Starting phenix.real_space_refine
on Wed Mar  5 21:25:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dha_27434/03_2025/8dha_27434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dha_27434/03_2025/8dha_27434.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2025/8dha_27434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2025/8dha_27434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2025/8dha_27434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2025/8dha_27434.cif"
  }
  resolution = 3.8
  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=   0.014
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      16      5.16       5
     C    2234      2.51       5
     N     596      2.21       5
     O     664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3510
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 773
          Classifications: {'peptide': 94}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 89}
    Chain: "B"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1622
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 188}
    Chain: "C"
      Number of atoms: 1087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1087
          Classifications: {'peptide': 141}
          Link IDs: {'PTRANS': 6, 'TRANS': 134}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "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
  Time building chain proxies: 3.60, per 1000 atoms: 1.03
  Number of scatterers: 3510
  At special positions: 0
  Unit cell: (103.786, 72.7693, 95.4352, 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      16     16.00
     O     664      8.00
     N     596      7.00
     C    2234      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 411 " - pdb=" SG  CYS A 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " 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 901 " - " ASN A 345 "
      " NAG B 901 " - " ASN B 622 "
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 416.6 milliseconds
  

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  844

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      25.7% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.739A  pdb=" N   VAL B 532 " --> pdb=" O   PRO B 529 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 26
    Processing helix  chain 'C' and resid 50 through 67
    Processing helix  chain 'C' and resid 70 through 94
    Processing helix  chain 'C' and resid 107 through 117
      removed outlier: 3.554A  pdb=" N   ASP C 111 " --> pdb=" O   PRO C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 141
      removed outlier: 4.393A  pdb=" N   ASP C 141 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339
      removed outlier: 5.963A  pdb=" N   ILE A 338 " --> pdb=" O   TYR A 424 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 408 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 365 " --> pdb=" O   CYS A 411 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339
      removed outlier: 5.963A  pdb=" N   ILE A 338 " --> pdb=" O   TYR A 424 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 408 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347
      removed outlier: 3.788A  pdb=" N   ALA A 346 " --> pdb=" O   PHE A 391 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 354
    Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.516A  pdb=" N   MET B 443 " --> pdb=" O   PHE B 498 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   CYS B 445 " --> pdb=" O   CYS B 496 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   CYS B 496 " --> pdb=" O   CYS B 445 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TRP B 447 " --> pdb=" O   TYR B 494 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR B 494 " --> pdb=" O   TRP B 447 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 482 through 483
      removed outlier: 3.768A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASN B 514 " --> pdb=" O   THR B 459 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLN B 461 " --> pdb=" O   ARG B 512 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG B 512 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B 463 " --> pdb=" O   TRP B 510 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B 520 " --> pdb=" O   ILE B 513 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   HIS B 515 " --> pdb=" O   GLY B 518 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLY B 518 " --> pdb=" O   HIS B 515 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483
      removed outlier: 3.768A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASN B 514 " --> pdb=" O   THR B 459 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLN B 461 " --> pdb=" O   ARG B 512 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG B 512 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B 463 " --> pdb=" O   TRP B 510 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   TYR B 507 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL B 527 " --> pdb=" O   TYR B 507 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   MET B 509 " --> pdb=" O   THR B 525 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR B 525 " --> pdb=" O   MET B 509 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 542 through 545
      removed outlier: 3.816A  pdb=" N   LYS B 542 " --> pdb=" O   SER B 555 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   SER B 555 " --> pdb=" O   LYS B 542 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   VAL B 554 " --> pdb=" O   ALA B 594 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 582 through 586
      removed outlier: 3.933A  pdb=" N   VAL B 607 " --> pdb=" O   ALA B 627 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA B 627 " --> pdb=" O   VAL B 607 " (cutoff:3.500A)

    137 hydrogen bonds defined for protein.
