Starting phenix.real_space_refine
on Tue Mar 11 21:37:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dln_27507/03_2025/8dln_27507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dln_27507/03_2025/8dln_27507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dln_27507/03_2025/8dln_27507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dln_27507/03_2025/8dln_27507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dln_27507/03_2025/8dln_27507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dln_27507/03_2025/8dln_27507.cif"
  }
  resolution = 3.04
  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=   0.031
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    4190      2.51       5
     N    1078      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: {'PTRANS': 27, '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: 5.23, per 1000 atoms: 0.80
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (77, 85, 123, 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    1248      8.00
     N    1078      7.00
     C    4190      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: 1.51
  Conformation dependent library (CDL) restraints added in 885.9 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:
      38 helices and 7 sheets defined
      57.0% 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 364 through 370
      removed outlier: 4.403A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    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: 3.725A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.697A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.563A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.727A  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: 4.072A  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 147 through 155
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.732A  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: 3.762A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.743A  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: 3.795A  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: 3.585A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.693A  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: 4.294A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.924A  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
      removed outlier: 3.526A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.318A  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: 3.665A  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: 4.425A  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: 3.877A  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: 3.985A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.814A  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: 3.790A  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: 6.052A  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: 6.363A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    912 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: 1.85

  Time building geometry restraints manager: 1.83 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: 2079
        1.35 -     1.47: 1795
        1.47 -     1.60: 2804
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6736
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.23e+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 5.26e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.72e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.65e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.53e+00
  ... (remaining 6731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8794
        2.00 -     4.00: 314
        4.00 -     6.00: 35
        6.00 -     8.00: 7
        8.00 -    10.00: 5
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  123.90  -10.00 1.80e+00 3.09e-01 3.09e+01
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.33   -5.97 1.42e+00 4.96e-01 1.77e+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  123.02   -8.62 2.30e+00 1.89e-01 1.41e+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  116.03   -3.43 1.00e+00 1.00e+00 1.18e+01
  angle pdb=" C   TYR B 495 "
        pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     110.78  105.54    5.24 1.60e+00 3.91e-01 1.07e+01
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 3688
       17.19 -    34.37: 310
       34.37 -    51.55: 44
       51.55 -    68.74: 12
       68.74 -    85.92: 11
  Dihedral angle restraints: 4065
    sinusoidal: 1726
      harmonic: 2339
  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  -46.48  -39.52     1      1.00e+01 1.00e-02 2.19e+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   14.60   64.40     1      2.00e+01 2.50e-03 1.36e+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 -130.75    8.15     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 4062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 701
       0.052 -    0.105: 197
       0.105 -    0.157: 64
       0.157 -    0.209: 14
       0.209 -    0.261: 2
  Chirality restraints: 978
  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    2.25    0.26 2.00e-01 2.50e+01 1.71e+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   -2.38   -0.25 2.00e-01 2.50e+01 1.55e+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    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 975 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.030 2.00e-02 2.50e+03   1.88e-02 7.09e+00
        pdb=" CG  TYR B 495 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "   -0.003 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   6.41e-02 6.58e+00
        pdb=" N   PRO E 590 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.043 5.00e-02 4.00e+02   6.39e-02 6.53e+00
        pdb=" N   PRO E 500 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1941
        2.82 -     3.34: 5987
        3.34 -     3.86: 11373
        3.86 -     4.38: 12873
        4.38 -     4.90: 22360
  Nonbonded interactions: 54534
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.366 3.120
  ... (remaining 54529 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:             4.580
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.910
  Find NCS groups from input model:        0.080
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
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   0.064   6736  Z= 0.344
  Angle     :  0.860  10.004   9155  Z= 0.481
  Chirality :  0.056   0.261    978
  Planarity :  0.007   0.064   1177
  Dihedral  : 13.351  85.924   2547
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.57 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 793
  helix:  0.33 (0.22), residues: 387
  sheet:  1.07 (0.72), residues: 43
  loop : -0.73 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  69 
 HIS   0.007   0.001   HIS E  34 
 PHE   0.027   0.003   PHE E 369 
 TYR   0.043   0.002   TYR B 495 
 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
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8276 (m-30) cc_final: 0.7950 (m-30)
REVERT: E  143 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8945 (mp)
REVERT: E  562 LYS cc_start: 0.9196 (tttt) cc_final: 0.8983 (tttp)
REVERT: E  589 GLU cc_start: 0.7916 (tp30) cc_final: 0.7473 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2523
  time to fit residues: 36.6636
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  143 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0070
   chunk 33 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
E 374 HIS
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.071191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.054939 restraints weight = 18772.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 3.30
r_work: 0.2769 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6736  Z= 0.193
  Angle     :  0.557   9.218   9155  Z= 0.285
  Chirality :  0.042   0.140    978
  Planarity :  0.005   0.041   1177
  Dihedral  :  5.206  49.543   1015
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.29 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.28), residues: 793
  helix:  1.52 (0.25), residues: 383
  sheet:  0.87 (0.72), residues: 43
  loop : -0.15 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.005   0.000   ARG E 559 

