Starting phenix.real_space_refine
on Wed Mar 12 14:19:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tem_41191/03_2025/8tem_41191.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tem_41191/03_2025/8tem_41191.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tem_41191/03_2025/8tem_41191.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tem_41191/03_2025/8tem_41191.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tem_41191/03_2025/8tem_41191.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tem_41191/03_2025/8tem_41191.cif"
  }
  resolution = 3.02
  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=   0.002
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      58      5.16       5
     C    5302      2.51       5
     N    1294      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 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: 7992
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3996
          Classifications: {'peptide': 505}
          Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 473}
          Chain breaks: 2
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.24, per 1000 atoms: 0.91
  Number of scatterers: 7992
  At special positions: 0
  Unit cell: (97.11, 117.03, 81.34, 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      58     16.00
     O    1338      8.00
     N    1294      7.00
     C    5302      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.94
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      80.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 19
    Processing helix  chain 'A' and resid 21 through 33
      removed outlier: 3.973A  pdb=" N   GLY A  33 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 62
      removed outlier: 3.921A  pdb=" N   ILE A  49 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 67 through 86
    Processing helix  chain 'A' and resid 96 through 112
      removed outlier: 3.508A  pdb=" N   ALA A 112 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 142
    Processing helix  chain 'A' and resid 143 through 151
      removed outlier: 3.548A  pdb=" N   ILE A 147 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE A 148 " --> pdb=" O   CYS A 145 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   ASN A 149 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 178
      removed outlier: 3.534A  pdb=" N   GLY A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 192
    Processing helix  chain 'A' and resid 193 through 219
    Processing helix  chain 'A' and resid 228 through 252
      removed outlier: 6.664A  pdb=" N   VAL A 240 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
      Proline residue:  A 241  - end of helix
    Processing helix  chain 'A' and resid 253 through 258
      removed outlier: 4.505A  pdb=" N   GLY A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL A 258 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.797A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 297
    Processing helix  chain 'A' and resid 297 through 320
      removed outlier: 3.613A  pdb=" N   MET A 303 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A 313 " --> pdb=" O   TYR A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 331 through 350
    Processing helix  chain 'A' and resid 359 through 368
    Processing helix  chain 'A' and resid 464 through 480
      removed outlier: 3.533A  pdb=" N   LEU A 468 " --> pdb=" O   ARG A 464 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL A 478 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA A 479 " --> pdb=" O   GLY A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 485
    Processing helix  chain 'A' and resid 488 through 503
      removed outlier: 3.689A  pdb=" N   LEU A 492 " --> pdb=" O   PRO A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 517
    Processing helix  chain 'A' and resid 519 through 521
      No H-bonds generated for 'chain 'A' and resid 519 through 521'
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.964A  pdb=" N   VAL A 526 " --> pdb=" O   ARG A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 538
    Processing helix  chain 'A' and resid 539 through 562
      removed outlier: 3.587A  pdb=" N   TRP A 562 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 568
    Processing helix  chain 'A' and resid 569 through 589
      removed outlier: 3.540A  pdb=" N   MET A 573 " --> pdb=" O   MET A 569 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 577 " --> pdb=" O   MET A 573 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ILE A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      Proline residue:  A 579  - end of helix
      removed outlier: 4.394A  pdb=" N   LEU A 585 " --> pdb=" O   ARG A 581 " (cutoff:3.500A)
      Proline residue:  A 586  - end of helix
    Processing helix  chain 'A' and resid 591 through 598