    375 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: 0.95

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1122
        1.34 -     1.46: 788
        1.46 -     1.58: 1658
        1.58 -     1.70: 1
        1.70 -     1.81: 19
  Bond restraints: 3588
  Sorted by residual:
  bond pdb=" CB  PRO B 472 "
       pdb=" CG  PRO B 472 "
    ideal  model  delta    sigma   weight residual
    1.492  1.614 -0.122 5.00e-02 4.00e+02 5.94e+00
  bond pdb=" C2  NAG A 901 "
       pdb=" N2  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.439  1.463 -0.024 2.00e-02 2.50e+03 1.40e+00
  bond pdb=" C1  NAG B 901 "
       pdb=" O5  NAG B 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.39e+00
  bond pdb=" C5  NAG A 901 "
       pdb=" O5  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C5  NAG B 901 "
       pdb=" O5  NAG B 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.10e+00
  ... (remaining 3583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 4777
        2.22 -     4.44: 91
        4.44 -     6.67: 11
        6.67 -     8.89: 4
        8.89 -    11.11: 1
  Bond angle restraints: 4884
  Sorted by residual:
  angle pdb=" CA  SER B 450 "
        pdb=" C   SER B 450 "
        pdb=" N   THR B 451 "
      ideal   model   delta    sigma   weight residual
     116.84  125.69   -8.85 1.71e+00 3.42e-01 2.68e+01
  angle pdb=" CA  PRO B 472 "
        pdb=" N   PRO B 472 "
        pdb=" CD  PRO B 472 "
      ideal   model   delta    sigma   weight residual
     112.00  104.86    7.14 1.40e+00 5.10e-01 2.60e+01
  angle pdb=" CA  SER B 450 "
        pdb=" C   SER B 450 "
        pdb=" O   SER B 450 "
      ideal   model   delta    sigma   weight residual
     120.51  115.41    5.10 1.43e+00 4.89e-01 1.27e+01
  angle pdb=" N   LYS C   5 "
        pdb=" CA  LYS C   5 "
        pdb=" C   LYS C   5 "
      ideal   model   delta    sigma   weight residual
     111.28  107.66    3.62 1.09e+00 8.42e-01 1.10e+01
  angle pdb=" CA  LEU C 104 "
        pdb=" CB  LEU C 104 "
        pdb=" CG  LEU C 104 "
      ideal   model   delta    sigma   weight residual
     116.30  127.41  -11.11 3.50e+00 8.16e-02 1.01e+01
  ... (remaining 4879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 1869
       17.93 -    35.86: 279
       35.86 -    53.79: 56
       53.79 -    71.72: 9
       71.72 -    89.64: 4
  Dihedral angle restraints: 2217
    sinusoidal: 919
      harmonic: 1298
  Sorted by residual:
  dihedral pdb=" CB  CYS B 486 "
           pdb=" SG  CYS B 486 "
           pdb=" SG  CYS B 496 "
           pdb=" CB  CYS B 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.09   37.91     1      1.00e+01 1.00e-02 2.03e+01
  dihedral pdb=" CB  GLU B 435 "
           pdb=" CG  GLU B 435 "
           pdb=" CD  GLU B 435 "
           pdb=" OE1 GLU B 435 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.64  -89.64     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CG  ARG C  35 "
           pdb=" CD  ARG C  35 "
           pdb=" NE  ARG C  35 "
           pdb=" CZ  ARG C  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.34  -44.66     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 2214 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 381
       0.039 -    0.077: 135
       0.077 -    0.116: 47
       0.116 -    0.154: 7
       0.154 -    0.193: 2
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" C1  NAG B 901 "
            pdb=" ND2 ASN B 622 "
            pdb=" C2  NAG B 901 "
            pdb=" O5  NAG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" C2  NAG A 901 "
            pdb=" C1  NAG A 901 "
            pdb=" C3  NAG A 901 "
            pdb=" N2  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.18 2.00e-01 2.50e+01 7.89e-01
  chirality pdb=" CB  VAL C 113 "
            pdb=" CA  VAL C 113 "
            pdb=" CG1 VAL C 113 "
            pdb=" CG2 VAL C 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.01e-01
  ... (remaining 569 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 471 "    0.048 5.00e-02 4.00e+02   6.92e-02 7.67e+00
        pdb=" N   PRO B 472 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 472 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 472 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 374 "    0.038 5.00e-02 4.00e+02   5.81e-02 5.39e+00
        pdb=" N   PRO A 375 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 447 "    0.012 2.00e-02 2.50e+03   1.21e-02 3.66e+00
        pdb=" CG  TRP B 447 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 447 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 447 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 447 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 447 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 447 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 447 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 447 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 447 "    0.002 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 139
