Starting phenix.real_space_refine
on Sun Apr 27 17:24:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jj6_61517/04_2025/9jj6_61517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jj6_61517/04_2025/9jj6_61517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jj6_61517/04_2025/9jj6_61517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jj6_61517/04_2025/9jj6_61517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jj6_61517/04_2025/9jj6_61517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jj6_61517/04_2025/9jj6_61517.cif"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
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      38      5.16       5
     C    4023      2.51       5
     N    1040      2.21       5
     O    1213      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6314
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1407
          Classifications: {'peptide': 181}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 167}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 4817
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 590, 4810
          Classifications: {'peptide': 590}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 563}
      Conformer: "B"
        Number of residues, atoms: 590, 4810
          Classifications: {'peptide': 590}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 563}
          bond proxies already assigned to first conformer: 4934
    Chain: "A"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 90
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 7.24, per 1000 atoms: 1.15
  Number of scatterers: 6314
  At special positions: 0
  Unit cell: (76.65, 83.95, 110.23, 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      38     16.00
     O    1213      8.00
     N    1040      7.00
     C    4023      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 418 " - pdb=" SG  CYS B 471 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 430 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 495 " - pdb=" SG  CYS B 516 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1458

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      56.7% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'B' and resid 378 through 383
    Processing helix  chain 'B' and resid 388 through 392
    Processing helix  chain 'B' and resid 403 through 410
      removed outlier: 3.726A  pdb=" N   LEU B 410 " --> pdb=" O   LYS B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 450
      removed outlier: 4.798A  pdb=" N   SER B 447 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 4.324A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.806A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLN A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.594A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.532A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.585A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 175
      No H-bonds generated for 'chain 'A' and resid 173 through 175'
    Processing helix  chain 'A' and resid 176 through 193
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 250
      removed outlier: 3.770A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.786A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.581A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 386
      removed outlier: 3.549A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP A 382 " --> pdb=" O   HIS A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.887A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
      removed outlier: 3.620A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.432A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.989A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.764A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.773A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 393 through 397
      removed outlier: 3.596A  pdb=" N   ASN B 393 " --> pdb=" O   TYR B 438 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER B 433 " --> pdb=" O   THR B 556 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 502 through 505
      removed outlier: 3.621A  pdb=" N   GLY B 502 " --> pdb=" O   GLY B 499 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   ASN B 490 " --> pdb=" O   ALA B 541 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ALA B 541 " --> pdb=" O   ASN B 490 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   ILE B 492 " --> pdb=" O   GLN B 539 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   GLN B 539 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.820A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.014A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    313 hydrogen bonds defined for protein.
    881 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: 1.88 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1039
        1.31 -     1.43: 1807
        1.43 -     1.56: 3577
        1.56 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6485
  Sorted by residual:
  bond pdb=" C7  NAG A 701 "