    Processing helix  chain 'B' and resid 8 through 19
    Processing helix  chain 'B' and resid 21 through 33
      removed outlier: 3.974A  pdb=" N   GLY B  33 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 62
      removed outlier: 3.921A  pdb=" N   ILE B  49 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 67 through 86
    Processing helix  chain 'B' and resid 96 through 112
      removed outlier: 3.508A  pdb=" N   ALA B 112 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 142
    Processing helix  chain 'B' and resid 143 through 151
      removed outlier: 3.548A  pdb=" N   ILE B 147 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE B 148 " --> pdb=" O   CYS B 145 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   ASN B 149 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 178
      removed outlier: 3.535A  pdb=" N   GLY B 156 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 192
    Processing helix  chain 'B' and resid 193 through 219
    Processing helix  chain 'B' and resid 228 through 252
      removed outlier: 6.662A  pdb=" N   VAL B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
      Proline residue:  B 241  - end of helix
    Processing helix  chain 'B' and resid 253 through 258
      removed outlier: 4.505A  pdb=" N   GLY B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL B 258 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.797A  pdb=" N   LEU B 287 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 297
    Processing helix  chain 'B' and resid 297 through 320
      removed outlier: 3.613A  pdb=" N   MET B 303 " --> pdb=" O   ILE B 299 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 313 " --> pdb=" O   TYR B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 325
    Processing helix  chain 'B' and resid 331 through 350
    Processing helix  chain 'B' and resid 359 through 368
    Processing helix  chain 'B' and resid 464 through 480
      removed outlier: 3.532A  pdb=" N   LEU B 468 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL B 478 " --> pdb=" O   VAL B 474 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ALA B 479 " --> pdb=" O   GLY B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 485
    Processing helix  chain 'B' and resid 488 through 503
      removed outlier: 3.688A  pdb=" N   LEU B 492 " --> pdb=" O   PRO B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 517
    Processing helix  chain 'B' and resid 519 through 521
      No H-bonds generated for 'chain 'B' and resid 519 through 521'
    Processing helix  chain 'B' and resid 522 through 528
      removed outlier: 3.965A  pdb=" N   VAL B 526 " --> pdb=" O   ARG B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 533 through 538
    Processing helix  chain 'B' and resid 539 through 562
      removed outlier: 3.587A  pdb=" N   TRP B 562 " --> pdb=" O   PHE B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 568
    Processing helix  chain 'B' and resid 569 through 589
      removed outlier: 3.540A  pdb=" N   MET B 573 " --> pdb=" O   MET B 569 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B 577 " --> pdb=" O   MET B 573 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ILE B 578 " --> pdb=" O   ILE B 574 " (cutoff:3.500A)
      Proline residue:  B 579  - end of helix
      removed outlier: 4.394A  pdb=" N   LEU B 585 " --> pdb=" O   ARG B 581 " (cutoff:3.500A)
      Proline residue:  B 586  - end of helix
    Processing helix  chain 'B' and resid 591 through 598
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94
    Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532
    Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94
    Processing sheet with id=AA4, first strand: chain 'B' and resid 531 through 532

    530 hydrogen bonds defined for protein.
    1530 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: 2.31

  Time building geometry restraints manager: 2.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2420
        1.34 -     1.46: 2020
        1.46 -     1.58: 3678
        1.58 -     1.70: 0
        1.70 -     1.81: 100
  Bond restraints: 8218
  Sorted by residual:
  bond pdb=" N   PHE A   5 "
       pdb=" CA  PHE A   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   PHE B   5 "
       pdb=" CA  PHE B   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" CB  LYS B 260 "
       pdb=" CG  LYS B 260 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.54e+00
  bond pdb=" CB  LYS A 260 "
       pdb=" CG  LYS A 260 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.54e+00
  bond pdb=" CA  ILE B 181 "
       pdb=" CB  ILE B 181 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.012 1.29e-02 6.01e+03 8.54e-01
  ... (remaining 8213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 10772
        1.26 -     2.51: 292
        2.51 -     3.77: 70
