications: {'peptide': 494}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 27, 'TRANS': 466}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 404
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 416
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "M"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 101
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'2OP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'2OP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 5.60, per 1000 atoms: 0.62
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (95.57, 92.7029, 141.444, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P      46     15.00
     O    1789      8.00
     N    1530      7.00
     C    5631      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 10 sheets defined
      39.7% alpha, 20.9% beta
      12 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 3.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 48
    Processing helix  chain 'A' and resid 87 through 96
    Processing helix  chain 'A' and resid 106 through 123
      removed outlier: 3.676A  pdb=" N   ILE A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 157
    Processing helix  chain 'A' and resid 198 through 222
      removed outlier: 9.357A  pdb=" N   GLU A 218 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   ASP A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 234
    Processing helix  chain 'A' and resid 299 through 303
      removed outlier: 4.543A  pdb=" N   THR A 303 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 308
      No H-bonds generated for 'chain 'A' and resid 306 through 308'
    Processing helix  chain 'A' and resid 324 through 332
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 352 through 356
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 426 through 430
      removed outlier: 3.829A  pdb=" N   LEU A 430 " --> pdb=" O   MET A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 461
      removed outlier: 3.582A  pdb=" N   ASP A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 482
      removed outlier: 3.574A  pdb=" N   ILE A 482 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 500
      removed outlier: 3.702A  pdb=" N   GLN A 488 " --> pdb=" O   ASN A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 517
    Processing helix  chain 'A' and resid 519 through 526
    Processing helix  chain 'A' and resid 526 through 537
    Processing helix  chain 'B' and resid 45 through 50
    Processing helix  chain 'B' and resid 58 through 78
    Processing helix  chain 'B' and resid 112 through 121
    Processing helix  chain 'B' and resid 123 through 136
    Processing helix  chain 'B' and resid 142 through 156
    Processing helix  chain 'B' and resid 179 through 196
    Processing helix  chain 'B' and resid 238 through 251
      removed outlier: 3.935A  pdb=" N   THR B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 314
      No H-bonds generated for 'chain 'B' and resid 312 through 314'
    Processing helix  chain 'B' and resid 330 through 338
      removed outlier: 3.788A  pdb=" N   LYS B 338 " --> pdb=" O   THR B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 356
      No H-bonds generated for 'chain 'B' and resid 354 through 356'
    Processing helix  chain 'B' and resid 377 through 393
      removed outlier: 3.538A  pdb=" N   LEU B 381 " --> pdb=" O   GLY B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 443
    Processing helix  chain 'B' and resid 455 through 469
    Processing helix  chain 'B' and resid 474 through 478
      removed outlier: 4.159A  pdb=" N   PHE B 478 " --> pdb=" O   SER B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 495
      removed outlier: 3.537A  pdb=" N   ARG B 488 " --> pdb=" O   GLN B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 519
    Processing helix  chain 'B' and resid 520 through 530
    Processing helix  chain 'M' and resid 9 through 13
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84
