Starting phenix.real_space_refine
on Fri Feb 14 01:34:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7adm_11731/02_2025/7adm_11731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7adm_11731/02_2025/7adm_11731.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7adm_11731/02_2025/7adm_11731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7adm_11731/02_2025/7adm_11731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7adm_11731/02_2025/7adm_11731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7adm_11731/02_2025/7adm_11731.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       3      5.16       5
     C    3083      2.51       5
     N     851      2.21       5
     O     990      1.98       5
     H    4799      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9726
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 9726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 9726
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 22, 'TRANS': 591}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 4.97, per 1000 atoms: 0.51
  Number of scatterers: 9726
  At special positions: 0
  Unit cell: (100.57, 90.4, 110.74, 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       3     16.00
     O     990      8.00
     N     851      7.00
     C    3083      6.00
     H    4799      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.41
  Conformation dependent library (CDL) restraints added in 615.2 milliseconds
  

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1144

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 6 sheets defined
      33.1% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'C' and resid 152 through 158
    Processing helix  chain 'C' and resid 181 through 195
      removed outlier: 3.842A  pdb=" N   GLN C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA C 189 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 218
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'C' and resid 226 through 232
      removed outlier: 3.669A  pdb=" N   SER C 230 " --> pdb=" O   ASP C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 234
      No H-bonds generated for 'chain 'C' and resid 233 through 234'
    Processing helix  chain 'C' and resid 235 through 237
      No H-bonds generated for 'chain 'C' and resid 235 through 237'
    Processing helix  chain 'C' and resid 238 through 254
      removed outlier: 3.561A  pdb=" N   GLN C 243 " --> pdb=" O   SER C 239 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ASN C 244 " --> pdb=" O   GLY C 240 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU C 247 " --> pdb=" O   GLN C 243 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ARG C 248 " --> pdb=" O   ASN C 244 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   TYR C 249 " --> pdb=" O   THR C 245 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LYS C 251 " --> pdb=" O   GLU C 247 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   MET C 252 " --> pdb=" O   ARG C 248 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ASP C 254 " --> pdb=" O   LYS C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 263
      removed outlier: 4.162A  pdb=" N   LYS C 263 " --> pdb=" O   ASN C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 269
      removed outlier: 4.051A  pdb=" N   LYS C 268 " --> pdb=" O   GLU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 289
      removed outlier: 4.193A  pdb=" N   ILE C 285 " --> pdb=" O   ASN C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 291
      No H-bonds generated for 'chain 'C' and resid 290 through 291'
    Processing helix  chain 'C' and resid 292 through 296
    Processing helix  chain 'C' and resid 300 through 309
      removed outlier: 3.580A  pdb=" N   LEU C 307 " --> pdb=" O   SER C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 337
    Processing helix  chain 'C' and resid 338 through 351
      removed outlier: 3.907A  pdb=" N   SER C 349 " --> pdb=" O   ARG C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 363 through 369
    Processing helix  chain 'C' and resid 380 through 389
      removed outlier: 4.057A  pdb=" N   TYR C 384 " --> pdb=" O   VAL C 380 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS C 387 " --> pdb=" O   PRO C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 426 through 431
    Processing helix  chain 'C' and resid 432 through 442
      removed outlier: 3.582A  pdb=" N   GLN C 440 " --> pdb=" O   ILE C 436 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 463 through 469
    Processing helix  chain 'C' and resid 519 through 523