        3.77 -     5.02: 26
        5.02 -     6.28: 4
  Bond angle restraints: 11164
  Sorted by residual:
  angle pdb=" CB  LYS A 260 "
        pdb=" CG  LYS A 260 "
        pdb=" CD  LYS A 260 "
      ideal   model   delta    sigma   weight residual
     111.30  117.29   -5.99 2.30e+00 1.89e-01 6.78e+00
  angle pdb=" CB  LYS B 260 "
        pdb=" CG  LYS B 260 "
        pdb=" CD  LYS B 260 "
      ideal   model   delta    sigma   weight residual
     111.30  117.29   -5.99 2.30e+00 1.89e-01 6.78e+00
  angle pdb=" CA  LYS B 260 "
        pdb=" CB  LYS B 260 "
        pdb=" CG  LYS B 260 "
      ideal   model   delta    sigma   weight residual
     114.10  118.77   -4.67 2.00e+00 2.50e-01 5.45e+00
  angle pdb=" CA  LYS A 260 "
        pdb=" CB  LYS A 260 "
        pdb=" CG  LYS A 260 "
      ideal   model   delta    sigma   weight residual
     114.10  118.74   -4.64 2.00e+00 2.50e-01 5.38e+00
  angle pdb=" N   PHE A   8 "
        pdb=" CA  PHE A   8 "
        pdb=" CB  PHE A   8 "
      ideal   model   delta    sigma   weight residual
     113.65  110.38    3.27 1.47e+00 4.63e-01 4.94e+00
  ... (remaining 11159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 4181
       17.24 -    34.47: 441
       34.47 -    51.71: 144
       51.71 -    68.94: 24
       68.94 -    86.18: 24
  Dihedral angle restraints: 4814
    sinusoidal: 1910
      harmonic: 2904
  Sorted by residual:
  dihedral pdb=" CA  LYS B 590 "
           pdb=" C   LYS B 590 "
           pdb=" N   GLY B 591 "
           pdb=" CA  GLY B 591 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.96   18.04     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  LYS A 590 "
           pdb=" C   LYS A 590 "
           pdb=" N   GLY A 591 "
           pdb=" CA  GLY A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.00   18.00     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  SER B 521 "
           pdb=" C   SER B 521 "
           pdb=" N   ARG B 522 "
           pdb=" CA  ARG B 522 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.87  -16.13     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 4811 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 835
       0.030 -    0.060: 270
       0.060 -    0.090: 104
       0.090 -    0.120: 41
       0.120 -    0.150: 10
  Chirality restraints: 1260
  Sorted by residual:
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  ILE B 358 "
            pdb=" N   ILE B 358 "
            pdb=" C   ILE B 358 "
            pdb=" CB  ILE B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  ILE B 181 "
            pdb=" N   ILE B 181 "
            pdb=" C   ILE B 181 "
            pdb=" CB  ILE B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 1257 not shown)

  Planarity restraints: 1380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 258 "   -0.023 5.00e-02 4.00e+02   3.54e-02 2.00e+00
        pdb=" N   PRO B 259 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 258 "   -0.023 5.00e-02 4.00e+02   3.52e-02 1.99e+00
        pdb=" N   PRO A 259 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 259 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 259 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A   6 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO A   7 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A   7 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A   7 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1377 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 81
        2.65 -     3.22: 7793
        3.22 -     3.78: 12758
        3.78 -     4.34: 17401
        4.34 -     4.90: 28722
  Nonbonded interactions: 66755
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 144 "
            pdb=" OH  TYR B 309 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   ALA A 144 "
            pdb=" OH  TYR A 309 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   LEU A  58 "
            pdb=" OG1 THR A  62 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   LEU B  58 "
            pdb=" OG1 THR B  62 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OE2 GLU A 178 "
            pdb=" OG1 THR A 489 "
     model   vdw
     2.184 3.040
  ... (remaining 66750 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             2.350
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.280
  Find NCS groups from input model:        0.140
  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:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
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      :  0.003   0.037   8218  Z= 0.206
  Angle     :  0.557   6.276  11164  Z= 0.284
  Chirality :  0.038   0.150   1260
  Planarity :  0.004   0.035   1380
  Dihedral  : 17.161  86.177   2946
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 18.50 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  1.84 (0.27), residues: 998
