Starting phenix.real_space_refine
on Tue Mar 11 16:55:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xyo_38779/03_2025/8xyo_38779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xyo_38779/03_2025/8xyo_38779.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xyo_38779/03_2025/8xyo_38779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xyo_38779/03_2025/8xyo_38779.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xyo_38779/03_2025/8xyo_38779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xyo_38779/03_2025/8xyo_38779.cif"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      35      5.16       5
     C    4074      2.51       5
     N    1047      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6369
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4739
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 578, 4729
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 24, 'TRANS': 553}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 578, 4729
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 24, 'TRANS': 553}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4850
    Chain: "B"
      Number of atoms: 1531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1531
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 85
          Unusual residues: {' ZN': 1, 'NAG': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    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
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A  34 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A  34 " occ=0.50
  Time building chain proxies: 6.58, per 1000 atoms: 1.03
  Number of scatterers: 6369
  At special positions: 0
  Unit cell: (73.95, 93.5, 124.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      35     16.00
     O    1212      8.00
     N    1047      7.00
     C    4074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    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

  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 A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 103 "
      " NAG A 704 " - " ASN A  53 "
      " NAG A 705 " - " ASN A 322 "
      " NAG A 706 " - " ASN A 432 "
      " NAG B1301 " - " ASN B 343 "
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 707 "
        pdb="ZN    ZN A 707 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 707 " - pdb=" NE2 HIS A 374 "


  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      58.0% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.703A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.783A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.919A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.835A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.765A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    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 252
      removed outlier: 4.023A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.611A  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 281
      removed outlier: 4.162A  pdb=" N   SER A 280 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    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: 3.735A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.850A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 413
    Processing helix  chain 'A' and resid 414 through 420
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.686A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    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: 4.055A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ALA A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA A 532 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.524A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.882A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.716A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      removed outlier: 3.543A  pdb=" N   LEU A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    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 389
      removed outlier: 4.156A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.344A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 357
    Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.711A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474

    313 hydrogen bonds defined for protein.
    874 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: 1.61

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2025
        1.34 -     1.46: 1534
        1.46 -     1.58: 2932
        1.58 -     1.70: 0
        1.70 -     1.81: 56
  Bond restraints: 6547
  Sorted by residual:
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.22e+00
  bond pdb=" C   TYR B 495 "