    Processing helix  chain 'C' and resid 566 through 576
    Processing helix  chain 'C' and resid 599 through 603
    Processing helix  chain 'C' and resid 654 through 658
      removed outlier: 3.963A  pdb=" N   LEU C 657 " --> pdb=" O   SER C 654 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 697 through 710
      removed outlier: 3.693A  pdb=" N   TYR C 707 " --> pdb=" O   ASN C 703 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   PHE C 708 " --> pdb=" O   LEU C 704 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TYR C 710 " --> pdb=" O   LYS C 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 131 through 133
      removed outlier: 7.292A  pdb=" N   GLU C 140 " --> pdb=" O   VAL C 178 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   VAL C 178 " --> pdb=" O   GLU C 140 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   GLU C 142 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU C 144 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LYS C 174 " --> pdb=" O   GLU C 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 312 through 313
    Processing sheet with id=AA3, first strand: chain 'C' and resid 318 through 321
      removed outlier: 3.735A  pdb=" N   GLU C 325 " --> pdb=" O   ASN C 321 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 375 through 379
      removed outlier: 3.831A  pdb=" N   ARG C 397 " --> pdb=" O   ASP C 420 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   TYR C 449 " --> pdb=" O   GLU C 478 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   PHE C 480 " --> pdb=" O   TYR C 449 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   ILE C 451 " --> pdb=" O   PHE C 480 " (cutoff:3.500A)
      removed outlier: 11.170A  pdb=" N   ASP C 473 " --> pdb=" O   ILE C 499 " (cutoff:3.500A)
      removed outlier: 10.302A  pdb=" N   GLU C 501 " --> pdb=" O   ASP C 473 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   GLN C 475 " --> pdb=" O   GLU C 501 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   SER C 503 " --> pdb=" O   GLN C 475 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   LEU C 477 " --> pdb=" O   SER C 503 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   TYR C 505 " --> pdb=" O   LEU C 477 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   LEU C 479 " --> pdb=" O   TYR C 505 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 554 through 555
      removed outlier: 6.097A  pdb=" N   LEU C 554 " --> pdb=" O   ASP C 610 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 650 through 651
      removed outlier: 6.695A  pdb=" N   PHE C 650 " --> pdb=" O   ARG C 689 " (cutoff:3.500A)

    120 hydrogen bonds defined for protein.
    318 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: 3.17

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        0.89 -     1.08: 1364
        1.08 -     1.26: 4304
        1.26 -     1.45: 1327
        1.45 -     1.63: 2819
        1.63 -     1.81: 6
  Bond restraints: 9820
  Sorted by residual:
  bond pdb=" CD2 TYR C 539 "
       pdb=" HD2 TYR C 539 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   ARG C 450 "
       pdb=" H   ARG C 450 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   GLY C 593 "
       pdb=" H   GLY C 593 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" NE2 GLN C 153 "
       pdb="HE22 GLN C 153 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   LYS C 272 "
       pdb=" H   LYS C 272 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 9815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 12480
        1.97 -     3.95: 3936
        3.95 -     5.92: 805
        5.92 -     7.90: 423
        7.90 -     9.87: 59
  Bond angle restraints: 17703
  Sorted by residual:
  angle pdb=" N   LYS C 500 "
        pdb=" CA  LYS C 500 "
        pdb=" C   LYS C 500 "
      ideal   model   delta    sigma   weight residual
     111.28  121.15   -9.87 1.35e+00 5.49e-01 5.35e+01
  angle pdb=" CA  ASP C 420 "
        pdb=" CB  ASP C 420 "
        pdb=" CG  ASP C 420 "
      ideal   model   delta    sigma   weight residual
     112.60  119.90   -7.30 1.00e+00 1.00e+00 5.33e+01
  angle pdb=" CA  HIS C 590 "
        pdb=" CB  HIS C 590 "
        pdb=" CG  HIS C 590 "
      ideal   model   delta    sigma   weight residual
     113.80  121.09   -7.29 1.00e+00 1.00e+00 5.32e+01
  angle pdb=" CA  ASP C 483 "
        pdb=" CB  ASP C 483 "
        pdb=" CG  ASP C 483 "
      ideal   model   delta    sigma   weight residual
     112.60  119.84   -7.24 1.00e+00 1.00e+00 5.24e+01
  angle pdb=" CA  ASP C 557 "
        pdb=" CB  ASP C 557 "