      removed outlier: 5.194A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU A  58 " --> pdb=" O   VAL A  79 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LEU A  83 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ILE A  54 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   ALA A  55 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL A  10 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   VAL A  57 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   LEU A  12 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   PHE A  59 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   MET A  14 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ARG A 130 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   GLN A 162 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ILE A 132 " --> pdb=" O   GLN A 162 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   PHE A 164 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ILE A 134 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   TYR A 225 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 165 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 253
      removed outlier: 6.913A  pdb=" N   VAL A 361 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   LEU A 268 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 9.917A  pdb=" N   ASN A 359 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   ASN A 359 " --> pdb=" O   TYR A 421 " (cutoff:3.500A)
      removed outlier: 11.930A  pdb=" N   TYR A 421 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 10.122A  pdb=" N   VAL A 361 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 11.031A  pdb=" N   LEU A 419 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
      removed outlier: 9.948A  pdb=" N   LYS A 363 " --> pdb=" O   GLU A 417 " (cutoff:3.500A)
      removed outlier: 10.850A  pdb=" N   GLU A 417 " --> pdb=" O   LYS A 363 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   MET A 389 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLY A 344 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ARG A 394 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   VAL A 342 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   ALA A 396 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   PHE A 340 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 280
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 297
    Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322
    Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AA7, first strand: chain 'A' and resid 540 through 541
    Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 109
      removed outlier: 7.161A  pdb=" N   LEU B 105 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
      removed outlier: 8.779A  pdb=" N   PHE B  87 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   GLU B 107 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   VAL B  85 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP B  43 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS B 164 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 8.724A  pdb=" N   ASP B 201 " --> pdb=" O   LYS B 164 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE B 166 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   MET B 203 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 168 " --> pdb=" O   MET B 203 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262
      removed outlier: 7.825A  pdb=" N   VAL B 394 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 350 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   PHE B 350 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B 397 " --> pdb=" O   MET B 348 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 419 through 420
      removed outlier: 6.882A  pdb=" N   GLU B 419 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 3.28

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1428
        1.29 -     1.42: 2464
        1.42 -     1.55: 5244
        1.55 -     1.69: 89
        1.69 -     1.82: 67
  Bond restraints: 9292
  Sorted by residual:
  bond pdb=" CB  GLN B 320 "
       pdb=" CG  GLN B 320 "
    ideal  model  delta    sigma   weight residual
    1.520  1.340  0.180 3.00e-02 1.11e+03 3.59e+01
  bond pdb=" CZ  ARG B 318 "
       pdb=" NH2 ARG B 318 "
    ideal  model  delta    sigma   weight residual
    1.330  1.259  0.071 1.30e-02 5.92e+03 3.00e+01
  bond pdb=" O14 IHP B 801 "
       pdb=" P4  IHP B 801 "
    ideal  model  delta    sigma   weight residual
    1.671  1.571  0.100 2.00e-02 2.50e+03 2.49e+01
  bond pdb=" CZ  ARG B 318 "
       pdb=" NH1 ARG B 318 "
    ideal  model  delta    sigma   weight residual
    1.323  1.260  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" O12 IHP B 801 "
       pdb=" P2  IHP B 801 "
    ideal  model  delta    sigma   weight residual
