Starting phenix.real_space_refine
on Tue Feb 11 21:32:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dlq_27510/02_2025/8dlq_27510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dlq_27510/02_2025/8dlq_27510.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dlq_27510/02_2025/8dlq_27510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dlq_27510/02_2025/8dlq_27510.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dlq_27510/02_2025/8dlq_27510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dlq_27510/02_2025/8dlq_27510.cif"
  }
  resolution = 2.77
  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=   0.035
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    1077      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6552
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1592
          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: 3.33, per 1000 atoms: 0.51
  Number of scatterers: 6552
  At special positions: 0
  Unit cell: (80, 83, 122, 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    1077      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: 1.42
  Conformation dependent library (CDL) restraints added in 964.6 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:
      40 helices and 7 sheets defined
      57.8% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  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 405 through 410
      removed outlier: 4.013A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.568A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.645A  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: 3.692A  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: 4.030A  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: 3.693A  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: 3.742A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.707A  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: 3.793A  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
    Processing helix  chain 'E' and resid 365 through 385
    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: 4.296A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.890A  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: 3.509A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.315A  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: 3.654A  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: 4.420A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.630A  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: 3.851A  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: 3.864A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.739A  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: 3.578A  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: 6.123A  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: 6.521A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    326 hydrogen bonds defined for protein.
    924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 1.70 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: 1810
        1.47 -     1.60: 2788
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" C1  NAG E 701 "
       pdb=" O5  NAG E 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 6.95e+00
  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 6.52e+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 5.58e+00
  bond pdb=" C   GLU E 145 "
       pdb=" N   PRO E 146 "
    ideal  model  delta    sigma   weight residual
    1.334  1.388 -0.054 2.34e-02 1.83e+03 5.31e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 8629
        1.80 -     3.61: 455
        3.61 -     5.41: 49
        5.41 -     7.21: 15
        7.21 -     9.01: 6
  Bond angle restraints: 9154
  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  122.91   -9.01 1.80e+00 3.09e-01 2.51e+01
  angle pdb=" CA  TYR E 385 "
        pdb=" CB  TYR E 385 "
        pdb=" CG  TYR E 385 "
      ideal   model   delta    sigma   weight residual
     113.90  122.12   -8.22 1.80e+00 3.09e-01 2.08e+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  128.19   -5.83 1.42e+00 4.96e-01 1.69e+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=" CA  ASN B 360 "
        pdb=" CB  ASN B 360 "
        pdb=" CG  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     112.60  115.96   -3.36 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 9149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 3690
       16.95 -    33.90: 309
       33.90 -    50.85: 38
       50.85 -    67.80: 17
       67.80 -    84.75: 10
  Dihedral angle restraints: 4064
    sinusoidal: 1725
      harmonic: 2339
  Sorted by residual:
  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   15.31   63.69     1      2.00e+01 2.50e-03 1.34e+01
  dihedral pdb=" SG  CYS E 133 "
           pdb=" CB  CYS E 141 "
           pdb=" SG  CYS E 141 "
           pdb=" CA  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   16.53   62.47     1      2.00e+01 2.50e-03 1.29e+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 -130.95    8.35     0      2.50e+00 1.60e-01 1.12e+01
  ... (remaining 4061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 687
       0.053 -    0.106: 213
       0.106 -    0.159: 63
       0.159 -    0.212: 14
       0.212 -    0.265: 2
  Chirality restraints: 979
  Sorted by residual:
  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   -2.36   -0.26 2.00e-01 2.50e+01 1.75e+00
  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 1.69e+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 1.09e+00
  ... (remaining 976 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.014 2.00e-02 2.50e+03   2.91e-02 8.48e+00
        pdb=" C   ARG E 169 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.030 2.00e-02 2.50e+03   1.96e-02 7.68e+00
        pdb=" CG  TYR B 495 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.046 5.00e-02 4.00e+02   6.90e-02 7.62e+00
        pdb=" N   PRO E 590 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1891
        2.82 -     3.34: 6027
        3.34 -     3.86: 11482
        3.86 -     4.38: 13057
        4.38 -     4.90: 22523
  Nonbonded interactions: 54980
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" OH  TYR E 237 "
            pdb=" O   VAL E 485 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.384 3.040
  ... (remaining 54975 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:             12.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     17.930
  Find NCS groups from input model:        0.050
  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:15.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
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      :  0.006   0.083   6735  Z= 0.375
  Angle     :  0.909   9.012   9154  Z= 0.520
  Chirality :  0.059   0.265    979
  Planarity :  0.007   0.069   1176
  Dihedral  : 13.162  84.755   2546
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.29 %
    Favored  : 95.29 %
  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:  0.35 (0.27), residues: 793
  helix:  0.75 (0.24), residues: 391
  sheet:  1.02 (0.65), residues: 42
  loop : -0.35 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 566 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.029   0.003   PHE E 369 
 TYR   0.046   0.002   TYR B 495 
 ARG   0.010   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
  93 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.841 
Fit side-chains
REVERT: B  386 LYS cc_start: 0.8764 (pttm) cc_final: 0.8134 (pttm)
REVERT: B  390 LEU cc_start: 0.8852 (mt) cc_final: 0.8415 (mt)
REVERT: E  117 ASN cc_start: 0.8976 (t0) cc_final: 0.8351 (p0)
REVERT: E  121 ASN cc_start: 0.8679 (m-40) cc_final: 0.8439 (m110)
  outliers start: 3
  outliers final: 0
  residues processed: 93
  average time/residue: 1.5052
  time to fit residues: 146.4473
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 498 GLN
E  42 GLN
E 374 HIS
E 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.049833 restraints weight = 17467.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 3.09
r_work: 0.2659 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6735  Z= 0.234
  Angle     :  0.568   9.102   9154  Z= 0.294
  Chirality :  0.042   0.147    979
  Planarity :  0.005   0.042   1176
  Dihedral  :  5.017  49.335   1013
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.29 %
    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:  1.10 (0.28), residues: 793
  helix:  1.47 (0.25), residues: 398
  sheet:  1.00 (0.73), residues: 42
  loop : -0.08 (0.31), residues: 353