  helix:  1.38 (0.19), residues: 726
  sheet:  None (None), residues: 0
  loop :  1.12 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 230 
 HIS   0.002   0.001   HIS A 312 
 PHE   0.014   0.001   PHE B 570 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.003   0.001   ARG A 523 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A  157 GLU cc_start: 0.8219 (mm-30) cc_final: 0.6878 (mt-10)
REVERT: B  157 GLU cc_start: 0.8236 (mm-30) cc_final: 0.6869 (mt-10)
  outliers start: 16
  outliers final: 8
  residues processed: 112
  average time/residue: 0.2365
  time to fit residues: 34.8049
Evaluate side-chains
  104 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0470
   chunk 51 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.5684

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.156967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.124847 restraints weight = 9625.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.13
r_work: 0.3193 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8218  Z= 0.266
  Angle     :  0.592   6.443  11164  Z= 0.297
  Chirality :  0.044   0.169   1260
  Planarity :  0.005   0.039   1380
  Dihedral  :  4.365  31.074   1096
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.40 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.27), residues: 998
  helix:  1.51 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop :  1.45 (0.43), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 312 
 PHE   0.009   0.001   PHE A 534 
 TYR   0.012   0.002   TYR A 226 
 ARG   0.003   0.000   ARG A 150 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A   60 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6524 (mtt-85)
REVERT: A   70 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.6774 (mp10)
REVERT: A  463 GLN cc_start: 0.4506 (OUTLIER) cc_final: 0.4043 (pm20)
REVERT: A  469 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6987 (mt)
REVERT: A  562 TRP cc_start: 0.8074 (m-10) cc_final: 0.7696 (m-10)
REVERT: B   60 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6521 (mtt-85)
REVERT: B   70 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.6782 (mp10)
REVERT: B  463 GLN cc_start: 0.4440 (OUTLIER) cc_final: 0.3941 (pm20)
REVERT: B  562 TRP cc_start: 0.8079 (m-10) cc_final: 0.7699 (m-10)
  outliers start: 26
  outliers final: 12
  residues processed: 122
  average time/residue: 0.2579
  time to fit residues: 40.6466
Evaluate side-chains
  114 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ARG
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain B residue   60 ARG
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  604 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 92 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.157747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.125364 restraints weight = 9735.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.15
r_work: 0.3177 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8218  Z= 0.175
  Angle     :  0.503   6.405  11164  Z= 0.250
  Chirality :  0.041   0.157   1260
  Planarity :  0.004   0.032   1380
  Dihedral  :  3.738  22.383   1084
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.99 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.27), residues: 998
  helix:  1.79 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop :  1.38 (0.43), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 247 
 HIS   0.002   0.001   HIS A 531 
 PHE   0.011   0.001   PHE A 534 
 TYR   0.009   0.001   TYR A 103 
 ARG   0.002   0.000   ARG B 113 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.6763 (mp10)
REVERT: A  187 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6618 (mt0)
REVERT: A  463 GLN cc_start: 0.4510 (OUTLIER) cc_final: 0.4033 (pm20)
REVERT: A  469 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6879 (mt)
REVERT: B   70 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6747 (mp10)
REVERT: B  187 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6690 (mt0)
REVERT: B  463 GLN cc_start: 0.4473 (OUTLIER) cc_final: 0.3965 (pm20)
  outliers start: 19
  outliers final: 6
  residues processed: 117
  average time/residue: 0.2353
  time to fit residues: 36.1370
Evaluate side-chains
  112 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0980
   chunk 77 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.157275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.125303 restraints weight = 9752.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.16
r_work: 0.3194 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8218  Z= 0.156
  Angle     :  0.497   6.304  11164  Z= 0.247
  Chirality :  0.041   0.156   1260
  Planarity :  0.005   0.050   1380
  Dihedral  :  3.664  21.875   1084
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.82 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.27), residues: 998