    1.675  1.586  0.089 2.00e-02 2.50e+03 1.96e+01
  ... (remaining 9287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.09: 12400
        4.09 -     8.18: 302
        8.18 -    12.27: 5
       12.27 -    16.36: 1
       16.36 -    20.45: 1
  Bond angle restraints: 12709
  Sorted by residual:
  angle pdb=" CB  GLN B 320 "
        pdb=" CG  GLN B 320 "
        pdb=" CD  GLN B 320 "
      ideal   model   delta    sigma   weight residual
     112.60  133.05  -20.45 1.70e+00 3.46e-01 1.45e+02
  angle pdb=" CA  GLN B 320 "
        pdb=" CB  GLN B 320 "
        pdb=" CG  GLN B 320 "
      ideal   model   delta    sigma   weight residual
     114.10  126.57  -12.47 2.00e+00 2.50e-01 3.89e+01
  angle pdb=" OE1 GLN B 320 "
        pdb=" CD  GLN B 320 "
        pdb=" NE2 GLN B 320 "
      ideal   model   delta    sigma   weight residual
     122.60  117.36    5.24 1.00e+00 1.00e+00 2.74e+01
  angle pdb=" O   GLY A 313 "
        pdb=" C   GLY A 313 "
        pdb=" N   PHE A 314 "
      ideal   model   delta    sigma   weight residual
     123.65  118.92    4.73 9.20e-01 1.18e+00 2.64e+01
  angle pdb=" C4'  DA D   7 "
        pdb=" C3'  DA D   7 "
        pdb=" O3'  DA D   7 "
      ideal   model   delta    sigma   weight residual
     110.00  102.35    7.65 1.50e+00 4.44e-01 2.60e+01
  ... (remaining 12704 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.39: 5110
       23.39 -    46.77: 372
       46.77 -    70.15: 121
       70.15 -    93.54: 14
       93.54 -   116.92: 4
  Dihedral angle restraints: 5621
    sinusoidal: 2627
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" C   LEU A 108 "
           pdb=" N   LEU A 108 "
           pdb=" CA  LEU A 108 "
           pdb=" CB  LEU A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.02   14.42     0      2.50e+00 1.60e-01 3.33e+01
  dihedral pdb=" CA  LYS A 413 "
           pdb=" C   LYS A 413 "
           pdb=" N   HIS A 414 "
           pdb=" CA  HIS A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.25   28.75     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  GLU B  91 "
           pdb=" C   GLU B  91 "
           pdb=" N   LYS B  92 "
           pdb=" CA  LYS B  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.09   25.91     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 5618 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1179
       0.107 -    0.215: 217
       0.215 -    0.322: 30
       0.322 -    0.429: 2
       0.429 -    0.536: 2
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" CA  LEU A 108 "
            pdb=" N   LEU A 108 "
            pdb=" C   LEU A 108 "
            pdb=" CB  LEU A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.20e+00
  chirality pdb=" CA  PHE B 159 "
            pdb=" N   PHE B 159 "
            pdb=" C   PHE B 159 "
            pdb=" CB  PHE B 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" CG  LEU B  57 "
            pdb=" CB  LEU B  57 "
            pdb=" CD1 LEU B  57 "
            pdb=" CD2 LEU B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.20   -0.39 2.00e-01 2.50e+01 3.76e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA D   1 "    0.355 2.00e-02 2.50e+03   1.51e-01 6.30e+02
        pdb=" N9   DA D   1 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8   DA D   1 "   -0.095 2.00e-02 2.50e+03
        pdb=" N7   DA D   1 "   -0.097 2.00e-02 2.50e+03
        pdb=" C5   DA D   1 "   -0.093 2.00e-02 2.50e+03
        pdb=" C6   DA D   1 "    0.028 2.00e-02 2.50e+03
        pdb=" N6   DA D   1 "    0.242 2.00e-02 2.50e+03
        pdb=" N1   DA D   1 "    0.030 2.00e-02 2.50e+03
        pdb=" C2   DA D   1 "   -0.053 2.00e-02 2.50e+03
        pdb=" N3   DA D   1 "   -0.114 2.00e-02 2.50e+03
        pdb=" C4   DA D   1 "   -0.133 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  14 "   -0.188 2.00e-02 2.50e+03   1.22e-01 3.72e+02
        pdb=" N1   DT C  14 "    0.121 2.00e-02 2.50e+03
        pdb=" C2   DT C  14 "    0.141 2.00e-02 2.50e+03
        pdb=" O2   DT C  14 "   -0.141 2.00e-02 2.50e+03
        pdb=" N3   DT C  14 "    0.128 2.00e-02 2.50e+03
        pdb=" C4   DT C  14 "    0.022 2.00e-02 2.50e+03
        pdb=" O4   DT C  14 "   -0.155 2.00e-02 2.50e+03
        pdb=" C5   DT C  14 "    0.035 2.00e-02 2.50e+03
        pdb=" C7   DT C  14 "   -0.073 2.00e-02 2.50e+03
        pdb=" C6   DT C  14 "    0.108 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC C   7 "   -0.155 2.00e-02 2.50e+03   8.46e-02 1.61e+02
