Starting phenix.real_space_refine
on Tue Feb 11 22:09:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sy0_25512/02_2025/7sy0_25512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sy0_25512/02_2025/7sy0_25512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sy0_25512/02_2025/7sy0_25512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sy0_25512/02_2025/7sy0_25512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sy0_25512/02_2025/7sy0_25512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sy0_25512/02_2025/7sy0_25512.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.029
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      37      5.16       5
     C    4186      2.51       5
     N    1081      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6553
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1593
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.73, per 1000 atoms: 0.72
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (79, 84, 121, 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      37     16.00
     O    1249      8.00
     N    1081      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 995.7 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      57.3% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.708A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.162A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU E  39 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.781A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.028A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 146 through 155
      removed outlier: 3.933A  pdb=" N   ILE E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.725A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.669A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.784A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 301
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.541A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.701A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.235A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.310A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.726A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.458A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.931A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.911A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.620A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 5.966A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.313A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    918 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: 1.81

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2086
        1.35 -     1.47: 1795
        1.47 -     1.60: 2796
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.64e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.20e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.35e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 3.95e+00
  bond pdb=" C   SER E 611 "
       pdb=" N   PRO E 612 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.73e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 8817
        2.05 -     4.10: 289
        4.10 -     6.15: 36
        6.15 -     8.20: 6
        8.20 -    10.24: 4
  Bond angle restraints: 9152
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.82  128.96   -6.14 1.42e+00 4.96e-01 1.87e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  123.65   -9.25 2.30e+00 1.89e-01 1.62e+01
  angle pdb=" CB  MET E 323 "
        pdb=" CG  MET E 323 "
        pdb=" SD  MET E 323 "
      ideal   model   delta    sigma   weight residual
     112.70  122.94  -10.24 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  115.96   -3.36 1.00e+00 1.00e+00 1.13e+01
  angle pdb=" N   LYS E 234 "
        pdb=" CA  LYS E 234 "
        pdb=" C   LYS E 234 "
      ideal   model   delta    sigma   weight residual
     113.16  117.68   -4.52 1.42e+00 4.96e-01 1.01e+01
  ... (remaining 9147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 3688
       17.12 -    34.25: 314
       34.25 -    51.37: 43
       51.37 -    68.50: 11
       68.50 -    85.62: 12
  Dihedral angle restraints: 4068
    sinusoidal: 1730
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -42.93  -43.07     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   17.52   61.48     1      2.00e+01 2.50e-03 1.25e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.76    8.16     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 4065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 724
       0.055 -    0.109: 197