       pdb=" N2  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.346  1.473 -0.127 2.00e-02 2.50e+03 4.01e+01
  bond pdb=" C7  NAG A 704 "
       pdb=" N2  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.346  1.473 -0.127 2.00e-02 2.50e+03 4.01e+01
  bond pdb=" C7  NAG A 705 "
       pdb=" N2  NAG A 705 "
    ideal  model  delta    sigma   weight residual
    1.346  1.472 -0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C7  NAG A 703 "
       pdb=" N2  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.346  1.472 -0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C7  NAG A 702 "
       pdb=" N2  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.346  1.472 -0.126 2.00e-02 2.50e+03 3.94e+01
  ... (remaining 6480 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 8611
        1.82 -     3.64: 146
        3.64 -     5.46: 40
        5.46 -     7.27: 19
        7.27 -     9.09: 2
  Bond angle restraints: 8818
  Sorted by residual:
  angle pdb=" CA  PRO A 346 "
        pdb=" N   PRO A 346 "
        pdb=" CD  PRO A 346 "
      ideal   model   delta    sigma   weight residual
     112.00  105.67    6.33 1.40e+00 5.10e-01 2.04e+01
  angle pdb=" N   PRO A 346 "
        pdb=" CD  PRO A 346 "
        pdb=" CG  PRO A 346 "
      ideal   model   delta    sigma   weight residual
     103.20   97.00    6.20 1.50e+00 4.44e-01 1.71e+01
  angle pdb=" CB  MET A 190 "
        pdb=" CG  MET A 190 "
        pdb=" SD  MET A 190 "
      ideal   model   delta    sigma   weight residual
     112.70  121.79   -9.09 3.00e+00 1.11e-01 9.19e+00
  angle pdb=" C   PRO A 492 "
        pdb=" N   HIS A 493 "
        pdb=" CA  HIS A 493 "
      ideal   model   delta    sigma   weight residual
     122.99  118.86    4.13 1.41e+00 5.03e-01 8.57e+00
  angle pdb=" CB  PRO A 346 "
        pdb=" CG  PRO A 346 "
        pdb=" CD  PRO A 346 "
      ideal   model   delta    sigma   weight residual
     106.10   97.03    9.07 3.20e+00 9.77e-02 8.03e+00
  ... (remaining 8813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.61: 3415
       22.61 -    45.22: 332
       45.22 -    67.83: 61
       67.83 -    90.44: 14
       90.44 -   113.05: 117
  Dihedral angle restraints: 3939
    sinusoidal: 1674
      harmonic: 2265
  Sorted by residual:
  dihedral pdb=" CA  MET A 462 "
           pdb=" C   MET A 462 "
           pdb=" N   VAL A 463 "
           pdb=" CA  VAL A 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.73   24.27     0      5.00e+00 4.00e-02 2.36e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.84   34.84     1      1.00e+01 1.00e-02 1.72e+01
  dihedral pdb=" N2  NAG A 702 "
           pdb=" C1  NAG A 702 "
           pdb=" C2  NAG A 702 "
           pdb=" O5  NAG A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -65.14 -113.05     1      3.00e+01 1.11e-03 1.48e+01
  ... (remaining 3936 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 654
       0.035 -    0.070: 211
       0.070 -    0.104: 68
       0.104 -    0.139: 19
       0.139 -    0.174: 2
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" CB  THR A 122 "
            pdb=" CA  THR A 122 "
            pdb=" OG1 THR A 122 "
            pdb=" CG2 THR A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  MET A 462 "
            pdb=" N   MET A 462 "
            pdb=" C   MET A 462 "
            pdb=" CB  MET A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.28e-01
  chirality pdb=" CA  TYR A 385 "
            pdb=" N   TYR A 385 "
            pdb=" C   TYR A 385 "
            pdb=" CB  TYR A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.76e-01
  ... (remaining 951 not shown)

  Planarity restraints: 1130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 345 "    0.038 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO A 346 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 134 "    0.035 5.00e-02 4.00e+02   5.43e-02 4.71e+00
        pdb=" N   PRO A 135 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 135 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 135 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A  42 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.87e+00
        pdb=" CD  GLN A  42 "   -0.029 2.00e-02 2.50e+03
        pdb=" OE1 GLN A  42 "    0.011 2.00e-02 2.50e+03
        pdb=" NE2 GLN A  42 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1127 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1236
        2.77 -     3.30: 5951
        3.30 -     3.84: 11089
        3.84 -     4.37: 13152
        4.37 -     4.90: 22749
  Nonbonded interactions: 54177
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER B 433 "
            pdb=" OG1 THR B 556 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER A 170 "
            pdb=" OE1 GLU A 171 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   GLY A 268 "
            pdb=" ND2 ASN A 277 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OG  SER A 331 "
            pdb=" O   ILE A 358 "
     model   vdw
     2.268 3.040
  ... (remaining 54172 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.29 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:             2.710