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   0.018   0.001   PHE E 369 
 TYR   0.024   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: B  518 LEU cc_start: 0.8465 (tm) cc_final: 0.8256 (mt)
REVERT: B  528 LYS cc_start: 0.3719 (OUTLIER) cc_final: 0.3089 (pttp)
REVERT: E  117 ASN cc_start: 0.9121 (t0) cc_final: 0.8429 (p0)
REVERT: E  121 ASN cc_start: 0.8975 (m-40) cc_final: 0.8642 (m110)
  outliers start: 11
  outliers final: 3
  residues processed: 67
  average time/residue: 1.4883
  time to fit residues: 104.6748
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 39 optimal weight:    0.1980
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.066339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.049689 restraints weight = 17502.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 3.03
r_work: 0.2662 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6735  Z= 0.223
  Angle     :  0.556  10.826   9154  Z= 0.284
  Chirality :  0.041   0.129    979
  Planarity :  0.004   0.042   1176
  Dihedral  :  4.891  52.103   1013
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.13 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.43 %
    Favored  : 86.00 %
  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:  1.45 (0.29), residues: 793
  helix:  1.77 (0.26), residues: 392
  sheet:  0.87 (0.77), residues: 43
  loop :  0.15 (0.31), residues: 358

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   0.018   0.001   PHE E 369 
 TYR   0.022   0.001   TYR B 495 
 ARG   0.004   0.000   ARG B 346 

*********************** 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
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: B  528 LYS cc_start: 0.3621 (OUTLIER) cc_final: 0.3351 (pttp)
REVERT: E  117 ASN cc_start: 0.9144 (t0) cc_final: 0.8674 (p0)
REVERT: E  291 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8034 (pp)
REVERT: E  483 GLU cc_start: 0.8992 (tp30) cc_final: 0.8528 (tm-30)
  outliers start: 11
  outliers final: 2
  residues processed: 61
  average time/residue: 1.4735
  time to fit residues: 94.4089
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0270
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.1844

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.064752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.047988 restraints weight = 18038.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 3.06
r_work: 0.2614 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6735  Z= 0.293
  Angle     :  0.562  10.561   9154  Z= 0.284
  Chirality :  0.042   0.129    979
  Planarity :  0.004   0.042   1176
  Dihedral  :  4.924  52.717   1013
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.29 %
    Favored  : 85.71 %
  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:  1.53 (0.29), residues: 793
  helix:  1.80 (0.26), residues: 392
  sheet:  0.97 (0.79), residues: 42
  loop :  0.24 (0.32), residues: 359

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   0.019   0.002   PHE E 369 
 TYR   0.022   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

*********************** 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
  71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9152 (t80) cc_final: 0.8921 (t80)
REVERT: B  518 LEU cc_start: 0.8581 (tm) cc_final: 0.8377 (mt)
REVERT: B  528 LYS cc_start: 0.3814 (OUTLIER) cc_final: 0.3237 (pttp)
REVERT: E  483 GLU cc_start: 0.8993 (tp30) cc_final: 0.8547 (tm-30)
  outliers start: 14
  outliers final: 3
  residues processed: 66
  average time/residue: 1.5207
  time to fit residues: 105.3608
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0010
   chunk 26 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.4764