        pdb=" CG  ASP C 557 "
      ideal   model   delta    sigma   weight residual
     112.60  118.53   -5.93 1.00e+00 1.00e+00 3.51e+01
  ... (remaining 17698 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 4132
       17.31 -    34.62: 331
       34.62 -    51.92: 95
       51.92 -    69.23: 55
       69.23 -    86.54: 12
  Dihedral angle restraints: 4625
    sinusoidal: 2539
      harmonic: 2086
  Sorted by residual:
  dihedral pdb=" CA  ILE C 499 "
           pdb=" C   ILE C 499 "
           pdb=" N   LYS C 500 "
           pdb=" CA  LYS C 500 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.87   29.13     0      5.00e+00 4.00e-02 3.40e+01
  dihedral pdb=" CA  LYS C 500 "
           pdb=" C   LYS C 500 "
           pdb=" N   GLU C 501 "
           pdb=" CA  GLU C 501 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.99   29.01     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  LYS C 497 "
           pdb=" C   LYS C 497 "
           pdb=" N   ASN C 498 "
           pdb=" CA  ASN C 498 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.90   28.10     0      5.00e+00 4.00e-02 3.16e+01
  ... (remaining 4622 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 437
       0.093 -    0.185: 229
       0.185 -    0.277: 40
       0.277 -    0.369: 8
       0.369 -    0.461: 3
  Chirality restraints: 717
  Sorted by residual:
  chirality pdb=" CA  LYS C 500 "
            pdb=" N   LYS C 500 "
            pdb=" C   LYS C 500 "
            pdb=" CB  LYS C 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" CA  SER C 717 "
            pdb=" N   SER C 717 "
            pdb=" C   SER C 717 "
            pdb=" CB  SER C 717 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.19e+00
  chirality pdb=" CA  ASP C 557 "
            pdb=" N   ASP C 557 "
            pdb=" C   ASP C 557 "
            pdb=" CB  ASP C 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.09e+00
  ... (remaining 714 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 337 "    0.247 2.00e-02 2.50e+03   1.00e-01 3.02e+02
        pdb=" CG  TYR C 337 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 337 "   -0.099 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 337 "   -0.067 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 337 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 337 "   -0.058 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 337 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR C 337 "    0.176 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 337 "   -0.074 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 337 "   -0.039 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 337 "    0.015 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 337 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 580 "   -0.162 9.50e-02 1.11e+02   1.04e-01 1.79e+02
        pdb=" NE  ARG C 580 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 580 "   -0.029 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 580 "   -0.024 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 580 "   -0.052 2.00e-02 2.50e+03
        pdb="HH11 ARG C 580 "    0.142 2.00e-02 2.50e+03
        pdb="HH12 ARG C 580 "   -0.152 2.00e-02 2.50e+03
        pdb="HH21 ARG C 580 "   -0.015 2.00e-02 2.50e+03
        pdb="HH22 ARG C 580 "    0.150 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 527 "    0.173 2.00e-02 2.50e+03   6.64e-02 1.77e+02
        pdb=" CG  TRP C 527 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 527 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 527 "   -0.064 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 527 "   -0.083 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 527 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 527 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 527 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 527 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 527 "    0.048 2.00e-02 2.50e+03
        pdb=" HD1 TRP C 527 "    0.054 2.00e-02 2.50e+03
        pdb=" HE1 TRP C 527 "   -0.015 2.00e-02 2.50e+03
        pdb=" HE3 TRP C 527 "   -0.083 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C 527 "    0.027 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C 527 "   -0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP C 527 "    0.095 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 890
        2.22 -     2.82: 18202
        2.82 -     3.41: 26010
        3.41 -     4.01: 33717
        4.01 -     4.60: 49631
  Nonbonded interactions: 128450
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C 456 "