        pdb=" N1   DC C   7 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DC C   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DC C   7 "    0.119 2.00e-02 2.50e+03
        pdb=" N3   DC C   7 "   -0.036 2.00e-02 2.50e+03
        pdb=" C4   DC C   7 "   -0.028 2.00e-02 2.50e+03
        pdb=" N4   DC C   7 "   -0.081 2.00e-02 2.50e+03
        pdb=" C5   DC C   7 "    0.077 2.00e-02 2.50e+03
        pdb=" C6   DC C   7 "    0.109 2.00e-02 2.50e+03
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1288
        2.79 -     3.31: 9097
        3.31 -     3.84: 14986
        3.84 -     4.37: 17397
        4.37 -     4.90: 28012
  Nonbonded interactions: 70780
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 324 "
            pdb=" OD2 ASP A 327 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG1 THR A  61 "
            pdb=" O   GLY A  63 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LYS B 265 "
            pdb=" NZ  LYS B 265 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   GLY A  17 "
            pdb=" OG  SER A  21 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ILE A 197 "
            pdb=" NZ  LYS A 202 "
     model   vdw
     2.345 3.120
  ... (remaining 70775 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 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:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.550
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
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      :  0.012   0.180   9293  Z= 0.657
  Angle     :  1.665  20.454  12709  Z= 1.075
  Chirality :  0.085   0.536   1430
  Planarity :  0.017   0.173   1482
  Dihedral  : 18.011 116.920   3667
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.85 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.20 %
  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: -0.52 (0.24), residues: 1007
  helix: -0.29 (0.25), residues: 354
  sheet:  0.52 (0.38), residues: 156
  loop : -0.57 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.077   0.016   TRP A 276 
 HIS   0.014   0.003   HIS B 360 
 PHE   0.060   0.010   PHE A 409 
 TYR   0.111   0.015   TYR B 217 
 ARG   0.012   0.001   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15671 (  403)
  hydrogen bonds       : angle       7.91297 ( 1092)
  covalent geometry    : bond        0.01171 ( 9292)
  covalent geometry    : angle       1.66530 (12709)
  Misc. bond           : bond        0.01948 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9320 (mmt) cc_final: 0.8968 (mmm)
REVERT: A  208 VAL cc_start: 0.9637 (t) cc_final: 0.9428 (t)
REVERT: A  292 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7806 (tm-30)
REVERT: A  427 MET cc_start: 0.9567 (tmm) cc_final: 0.9040 (tmm)
REVERT: A  461 MET cc_start: 0.9015 (mpp) cc_final: 0.8790 (mmp)
REVERT: B   41 LEU cc_start: 0.9299 (mm) cc_final: 0.9076 (mm)
REVERT: B   62 MET cc_start: 0.9120 (tpp) cc_final: 0.8805 (tpp)
REVERT: B   68 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9225 (mm-40)
REVERT: B  287 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8898 (mmmt)
REVERT: B  488 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8961 (tpp80)
REVERT: B  514 MET cc_start: 0.9705 (mtp) cc_final: 0.9173 (mtp)
REVERT: B  518 LEU cc_start: 0.9683 (mt) cc_final: 0.9448 (mt)
  outliers start: 8
  outliers final: 2
  residues processed: 90
  average time/residue: 0.2362
  time to fit residues: 29.7944
Evaluate side-chains
  69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  488 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0470
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.3884

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 432 GLN
A 511 HIS
B  68 GLN
B 152 ASN
B 176 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.059928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.041689 restraints weight = 42704.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 4.89
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9293  Z= 0.152
  Angle     :  0.669   6.979  12709  Z= 0.352
  Chirality :  0.044   0.171   1430
  Planarity :  0.004   0.043   1482
  Dihedral  : 19.393 103.428   1568
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.14 %
    Favored  : 88.44 %
  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:  0.18 (0.25), residues: 1007
  helix:  0.80 (0.27), residues: 355
  sheet:  0.33 (0.37), residues: 165