       0.109 -    0.164: 46
       0.164 -    0.218: 7
       0.218 -    0.273: 3
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  VAL E 318 "
            pdb=" CA  VAL E 318 "
            pdb=" CG1 VAL E 318 "
            pdb=" CG2 VAL E 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 974 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E  36 "    0.025 2.00e-02 2.50e+03   4.97e-02 2.47e+01
        pdb=" C   ALA E  36 "   -0.086 2.00e-02 2.50e+03
        pdb=" O   ALA E  36 "    0.032 2.00e-02 2.50e+03
        pdb=" N   GLU E  37 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.017 2.00e-02 2.50e+03   3.46e-02 1.20e+01
        pdb=" C   ARG E 169 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.022 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  32 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.31e+00
        pdb=" C   PHE E  32 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   PHE E  32 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASN E  33 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1834
        2.82 -     3.34: 5957
        3.34 -     3.86: 11435
        3.86 -     4.38: 12999
        4.38 -     4.90: 22431
  Nonbonded interactions: 54656
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 500 "
            pdb=" OH  TYR E  41 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.338 3.040
  ... (remaining 54651 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.020
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.200
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
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      :  0.005   0.057   6735  Z= 0.327
  Angle     :  0.843  10.244   9152  Z= 0.460
  Chirality :  0.055   0.273    977
  Planarity :  0.007   0.065   1178
  Dihedral  : 13.353  85.622   2550
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.26), residues: 793
  helix: -0.06 (0.23), residues: 387
  sheet:  0.55 (0.66), residues: 52
  loop : -0.63 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.030   0.003   PHE E 369 
 TYR   0.032   0.002   TYR E 385 
 ARG   0.011   0.001   ARG E 460 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: E  142 LEU cc_start: 0.9130 (mt) cc_final: 0.8923 (mt)
REVERT: E  149 ASN cc_start: 0.9200 (m-40) cc_final: 0.8949 (m-40)
REVERT: E  249 MET cc_start: 0.9324 (ttm) cc_final: 0.9031 (ttp)
REVERT: E  290 ASN cc_start: 0.8984 (t0) cc_final: 0.8685 (t0)
REVERT: E  347 THR cc_start: 0.8821 (m) cc_final: 0.8354 (p)
REVERT: E  371 THR cc_start: 0.9207 (m) cc_final: 0.8930 (p)
REVERT: E  441 LYS cc_start: 0.8993 (tttp) cc_final: 0.8572 (ttmm)
REVERT: E  455 MET cc_start: 0.8781 (tmm) cc_final: 0.8460 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 1.3349
  time to fit residues: 177.6051
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0470
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
E 154 ASN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.077169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.059372 restraints weight = 18170.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 3.46
r_work: 0.2836 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6735  Z= 0.204
  Angle     :  0.565   9.284   9152  Z= 0.294
  Chirality :  0.041   0.143    977
  Planarity :  0.005   0.039   1178
  Dihedral  :  4.991  48.531   1013
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.57 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.28), residues: 793
  helix:  1.01 (0.25), residues: 403
  sheet:  0.86 (0.75), residues: 43
  loop : -0.10 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 466 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.768 
Fit side-chains
REVERT: B  484 GLU cc_start: 0.8774 (tt0) cc_final: 0.8528 (tp30)
REVERT: E   55 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8664 (p)
REVERT: E  149 ASN cc_start: 0.9210 (m-40) cc_final: 0.8885 (m110)
REVERT: E  224 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8216 (pp20)
REVERT: E  249 MET cc_start: 0.9302 (ttm) cc_final: 0.9006 (ttp)
REVERT: E  347 THR cc_start: 0.8791 (m) cc_final: 0.8318 (p)
REVERT: E  360 MET cc_start: 0.9131 (ttp) cc_final: 0.8862 (ttm)
REVERT: E  366 MET cc_start: 0.8585 (ttp) cc_final: 0.8380 (ttm)
REVERT: E  371 THR cc_start: 0.9155 (m) cc_final: 0.8943 (p)
REVERT: E  441 LYS cc_start: 0.8979 (tttp) cc_final: 0.8597 (ttmm)
REVERT: E  455 MET cc_start: 0.9107 (tmm) cc_final: 0.8847 (tmm)
REVERT: E  474 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7312 (mmt)
REVERT: E  578 ASN cc_start: 0.8508 (t0) cc_final: 0.8221 (p0)