            pdb=" HG  SER C 482 "
     model   vdw
     1.629 2.450
  nonbonded pdb=" HH  TYR C 388 "
            pdb=" OD2 ASP C 442 "
     model   vdw
     1.635 2.450
  nonbonded pdb=" HH  TYR C 167 "
            pdb=" OD2 ASP C 347 "
     model   vdw
     1.645 2.450
  nonbonded pdb=" O   GLU C 382 "
            pdb=" HG  SER C 385 "
     model   vdw
     1.645 2.450
  nonbonded pdb=" O   GLN C 587 "
            pdb=" HG  SER C 604 "
     model   vdw
     1.657 2.450
  ... (remaining 128445 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  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:             0.160
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.270
  Find NCS groups from input model:        0.070
  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:   27.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
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      :  0.013   0.105   5021  Z= 0.858
  Angle     :  1.978   9.870   6770  Z= 1.320
  Chirality :  0.108   0.461    717
  Planarity :  0.015   0.121    897
  Dihedral  : 15.369  86.540   1914
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.93 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  6.79 %
    Favored  : 92.48 %
  Cbeta Deviations :  0.52 %
  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: -2.91 (0.30), residues: 612
  helix: -3.29 (0.30), residues: 152
  sheet:  1.91 (1.10), residues: 22
  loop : -1.73 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.121   0.035   TRP C 527 
 HIS   0.011   0.004   HIS C 170 
 PHE   0.067   0.014   PHE C 625 
 TYR   0.215   0.021   TYR C 337 
 ARG   0.007   0.001   ARG C 362 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7354 (mttt)
REVERT: C  298 LYS cc_start: 0.6752 (ttmt) cc_final: 0.6397 (tttp)
REVERT: C  345 ARG cc_start: 0.7148 (ttm170) cc_final: 0.6738 (ttm-80)
REVERT: C  365 ASP cc_start: 0.7718 (t70) cc_final: 0.7381 (t0)
REVERT: C  425 ASN cc_start: 0.6655 (t0) cc_final: 0.6023 (t0)
REVERT: C  437 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: C  538 GLU cc_start: 0.4530 (OUTLIER) cc_final: 0.2603 (tt0)
REVERT: C  607 THR cc_start: 0.8431 (p) cc_final: 0.8214 (t)
REVERT: C  639 THR cc_start: 0.9016 (p) cc_final: 0.8533 (p)
REVERT: C  701 ARG cc_start: 0.5563 (mtt180) cc_final: 0.5317 (tpp80)
REVERT: C  712 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6346 (mm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 129
  average time/residue: 0.5130
  time to fit residues: 79.2587
Evaluate side-chains
  84 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  377 LYS
Chi-restraints excluded: chain C residue  538 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
C 212 ASN
C 290 ASN
C 293 GLN
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 590 HIS
C 663 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.177113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.151070 restraints weight = 20191.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.157002 restraints weight = 8922.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.160911 restraints weight = 5255.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5021  Z= 0.198
  Angle     :  0.644   5.050   6770  Z= 0.357
  Chirality :  0.042   0.143    717
  Planarity :  0.004   0.036    897
  Dihedral  :  7.598  50.451    678
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.64 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 (0.32), residues: 612
  helix: -2.12 (0.36), residues: 148
  sheet:  1.86 (1.00), residues: 32
  loop : -1.50 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 527 
 HIS   0.009   0.002   HIS C 590 
 PHE   0.016   0.002   PHE C 206 
 TYR   0.014   0.002   TYR C 644 
 ARG   0.006   0.001   ARG C 154 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  96 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 LYS cc_start: 0.6760 (mmtm) cc_final: 0.6325 (mttt)
REVERT: C  338 ASN cc_start: 0.8353 (t0) cc_final: 0.7844 (t0)
REVERT: C  345 ARG cc_start: 0.7389 (ttm170) cc_final: 0.6847 (ttm-80)
REVERT: C  356 TYR cc_start: 0.8639 (p90) cc_final: 0.8126 (p90)
REVERT: C  365 ASP cc_start: 0.7756 (t70) cc_final: 0.7491 (t70)
REVERT: C  567 GLU cc_start: 0.7414 (tp30) cc_final: 0.6810 (mt-10)
REVERT: C  634 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7795 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 93
  average time/residue: 0.4278
  time to fit residues: 49.8674
Evaluate side-chains
  68 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  168 GLN
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  377 LYS