  loop : -0.38 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 247 
 HIS   0.005   0.001   HIS A 131 
 PHE   0.018   0.001   PHE A  31 
 TYR   0.016   0.001   TYR A 264 
 ARG   0.006   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05576 (  403)
  hydrogen bonds       : angle       5.80851 ( 1092)
  covalent geometry    : bond        0.00323 ( 9292)
  covalent geometry    : angle       0.66949 (12709)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.9715 (tpp) cc_final: 0.9514 (tmm)
REVERT: A  427 MET cc_start: 0.9620 (tmm) cc_final: 0.9093 (tmm)
REVERT: A  461 MET cc_start: 0.9116 (mpp) cc_final: 0.8802 (mmp)
REVERT: B   62 MET cc_start: 0.9146 (tpp) cc_final: 0.8917 (tpp)
REVERT: B  287 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8882 (mmmt)
REVERT: B  518 LEU cc_start: 0.9684 (mt) cc_final: 0.9455 (mt)
  outliers start: 13
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2483
  time to fit residues: 28.9356
Evaluate side-chains
  69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 GLN
A 415 ASN
A 452 ASN
A 511 HIS
A 517 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.057947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.039342 restraints weight = 45278.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 4.97
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9293  Z= 0.241
  Angle     :  0.666   7.738  12709  Z= 0.352
  Chirality :  0.043   0.156   1430
  Planarity :  0.004   0.050   1482
  Dihedral  : 19.028 102.334   1554
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.01 %
    Favored  : 88.00 %
  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:  0.22 (0.25), residues: 1007
  helix:  1.02 (0.27), residues: 355
  sheet:  0.07 (0.38), residues: 164
  loop : -0.41 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 247 
 HIS   0.005   0.001   HIS A 382 
 PHE   0.014   0.002   PHE A  31 
 TYR   0.012   0.002   TYR A 264 
 ARG   0.006   0.001   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05430 (  403)
  hydrogen bonds       : angle       5.54506 ( 1092)
  covalent geometry    : bond        0.00530 ( 9292)
  covalent geometry    : angle       0.66578 (12709)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.9656 (tmm) cc_final: 0.9101 (tmm)
REVERT: A  461 MET cc_start: 0.9189 (mpp) cc_final: 0.8842 (mmp)
REVERT: B   62 MET cc_start: 0.9197 (tpp) cc_final: 0.8841 (tpp)
REVERT: B  518 LEU cc_start: 0.9669 (mt) cc_final: 0.9431 (mt)
  outliers start: 9
  outliers final: 5
  residues processed: 72
  average time/residue: 0.2217
  time to fit residues: 23.3491
Evaluate side-chains
  71 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 59 optimal weight:    0.0010
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 61 optimal weight:   20.0000
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 511 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.060068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.041591 restraints weight = 42888.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 4.93
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9293  Z= 0.115
  Angle     :  0.606   9.095  12709  Z= 0.308
  Chirality :  0.041   0.180   1430
  Planarity :  0.003   0.045   1482
  Dihedral  : 18.852  96.616   1554
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.32 %
    Favored  : 86.48 %
  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:  0.61 (0.26), residues: 1007
  helix:  1.32 (0.28), residues: 355
  sheet:  0.49 (0.38), residues: 163
  loop : -0.25 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 204 
 PHE   0.020   0.001   PHE A  31 
 TYR   0.011   0.001   TYR B 217 
 ARG   0.003   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 (  403)
  hydrogen bonds       : angle       5.05950 ( 1092)
  covalent geometry    : bond        0.00239 ( 9292)
  covalent geometry    : angle       0.60565 (12709)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9480 (tpp) cc_final: 0.9142 (tpp)
REVERT: A  115 MET cc_start: 0.9756 (tpp) cc_final: 0.9534 (tmm)
REVERT: A  427 MET cc_start: 0.9645 (tmm) cc_final: 0.9195 (tmm)
REVERT: A  461 MET cc_start: 0.9148 (tpp) cc_final: 0.8780 (mmp)
REVERT: B   62 MET cc_start: 0.9093 (tpp) cc_final: 0.8718 (tpp)
REVERT: B  497 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9037 (pp)
REVERT: B  518 LEU cc_start: 0.9650 (mt) cc_final: 0.9431 (mt)
REVERT: M    9 ARG cc_start: 0.8816 (ptm-80) cc_final: 0.8580 (ptm-80)