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.066512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.049758 restraints weight = 17666.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 3.06
r_work: 0.2663 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6735  Z= 0.174
  Angle     :  0.515   9.171   9154  Z= 0.258
  Chirality :  0.039   0.125    979
  Planarity :  0.003   0.041   1176
  Dihedral  :  4.720  54.851   1013
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.14 %
    Favored  : 85.00 %
  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:  1.49 (0.30), residues: 793
  helix:  1.73 (0.26), residues: 406
  sheet:  0.85 (0.79), residues: 43
  loop :  0.22 (0.33), residues: 344

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   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR E 613 
 ARG   0.005   0.000   ARG B 346 

*********************** 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
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9144 (t80) cc_final: 0.8901 (t80)
REVERT: B  518 LEU cc_start: 0.8597 (tm) cc_final: 0.8396 (mt)
REVERT: B  528 LYS cc_start: 0.3840 (OUTLIER) cc_final: 0.3367 (pttp)
REVERT: E  483 GLU cc_start: 0.8969 (tp30) cc_final: 0.8509 (tm-30)
REVERT: E  613 TYR cc_start: 0.6311 (t80) cc_final: 0.6076 (t80)
  outliers start: 13
  outliers final: 4
  residues processed: 63
  average time/residue: 1.5558
  time to fit residues: 102.6583
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0170
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0170
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.066412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.049696 restraints weight = 17528.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 3.04
r_work: 0.2663 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6735  Z= 0.183
  Angle     :  0.511   8.268   9154  Z= 0.256
  Chirality :  0.039   0.125    979
  Planarity :  0.003   0.042   1176
  Dihedral  :  4.621  55.268   1013
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.57 %
    Favored  : 84.43 %
  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:  1.59 (0.30), residues: 793
  helix:  1.79 (0.26), residues: 406
  sheet:  0.97 (0.80), residues: 42
  loop :  0.28 (0.33), residues: 345

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   0.015   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

*********************** 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
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9200 (t80) cc_final: 0.8955 (t80)
REVERT: B  528 LYS cc_start: 0.3838 (OUTLIER) cc_final: 0.3439 (pttp)
REVERT: E  483 GLU cc_start: 0.8953 (tp30) cc_final: 0.8560 (tm-30)
REVERT: E  613 TYR cc_start: 0.6294 (t80) cc_final: 0.6035 (t80)
  outliers start: 14
  outliers final: 5
  residues processed: 61
  average time/residue: 1.4441
  time to fit residues: 92.5597
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 52 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.064633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.047959 restraints weight = 17767.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 3.02
r_work: 0.2617 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6735  Z= 0.279
  Angle     :  0.563  12.292   9154  Z= 0.280
  Chirality :  0.041   0.129    979
  Planarity :  0.004   0.040   1176
  Dihedral  :  4.741  55.527   1013
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.71 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.30), residues: 793
  helix:  1.74 (0.26), residues: 406
  sheet:  1.03 (0.80), residues: 42
  loop :  0.32 (0.34), residues: 345

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   0.018   0.001   PHE E 369 
 TYR   0.020   0.001   TYR B 495 
 ARG   0.007   0.001   ARG B 346 

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9211 (t80) cc_final: 0.8967 (t80)
REVERT: B  518 LEU cc_start: 0.8603 (tm) cc_final: 0.8390 (mt)
REVERT: B  528 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3517 (pttp)
REVERT: E  483 GLU cc_start: 0.8986 (tp30) cc_final: 0.8600 (tm-30)
REVERT: E  613 TYR cc_start: 0.6522 (t80) cc_final: 0.6285 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 62
  average time/residue: 1.3674
  time to fit residues: 89.3514
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  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0170
   chunk 24 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.049576 restraints weight = 17616.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 3.01
r_work: 0.2656 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6735  Z= 0.188
  Angle     :  0.545  11.690   9154  Z= 0.269
  Chirality :  0.040   0.126    979
  Planarity :  0.003   0.040   1176
  Dihedral  :  4.638  56.098   1013
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.71 %
    Favored  : 83.14 %
  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:  1.62 (0.30), residues: 793
  helix:  1.78 (0.26), residues: 406
  sheet:  0.98 (0.79), residues: 42
  loop :  0.33 (0.34), residues: 345

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   0.016   0.001   TYR B 495 
 ARG   0.008   0.000   ARG B 346 