Chi-restraints excluded: chain C residue  413 LEU
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 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 = 0.4010 r_free = 0.4010 target = 0.173732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.144938 restraints weight = 21362.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.151188 restraints weight = 9635.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155308 restraints weight = 5831.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5021  Z= 0.251
  Angle     :  0.595   4.840   6770  Z= 0.326
  Chirality :  0.041   0.148    717
  Planarity :  0.004   0.066    897
  Dihedral  :  6.406  33.091    675
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.66 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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: -2.08 (0.32), residues: 612
  helix: -1.87 (0.37), residues: 162
  sheet:  1.94 (1.01), residues: 32
  loop : -1.53 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 527 
 HIS   0.014   0.003   HIS C 590 
 PHE   0.012   0.001   PHE C 206 
 TYR   0.011   0.001   TYR C 578 
 ARG   0.009   0.001   ARG C 346 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 LYS cc_start: 0.6957 (mmtm) cc_final: 0.6527 (mttt)
REVERT: C  345 ARG cc_start: 0.7363 (ttm170) cc_final: 0.6779 (ttm-80)
REVERT: C  365 ASP cc_start: 0.7566 (t70) cc_final: 0.7036 (t0)
REVERT: C  377 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7489 (tttt)
REVERT: C  474 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7302 (mt)
REVERT: C  494 LEU cc_start: 0.6108 (mt) cc_final: 0.5845 (mt)
REVERT: C  567 GLU cc_start: 0.7391 (tp30) cc_final: 0.6734 (mt-10)
REVERT: C  634 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7793 (mt-10)
REVERT: C  701 ARG cc_start: 0.5779 (mtt180) cc_final: 0.5523 (tpp80)
  outliers start: 11
  outliers final: 6
  residues processed: 82
  average time/residue: 0.3953
  time to fit residues: 41.2832
Evaluate side-chains
  72 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  377 LYS
Chi-restraints excluded: chain C residue  413 LEU
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 453 ASN
C 529 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.174035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148141 restraints weight = 20672.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.154176 restraints weight = 8885.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.158106 restraints weight = 5172.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5021  Z= 0.211
  Angle     :  0.542   4.846   6770  Z= 0.295
  Chirality :  0.040   0.137    717
  Planarity :  0.004   0.082    897
  Dihedral  :  6.024  33.653    675
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.21 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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: -1.95 (0.33), residues: 612
  helix: -1.63 (0.38), residues: 162
  sheet:  0.89 (0.94), residues: 42
  loop : -1.45 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 527 
 HIS   0.009   0.002   HIS C 590 
 PHE   0.009   0.001   PHE C 390 
 TYR   0.009   0.001   TYR C 388 
 ARG   0.008   0.000   ARG C 346 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  158 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7511 (tpp-160)
REVERT: C  190 LYS cc_start: 0.7109 (mmtm) cc_final: 0.6713 (mttt)
REVERT: C  308 GLU cc_start: 0.6431 (tp30) cc_final: 0.5976 (tp30)
REVERT: C  345 ARG cc_start: 0.7265 (ttm170) cc_final: 0.6718 (ttm-80)
REVERT: C  356 TYR cc_start: 0.8625 (p90) cc_final: 0.8111 (p90)
REVERT: C  365 ASP cc_start: 0.7562 (t70) cc_final: 0.7079 (t0)
REVERT: C  425 ASN cc_start: 0.7713 (t0) cc_final: 0.7480 (t0)
REVERT: C  538 GLU cc_start: 0.4547 (OUTLIER) cc_final: 0.2912 (tt0)
REVERT: C  567 GLU cc_start: 0.7385 (tp30) cc_final: 0.6768 (mt-10)
REVERT: C  634 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7922 (mt-10)
REVERT: C  701 ARG cc_start: 0.5706 (mtt180) cc_final: 0.5354 (tpp80)
  outliers start: 12
  outliers final: 8
  residues processed: 75
  average time/residue: 0.3761
  time to fit residues: 36.5180
Evaluate side-chains
  74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  350 GLU
Chi-restraints excluded: chain C residue  413 LEU
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  538 GLU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  573 LEU
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    0.2980