  outliers start: 11
  outliers final: 4
  residues processed: 78
  average time/residue: 0.1857
  time to fit residues: 21.7945
Evaluate side-chains
  73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  497 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 91 optimal weight:    0.0980
   chunk 26 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 28 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.059849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.041242 restraints weight = 43757.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 5.01
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9293  Z= 0.121
  Angle     :  0.597   8.520  12709  Z= 0.302
  Chirality :  0.041   0.196   1430
  Planarity :  0.003   0.045   1482
  Dihedral  : 18.703  94.196   1554
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.98 %
    Favored  : 85.61 %
  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:  0.64 (0.26), residues: 1007
  helix:  1.38 (0.28), residues: 355
  sheet:  0.44 (0.39), residues: 160
  loop : -0.22 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 382 
 PHE   0.023   0.001   PHE A  31 
 TYR   0.010   0.001   TYR A 264 
 ARG   0.002   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04309 (  403)
  hydrogen bonds       : angle       4.95774 ( 1092)
  covalent geometry    : bond        0.00261 ( 9292)
  covalent geometry    : angle       0.59696 (12709)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9461 (tpp) cc_final: 0.9209 (tpp)
REVERT: A  115 MET cc_start: 0.9753 (tpp) cc_final: 0.9546 (tmm)
REVERT: A  427 MET cc_start: 0.9640 (tmm) cc_final: 0.9215 (tmm)
REVERT: A  461 MET cc_start: 0.9147 (tpp) cc_final: 0.8763 (mmp)
REVERT: B   62 MET cc_start: 0.9096 (tpp) cc_final: 0.8693 (tpp)
REVERT: B  497 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9047 (pp)
REVERT: B  514 MET cc_start: 0.9738 (mtm) cc_final: 0.9492 (mtt)
REVERT: B  518 LEU cc_start: 0.9657 (mt) cc_final: 0.9440 (mt)
  outliers start: 13
  outliers final: 9
  residues processed: 76
  average time/residue: 0.2622
  time to fit residues: 29.7813
Evaluate side-chains
  76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0970
   chunk 73 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 88 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** 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 = 0.3423 r_free = 0.3423 target = 0.059603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.040988 restraints weight = 44268.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 5.01
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9293  Z= 0.130
  Angle     :  0.607  11.319  12709  Z= 0.302
  Chirality :  0.041   0.226   1430
  Planarity :  0.003   0.048   1482
  Dihedral  : 18.513  89.358   1554
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.52 %
    Favored  : 85.06 %
  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:  0.68 (0.26), residues: 1007
  helix:  1.44 (0.28), residues: 355
  sheet:  0.39 (0.40), residues: 160
  loop : -0.19 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 486 
 PHE   0.019   0.001   PHE A  31 
 TYR   0.009   0.001   TYR A 264 
 ARG   0.003   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04122 (  403)
  hydrogen bonds       : angle       4.88787 ( 1092)
  covalent geometry    : bond        0.00285 ( 9292)
  covalent geometry    : angle       0.60686 (12709)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8690 (t) cc_final: 0.8403 (t)
REVERT: A  427 MET cc_start: 0.9645 (tmm) cc_final: 0.9226 (tmm)
REVERT: A  461 MET cc_start: 0.9152 (tpp) cc_final: 0.8773 (mmp)
REVERT: B   62 MET cc_start: 0.9072 (tpp) cc_final: 0.8620 (tpp)
REVERT: B  203 MET cc_start: 0.9451 (mmp) cc_final: 0.9106 (mmp)
REVERT: B  518 LEU cc_start: 0.9638 (mt) cc_final: 0.9405 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 73
  average time/residue: 0.2632
  time to fit residues: 28.9410
Evaluate side-chains
  74 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 41 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** 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 = 0.3415 r_free = 0.3415 target = 0.058930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.040550 restraints weight = 44434.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 4.94
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9293  Z= 0.164
  Angle     :  0.641  11.541  12709  Z= 0.318
