Starting phenix.real_space_refine
on Tue Mar 11 21:06:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sxy_25510/03_2025/7sxy_25510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sxy_25510/03_2025/7sxy_25510.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2025/7sxy_25510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2025/7sxy_25510.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2025/7sxy_25510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2025/7sxy_25510.cif"
  }
  resolution = 2.79
  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=  -0.002 sd=   0.036
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    4191      2.51       5
     N    1080      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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6557
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    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: 7.33, per 1000 atoms: 1.12
  Number of scatterers: 6557
  At special positions: 0
  Unit cell: (80, 83, 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    1080      7.00
     C    4191      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=2.02

  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: 1.54
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1502

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      57.8% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  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 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.674A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.832A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (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: 3.742A  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: 4.034A  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: 3.942A  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: 3.707A  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: 3.682A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.762A  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: 3.765A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.545A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.658A  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: 4.219A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.947A  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: 4.344A  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: 3.706A  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: 4.397A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.623A  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: 3.905A  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: 3.860A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.772A  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: 3.657A  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: 6.069A  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: 6.304A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    917 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: 1.88

  Time building geometry restraints manager: 1.90 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: 2087
        1.35 -     1.47: 1785
        1.47 -     1.60: 2811
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6741
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.50e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.63e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.38e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.07e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.75e+00
  ... (remaining 6736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 8820
        2.02 -     4.05: 297
        4.05 -     6.07: 35
        6.07 -     8.09: 7
        8.09 -    10.12: 4
  Bond angle restraints: 9163
  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  128.94   -6.12 1.42e+00 4.96e-01 1.86e+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  123.47   -9.07 2.30e+00 1.89e-01 1.55e+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  115.98   -3.38 1.00e+00 1.00e+00 1.14e+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  122.82  -10.12 3.00e+00 1.11e-01 1.14e+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  117.77   -4.61 1.42e+00 4.96e-01 1.05e+01
  ... (remaining 9158 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 3701
       17.13 -    34.25: 306
       34.25 -    51.37: 42
       51.37 -    68.50: 10
       68.50 -    85.62: 12
  Dihedral angle restraints: 4071
    sinusoidal: 1729
      harmonic: 2342
  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  -43.13  -42.87     1      1.00e+01 1.00e-02 2.56e+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   16.37   62.63     1      2.00e+01 2.50e-03 1.30e+01
  dihedral pdb=" CA  ALA E 396 "
           pdb=" C   ALA E 396 "
           pdb=" N   ASN E 397 "
           pdb=" CA  ASN E 397 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.63   16.37     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4068 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 698
       0.051 -    0.102: 202
       0.102 -    0.153: 63
       0.153 -    0.203: 13
       0.203 -    0.254: 3
  Chirality restraints: 979
  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    2.26    0.25 2.00e-01 2.50e+01 1.62e+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   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ASN E 437 "
            pdb=" N   ASN E 437 "
            pdb=" C   ASN E 437 "
            pdb=" CB  ASN E 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 976 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.017 2.00e-02 2.50e+03   3.40e-02 1.16e+01