*********************** 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
  76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8693 (m-30) cc_final: 0.8170 (m-30)
REVERT: E  143 LEU cc_start: 0.9379 (mp) cc_final: 0.9168 (mt)
REVERT: E  149 ASN cc_start: 0.9283 (m-40) cc_final: 0.9058 (m-40)
REVERT: E  152 MET cc_start: 0.8267 (mmp) cc_final: 0.7929 (mmt)
REVERT: E  249 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8833 (mtm)
REVERT: E  471 ASP cc_start: 0.8618 (p0) cc_final: 0.8121 (t0)
REVERT: E  474 MET cc_start: 0.8501 (mmt) cc_final: 0.7983 (mmt)
REVERT: E  577 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8666 (mttm)
  outliers start: 6
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2726
  time to fit residues: 24.9412
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  458 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0270
   chunk 39 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3304 r_free = 0.3304 target = 0.070495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.054276 restraints weight = 18906.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 3.26
r_work: 0.2791 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6736  Z= 0.179
  Angle     :  0.514   8.207   9155  Z= 0.262
  Chirality :  0.040   0.132    978
  Planarity :  0.004   0.043   1177
  Dihedral  :  4.806  50.389   1013
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  8.43 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.29), residues: 793
  helix:  1.83 (0.26), residues: 383
  sheet:  0.77 (0.73), residues: 43
  loop :  0.19 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.014   0.001   TYR B 495 
 ARG   0.004   0.000   ARG E 559 

*********************** 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
  71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  145 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8466 (tm-30)
REVERT: E  149 ASN cc_start: 0.9308 (m-40) cc_final: 0.9093 (m110)
REVERT: E  249 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8875 (mtm)
REVERT: E  471 ASP cc_start: 0.8572 (p0) cc_final: 0.7969 (t0)
REVERT: E  577 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8705 (mttm)
  outliers start: 9
  outliers final: 3
  residues processed: 67
  average time/residue: 0.2664
  time to fit residues: 22.5769
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  458 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    0.1980
   chunk 19 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3297 r_free = 0.3297 target = 0.070203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.054017 restraints weight = 19183.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 3.28
r_work: 0.2782 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6736  Z= 0.179
  Angle     :  0.510   7.179   9155  Z= 0.259
  Chirality :  0.040   0.129    978
  Planarity :  0.004   0.044   1177
  Dihedral  :  4.711  51.437   1013
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  8.43 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.29), residues: 793
  helix:  1.88 (0.26), residues: 388
  sheet:  0.82 (0.74), residues: 43
  loop :  0.31 (0.32), residues: 362

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   0.013   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.003   0.000   ARG E 559 