  Chirality :  0.042   0.239   1430
  Planarity :  0.003   0.048   1482
  Dihedral  : 18.374  85.550   1554
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.41 %
    Favored  : 84.95 %
  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:  0.67 (0.26), residues: 1007
  helix:  1.47 (0.28), residues: 355
  sheet:  0.35 (0.40), residues: 160
  loop : -0.22 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.016   0.001   PHE A  31 
 TYR   0.009   0.001   TYR A 264 
 ARG   0.003   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  403)
  hydrogen bonds       : angle       4.92349 ( 1092)
  covalent geometry    : bond        0.00363 ( 9292)
  covalent geometry    : angle       0.64074 (12709)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8808 (t) cc_final: 0.8488 (t)
REVERT: A  427 MET cc_start: 0.9655 (tmm) cc_final: 0.9224 (tmm)
REVERT: A  461 MET cc_start: 0.9158 (tpp) cc_final: 0.8772 (mmp)
REVERT: B  203 MET cc_start: 0.9337 (mmp) cc_final: 0.9086 (mmp)
REVERT: B  348 MET cc_start: 0.8773 (mmm) cc_final: 0.8374 (mtt)
REVERT: B  497 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9082 (pp)
REVERT: B  518 LEU cc_start: 0.9633 (mt) cc_final: 0.9407 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 75
  average time/residue: 0.2656
  time to fit residues: 29.6877
Evaluate side-chains
  77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0170
   chunk 45 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0870
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
A 511 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.060357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.042016 restraints weight = 44353.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 4.95
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9293  Z= 0.109
  Angle     :  0.634  11.372  12709  Z= 0.304
  Chirality :  0.041   0.258   1430
  Planarity :  0.003   0.043   1482
  Dihedral  : 18.229  80.400   1554
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.63 %
    Favored  : 84.84 %
  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:  0.71 (0.26), residues: 1007
  helix:  1.42 (0.28), residues: 355
  sheet:  0.44 (0.40), residues: 160
  loop : -0.14 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 247 
 HIS   0.002   0.000   HIS B 486 
 PHE   0.019   0.001   PHE A  31 
 TYR   0.009   0.001   TYR A 264 
 ARG   0.004   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  403)
  hydrogen bonds       : angle       4.76908 ( 1092)
  covalent geometry    : bond        0.00229 ( 9292)
  covalent geometry    : angle       0.63424 (12709)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.9644 (tmm) cc_final: 0.9241 (tmm)
REVERT: A  461 MET cc_start: 0.9150 (tpp) cc_final: 0.8727 (mmp)
REVERT: B  203 MET cc_start: 0.9392 (mmp) cc_final: 0.9105 (mmp)
REVERT: B  336 GLU cc_start: 0.9540 (tt0) cc_final: 0.9334 (tm-30)
REVERT: B  347 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9340 (tp)
REVERT: B  348 MET cc_start: 0.8714 (mmm) cc_final: 0.8331 (mtt)
REVERT: B  462 MET cc_start: 0.8775 (ptp) cc_final: 0.8572 (ptp)
REVERT: B  469 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9025 (mm)
REVERT: B  497 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9107 (pp)
REVERT: B  518 LEU cc_start: 0.9619 (mt) cc_final: 0.9408 (mt)
REVERT: M    9 ARG cc_start: 0.8903 (ptm-80) cc_final: 0.8637 (ptm-80)
  outliers start: 14
  outliers final: 8
  residues processed: 76
  average time/residue: 0.2030
  time to fit residues: 22.5197
Evaluate side-chains
  76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 103 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   chunk 86 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.059925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.041533 restraints weight = 43677.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 4.96
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9293  Z= 0.124
  Angle     :  0.629  10.651  12709  Z= 0.305
  Chirality :  0.041   0.254   1430
  Planarity :  0.003   0.044   1482
  Dihedral  : 18.135  77.099   1554
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.85 %
    Favored  : 84.84 %
  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:  0.75 (0.26), residues: 1007
  helix:  1.46 (0.28), residues: 355
  sheet:  0.44 (0.41), residues: 160
  loop : -0.11 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 486 
 PHE   0.017   0.001   PHE A  31 