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 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 = 0.4040 r_free = 0.4040 target = 0.176350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.148432 restraints weight = 21085.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.154830 restraints weight = 9365.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.159022 restraints weight = 5604.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.4640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5021  Z= 0.153
  Angle     :  0.494   4.645   6770  Z= 0.266
  Chirality :  0.039   0.132    717
  Planarity :  0.004   0.068    897
  Dihedral  :  5.271  29.427    671
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.03 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.33), residues: 612
  helix: -1.10 (0.41), residues: 155
  sheet:  1.47 (0.96), residues: 37
  loop : -1.42 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 527 
 HIS   0.005   0.001   HIS C 590 
 PHE   0.008   0.001   PHE C 390 
 TYR   0.017   0.001   TYR C 578 
 ARG   0.006   0.000   ARG C 346 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  83 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  158 ARG cc_start: 0.7903 (tpp-160) cc_final: 0.7474 (tpp-160)
REVERT: C  190 LYS cc_start: 0.7039 (mmtm) cc_final: 0.6663 (mttt)
REVERT: C  308 GLU cc_start: 0.6589 (tp30) cc_final: 0.6209 (tp30)
REVERT: C  356 TYR cc_start: 0.8603 (p90) cc_final: 0.8026 (p90)
REVERT: C  365 ASP cc_start: 0.7590 (t70) cc_final: 0.7278 (t0)
REVERT: C  425 ASN cc_start: 0.7773 (t0) cc_final: 0.7565 (t0)
REVERT: C  538 GLU cc_start: 0.4173 (OUTLIER) cc_final: 0.2448 (tt0)
REVERT: C  567 GLU cc_start: 0.7326 (tp30) cc_final: 0.6830 (mt-10)
REVERT: C  573 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7465 (mp)
REVERT: C  634 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8017 (mt-10)
REVERT: C  701 ARG cc_start: 0.5808 (mtt180) cc_final: 0.5375 (tpp80)
  outliers start: 14
  outliers final: 8
  residues processed: 80
  average time/residue: 0.3060
  time to fit residues: 32.7139
Evaluate side-chains
  71 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  426 ASP
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  538 GLU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  573 LEU
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 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 = 0.4004 r_free = 0.4004 target = 0.172784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.144574 restraints weight = 21110.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.150898 restraints weight = 9473.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.155087 restraints weight = 5691.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.4851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5021  Z= 0.194
  Angle     :  0.509   4.680   6770  Z= 0.275
  Chirality :  0.039   0.135    717
  Planarity :  0.004   0.059    897
  Dihedral  :  5.208  28.837    671
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.68 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.33), residues: 612
  helix: -0.91 (0.42), residues: 155
  sheet:  1.23 (1.11), residues: 27
  loop : -1.35 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 286 
 HIS   0.010   0.002   HIS C 590 
 PHE   0.008   0.001   PHE C 390 
 TYR   0.007   0.001   TYR C 167 
 ARG   0.004   0.000   ARG C 346 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  158 ARG cc_start: 0.7930 (tpp-160) cc_final: 0.7486 (tpp-160)
REVERT: C  190 LYS cc_start: 0.7150 (mmtm) cc_final: 0.6710 (mttt)
REVERT: C  308 GLU cc_start: 0.6561 (tp30) cc_final: 0.6234 (tp30)
REVERT: C  356 TYR cc_start: 0.8671 (p90) cc_final: 0.8069 (p90)
REVERT: C  365 ASP cc_start: 0.7597 (t70) cc_final: 0.7353 (t0)
REVERT: C  425 ASN cc_start: 0.7896 (t0) cc_final: 0.7674 (t0)
REVERT: C  538 GLU cc_start: 0.4321 (OUTLIER) cc_final: 0.2580 (tt0)
REVERT: C  565 SER cc_start: 0.8866 (t) cc_final: 0.8421 (p)
REVERT: C  567 GLU cc_start: 0.7453 (tp30) cc_final: 0.6874 (mt-10)
REVERT: C  634 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8039 (mt-10)
REVERT: C  701 ARG cc_start: 0.5747 (mtt180) cc_final: 0.5254 (tpp80)
  outliers start: 13
  outliers final: 11
  residues processed: 72
  average time/residue: 0.3261
  time to fit residues: 31.2490
Evaluate side-chains
  73 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  350 GLU
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  426 ASP
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  538 GLU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  573 LEU
Chi-restraints excluded: chain C residue  681 ASN