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.190
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
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      :  0.007   0.127   6491  Z= 0.334
  Angle     :  0.662   9.092   8830  Z= 0.312
  Chirality :  0.040   0.174    954
  Planarity :  0.005   0.056   1130
  Dihedral  : 28.525 113.046   2463
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 24.34 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  0.54 (0.31), residues: 764
  helix:  0.94 (0.27), residues: 384
  sheet: -0.77 (0.58), residues: 73
  loop :  0.08 (0.38), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.013   0.001   PHE A 315 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17227 (  313)
  hydrogen bonds       : angle       6.72880 (  881)
  SS BOND              : bond        0.00137 (    6)
  SS BOND              : angle       0.58815 (   12)
  covalent geometry    : bond        0.00679 ( 6485)
  covalent geometry    : angle       0.66216 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.669 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 77
  average time/residue: 1.0275
  time to fit residues: 84.2709
Evaluate side-chains
  75 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  280 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0770
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B 393 ASN
B 506 GLN
A  42 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.189024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.135898 restraints weight = 12989.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 3.25
r_work: 0.3209 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.0939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6491  Z= 0.126
  Angle     :  0.644  10.211   8830  Z= 0.294
  Chirality :  0.043   0.250    954
  Planarity :  0.004   0.050   1130
  Dihedral  : 13.171  60.799    984
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.85 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  0.97 (0.31), residues: 764
  helix:  1.28 (0.27), residues: 389
  sheet: -0.52 (0.58), residues: 72
  loop :  0.27 (0.38), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.007   0.001   HIS A 378 
 PHE   0.012   0.001   PHE A 315 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  313)
  hydrogen bonds       : angle       4.64546 (  881)
  SS BOND              : bond        0.00158 (    6)
  SS BOND              : angle       0.56892 (   12)
  covalent geometry    : bond        0.00287 ( 6485)
  covalent geometry    : angle       0.64434 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
REVERT: B  540 SER cc_start: 0.8176 (t) cc_final: 0.7903 (p)
REVERT: A   24 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7226 (mt0)
REVERT: A   70 SER cc_start: 0.8115 (m) cc_final: 0.7663 (p)
REVERT: A  171 GLU cc_start: 0.7187 (mp0) cc_final: 0.6754 (OUTLIER)
REVERT: A  480 MET cc_start: 0.7812 (mtt) cc_final: 0.7554 (mtt)
  outliers start: 16
  outliers final: 6
  residues processed: 89
  average time/residue: 0.9720
  time to fit residues: 92.3442
Evaluate side-chains
  71 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0370
   chunk 37 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 2 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.5462

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

Flipped N/Q/H residues before XYZ refinement:
B 503 ASN
A  42 GLN
A  64 ASN
A 194 ASN
A 586 ASN
A 599 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.185019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.149654 restraints weight = 15753.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 4.80
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6491  Z= 0.218
  Angle     :  0.610   8.372   8830  Z= 0.303
  Chirality :  0.044   0.162    954
  Planarity :  0.004   0.048   1130
  Dihedral  :  7.156  55.715    981
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.53 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  0.65 (0.31), residues: 764
  helix:  0.99 (0.26), residues: 389
  sheet: -0.71 (0.59), residues: 73
  loop :  0.17 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 165 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.016   0.002   PHE A 315 
 TYR   0.014   0.002   TYR A 385 
 ARG   0.003   0.001   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04828 (  313)
  hydrogen bonds       : angle       4.64389 (  881)
  SS BOND              : bond        0.00249 (    6)
  SS BOND              : angle       0.83140 (   12)
  covalent geometry    : bond        0.00531 ( 6485)
  covalent geometry    : angle       0.60979 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 1.177 
Fit side-chains
REVERT: B  540 SER cc_start: 0.8016 (t) cc_final: 0.7761 (p)
REVERT: B  543 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6463 (ttp)
REVERT: A   24 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7506 (mt0)
REVERT: A  171 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6626 (mp0)
  outliers start: 26
  outliers final: 10
  residues processed: 93