        pdb=" C   ARG E 169 "   -0.059 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  TRP E 168 "    0.014 2.00e-02 2.50e+03   2.73e-02 7.43e+00
        pdb=" C   TRP E 168 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   TRP E 168 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ARG E 169 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.043 5.00e-02 4.00e+02   6.54e-02 6.84e+00
        pdb=" N   PRO E 590 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1911
        2.82 -     3.34: 6008
        3.34 -     3.86: 11540
        3.86 -     4.38: 13065
        4.38 -     4.90: 22546
  Nonbonded interactions: 55070
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG1 THR B 500 "
            pdb=" OH  TYR E  41 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OH  TYR E 237 "
            pdb=" O   VAL E 485 "
     model   vdw
     2.353 3.040
  ... (remaining 55065 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=0.50 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:             5.000
  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:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     23.440
  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:13.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
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   6741  Z= 0.343
  Angle     :  0.840  10.116   9163  Z= 0.455
  Chirality :  0.056   0.254    979
  Planarity :  0.007   0.065   1179
  Dihedral  : 13.174  85.622   2551
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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: -0.48 (0.26), residues: 794
  helix: -0.05 (0.23), residues: 396
  sheet:  0.71 (0.65), residues: 52
  loop : -0.67 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 473 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.029   0.003   PHE E 369 
 TYR   0.033   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)
************************************************

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: E  156 LEU cc_start: 0.9544 (mm) cc_final: 0.8932 (tm)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 1.5764
  time to fit residues: 118.7458
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.1562

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 ASN
** E  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E 325 GLN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.069292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.051083 restraints weight = 26988.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 3.83
r_work: 0.2650 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6741  Z= 0.283
  Angle     :  0.603   7.826   9163  Z= 0.309
  Chirality :  0.043   0.159    979
  Planarity :  0.005   0.046   1179
  Dihedral  :  5.120  51.252   1014
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.13 %
    Favored  : 91.01 %
  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:  0.72 (0.28), residues: 794
  helix:  1.04 (0.25), residues: 396
  sheet:  0.73 (0.67), residues: 53
  loop : -0.11 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.019   0.002   PHE E 400 
 TYR   0.016   0.001   TYR E 385 
 ARG   0.004   0.000   ARG E 219 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.751 
Fit side-chains
REVERT: B  386 LYS cc_start: 0.8992 (ptpp) cc_final: 0.8792 (ptpp)
REVERT: B  458 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8989 (mtpp)
REVERT: B  471 GLU cc_start: 0.8965 (tp30) cc_final: 0.8699 (tp30)
REVERT: E   91 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8778 (tm)
REVERT: E  249 MET cc_start: 0.8911 (ttm) cc_final: 0.8658 (mtt)
REVERT: E  408 MET cc_start: 0.9485 (mmt) cc_final: 0.9252 (mmt)
  outliers start: 6
  outliers final: 2
  residues processed: 53
  average time/residue: 1.5226
  time to fit residues: 84.6875
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  458 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0870
   chunk 66 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 71 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E 117 ASN
E 374 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.070530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.052411 restraints weight = 24362.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.65
r_work: 0.2707 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6741  Z= 0.186
  Angle     :  0.524   6.669   9163  Z= 0.268
  Chirality :  0.040   0.142    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.807  53.689   1014
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.56 %
    Favored  : 89.73 %
  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:  1.02 (0.29), residues: 794
  helix:  1.30 (0.26), residues: 399
  sheet:  0.63 (0.68), residues: 53
  loop :  0.05 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 219 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.744 
Fit side-chains
REVERT: B  471 GLU cc_start: 0.8957 (tp30) cc_final: 0.8742 (tp30)
REVERT: E   91 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8791 (tm)
REVERT: E  249 MET cc_start: 0.8873 (ttm) cc_final: 0.8653 (mtt)
REVERT: E  332 MET cc_start: 0.9140 (ttp) cc_final: 0.8732 (ptm)
REVERT: E  366 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8302 (ttp)
  outliers start: 5
  outliers final: 2
  residues processed: 50
  average time/residue: 1.4989
  time to fit residues: 79.1500
Evaluate side-chains
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  259 ILE
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 41 optimal weight:    0.3980