       pdb=" N   GLY B 496 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 2.13e+00
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.70e+00
  bond pdb=" C1  NAG A 706 "
       pdb=" O5  NAG A 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.69e+00
  ... (remaining 6542 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 8478
        1.25 -     2.49: 327
        2.49 -     3.74: 71
        3.74 -     4.99: 19
        4.99 -     6.23: 2
  Bond angle restraints: 8897
  Sorted by residual:
  angle pdb=" C   THR A 334 "
        pdb=" N   ASP A 335 "
        pdb=" CA  ASP A 335 "
      ideal   model   delta    sigma   weight residual
     121.20  125.70   -4.50 1.40e+00 5.10e-01 1.03e+01
  angle pdb=" N   LYS A 234 "
        pdb=" CA  LYS A 234 "
        pdb=" C   LYS A 234 "
      ideal   model   delta    sigma   weight residual
     113.25  116.69   -3.44 1.30e+00 5.92e-01 7.02e+00
  angle pdb=" C   PRO A  84 "
        pdb=" N   LEU A  85 "
        pdb=" CA  LEU A  85 "
      ideal   model   delta    sigma   weight residual
     121.54  126.24   -4.70 1.91e+00 2.74e-01 6.06e+00
  angle pdb=" C   TYR B 495 "
        pdb=" N   GLY B 496 "
        pdb=" CA  GLY B 496 "
      ideal   model   delta    sigma   weight residual
     122.29  120.31    1.98 8.90e-01 1.26e+00 4.93e+00
  angle pdb=" CA  TRP A 165 "
        pdb=" CB  TRP A 165 "
        pdb=" CG  TRP A 165 "
      ideal   model   delta    sigma   weight residual
     113.60  117.33   -3.73 1.90e+00 2.77e-01 3.86e+00
  ... (remaining 8892 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3590
       17.79 -    35.57: 271
       35.57 -    53.36: 48
       53.36 -    71.14: 12
       71.14 -    88.93: 14
  Dihedral angle restraints: 3935
    sinusoidal: 1669
      harmonic: 2266
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.04  -80.04     1      1.00e+01 1.00e-02 7.94e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -48.28  -37.72     1      1.00e+01 1.00e-02 2.01e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.30  -36.30     1      1.00e+01 1.00e-02 1.86e+01
  ... (remaining 3932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 508
       0.028 -    0.056: 292
       0.056 -    0.085: 91
       0.085 -    0.113: 47
       0.113 -    0.141: 11
  Chirality restraints: 949
  Sorted by residual:
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  PRO B 491 "
            pdb=" N   PRO B 491 "
            pdb=" C   PRO B 491 "
            pdb=" CB  PRO B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A  90 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 946 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 475 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.46e+00
        pdb=" C   LYS A 475 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   LYS A 475 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 476 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 473 "   -0.007 2.00e-02 2.50e+03   1.50e-02 2.24e+00
        pdb=" C   TRP A 473 "    0.026 2.00e-02 2.50e+03
        pdb=" O   TRP A 473 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   MET A 474 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 335 "    0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO A 336 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 336 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 336 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 69
        2.66 -     3.22: 5794
        3.22 -     3.78: 9374
        3.78 -     4.34: 12820
        4.34 -     4.90: 21900
  Nonbonded interactions: 49957
  Sorted by model distance:
  nonbonded pdb=" CD  GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.097 2.460
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.098 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.105 2.230
  nonbonded pdb=" OD1 ASP B 442 "
            pdb=" OH  TYR B 451 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   ASP A 431 "
            pdb=" OG1 THR A 434 "
     model   vdw
     2.227 3.040
  ... (remaining 49952 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     22.230
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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      :  0.004   0.038   6547  Z= 0.274
  Angle     :  0.593   6.234   8897  Z= 0.320
  Chirality :  0.042   0.141    949
  Planarity :  0.004   0.037   1141
  Dihedral  : 13.686  88.931   2471
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  0.35 (0.30), residues: 768
  helix:  1.20 (0.27), residues: 395
  sheet:  0.42 (0.66), residues: 60
  loop : -1.05 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.017   0.002   PHE A 512 
 TYR   0.016   0.001   TYR A 158 