*********************** 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
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8659 (m-30) cc_final: 0.8155 (m-30)
REVERT: E   22 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8438 (tm-30)
REVERT: E  145 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8425 (tm-30)
REVERT: E  149 ASN cc_start: 0.9302 (m-40) cc_final: 0.9078 (m110)
REVERT: E  152 MET cc_start: 0.8297 (mmp) cc_final: 0.7872 (mmt)
REVERT: E  249 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8899 (mtm)
REVERT: E  471 ASP cc_start: 0.8644 (p0) cc_final: 0.8166 (t0)
REVERT: E  577 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8760 (mttm)
  outliers start: 11
  outliers final: 3
  residues processed: 66
  average time/residue: 0.2622
  time to fit residues: 21.7840
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 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:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0470
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
E  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.069382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.053029 restraints weight = 19053.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 3.33
r_work: 0.2734 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6736  Z= 0.182
  Angle     :  0.504   6.496   9155  Z= 0.256
  Chirality :  0.040   0.126    978
  Planarity :  0.004   0.043   1177
  Dihedral  :  4.631  52.417   1013
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.00 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.29), residues: 793
  helix:  1.82 (0.25), residues: 402
  sheet:  1.02 (0.78), residues: 43
  loop :  0.41 (0.32), residues: 348

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   0.013   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 

*********************** 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
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8689 (m-30) cc_final: 0.8144 (m-30)
REVERT: B  467 ASP cc_start: 0.8818 (t0) cc_final: 0.8605 (t0)
REVERT: E   22 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8447 (tm-30)
REVERT: E  145 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8384 (tm-30)
REVERT: E  149 ASN cc_start: 0.9271 (m-40) cc_final: 0.9054 (m110)
REVERT: E  152 MET cc_start: 0.8323 (mmp) cc_final: 0.7944 (mmt)
REVERT: E  249 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8878 (mtm)
REVERT: E  471 ASP cc_start: 0.8700 (p0) cc_final: 0.8158 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 64
  average time/residue: 0.2647
  time to fit residues: 21.7017
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
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 10 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3219 r_free = 0.3219 target = 0.066510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.050227 restraints weight = 19102.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 3.23
r_work: 0.2649 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   6736  Z= 0.360
  Angle     :  0.605  10.169   9155  Z= 0.306
  Chirality :  0.043   0.143    978
  Planarity :  0.004   0.040   1177
  Dihedral  :  5.030  52.645   1013
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.57 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.29), residues: 793
  helix:  1.75 (0.25), residues: 401
  sheet:  0.89 (0.76), residues: 43
  loop :  0.53 (0.33), residues: 349

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   0.002   PHE E 369 
 TYR   0.017   0.001   TYR E 385 
 ARG   0.003   0.001   ARG E 273 

*********************** 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: 8
    poor density    : 58
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  467 ASP cc_start: 0.8896 (t0) cc_final: 0.8547 (t0)
REVERT: E  249 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8907 (mtm)
  outliers start: 8
  outliers final: 4
  residues processed: 62
  average time/residue: 0.2743
  time to fit residues: 21.7120
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
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 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 62 optimal weight:    0.4980
   chunk 67 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.5382

-------------------------------------------------------------------------------
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 = 0.3245 r_free = 0.3245 target = 0.068264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.051921 restraints weight = 19118.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 3.31
r_work: 0.2744 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6736  Z= 0.178
  Angle     :  0.540  10.787   9155  Z= 0.269
  Chirality :  0.040   0.130    978
  Planarity :  0.003   0.040   1177
  Dihedral  :  4.786  53.391   1013
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.57 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.29), residues: 793
  helix:  1.77 (0.25), residues: 403
  sheet:  0.92 (0.77), residues: 43
  loop :  0.49 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 