  outliers start: 13
  outliers final: 4
  residues processed: 66
  average time/residue: 1.2044
  time to fit residues: 84.1731
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0980
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** E 374 HIS ** 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 = 0.3337 r_free = 0.3337 target = 0.075957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.057957 restraints weight = 18172.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 3.44
r_work: 0.2810 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6735  Z= 0.210
  Angle     :  0.527   7.480   9152  Z= 0.271
  Chirality :  0.041   0.144    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.686  50.649   1013
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 10.71 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.23 (0.30), residues: 793
  helix:  1.45 (0.26), residues: 402
  sheet:  0.95 (0.79), residues: 42
  loop :  0.17 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 466 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: B  523 THR cc_start: 0.8531 (p) cc_final: 0.8271 (t)
REVERT: E  149 ASN cc_start: 0.9232 (m-40) cc_final: 0.8833 (m110)
REVERT: E  224 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8232 (pp20)
REVERT: E  249 MET cc_start: 0.9269 (ttm) cc_final: 0.8939 (ttp)
REVERT: E  347 THR cc_start: 0.8821 (m) cc_final: 0.8355 (p)
REVERT: E  371 THR cc_start: 0.9179 (m) cc_final: 0.8974 (p)
REVERT: E  441 LYS cc_start: 0.9041 (tttp) cc_final: 0.8580 (ttmm)
REVERT: E  455 MET cc_start: 0.9130 (tmm) cc_final: 0.8929 (tmm)
  outliers start: 13
  outliers final: 6
  residues processed: 64
  average time/residue: 1.2218
  time to fit residues: 83.5834
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 68 optimal weight:    0.2980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0050
   chunk 19 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.076440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.058515 restraints weight = 18311.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 3.46
r_work: 0.2819 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6735  Z= 0.175
  Angle     :  0.501   7.942   9152  Z= 0.257
  Chirality :  0.040   0.133    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.536  51.801   1013
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.71 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.54 (0.30), residues: 793
  helix:  1.73 (0.26), residues: 387
  sheet:  0.83 (0.79), residues: 42
  loop :  0.39 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 466 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8752 (p)
REVERT: E  149 ASN cc_start: 0.9260 (m-40) cc_final: 0.8883 (m110)
REVERT: E  224 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8219 (pp20)
REVERT: E  249 MET cc_start: 0.9282 (ttm) cc_final: 0.8959 (ttp)
REVERT: E  347 THR cc_start: 0.8895 (m) cc_final: 0.8455 (p)
REVERT: E  441 LYS cc_start: 0.9075 (tttp) cc_final: 0.8602 (ttmm)
REVERT: E  455 MET cc_start: 0.9159 (tmm) cc_final: 0.8956 (tmm)
REVERT: E  522 GLN cc_start: 0.8516 (tt0) cc_final: 0.8177 (tt0)
REVERT: E  578 ASN cc_start: 0.8606 (t0) cc_final: 0.8244 (p0)
  outliers start: 14
  outliers final: 6
  residues processed: 71
  average time/residue: 1.1260
  time to fit residues: 84.9320
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** 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 = 0.3318 r_free = 0.3318 target = 0.075083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.057030 restraints weight = 18189.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.45
r_work: 0.2787 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6735  Z= 0.227
  Angle     :  0.518   9.373   9152  Z= 0.266
  Chirality :  0.041   0.169    977
  Planarity :  0.004   0.039   1178
  Dihedral  :  4.549  52.136   1013
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.14 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.69 (0.30), residues: 793
  helix:  1.82 (0.27), residues: 387
  sheet:  0.84 (0.78), residues: 42
  loop :  0.52 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8752 (p)
REVERT: E  149 ASN cc_start: 0.9273 (m-40) cc_final: 0.8966 (m110)
REVERT: E  224 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8255 (pp20)
REVERT: E  249 MET cc_start: 0.9346 (ttm) cc_final: 0.9015 (ttp)
REVERT: E  323 MET cc_start: 0.9426 (mmm) cc_final: 0.9087 (mmm)
REVERT: E  347 THR cc_start: 0.8910 (m) cc_final: 0.8494 (p)
REVERT: E  366 MET cc_start: 0.8761 (ttp) cc_final: 0.8432 (ttm)
REVERT: E  441 LYS cc_start: 0.9082 (tttp) cc_final: 0.8624 (ttmm)