  helix:  2.05 (0.19), residues: 726
  sheet:  None (None), residues: 0
  loop :  1.06 (0.42), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 247 
 HIS   0.001   0.000   HIS A 531 
 PHE   0.021   0.001   PHE A 310 
 TYR   0.008   0.001   TYR B  22 
 ARG   0.003   0.000   ARG A  60 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6656 (mp10)
REVERT: A  187 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6650 (mt0)
REVERT: A  219 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8056 (mmm-85)
REVERT: A  463 GLN cc_start: 0.4451 (OUTLIER) cc_final: 0.4034 (pm20)
REVERT: B   70 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6675 (mp10)
REVERT: B  187 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6643 (mt0)
REVERT: B  219 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8053 (mmm-85)
REVERT: B  463 GLN cc_start: 0.4436 (OUTLIER) cc_final: 0.3979 (pm20)
  outliers start: 26
  outliers final: 14
  residues processed: 128
  average time/residue: 0.2314
  time to fit residues: 39.1617
Evaluate side-chains
  123 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  604 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0980
   chunk 68 optimal weight:    0.0060
   chunk 88 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.157598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.125674 restraints weight = 9630.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.16
r_work: 0.3163 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8218  Z= 0.152
  Angle     :  0.487   6.232  11164  Z= 0.242
  Chirality :  0.040   0.155   1260
  Planarity :  0.004   0.037   1380
  Dihedral  :  3.588  21.228   1084
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.57 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.27), residues: 998
  helix:  2.11 (0.19), residues: 726
  sheet:  None (None), residues: 0
  loop :  1.20 (0.42), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 247 
 HIS   0.001   0.000   HIS A 312 
 PHE   0.021   0.001   PHE B 310 
 TYR   0.008   0.001   TYR B 103 
 ARG   0.002   0.000   ARG A 153 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6690 (mp10)
REVERT: A  157 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8143 (mm-30)
REVERT: A  187 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6599 (mt0)
REVERT: A  219 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8046 (mmm-85)
REVERT: A  575 MET cc_start: 0.7056 (tpp) cc_final: 0.6590 (mpp)
REVERT: B   70 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6701 (mp10)
REVERT: B  157 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8129 (mm-30)
REVERT: B  187 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6586 (mt0)
REVERT: B  219 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8051 (mmm-85)
REVERT: B  463 GLN cc_start: 0.4437 (OUTLIER) cc_final: 0.4045 (pm20)
REVERT: B  575 MET cc_start: 0.7065 (tpp) cc_final: 0.6598 (mpp)
  outliers start: 23
  outliers final: 14
  residues processed: 127
  average time/residue: 0.2318
  time to fit residues: 39.1111
Evaluate side-chains
  126 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 64 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0060
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.159011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.126892 restraints weight = 9755.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.21
r_work: 0.3152 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8218  Z= 0.157
  Angle     :  0.489   6.182  11164  Z= 0.242
  Chirality :  0.040   0.157   1260
  Planarity :  0.004   0.039   1380
  Dihedral  :  3.597  22.318   1084
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.39 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.67 (0.27), residues: 998
  helix:  2.07 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop :  1.14 (0.43), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 247 
 HIS   0.001   0.000   HIS B 312 
 PHE   0.024   0.001   PHE A 310 
 TYR   0.008   0.001   TYR B 103 
 ARG   0.001   0.000   ARG A 184 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.5569 (mtm) cc_final: 0.5287 (mtm)
REVERT: A   70 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.6713 (mp10)
REVERT: A  119 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6445 (m-30)
REVERT: A  187 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6662 (mt0)
REVERT: A  219 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8071 (mmm-85)
REVERT: A  463 GLN cc_start: 0.4300 (OUTLIER) cc_final: 0.3899 (pm20)
REVERT: A  575 MET cc_start: 0.7170 (tpp) cc_final: 0.6674 (mpp)
REVERT: B   70 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.6710 (mp10)
REVERT: B  119 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6458 (m-30)
REVERT: B  187 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6607 (mt0)