*********************** 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: 8
    poor density    : 51
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.9241 (pt0) cc_final: 0.8815 (pm20)
REVERT: B  369 TYR cc_start: 0.9191 (t80) cc_final: 0.8952 (t80)
REVERT: B  462 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8564 (mmmm)
REVERT: B  518 LEU cc_start: 0.8648 (tm) cc_final: 0.8427 (mt)
REVERT: B  528 LYS cc_start: 0.3855 (OUTLIER) cc_final: 0.3495 (pttp)
REVERT: E  291 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8058 (pp)
REVERT: E  483 GLU cc_start: 0.8974 (tp30) cc_final: 0.8541 (tm-30)
REVERT: E  613 TYR cc_start: 0.6379 (t80) cc_final: 0.6054 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 56
  average time/residue: 1.4801
  time to fit residues: 87.0874
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  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 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 63 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0470
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0040
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.4890

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.066550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.049920 restraints weight = 17805.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 3.05
r_work: 0.2668 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6735  Z= 0.180
  Angle     :  0.544  11.322   9154  Z= 0.267
  Chirality :  0.040   0.125    979
  Planarity :  0.003   0.041   1176
  Dihedral  :  4.529  56.206   1013
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 16.14 %
    Favored  : 82.86 %
  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:  1.67 (0.30), residues: 793
  helix:  1.83 (0.26), residues: 406
  sheet:  1.02 (0.78), residues: 42
  loop :  0.36 (0.34), residues: 345

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   0.016   0.001   TYR B 495 
 ARG   0.008   0.000   ARG B 346 

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.9218 (pt0) cc_final: 0.8798 (pm20)
REVERT: B  462 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8584 (mmmm)
REVERT: B  518 LEU cc_start: 0.8665 (tm) cc_final: 0.8440 (mt)
REVERT: B  528 LYS cc_start: 0.3985 (OUTLIER) cc_final: 0.3515 (pttp)
REVERT: E  291 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8042 (pp)
REVERT: E  480 MET cc_start: 0.9027 (mtp) cc_final: 0.8775 (mtm)
REVERT: E  483 GLU cc_start: 0.8962 (tp30) cc_final: 0.8541 (tm-30)
REVERT: E  613 TYR cc_start: 0.6391 (t80) cc_final: 0.6060 (t80)
  outliers start: 7
  outliers final: 4
  residues processed: 57
  average time/residue: 1.4390
  time to fit residues: 86.3102
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
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 37 optimal weight:    2.9990
   chunk 69 optimal weight:    0.4980
   chunk 76 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.064254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.047465 restraints weight = 17964.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 3.06
r_work: 0.2609 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6735  Z= 0.312
  Angle     :  0.589  11.156   9154  Z= 0.294
  Chirality :  0.042   0.129    979
  Planarity :  0.004   0.041   1176
  Dihedral  :  4.775  55.789   1013
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.29 %
    Favored  : 82.57 %
  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:  1.59 (0.30), residues: 793
  helix:  1.74 (0.26), residues: 406
  sheet:  0.95 (0.77), residues: 42
  loop :  0.36 (0.34), residues: 345

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   0.017   0.001   PHE E 369 
 TYR   0.020   0.001   TYR B 369 
 ARG   0.009   0.001   ARG B 346 

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: B  462 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8571 (mmmm)
REVERT: B  518 LEU cc_start: 0.8639 (tm) cc_final: 0.8402 (mt)
REVERT: B  528 LYS cc_start: 0.4044 (OUTLIER) cc_final: 0.3628 (pttp)
REVERT: E  483 GLU cc_start: 0.8985 (tp30) cc_final: 0.8605 (tm-30)
REVERT: E  613 TYR cc_start: 0.6585 (t80) cc_final: 0.6227 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 58
  average time/residue: 1.4993
  time to fit residues: 91.2438
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 46 optimal weight:    0.3980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.065324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.048649 restraints weight = 18059.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 3.06
r_work: 0.2638 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6735  Z= 0.217
  Angle     :  0.557  11.002   9154  Z= 0.275
  Chirality :  0.040   0.127    979
  Planarity :  0.003   0.041   1176
  Dihedral  :  4.683  56.618   1013
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 17.14 %
    Favored  : 82.29 %
  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:  1.61 (0.30), residues: 793
  helix:  1.76 (0.26), residues: 407
  sheet:  0.89 (0.78), residues: 42
  loop :  0.38 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.008   0.000   ARG B 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4367.99 seconds
wall clock time: 78 minutes 31.52 seconds (4711.52 seconds total)