 ARG   0.003   0.000   ARG A 204 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7343 (tt0) cc_final: 0.7074 (tt0)
REVERT: A  231 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: A  243 TYR cc_start: 0.7578 (t80) cc_final: 0.7359 (t80)
REVERT: A  299 ASP cc_start: 0.8028 (m-30) cc_final: 0.7727 (m-30)
REVERT: A  435 GLU cc_start: 0.7294 (mp0) cc_final: 0.6706 (mp0)
REVERT: A  491 VAL cc_start: 0.8438 (t) cc_final: 0.8130 (p)
REVERT: A  512 PHE cc_start: 0.8588 (t80) cc_final: 0.8384 (t80)
REVERT: A  515 TYR cc_start: 0.8382 (m-80) cc_final: 0.7475 (m-80)
REVERT: A  564 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7257 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1884
  time to fit residues: 39.8127
Evaluate side-chains
  137 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 522 GLN
A 524 GLN
B 354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.101200 restraints weight = 19411.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.46
r_work: 0.3166 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6547  Z= 0.352
  Angle     :  0.613   7.144   8897  Z= 0.323
  Chirality :  0.046   0.210    949
  Planarity :  0.005   0.039   1141
  Dihedral  :  6.120  55.641    988
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  6.34 %
    Favored  : 92.18 %
  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:  0.39 (0.30), residues: 768
  helix:  1.41 (0.27), residues: 383
  sheet:  0.28 (0.67), residues: 61
  loop : -1.16 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 165 
 HIS   0.008   0.002   HIS A 401 
 PHE   0.020   0.002   PHE A 512 
 TYR   0.016   0.002   TYR A 158 
 ARG   0.006   0.001   ARG A 177 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8294 (tttt) cc_final: 0.8081 (tttt)
REVERT: A   75 GLU cc_start: 0.7743 (tt0) cc_final: 0.7478 (tt0)
REVERT: A  202 TYR cc_start: 0.8481 (t80) cc_final: 0.8093 (t80)
REVERT: A  231 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7960 (mm-30)
REVERT: A  243 TYR cc_start: 0.7509 (t80) cc_final: 0.7207 (t80)
REVERT: A  299 ASP cc_start: 0.7886 (m-30) cc_final: 0.7643 (m-30)
REVERT: A  435 GLU cc_start: 0.7355 (mp0) cc_final: 0.6858 (mp0)
REVERT: A  474 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7250 (mpp)
REVERT: A  491 VAL cc_start: 0.8428 (t) cc_final: 0.8099 (p)
REVERT: A  564 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7216 (mm-30)
REVERT: B  395 VAL cc_start: 0.8268 (p) cc_final: 0.7982 (t)
  outliers start: 10
  outliers final: 6
  residues processed: 155
  average time/residue: 0.1995
  time to fit residues: 42.7488
Evaluate side-chains
  143 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  534 LYS
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 44 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.110175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099314 restraints weight = 20638.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.72
r_work: 0.3129 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6547  Z= 0.281
  Angle     :  0.563   5.505   8897  Z= 0.297
  Chirality :  0.044   0.229    949
  Planarity :  0.005   0.057   1141
  Dihedral  :  5.483  55.098    988
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  8.55 %
    Favored  : 89.68 %
  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:  0.47 (0.30), residues: 768
  helix:  1.47 (0.27), residues: 383
  sheet:  0.24 (0.66), residues: 61
  loop : -1.10 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.008   0.001   HIS A 401 
 PHE   0.015   0.002   PHE A 369 
 TYR   0.016   0.002   TYR A 158 
 ARG   0.010   0.001   ARG A 192 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8103 (tttt) cc_final: 0.7874 (tttt)
REVERT: A   75 GLU cc_start: 0.7617 (tt0) cc_final: 0.7318 (tt0)
REVERT: A  150 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7528 (mm-30)
REVERT: A  202 TYR cc_start: 0.8323 (t80) cc_final: 0.7860 (t80)
REVERT: A  243 TYR cc_start: 0.7431 (t80) cc_final: 0.7084 (t80)
REVERT: A  299 ASP cc_start: 0.7852 (m-30) cc_final: 0.7603 (m-30)
REVERT: A  435 GLU cc_start: 0.7347 (mp0) cc_final: 0.6772 (mp0)
REVERT: A  491 VAL cc_start: 0.8428 (t) cc_final: 0.8061 (p)
REVERT: A  564 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7363 (mm-30)
REVERT: B  395 VAL cc_start: 0.8203 (p) cc_final: 0.7916 (t)
REVERT: B  451 TYR cc_start: 0.8228 (m-80) cc_final: 0.7898 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 155
  average time/residue: 0.1835
  time to fit residues: 38.3283
Evaluate side-chains
  153 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 145
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 57 optimal weight:    0.2980
   chunk 20 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0030