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 HIS    A ** 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 = 0.3288 r_free = 0.3288 target = 0.070286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.052172 restraints weight = 24410.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.64
r_work: 0.2699 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6741  Z= 0.196
  Angle     :  0.515   6.576   9163  Z= 0.263
  Chirality :  0.040   0.140    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.684  54.111   1014
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.27 %
    Favored  : 89.73 %
  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:  1.20 (0.29), residues: 794
  helix:  1.48 (0.26), residues: 392
  sheet:  0.75 (0.69), residues: 53
  loop :  0.12 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.016   0.001   TYR E  50 
 ARG   0.003   0.000   ARG B 403 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.749 
Fit side-chains
REVERT: E   91 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8768 (tm)
REVERT: E  249 MET cc_start: 0.8842 (ttm) cc_final: 0.8607 (mtt)
REVERT: E  332 MET cc_start: 0.9117 (ttp) cc_final: 0.8896 (ttm)
REVERT: E  366 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8311 (ttp)
  outliers start: 7
  outliers final: 2
  residues processed: 48
  average time/residue: 1.4223
  time to fit residues: 71.9690
Evaluate side-chains
  48 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 HIS    A ** 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 = 0.3271 r_free = 0.3271 target = 0.069552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.050668 restraints weight = 38552.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 4.40
r_work: 0.2640 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2646
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6741  Z= 0.232
  Angle     :  0.522   6.761   9163  Z= 0.267
  Chirality :  0.041   0.143    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.667  54.626   1014
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.42 %
    Favored  : 89.59 %
  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:  1.32 (0.29), residues: 794
  helix:  1.54 (0.26), residues: 390
  sheet:  0.66 (0.69), residues: 53
  loop :  0.28 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 466 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8124 (p)
REVERT: E   91 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8793 (tm)
REVERT: E  249 MET cc_start: 0.8892 (ttm) cc_final: 0.8659 (mtt)
REVERT: E  332 MET cc_start: 0.9178 (ttp) cc_final: 0.8920 (ttm)
REVERT: E  366 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8381 (ttp)
REVERT: E  480 MET cc_start: 0.9159 (mtp) cc_final: 0.8927 (mtm)
  outliers start: 7
  outliers final: 1
  residues processed: 47
  average time/residue: 1.4281
  time to fit residues: 70.7144
Evaluate side-chains
  47 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0010
   chunk 23 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0070
   chunk 33 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.5004

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 ASN
** E  34 HIS    A ** 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 = 0.3297 r_free = 0.3297 target = 0.070771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.052695 restraints weight = 25275.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 3.70
r_work: 0.2711 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6741  Z= 0.165
  Angle     :  0.497   6.059   9163  Z= 0.252
  Chirality :  0.040   0.133    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.544  55.825   1014
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.99 %
    Favored  : 89.73 %
  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:  1.32 (0.29), residues: 794
  helix:  1.56 (0.26), residues: 391
  sheet:  0.97 (0.77), residues: 43
  loop :  0.21 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 403 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.672 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8233 (p)
REVERT: E   91 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8760 (tm)
REVERT: E  249 MET cc_start: 0.8819 (ttm) cc_final: 0.8586 (mtt)
REVERT: E  332 MET cc_start: 0.9140 (ttp) cc_final: 0.8933 (ttm)
REVERT: E  366 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8290 (ttp)
  outliers start: 9
  outliers final: 2
  residues processed: 51
  average time/residue: 1.3652
  time to fit residues: 73.4459
Evaluate side-chains
  49 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 47 optimal weight:    0.4980
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.069015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.050143 restraints weight = 39534.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 4.47
r_work: 0.2614 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6741  Z= 0.251
  Angle     :  0.536   6.795   9163  Z= 0.273
  Chirality :  0.041   0.144    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.617  55.029   1014
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.41 %
    Favored  : 88.87 %
  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:  1.46 (0.29), residues: 794
  helix:  1.60 (0.26), residues: 391
  sheet:  0.54 (0.71), residues: 53
  loop :  0.45 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.016   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 403 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.702 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8159 (p)
REVERT: E   91 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8780 (tm)
REVERT: E  152 MET cc_start: 0.8776 (mmm) cc_final: 0.8575 (tpt)