  average time/residue: 1.3036
  time to fit residues: 129.8613
Evaluate side-chains
  82 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 60 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0770
   chunk 33 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    0.3980
   chunk 4 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.3716

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

Flipped N/Q/H residues before XYZ refinement:
B 503 ASN
A  42 GLN
A 194 ASN
A 522 GLN
A 599 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.189458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.136730 restraints weight = 12115.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 3.01
r_work: 0.3206 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6491  Z= 0.101
  Angle     :  0.501   8.079   8830  Z= 0.253
  Chirality :  0.039   0.152    954
  Planarity :  0.004   0.047   1130
  Dihedral  :  5.610  56.881    981
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.97 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  1.07 (0.31), residues: 764
  helix:  1.36 (0.27), residues: 388
  sheet: -0.47 (0.62), residues: 72
  loop :  0.34 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.013   0.001   PHE A 315 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03660 (  313)
  hydrogen bonds       : angle       4.39402 (  881)
  SS BOND              : bond        0.00104 (    6)
  SS BOND              : angle       0.36674 (   12)
  covalent geometry    : bond        0.00224 ( 6485)
  covalent geometry    : angle       0.50165 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.664 
Fit side-chains
REVERT: B  540 SER cc_start: 0.8147 (t) cc_final: 0.7894 (p)
REVERT: A   24 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7208 (mt0)
REVERT: A   70 SER cc_start: 0.8145 (m) cc_final: 0.7710 (p)
REVERT: A  171 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6794 (mp0)
  outliers start: 16
  outliers final: 8
  residues processed: 91
  average time/residue: 1.0948
  time to fit residues: 105.9170
Evaluate side-chains
  81 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  433 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0470
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 2 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
B 503 ASN
A  42 GLN
A 194 ASN
A 586 ASN
A 599 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.186506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.129138 restraints weight = 12130.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.79
r_work: 0.3221 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6491  Z= 0.169
  Angle     :  0.545   8.395   8830  Z= 0.277
  Chirality :  0.041   0.169    954
  Planarity :  0.004   0.046   1130
  Dihedral  :  5.525  58.757    981
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.23 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  0.92 (0.31), residues: 764
  helix:  1.23 (0.26), residues: 389
  sheet: -0.58 (0.62), residues: 73
  loop :  0.29 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.015   0.001   PHE A 315 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.008   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  313)
  hydrogen bonds       : angle       4.44029 (  881)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       0.65620 (   12)
  covalent geometry    : bond        0.00407 ( 6485)
  covalent geometry    : angle       0.54499 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.669 
Fit side-chains
REVERT: B  540 SER cc_start: 0.8196 (t) cc_final: 0.7967 (p)
REVERT: B  543 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6365 (ttp)
REVERT: A   24 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7338 (mt0)
REVERT: A   89 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7077 (mp-120)
REVERT: A  171 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6825 (mp0)
  outliers start: 21
  outliers final: 8
  residues processed: 80
  average time/residue: 1.0430
  time to fit residues: 89.2827
Evaluate side-chains
  78 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 60 optimal weight:    0.4980
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 503 ASN
A  42 GLN
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.187663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.134344 restraints weight = 8187.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.24
r_work: 0.3228 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6491  Z= 0.125
  Angle     :  0.516   8.487   8830  Z= 0.263
  Chirality :  0.040   0.193    954
  Planarity :  0.004   0.046   1130
  Dihedral  :  5.211  59.625    981
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.41 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  1.09 (0.31), residues: 764
  helix:  1.30 (0.26), residues: 389
  sheet: -0.38 (0.63), residues: 72
  loop :  0.44 (0.38), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 315 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  313)
  hydrogen bonds       : angle       4.30913 (  881)
  SS BOND              : bond        0.00137 (    6)