 TYR   0.007   0.001   TYR B 217 
 ARG   0.003   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03841 (  403)
  hydrogen bonds       : angle       4.77588 ( 1092)
  covalent geometry    : bond        0.00274 ( 9292)
  covalent geometry    : angle       0.62933 (12709)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.9657 (tmm) cc_final: 0.9234 (tmm)
REVERT: A  461 MET cc_start: 0.9144 (tpp) cc_final: 0.8737 (mmp)
REVERT: B   62 MET cc_start: 0.9021 (ttt) cc_final: 0.8451 (tpp)
REVERT: B  203 MET cc_start: 0.9414 (mmp) cc_final: 0.9124 (mmp)
REVERT: B  336 GLU cc_start: 0.9547 (tt0) cc_final: 0.9342 (tm-30)
REVERT: B  348 MET cc_start: 0.8705 (mmm) cc_final: 0.8382 (mtt)
REVERT: B  497 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9130 (pp)
REVERT: B  518 LEU cc_start: 0.9629 (mt) cc_final: 0.9304 (pp)
  outliers start: 12
  outliers final: 9
  residues processed: 74
  average time/residue: 0.1769
  time to fit residues: 19.8125
Evaluate side-chains
  74 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  497 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 83 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 92 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 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 = 0.3427 r_free = 0.3427 target = 0.059463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.041119 restraints weight = 44103.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 4.93
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9293  Z= 0.145
  Angle     :  0.663  11.894  12709  Z= 0.327
  Chirality :  0.042   0.251   1430
  Planarity :  0.003   0.045   1482
  Dihedral  : 18.091  74.554   1554
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.63 %
    Favored  : 85.17 %
  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:  0.77 (0.26), residues: 1007
  helix:  1.49 (0.28), residues: 355
  sheet:  0.43 (0.41), residues: 160
  loop : -0.12 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 486 
 PHE   0.017   0.001   PHE A  31 
 TYR   0.008   0.001   TYR B 217 
 ARG   0.003   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03926 (  403)
  hydrogen bonds       : angle       4.86302 ( 1092)
  covalent geometry    : bond        0.00321 ( 9292)
  covalent geometry    : angle       0.66308 (12709)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.9663 (tmm) cc_final: 0.9229 (tmm)
REVERT: A  461 MET cc_start: 0.9176 (tpp) cc_final: 0.8931 (mmp)
REVERT: B  348 MET cc_start: 0.8712 (mmm) cc_final: 0.8393 (mtt)
REVERT: B  497 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9136 (pp)
REVERT: B  514 MET cc_start: 0.9659 (mtm) cc_final: 0.9298 (mtm)
REVERT: B  518 LEU cc_start: 0.9612 (mt) cc_final: 0.9395 (mt)
REVERT: M    9 ARG cc_start: 0.8939 (ptm-80) cc_final: 0.8663 (ptm-80)
  outliers start: 11
  outliers final: 10
  residues processed: 70
  average time/residue: 0.2529
  time to fit residues: 27.4118
Evaluate side-chains
  73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  497 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 90 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 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 = 0.3404 r_free = 0.3404 target = 0.058503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.040187 restraints weight = 44969.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 4.96
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9293  Z= 0.182
  Angle     :  0.711  16.969  12709  Z= 0.348
  Chirality :  0.043   0.314   1430
  Planarity :  0.003   0.045   1482
  Dihedral  : 18.081  72.441   1554
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.63 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.10 %
  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:  0.73 (0.26), residues: 1007
  helix:  1.52 (0.28), residues: 354
  sheet:  0.34 (0.41), residues: 160
  loop : -0.15 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 486 
 PHE   0.016   0.001   PHE A  31 
 TYR   0.008   0.001   TYR B 217 
 ARG   0.003   0.000   ARG M   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  403)
  hydrogen bonds       : angle       5.03764 ( 1092)
  covalent geometry    : bond        0.00402 ( 9292)
  covalent geometry    : angle       0.71075 (12709)
  Misc. bond           : bond        0.00015 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3785.02 seconds
wall clock time: 70 minutes 6.57 seconds (4206.57 seconds total)