  outliers start: 14
  outliers final: 7
  residues processed: 61
  average time/residue: 1.2414
  time to fit residues: 80.1692
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** 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 = 0.3334 r_free = 0.3334 target = 0.075870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.057997 restraints weight = 18094.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 3.42
r_work: 0.2808 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6735  Z= 0.171
  Angle     :  0.498  10.408   9152  Z= 0.254
  Chirality :  0.040   0.135    977
  Planarity :  0.003   0.038   1178
  Dihedral  :  4.435  53.935   1013
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.43 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.75 (0.30), residues: 793
  helix:  1.88 (0.27), residues: 388
  sheet:  0.61 (0.77), residues: 44
  loop :  0.56 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.009   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 204 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8803 (p)
REVERT: E   75 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8417 (mp0)
REVERT: E  149 ASN cc_start: 0.9307 (m-40) cc_final: 0.9015 (m110)
REVERT: E  224 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8275 (pp20)
REVERT: E  249 MET cc_start: 0.9289 (ttm) cc_final: 0.8940 (ttp)
REVERT: E  323 MET cc_start: 0.9387 (mmm) cc_final: 0.9003 (mmm)
REVERT: E  332 MET cc_start: 0.8525 (ttp) cc_final: 0.8259 (ppp)
REVERT: E  347 THR cc_start: 0.8901 (m) cc_final: 0.8516 (p)
REVERT: E  441 LYS cc_start: 0.9057 (tttp) cc_final: 0.8593 (tppp)
REVERT: E  455 MET cc_start: 0.9181 (tmm) cc_final: 0.8980 (tmm)
REVERT: E  552 GLN cc_start: 0.8978 (tp40) cc_final: 0.8577 (tm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 64
  average time/residue: 1.2022
  time to fit residues: 81.6216
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 42 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** 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 = 0.3332 r_free = 0.3332 target = 0.075731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.057763 restraints weight = 18225.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 3.46
r_work: 0.2809 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6735  Z= 0.189
  Angle     :  0.514   8.358   9152  Z= 0.260
  Chirality :  0.040   0.136    977
  Planarity :  0.004   0.038   1178
  Dihedral  :  4.397  54.000   1013
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.29 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.80 (0.30), residues: 793
  helix:  1.93 (0.27), residues: 387
  sheet:  0.61 (0.78), residues: 44
  loop :  0.59 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 515 
 ARG   0.009   0.000   ARG E 192 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8776 (p)
REVERT: E   75 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8393 (mp0)
REVERT: E  149 ASN cc_start: 0.9295 (m-40) cc_final: 0.9023 (m110)
REVERT: E  224 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (pp20)
REVERT: E  249 MET cc_start: 0.9342 (ttm) cc_final: 0.8996 (ttp)
REVERT: E  323 MET cc_start: 0.9385 (mmm) cc_final: 0.9016 (mmm)
REVERT: E  332 MET cc_start: 0.8610 (ttp) cc_final: 0.8331 (ppp)
REVERT: E  347 THR cc_start: 0.8918 (m) cc_final: 0.8555 (p)
REVERT: E  441 LYS cc_start: 0.9064 (tttp) cc_final: 0.8598 (tppp)
REVERT: E  455 MET cc_start: 0.9185 (tmm) cc_final: 0.8968 (tmm)
REVERT: E  552 GLN cc_start: 0.8974 (tp40) cc_final: 0.8569 (tm-30)
REVERT: E  578 ASN cc_start: 0.8560 (t0) cc_final: 0.8232 (p0)
  outliers start: 16
  outliers final: 7
  residues processed: 66
  average time/residue: 1.1196
  time to fit residues: 78.5257
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.073601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.055646 restraints weight = 18454.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.40
r_work: 0.2756 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6735  Z= 0.282
  Angle     :  0.548   8.302   9152  Z= 0.282
  Chirality :  0.042   0.150    977
  Planarity :  0.004   0.037   1178
  Dihedral  :  4.582  53.356   1013
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.14 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.82 (0.30), residues: 793
  helix:  1.87 (0.26), residues: 387
  sheet:  0.67 (0.79), residues: 44
  loop :  0.69 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 515 
 ARG   0.007   0.000   ARG E 192 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8672 (p)
REVERT: E   75 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8495 (mp0)