REVERT: B  219 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8085 (mmm-85)
REVERT: B  463 GLN cc_start: 0.4468 (OUTLIER) cc_final: 0.4048 (pm20)
REVERT: B  573 MET cc_start: 0.7666 (mmm) cc_final: 0.7051 (mtp)
REVERT: B  575 MET cc_start: 0.7152 (tpp) cc_final: 0.6635 (mpp)
  outliers start: 27
  outliers final: 13
  residues processed: 131
  average time/residue: 0.2199
  time to fit residues: 38.3307
Evaluate side-chains
  134 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   60 ARG
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.156723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.124923 restraints weight = 9790.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.24
r_work: 0.3123 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8218  Z= 0.182
  Angle     :  0.512   6.270  11164  Z= 0.254
  Chirality :  0.041   0.163   1260
  Planarity :  0.004   0.042   1380
  Dihedral  :  3.655  22.574   1084
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.45 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.27), residues: 998
  helix:  1.82 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop :  1.33 (0.44), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 247 
 HIS   0.001   0.001   HIS A  82 
 PHE   0.030   0.001   PHE B 310 
 TYR   0.008   0.001   TYR B 103 
 ARG   0.001   0.000   ARG A 587 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.5606 (mtm) cc_final: 0.5324 (mtm)
REVERT: A   70 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.6704 (mp10)
REVERT: A  157 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8214 (mm-30)
REVERT: A  187 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6644 (mt0)
REVERT: A  219 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8121 (mmm-85)
REVERT: A  463 GLN cc_start: 0.4368 (OUTLIER) cc_final: 0.3920 (pm20)
REVERT: A  575 MET cc_start: 0.7179 (tpp) cc_final: 0.6769 (mpp)
REVERT: B   70 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6709 (mp10)
REVERT: B  157 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8207 (mm-30)
REVERT: B  187 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6630 (mt0)
REVERT: B  219 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8121 (mmm-85)
REVERT: B  463 GLN cc_start: 0.4510 (OUTLIER) cc_final: 0.4016 (pm20)
REVERT: B  575 MET cc_start: 0.7235 (tpp) cc_final: 0.6815 (mpp)
  outliers start: 24
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2239
  time to fit residues: 37.3963
Evaluate side-chains
  128 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 79 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.8586

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.157799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.126456 restraints weight = 9806.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.09
r_work: 0.3164 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8218  Z= 0.172
  Angle     :  0.516   7.090  11164  Z= 0.254
  Chirality :  0.041   0.159   1260
  Planarity :  0.004   0.044   1380
  Dihedral  :  3.665  22.661   1084
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.10 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.27), residues: 998
  helix:  1.86 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop :  1.33 (0.44), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 247 
 HIS   0.001   0.000   HIS B 312 
 PHE   0.031   0.001   PHE A 310 
 TYR   0.007   0.001   TYR A 103 
 ARG   0.001   0.000   ARG A  18 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6828 (mp10)
REVERT: A  219 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8183 (mmm-85)
REVERT: A  463 GLN cc_start: 0.4490 (OUTLIER) cc_final: 0.4035 (pm20)
REVERT: A  575 MET cc_start: 0.7299 (tpp) cc_final: 0.6985 (tpt)
REVERT: B   70 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.6831 (mp10)
REVERT: B  187 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6719 (mt0)
REVERT: B  219 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8178 (mmm-85)
REVERT: B  463 GLN cc_start: 0.4494 (OUTLIER) cc_final: 0.4013 (pm20)
REVERT: B  575 MET cc_start: 0.7302 (tpp) cc_final: 0.6850 (mpp)
  outliers start: 23
  outliers final: 14
  residues processed: 129
  average time/residue: 0.2271
  time to fit residues: 38.8545
Evaluate side-chains
  126 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.0670
   chunk 57 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0370
   chunk 70 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0980
   chunk 59 optimal weight:    0.7980
   chunk 95 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.3196

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

Flipped N/Q/H residues before XYZ refinement:
A 317 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.160234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.129710 restraints weight = 9969.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.02