REVERT: E  156 LEU cc_start: 0.9511 (mm) cc_final: 0.9111 (tm)
REVERT: E  249 MET cc_start: 0.8833 (ttm) cc_final: 0.8569 (mtt)
REVERT: E  332 MET cc_start: 0.9158 (ttp) cc_final: 0.8936 (ttm)
REVERT: E  366 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8404 (ttp)
REVERT: E  480 MET cc_start: 0.9113 (mtp) cc_final: 0.8826 (mtm)
  outliers start: 5
  outliers final: 2
  residues processed: 49
  average time/residue: 1.4937
  time to fit residues: 77.0551
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.069286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.050677 restraints weight = 33566.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 4.18
r_work: 0.2631 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6741  Z= 0.228
  Angle     :  0.528   7.143   9163  Z= 0.269
  Chirality :  0.041   0.139    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.602  55.613   1014
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.41 %
    Favored  : 88.87 %
  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:  1.39 (0.29), residues: 794
  helix:  1.54 (0.26), residues: 394
  sheet:  0.45 (0.71), residues: 53
  loop :  0.42 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 403 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.706 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8205 (p)
REVERT: E   91 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8788 (tm)
REVERT: E  152 MET cc_start: 0.8824 (mmm) cc_final: 0.8616 (tpt)
REVERT: E  156 LEU cc_start: 0.9502 (mm) cc_final: 0.9105 (tm)
REVERT: E  249 MET cc_start: 0.8833 (ttm) cc_final: 0.8574 (mtt)
REVERT: E  325 GLN cc_start: 0.8863 (tt0) cc_final: 0.8649 (tt0)
REVERT: E  366 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8419 (ttp)
  outliers start: 5
  outliers final: 1
  residues processed: 51
  average time/residue: 1.4967
  time to fit residues: 80.6748
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.050341 restraints weight = 21648.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 3.45
r_work: 0.2648 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6741  Z= 0.263
  Angle     :  0.547   6.989   9163  Z= 0.279
  Chirality :  0.041   0.143    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.666  55.178   1014
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.41 %
    Favored  : 88.73 %
  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:  1.45 (0.29), residues: 794
  helix:  1.57 (0.26), residues: 392
  sheet:  0.45 (0.71), residues: 53
  loop :  0.49 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.016   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 403 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.754 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8183 (p)
REVERT: E   91 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8814 (tm)
REVERT: E  152 MET cc_start: 0.8818 (mmm) cc_final: 0.8609 (tpt)
REVERT: E  156 LEU cc_start: 0.9487 (mm) cc_final: 0.9077 (tm)
REVERT: E  249 MET cc_start: 0.8848 (ttm) cc_final: 0.8581 (mtt)
REVERT: E  332 MET cc_start: 0.9019 (ttp) cc_final: 0.8657 (ttm)
REVERT: E  366 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8426 (ttp)
REVERT: E  480 MET cc_start: 0.9050 (mtp) cc_final: 0.8766 (mtm)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 1.4475
  time to fit residues: 74.6877
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0770
   chunk 40 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.069447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.051273 restraints weight = 25181.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 3.69
r_work: 0.2660 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6741  Z= 0.196
  Angle     :  0.529   6.928   9163  Z= 0.270
  Chirality :  0.040   0.135    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.618  55.885   1014
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.56 %
    Favored  : 88.73 %
  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:  1.39 (0.29), residues: 794
  helix:  1.54 (0.26), residues: 394
  sheet:  0.38 (0.71), residues: 53
  loop :  0.44 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 245 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.774 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8255 (p)
REVERT: E  156 LEU cc_start: 0.9491 (mm) cc_final: 0.9081 (tm)
REVERT: E  249 MET cc_start: 0.8869 (ttm) cc_final: 0.8619 (mtt)
REVERT: E  332 MET cc_start: 0.9047 (ttp) cc_final: 0.8710 (ttm)
REVERT: E  366 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8423 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 49
  average time/residue: 1.5168
  time to fit residues: 78.2940
Evaluate side-chains
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN
E 522 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.069454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.051129 restraints weight = 28957.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 3.92
r_work: 0.2652 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6741  Z= 0.206
  Angle     :  0.529   6.872   9163  Z= 0.269
  Chirality :  0.040   0.135    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.588  55.806   1014
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.98 %
    Favored  : 88.45 %
  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:  1.36 (0.29), residues: 794
  helix:  1.44 (0.25), residues: 405
  sheet:  0.37 (0.71), residues: 53
  loop :  0.48 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.001   0.000   ARG B 466 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4863.61 seconds
wall clock time: 83 minutes 56.14 seconds (5036.14 seconds total)