REVERT: E  149 ASN cc_start: 0.9270 (m-40) cc_final: 0.8985 (m110)
REVERT: E  224 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8312 (pp20)
REVERT: E  249 MET cc_start: 0.9335 (ttm) cc_final: 0.8939 (ttp)
REVERT: E  347 THR cc_start: 0.8927 (m) cc_final: 0.8620 (p)
REVERT: E  441 LYS cc_start: 0.9094 (tttp) cc_final: 0.8641 (tppp)
REVERT: E  455 MET cc_start: 0.9218 (tmm) cc_final: 0.8984 (tmm)
  outliers start: 16
  outliers final: 7
  residues processed: 65
  average time/residue: 1.2844
  time to fit residues: 88.1158
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** 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 = 0.3282 r_free = 0.3282 target = 0.073120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.055063 restraints weight = 18595.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 3.42
r_work: 0.2732 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6735  Z= 0.314
  Angle     :  0.579   8.516   9152  Z= 0.298
  Chirality :  0.043   0.150    977
  Planarity :  0.004   0.036   1178
  Dihedral  :  4.721  53.594   1013
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.71 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.77 (0.30), residues: 793
  helix:  1.75 (0.26), residues: 393
  sheet:  0.92 (0.81), residues: 42
  loop :  0.71 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 400 
 TYR   0.013   0.001   TYR E 515 
 ARG   0.007   0.000   ARG E 192 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8580 (p)
REVERT: E   75 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8453 (mp0)
REVERT: E  149 ASN cc_start: 0.9230 (m-40) cc_final: 0.8947 (m110)
REVERT: E  224 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8306 (pp20)
REVERT: E  249 MET cc_start: 0.9316 (ttm) cc_final: 0.8955 (ttp)
REVERT: E  347 THR cc_start: 0.8894 (m) cc_final: 0.8590 (p)
REVERT: E  441 LYS cc_start: 0.9071 (tttp) cc_final: 0.8617 (tppp)
  outliers start: 11
  outliers final: 7
  residues processed: 61
  average time/residue: 1.1572
  time to fit residues: 75.0145
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** 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 = 0.3307 r_free = 0.3307 target = 0.074466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.056520 restraints weight = 18408.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.43
r_work: 0.2766 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6735  Z= 0.215
  Angle     :  0.559   9.608   9152  Z= 0.282
  Chirality :  0.041   0.137    977
  Planarity :  0.004   0.037   1178
  Dihedral  :  4.592  54.665   1013
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.00 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.82 (0.30), residues: 793
  helix:  1.79 (0.26), residues: 393
  sheet:  0.84 (0.80), residues: 42
  loop :  0.75 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 515 
 ARG   0.006   0.000   ARG E 192 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8643 (p)
REVERT: E  149 ASN cc_start: 0.9219 (m-40) cc_final: 0.8941 (m110)
REVERT: E  224 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8257 (pp20)
REVERT: E  249 MET cc_start: 0.9305 (ttm) cc_final: 0.8957 (ttp)
REVERT: E  347 THR cc_start: 0.8920 (m) cc_final: 0.8622 (p)
REVERT: E  441 LYS cc_start: 0.9069 (tttp) cc_final: 0.8612 (tppp)
REVERT: E  455 MET cc_start: 0.9107 (tmm) cc_final: 0.8663 (tpt)
REVERT: E  552 GLN cc_start: 0.8999 (tp40) cc_final: 0.8594 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 59
  average time/residue: 1.0979
  time to fit residues: 69.1607
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 63 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** 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 = 0.3310 r_free = 0.3310 target = 0.074464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.056554 restraints weight = 18686.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 3.47
r_work: 0.2774 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6735  Z= 0.205
  Angle     :  0.555   9.130   9152  Z= 0.280
  Chirality :  0.041   0.148    977
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.562  54.732   1013
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.86 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.82 (0.30), residues: 793
  helix:  1.83 (0.26), residues: 393
  sheet:  0.86 (0.79), residues: 42
  loop :  0.70 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 516 
 ARG   0.006   0.000   ARG E 192 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3912.01 seconds
wall clock time: 70 minutes 3.66 seconds (4203.66 seconds total)