  SS BOND              : angle       0.49546 (   12)
  covalent geometry    : bond        0.00294 ( 6485)
  covalent geometry    : angle       0.51640 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 1.069 
Fit side-chains
REVERT: B  540 SER cc_start: 0.8175 (t) cc_final: 0.7943 (p)
REVERT: B  543 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6273 (ttp)
REVERT: A   24 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7230 (mt0)
REVERT: A   35 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8379 (mt-10)
REVERT: A  171 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6857 (mp0)
REVERT: A  462 MET cc_start: 0.8101 (ptt) cc_final: 0.7657 (ptt)
  outliers start: 17
  outliers final: 9
  residues processed: 78
  average time/residue: 1.0071
  time to fit residues: 84.3408
Evaluate side-chains
  75 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 503 ASN
A  42 GLN
A 195 HIS
A 599 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.185970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.131390 restraints weight = 10002.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.46
r_work: 0.3244 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6491  Z= 0.147
  Angle     :  0.523   8.646   8830  Z= 0.267
  Chirality :  0.041   0.178    954
  Planarity :  0.004   0.045   1130
  Dihedral  :  5.128  58.829    981
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.41 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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 (0.31), residues: 764
  helix:  1.31 (0.26), residues: 387
  sheet: -0.40 (0.63), residues: 72
  loop :  0.35 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.015   0.001   PHE A 315 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.007   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04109 (  313)
  hydrogen bonds       : angle       4.30608 (  881)
  SS BOND              : bond        0.00166 (    6)
  SS BOND              : angle       0.58151 (   12)
  covalent geometry    : bond        0.00354 ( 6485)
  covalent geometry    : angle       0.52279 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 1.245 
Fit side-chains
REVERT: B  540 SER cc_start: 0.8199 (t) cc_final: 0.7958 (p)
REVERT: B  543 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6335 (ttp)
REVERT: A   24 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7292 (mt0)
REVERT: A  171 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6818 (mp0)
REVERT: A  548 THR cc_start: 0.8512 (m) cc_final: 0.8142 (p)
  outliers start: 17
  outliers final: 8
  residues processed: 80
  average time/residue: 1.0117
  time to fit residues: 87.2413
Evaluate side-chains
  76 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:   20.0000
   chunk 67 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 39 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 194 ASN
A 586 ASN
A 599 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.186508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.134689 restraints weight = 9771.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.62
r_work: 0.3248 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6491  Z= 0.138
  Angle     :  0.526   8.743   8830  Z= 0.267
  Chirality :  0.040   0.173    954
  Planarity :  0.004   0.045   1130
  Dihedral  :  4.647  36.041    980
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.41 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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 (0.31), residues: 764
  helix:  1.32 (0.26), residues: 389
  sheet: -0.39 (0.62), residues: 72
  loop :  0.43 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 478 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  313)
  hydrogen bonds       : angle       4.27867 (  881)
  SS BOND              : bond        0.00137 (    6)
  SS BOND              : angle       0.62025 (   12)
  covalent geometry    : bond        0.00329 ( 6485)
  covalent geometry    : angle       0.52546 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
REVERT: B  540 SER cc_start: 0.8173 (t) cc_final: 0.7924 (p)
REVERT: B  543 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6370 (ttp)
REVERT: A   24 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7295 (mt0)
REVERT: A  171 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6915 (mp0)
REVERT: A  548 THR cc_start: 0.8505 (m) cc_final: 0.8128 (p)
  outliers start: 17
  outliers final: 9
  residues processed: 82
  average time/residue: 1.0909
  time to fit residues: 95.8624
Evaluate side-chains
  78 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 73 optimal weight:    0.0470
   chunk 74 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
B 503 ASN
A  42 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.189099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.133455 restraints weight = 12104.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.68
r_work: 0.3147 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6491  Z= 0.117
  Angle     :  0.509   8.814   8830  Z= 0.258
  Chirality :  0.040   0.171    954