   chunk 12 optimal weight:    0.6980
   chunk 56 optimal weight:    0.2980
   chunk 60 optimal weight:    0.7980
   chunk 42 optimal weight:    0.1980
   chunk 5 optimal weight:    0.5980
   chunk 75 optimal weight:    0.0970
   overall best weight:    0.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.113020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.101664 restraints weight = 23621.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.92
r_work: 0.3149 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6547  Z= 0.156
  Angle     :  0.499   5.240   8897  Z= 0.264
  Chirality :  0.041   0.226    949
  Planarity :  0.004   0.045   1141
  Dihedral  :  4.871  55.168    988
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.03 %
    Favored  : 88.20 %
  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:  0.73 (0.30), residues: 768
  helix:  1.72 (0.27), residues: 379
  sheet:  0.46 (0.67), residues: 59
  loop : -1.00 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 401 
 PHE   0.010   0.001   PHE A 369 
 TYR   0.012   0.001   TYR B 396 
 ARG   0.015   0.001   ARG A 192 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8032 (tttt) cc_final: 0.7791 (tttt)
REVERT: A   75 GLU cc_start: 0.7598 (tt0) cc_final: 0.7277 (tt0)
REVERT: A  202 TYR cc_start: 0.8233 (t80) cc_final: 0.7898 (t80)
REVERT: A  243 TYR cc_start: 0.7355 (t80) cc_final: 0.7079 (t80)
REVERT: A  299 ASP cc_start: 0.7895 (m-30) cc_final: 0.7647 (m-30)
REVERT: A  360 MET cc_start: 0.7653 (ttp) cc_final: 0.7154 (ptm)
REVERT: A  435 GLU cc_start: 0.7383 (mp0) cc_final: 0.6798 (mp0)
REVERT: A  474 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7002 (mpp)
REVERT: A  491 VAL cc_start: 0.8370 (t) cc_final: 0.8006 (p)
REVERT: A  564 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7401 (mm-30)
REVERT: B  395 VAL cc_start: 0.8096 (p) cc_final: 0.7670 (t)
REVERT: B  433 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8108 (t)
  outliers start: 12
  outliers final: 6
  residues processed: 150
  average time/residue: 0.2047
  time to fit residues: 41.6100
Evaluate side-chains
  144 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 136
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 49 optimal weight:    0.1980
   chunk 38 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.109600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.099778 restraints weight = 15420.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.25
r_work: 0.3155 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6547  Z= 0.316
  Angle     :  0.570   5.789   8897  Z= 0.300
  Chirality :  0.044   0.243    949
  Planarity :  0.004   0.038   1141
  Dihedral  :  5.021  55.545    988
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.88 %
    Favored  : 87.76 %
  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:  0.67 (0.30), residues: 768
  helix:  1.60 (0.27), residues: 383
  sheet:  0.51 (0.68), residues: 59
  loop : -0.99 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 165 
 HIS   0.007   0.002   HIS A 241 
 PHE   0.017   0.002   PHE A 369 
 TYR   0.015   0.002   TYR A 158 
 ARG   0.004   0.001   ARG A 177 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8243 (tttt) cc_final: 0.8011 (tttt)
REVERT: A   75 GLU cc_start: 0.7790 (tt0) cc_final: 0.7472 (tt0)
REVERT: A  202 TYR cc_start: 0.8394 (t80) cc_final: 0.8007 (t80)
REVERT: A  299 ASP cc_start: 0.8041 (m-30) cc_final: 0.7809 (m-30)
REVERT: A  435 GLU cc_start: 0.7618 (mp0) cc_final: 0.7039 (mp0)
REVERT: A  474 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7345 (mpp)
REVERT: A  491 VAL cc_start: 0.8494 (t) cc_final: 0.8129 (p)
REVERT: A  564 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7517 (mm-30)
REVERT: B  395 VAL cc_start: 0.8272 (p) cc_final: 0.7977 (t)
REVERT: B  433 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8235 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 154
  average time/residue: 0.2036
  time to fit residues: 42.0057
Evaluate side-chains
  156 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  514 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 25 optimal weight:    0.0980
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.099202 restraints weight = 21859.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.82
r_work: 0.3108 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6547  Z= 0.264
  Angle     :  0.548   5.943   8897  Z= 0.288
  Chirality :  0.043   0.254    949
  Planarity :  0.004   0.037   1141
  Dihedral  :  4.967  54.566    988
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.06 %
    Favored  : 86.87 %
  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:  0.65 (0.30), residues: 768