r_work: 0.3203 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8218  Z= 0.137
  Angle     :  0.491   7.545  11164  Z= 0.244
  Chirality :  0.040   0.147   1260
  Planarity :  0.004   0.045   1380
  Dihedral  :  3.556  20.942   1084
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.03 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.27), residues: 998
  helix:  2.12 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop :  1.14 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 247 
 HIS   0.002   0.000   HIS A 312 
 PHE   0.030   0.001   PHE B 310 
 TYR   0.008   0.001   TYR A  22 
 ARG   0.002   0.000   ARG A  18 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7980 (mm-30)
REVERT: A  187 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6553 (mt0)
REVERT: A  219 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8043 (mmm-85)
REVERT: A  222 ARG cc_start: 0.7401 (ptp-110) cc_final: 0.7099 (mtm-85)
REVERT: A  308 TYR cc_start: 0.8088 (m-10) cc_final: 0.7541 (m-80)
REVERT: A  463 GLN cc_start: 0.4401 (OUTLIER) cc_final: 0.3996 (pm20)
REVERT: A  573 MET cc_start: 0.7568 (mmm) cc_final: 0.7294 (mtp)
REVERT: A  575 MET cc_start: 0.7280 (tpp) cc_final: 0.6995 (tpt)
REVERT: B  157 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7972 (mm-30)
REVERT: B  187 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6643 (mt0)
REVERT: B  219 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8032 (mmm-85)
REVERT: B  222 ARG cc_start: 0.7398 (ptp-110) cc_final: 0.7108 (mtm-85)
REVERT: B  573 MET cc_start: 0.7652 (mmm) cc_final: 0.7168 (mtp)
REVERT: B  575 MET cc_start: 0.7198 (tpp) cc_final: 0.6901 (tpt)
  outliers start: 15
  outliers final: 8
  residues processed: 131
  average time/residue: 0.2361
  time to fit residues: 40.3851
Evaluate side-chains
  127 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 96 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.157231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.126329 restraints weight = 9718.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.12
r_work: 0.3130 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8218  Z= 0.162
  Angle     :  0.514   8.310  11164  Z= 0.253
  Chirality :  0.041   0.155   1260
  Planarity :  0.004   0.045   1380
  Dihedral  :  3.569  21.870   1084
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.10 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.27), residues: 998
  helix:  2.06 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop :  1.10 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 247 
 HIS   0.001   0.000   HIS A 312 
 PHE   0.013   0.001   PHE A 570 
 TYR   0.006   0.001   TYR B 103 
 ARG   0.002   0.000   ARG A 522 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8308 (mm-30)
REVERT: A  187 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6741 (mt0)
REVERT: A  219 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8130 (mmm-85)
REVERT: A  222 ARG cc_start: 0.7441 (ptp-110) cc_final: 0.7108 (mtm-85)
REVERT: A  463 GLN cc_start: 0.4484 (OUTLIER) cc_final: 0.4108 (pm20)
REVERT: A  573 MET cc_start: 0.7933 (mmm) cc_final: 0.7561 (mtp)
REVERT: A  575 MET cc_start: 0.7245 (tpp) cc_final: 0.6939 (tpt)
REVERT: B  157 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: B  187 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6709 (mt0)
REVERT: B  219 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (mmm-85)
REVERT: B  222 ARG cc_start: 0.7441 (ptp-110) cc_final: 0.7112 (mtm-85)
REVERT: B  573 MET cc_start: 0.7984 (mmm) cc_final: 0.7401 (mtp)
REVERT: B  575 MET cc_start: 0.7161 (tpp) cc_final: 0.6864 (tpt)
  outliers start: 19
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2399
  time to fit residues: 40.0136
Evaluate side-chains
  127 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   chunk 8 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.156903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.125674 restraints weight = 9775.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.13
r_work: 0.3134 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8218  Z= 0.164
  Angle     :  0.523   8.460  11164  Z= 0.259
  Chirality :  0.041   0.154   1260
  Planarity :  0.004   0.045   1380
  Dihedral  :  3.589  21.821   1084
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.45 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.27), residues: 998
  helix:  2.02 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop :  1.10 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 247 
 HIS   0.001   0.000   HIS A 312 
 PHE   0.029   0.001   PHE B 310 
 TYR   0.006   0.001   TYR A  22 
 ARG   0.003   0.000   ARG A 522 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4244.54 seconds
wall clock time: 73 minutes 16.34 seconds (4396.34 seconds total)