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 529 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.168602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.143030 restraints weight = 21018.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.148910 restraints weight = 9067.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.152875 restraints weight = 5291.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   5021  Z= 0.333
  Angle     :  0.574   4.867   6770  Z= 0.312
  Chirality :  0.042   0.149    717
  Planarity :  0.005   0.050    897
  Dihedral  :  5.540  31.360    671
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.68 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -1.92 (0.33), residues: 612
  helix: -1.06 (0.42), residues: 155
  sheet:  0.25 (1.06), residues: 32
  loop : -1.56 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 286 
 HIS   0.016   0.003   HIS C 590 
 PHE   0.009   0.002   PHE C 206 
 TYR   0.011   0.001   TYR C 167 
 ARG   0.003   0.001   ARG C 430 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 LYS cc_start: 0.7395 (mmtm) cc_final: 0.6977 (mttt)
REVERT: C  365 ASP cc_start: 0.7676 (t70) cc_final: 0.7336 (t0)
REVERT: C  425 ASN cc_start: 0.7970 (t0) cc_final: 0.7769 (t0)
REVERT: C  538 GLU cc_start: 0.4469 (OUTLIER) cc_final: 0.2835 (tt0)
REVERT: C  565 SER cc_start: 0.8799 (t) cc_final: 0.8217 (p)
REVERT: C  567 GLU cc_start: 0.7611 (tp30) cc_final: 0.7069 (mt-10)
REVERT: C  634 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8102 (mt-10)
REVERT: C  701 ARG cc_start: 0.5662 (mtt180) cc_final: 0.5027 (tpp80)
  outliers start: 14
  outliers final: 11
  residues processed: 73
  average time/residue: 0.3143
  time to fit residues: 31.0362
Evaluate side-chains
  73 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  350 GLU
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  426 ASP
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  538 GLU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  573 LEU
Chi-restraints excluded: chain C residue  681 ASN
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 529 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.171606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.146090 restraints weight = 21053.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151903 restraints weight = 9251.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.155864 restraints weight = 5491.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.5109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5021  Z= 0.202
  Angle     :  0.513   4.628   6770  Z= 0.278
  Chirality :  0.039   0.139    717
  Planarity :  0.004   0.054    897
  Dihedral  :  5.227  28.890    671
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.86 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.33), residues: 612
  helix: -0.95 (0.42), residues: 155
  sheet:  0.85 (1.09), residues: 27
  loop : -1.49 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 527 
 HIS   0.009   0.002   HIS C 590 
 PHE   0.008   0.001   PHE C 390 
 TYR   0.007   0.001   TYR C 167 
 ARG   0.003   0.000   ARG C 346 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6856 (mttt)
REVERT: C  365 ASP cc_start: 0.7568 (t70) cc_final: 0.7200 (t0)
REVERT: C  474 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7130 (mt)
REVERT: C  538 GLU cc_start: 0.4469 (OUTLIER) cc_final: 0.2810 (tt0)
REVERT: C  565 SER cc_start: 0.8819 (t) cc_final: 0.8088 (p)
REVERT: C  567 GLU cc_start: 0.7450 (tp30) cc_final: 0.6920 (mt-10)
REVERT: C  634 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8071 (mt-10)
REVERT: C  701 ARG cc_start: 0.5639 (mtt180) cc_final: 0.4965 (tpp80)
  outliers start: 15
  outliers final: 11
  residues processed: 71
  average time/residue: 0.3388
  time to fit residues: 32.2134
Evaluate side-chains
  71 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  350 GLU
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  426 ASP
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  538 GLU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  573 LEU
Chi-restraints excluded: chain C residue  681 ASN
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.0164

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 ASN
C 529 ASN
C 703 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.171814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.145521 restraints weight = 20580.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.151676 restraints weight = 8843.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.155691 restraints weight = 5146.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.5285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5021  Z= 0.164