  helix:  1.55 (0.27), residues: 383
  sheet:  0.50 (0.68), residues: 59
  loop : -0.94 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 401 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.015   0.001   TYR A 158 
 ARG   0.003   0.000   ARG A 177 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8094 (tttt) cc_final: 0.7853 (tttt)
REVERT: A   75 GLU cc_start: 0.7606 (tt0) cc_final: 0.7294 (tt0)
REVERT: A  202 TYR cc_start: 0.8321 (t80) cc_final: 0.7845 (t80)
REVERT: A  299 ASP cc_start: 0.7964 (m-30) cc_final: 0.7717 (m-30)
REVERT: A  474 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7184 (mpp)
REVERT: A  491 VAL cc_start: 0.8413 (t) cc_final: 0.8048 (p)
REVERT: A  564 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: B  395 VAL cc_start: 0.8195 (p) cc_final: 0.7932 (t)
REVERT: B  433 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8145 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 151
  average time/residue: 0.2375
  time to fit residues: 49.0542
Evaluate side-chains
  155 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 29 optimal weight:    0.1980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.098604 restraints weight = 18192.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.51
r_work: 0.3118 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6547  Z= 0.322
  Angle     :  0.573   6.273   8897  Z= 0.302
  Chirality :  0.044   0.262    949
  Planarity :  0.004   0.038   1141
  Dihedral  :  5.057  55.269    988
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.65 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.30), residues: 768
  helix:  1.48 (0.27), residues: 383
  sheet:  0.55 (0.68), residues: 59
  loop : -0.99 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 165 
 HIS   0.006   0.002   HIS A 241 
 PHE   0.016   0.002   PHE A 369 
 TYR   0.016   0.002   TYR A 158 
 ARG   0.004   0.001   ARG A 177 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8087 (tttt) cc_final: 0.7836 (tttt)
REVERT: A   75 GLU cc_start: 0.7561 (tt0) cc_final: 0.7286 (tt0)
REVERT: A  299 ASP cc_start: 0.7956 (m-30) cc_final: 0.7740 (m-30)
REVERT: A  323 MET cc_start: 0.7767 (mtp) cc_final: 0.7493 (mmt)
REVERT: A  474 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7235 (mpp)
REVERT: A  491 VAL cc_start: 0.8416 (t) cc_final: 0.8052 (p)
REVERT: A  564 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7306 (mm-30)
REVERT: B  395 VAL cc_start: 0.8209 (p) cc_final: 0.7909 (t)
REVERT: B  433 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8129 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 159
  average time/residue: 0.1733
  time to fit residues: 36.9458
Evaluate side-chains
  161 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 72 optimal weight:    0.1980
   chunk 1 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.099276 restraints weight = 20652.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.71
r_work: 0.3118 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6547  Z= 0.258
  Angle     :  0.551   6.268   8897  Z= 0.291
  Chirality :  0.043   0.266    949
  Planarity :  0.004   0.037   1141
  Dihedral  :  4.978  54.854    988
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.24 %
    Favored  : 85.55 %
  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:  0.66 (0.30), residues: 768
  helix:  1.55 (0.27), residues: 383
  sheet:  0.55 (0.68), residues: 59
  loop : -0.94 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.023   0.001   PHE A 285 
 TYR   0.015   0.002   TYR A 158 
 ARG   0.003   0.000   ARG A 177 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8066 (tttt) cc_final: 0.7813 (tttt)
REVERT: A   75 GLU cc_start: 0.7581 (tt0) cc_final: 0.7283 (tt0)
REVERT: A  206 ASP cc_start: 0.7801 (t0) cc_final: 0.7561 (t0)
REVERT: A  299 ASP cc_start: 0.7946 (m-30) cc_final: 0.7729 (m-30)
REVERT: A  424 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7900 (mp)
REVERT: A  474 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7174 (mpp)
REVERT: A  491 VAL cc_start: 0.8395 (t) cc_final: 0.8021 (p)
REVERT: A  564 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: B  395 VAL cc_start: 0.8182 (p) cc_final: 0.7847 (t)
REVERT: B  433 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8130 (t)
  outliers start: 15
  outliers final: 10
  residues processed: 155
  average time/residue: 0.1807
  time to fit residues: 37.4601
Evaluate side-chains
  157 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 57 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0000
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:    0.3980
   overall best weight:    0.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.100474 restraints weight = 20174.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.67