*********************** 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
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  467 ASP cc_start: 0.8842 (t0) cc_final: 0.8627 (t0)
REVERT: B  471 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8950 (mm-30)
REVERT: E  152 MET cc_start: 0.8190 (mmp) cc_final: 0.7625 (mmt)
REVERT: E  249 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8878 (mtm)
REVERT: E  471 ASP cc_start: 0.8898 (p0) cc_final: 0.8234 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 59
  average time/residue: 0.2660
  time to fit residues: 20.1147
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
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 45 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3224 r_free = 0.3224 target = 0.067262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.050856 restraints weight = 19107.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 3.30
r_work: 0.2737 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6736  Z= 0.262
  Angle     :  0.571  10.212   9155  Z= 0.288
  Chirality :  0.042   0.194    978
  Planarity :  0.004   0.041   1177
  Dihedral  :  4.841  52.929   1013
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.86 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.29), residues: 793
  helix:  1.79 (0.25), residues: 402
  sheet:  0.39 (0.67), residues: 53
  loop :  0.57 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  467 ASP cc_start: 0.8858 (t0) cc_final: 0.8621 (t0)
REVERT: B  471 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8955 (mm-30)
REVERT: E  152 MET cc_start: 0.8253 (mmp) cc_final: 0.7725 (mmt)
REVERT: E  249 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8858 (mtm)
REVERT: E  471 ASP cc_start: 0.8889 (p0) cc_final: 0.8144 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.2644
  time to fit residues: 18.5492
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0970
   chunk 41 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3257 r_free = 0.3257 target = 0.068703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.052713 restraints weight = 19187.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 3.26
r_work: 0.2748 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6736  Z= 0.229
  Angle     :  0.554  10.025   9155  Z= 0.278
  Chirality :  0.041   0.180    978
  Planarity :  0.003   0.040   1177
  Dihedral  :  4.791  53.459   1013
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.86 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.29), residues: 793
  helix:  1.75 (0.25), residues: 403
  sheet:  0.79 (0.76), residues: 43
  loop :  0.52 (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  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 

*********************** 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: 7
    poor density    : 54
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  467 ASP cc_start: 0.8838 (t0) cc_final: 0.8631 (t0)
REVERT: B  471 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8969 (mm-30)
REVERT: E  152 MET cc_start: 0.8238 (mmp) cc_final: 0.7715 (mmt)
REVERT: E  249 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8835 (mtm)
REVERT: E  471 ASP cc_start: 0.8854 (p0) cc_final: 0.8130 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 57
  average time/residue: 0.2825
  time to fit residues: 20.7904
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3235 r_free = 0.3235 target = 0.067701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.051521 restraints weight = 19358.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 3.24
r_work: 0.2693 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6736  Z= 0.301
  Angle     :  0.590   9.879   9155  Z= 0.297
  Chirality :  0.043   0.168    978
  Planarity :  0.004   0.040   1177
  Dihedral  :  4.959  53.871   1013
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.00 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.29), residues: 793
  helix:  1.76 (0.25), residues: 401
  sheet:  0.10 (0.65), residues: 53
  loop :  0.62 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 403 

********************** 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
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  467 ASP cc_start: 0.8882 (t0) cc_final: 0.8581 (t0)
REVERT: B  471 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9002 (mm-30)
REVERT: E  152 MET cc_start: 0.8308 (mmp) cc_final: 0.7805 (mmt)
REVERT: E  249 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8877 (mtm)
REVERT: E  471 ASP cc_start: 0.8891 (p0) cc_final: 0.8151 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 53
  average time/residue: 0.3003
  time to fit residues: 20.3475
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    0.0870
   chunk 63 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 64 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3245 r_free = 0.3245 target = 0.068328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.051888 restraints weight = 19388.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.35
r_work: 0.2759 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6736  Z= 0.184
  Angle     :  0.547  11.304   9155  Z= 0.272
  Chirality :  0.040   0.167    978
  Planarity :  0.003   0.040   1177
  Dihedral  :  4.763  53.821   1013
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.14 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.29), residues: 793
  helix:  1.78 (0.25), residues: 403
  sheet:  0.14 (0.65), residues: 53
  loop :  0.60 (0.34), residues: 337

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   0.013   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3095.02 seconds
wall clock time: 54 minutes 0.14 seconds (3240.14 seconds total)