  Planarity :  0.004   0.044   1130
  Dihedral  :  4.393  33.947    980
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 21.99 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.31), residues: 764
  helix:  1.44 (0.26), residues: 389
  sheet: -0.34 (0.63), residues: 72
  loop :  0.47 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 478 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.017   0.001   PHE A 315 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  313)
  hydrogen bonds       : angle       4.21108 (  881)
  SS BOND              : bond        0.00148 (    6)
  SS BOND              : angle       0.50687 (   12)
  covalent geometry    : bond        0.00275 ( 6485)
  covalent geometry    : angle       0.50917 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: B  533 TYR cc_start: 0.8069 (m-80) cc_final: 0.7865 (m-80)
REVERT: B  540 SER cc_start: 0.8162 (t) cc_final: 0.7889 (p)
REVERT: B  543 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6266 (ttp)
REVERT: A   24 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7277 (mt0)
REVERT: A  171 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6778 (mp0)
REVERT: A  376 MET cc_start: 0.8498 (mmm) cc_final: 0.8216 (tpt)
REVERT: A  480 MET cc_start: 0.7914 (mtt) cc_final: 0.7618 (mtt)
REVERT: A  548 THR cc_start: 0.8450 (m) cc_final: 0.8083 (p)
  outliers start: 14
  outliers final: 8
  residues processed: 79
  average time/residue: 1.1023
  time to fit residues: 93.5959
Evaluate side-chains
  77 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    0.3980
   chunk 45 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 503 ASN
A  42 GLN
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.187056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.132512 restraints weight = 13233.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 3.28
r_work: 0.2961 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6491  Z= 0.150
  Angle     :  0.541   8.959   8830  Z= 0.274
  Chirality :  0.041   0.174    954
  Planarity :  0.004   0.043   1130
  Dihedral  :  4.533  35.123    980
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 22.58 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  1.15 (0.31), residues: 764
  helix:  1.41 (0.26), residues: 388
  sheet: -0.34 (0.63), residues: 72
  loop :  0.37 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 478 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.017   0.001   PHE A 315 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04098 (  313)
  hydrogen bonds       : angle       4.27466 (  881)
  SS BOND              : bond        0.00202 (    6)
  SS BOND              : angle       0.61321 (   12)
  covalent geometry    : bond        0.00364 ( 6485)
  covalent geometry    : angle       0.54072 ( 8818)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: B  540 SER cc_start: 0.8196 (t) cc_final: 0.7966 (p)
REVERT: B  543 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6229 (ttp)
REVERT: A   24 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7154 (mt0)
REVERT: A  171 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6907 (mp0)
REVERT: A  548 THR cc_start: 0.8528 (m) cc_final: 0.8134 (p)
  outliers start: 11
  outliers final: 8
  residues processed: 73
  average time/residue: 1.0274
  time to fit residues: 80.7283
Evaluate side-chains
  77 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 29 optimal weight:    0.0370
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 67 optimal weight:    0.1980
   chunk 66 optimal weight:    0.1980
   chunk 9 optimal weight:   10.0000
   overall best weight:    0.3458

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 154 ASN
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.190227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.147735 restraints weight = 6731.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 1.95
r_work: 0.3315 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6491  Z= 0.103
  Angle     :  0.501   9.421   8830  Z= 0.254
  Chirality :  0.039   0.169    954
  Planarity :  0.004   0.044   1130
  Dihedral  :  4.185  31.718    980
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 22.43 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    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:  1.38 (0.32), residues: 764
  helix:  1.58 (0.27), residues: 389
  sheet: -0.32 (0.63), residues: 72
  loop :  0.53 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 478 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.017   0.001   PHE A 315 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.005   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03534 (  313)
  hydrogen bonds       : angle       4.19138 (  881)
  SS BOND              : bond        0.00124 (    6)
  SS BOND              : angle       0.40149 (   12)
  covalent geometry    : bond        0.00235 ( 6485)
  covalent geometry    : angle       0.50072 ( 8818)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5082.10 seconds
wall clock time: 90 minutes 44.42 seconds (5444.42 seconds total)