  Angle     :  0.495   4.587   6770  Z= 0.267
  Chirality :  0.039   0.129    717
  Planarity :  0.004   0.051    897
  Dihedral  :  4.884  27.519    671
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.78 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.33), residues: 612
  helix: -0.59 (0.44), residues: 155
  sheet: -0.08 (0.83), residues: 42
  loop : -1.39 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 527 
 HIS   0.006   0.001   HIS C 590 
 PHE   0.008   0.001   PHE C 390 
 TYR   0.006   0.001   TYR C 578 
 ARG   0.003   0.000   ARG C 346 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6836 (mttt)
REVERT: C  538 GLU cc_start: 0.4427 (OUTLIER) cc_final: 0.2634 (tt0)
REVERT: C  567 GLU cc_start: 0.7406 (tp30) cc_final: 0.6946 (mt-10)
REVERT: C  634 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: C  701 ARG cc_start: 0.5651 (mtt180) cc_final: 0.4948 (tpp80)
  outliers start: 12
  outliers final: 8
  residues processed: 71
  average time/residue: 0.3193
  time to fit residues: 30.8054
Evaluate side-chains
  66 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  350 GLU
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  538 GLU
Chi-restraints excluded: chain C residue  645 ASN
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 6 optimal weight:    0.2980
   chunk 21 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 529 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.172161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.145887 restraints weight = 20643.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.152028 restraints weight = 8830.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.156088 restraints weight = 5127.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.5408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5021  Z= 0.165
  Angle     :  0.497   4.565   6770  Z= 0.270
  Chirality :  0.039   0.133    717
  Planarity :  0.004   0.050    897
  Dihedral  :  4.772  27.633    671
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.51 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.33), residues: 612
  helix: -0.61 (0.43), residues: 156
  sheet:  0.09 (0.84), residues: 42
  loop : -1.33 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 527 
 HIS   0.007   0.001   HIS C 590 
 PHE   0.008   0.001   PHE C 390 
 TYR   0.007   0.001   TYR C 337 
 ARG   0.003   0.000   ARG C 346 

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  500 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 LYS cc_start: 0.7206 (mmtm) cc_final: 0.6780 (mttt)
REVERT: C  538 GLU cc_start: 0.4403 (OUTLIER) cc_final: 0.2582 (tt0)
REVERT: C  567 GLU cc_start: 0.7429 (tp30) cc_final: 0.6952 (mt-10)
REVERT: C  634 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: C  701 ARG cc_start: 0.5468 (mtt180) cc_final: 0.5089 (tpp80)
  outliers start: 10
  outliers final: 7
  residues processed: 66
  average time/residue: 0.3307
  time to fit residues: 29.3459
Evaluate side-chains
  68 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  350 GLU
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  446 ILE
Chi-restraints excluded: chain C residue  538 GLU
Chi-restraints excluded: chain C residue  645 ASN
Chi-restraints excluded: chain C residue  704 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 9 optimal weight:    0.2980
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 529 ASN
C 703 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.173247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.147537 restraints weight = 20471.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.153510 restraints weight = 8846.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.157495 restraints weight = 5174.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.5496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5021  Z= 0.159
  Angle     :  0.487   4.565   6770  Z= 0.263
  Chirality :  0.038   0.129    717
  Planarity :  0.004   0.050    897
  Dihedral  :  4.647  26.664    671
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.15 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.34), residues: 612
  helix: -0.51 (0.43), residues: 156
  sheet: -0.36 (0.73), residues: 53
  loop : -1.33 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 527 
 HIS   0.006   0.001   HIS C 590 
 PHE   0.007   0.001   PHE C 390 
 TYR   0.008   0.001   TYR C 337 
 ARG   0.002   0.000   ARG C 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3577.71 seconds
wall clock time: 63 minutes 37.95 seconds (3817.95 seconds total)