r_work: 0.3140 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6547  Z= 0.210
  Angle     :  0.525   5.854   8897  Z= 0.277
  Chirality :  0.042   0.266    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  4.811  54.549    988
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.27 %
    Favored  : 84.81 %
  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:  0.78 (0.31), residues: 768
  helix:  1.64 (0.27), residues: 381
  sheet:  0.58 (0.69), residues: 59
  loop : -0.84 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.026   0.001   PHE A 285 
 TYR   0.015   0.001   TYR A 587 
 ARG   0.002   0.000   ARG A 177 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8094 (tttt) cc_final: 0.7870 (tttt)
REVERT: A   75 GLU cc_start: 0.7579 (tt0) cc_final: 0.7282 (tt0)
REVERT: A  206 ASP cc_start: 0.7808 (t0) cc_final: 0.7577 (t0)
REVERT: A  299 ASP cc_start: 0.7940 (m-30) cc_final: 0.7729 (m-30)
REVERT: A  424 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7833 (mp)
REVERT: A  474 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7160 (mpp)
REVERT: A  491 VAL cc_start: 0.8344 (t) cc_final: 0.7972 (p)
REVERT: A  564 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7340 (mm-30)
REVERT: B  433 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8117 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 146
  average time/residue: 0.1834
  time to fit residues: 35.7494
Evaluate side-chains
  146 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0470
   chunk 58 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0980
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.110364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098756 restraints weight = 25689.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 3.11
r_work: 0.3100 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6547  Z= 0.260
  Angle     :  0.552   6.000   8897  Z= 0.290
  Chirality :  0.043   0.276    949
  Planarity :  0.004   0.037   1141
  Dihedral  :  4.859  54.610    988
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.27 %
    Favored  : 84.96 %
  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:  0.74 (0.30), residues: 768
  helix:  1.59 (0.27), residues: 381
  sheet:  0.60 (0.68), residues: 59
  loop : -0.85 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.034   0.002   PHE A 285 
 TYR   0.015   0.002   TYR A 587 
 ARG   0.003   0.000   ARG A 177 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 145
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8120 (tttt) cc_final: 0.7901 (tttt)
REVERT: A   75 GLU cc_start: 0.7639 (tt0) cc_final: 0.7327 (tt0)
REVERT: A  206 ASP cc_start: 0.7877 (t0) cc_final: 0.7640 (t0)
REVERT: A  299 ASP cc_start: 0.7990 (m-30) cc_final: 0.7773 (m-30)
REVERT: A  424 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7890 (mp)
REVERT: A  474 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7148 (mpp)
REVERT: A  491 VAL cc_start: 0.8378 (t) cc_final: 0.8003 (p)
REVERT: A  564 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: B  433 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8136 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 152
  average time/residue: 0.1904
  time to fit residues: 38.9744
Evaluate side-chains
  157 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 145
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.0670
   chunk 75 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   chunk 14 optimal weight:    0.2980
   chunk 46 optimal weight:    0.7980
   chunk 74 optimal weight:    0.3980
   chunk 63 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.3518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.111323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.100043 restraints weight = 22227.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.86
r_work: 0.3136 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3134
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6547  Z= 0.208
  Angle     :  0.533   6.201   8897  Z= 0.279
  Chirality :  0.042   0.266    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  4.801  55.111    988
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.83 %
    Favored  : 84.96 %
  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:  0.84 (0.31), residues: 768
  helix:  1.69 (0.27), residues: 381
  sheet:  0.60 (0.69), residues: 59
  loop : -0.80 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.014   0.001   PHE A 285 
 TYR   0.015   0.001   TYR A 587 
 ARG   0.003   0.000   ARG A 192 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3813.44 seconds
wall clock time: 66 minutes 11.65 seconds (3971.65 seconds total)