        2.70 -     3.25: 3307
        3.25 -     3.80: 5152
        3.80 -     4.35: 5698
        4.35 -     4.90: 9630
  Nonbonded interactions: 23926
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 563 "
            pdb=" OG1 THR C  19 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   VAL C  64 "
            pdb=" OG  SER C  67 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LEU B 455 "
            pdb=" OG  SER B 458 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OH  TYR B 470 "
            pdb=" OD2 ASP C   9 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ILE B 511 "
            pdb=" OG  SER B 522 "
     model   vdw
     2.304 3.040
  ... (remaining 23921 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.370
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.100
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
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   0.122   3588  Z= 0.230
  Angle     :  0.763  11.108   4884  Z= 0.392
  Chirality :  0.045   0.193    572
  Planarity :  0.005   0.069    614
  Dihedral  : 17.096  89.644   1358
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 34.07 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  0.08 (0.41), residues: 433
  helix:  2.17 (0.52), residues: 106
  sheet:  0.30 (0.54), residues: 103
  loop : -1.15 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B 447 
 HIS   0.002   0.001   HIS A 349 
 PHE   0.012   0.001   PHE B 502 
 TYR   0.014   0.001   TYR B 605 
 ARG   0.006   0.000   ARG B 571 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 PHE cc_start: 0.9397 (m-80) cc_final: 0.8920 (m-10)
REVERT: B  504 LEU cc_start: 0.9139 (mp) cc_final: 0.8809 (tt)
REVERT: C   87 LEU cc_start: 0.8920 (mt) cc_final: 0.8684 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 87
  average time/residue: 0.1491
  time to fit residues: 15.9614
Evaluate side-chains
  82 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  569 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 608 GLN
C  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.105809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.072613 restraints weight = 10834.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.074248 restraints weight = 5915.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.075167 restraints weight = 4487.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3588  Z= 0.379
  Angle     :  0.772   9.048   4884  Z= 0.392
  Chirality :  0.047   0.223    572
  Planarity :  0.005   0.047    614
  Dihedral  :  6.609  49.881    518
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 27.65 %
    Favored  : 67.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.29 (0.41), residues: 433
  helix:  1.89 (0.50), residues: 110
  sheet:  0.20 (0.54), residues: 97
  loop : -1.49 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B 447 
 HIS   0.003   0.001   HIS A 349 
 PHE   0.013   0.002   PHE B 502 
 TYR   0.019   0.002   TYR B 605 
 ARG   0.005   0.001   ARG B 613 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  447 TRP cc_start: 0.8436 (p-90) cc_final: 0.7889 (p-90)
REVERT: B  499 GLN cc_start: 0.9290 (tp-100) cc_final: 0.8726 (tp-100)
REVERT: B  504 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8627 (tt)
REVERT: B  509 MET cc_start: 0.8273 (ppp) cc_final: 0.7188 (ppp)
  outliers start: 21
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1369
  time to fit residues: 15.8700
Evaluate side-chains
  84 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0570
   chunk 33 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
B 499 GLN
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  28 GLN
C  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.108344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.075172 restraints weight = 10651.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.076859 restraints weight = 5857.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.077850 restraints weight = 4462.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3588  Z= 0.197
  Angle     :  0.699   9.406   4884  Z= 0.340
  Chirality :  0.046   0.238    572
  Planarity :  0.004   0.049    614
  Dihedral  :  6.124  53.128    515
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 27.41 %
    Favored  : 66.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.23 (0.41), residues: 433
  helix:  1.90 (0.51), residues: 110
  sheet:  0.16 (0.53), residues: 98
  loop : -1.41 (0.39), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 366 
 HIS   0.002   0.001   HIS B 465 
 PHE   0.017   0.002   PHE B 568 
 TYR   0.014   0.001   TYR B 605 
 ARG   0.002   0.000   ARG B 613 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5306 (t)
REVERT: A  417 HIS cc_start: 0.5960 (OUTLIER) cc_final: 0.5635 (t-90)
REVERT: B  447 TRP cc_start: 0.8393 (p-90) cc_final: 0.7523 (p-90)
REVERT: B  504 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8548 (tt)
REVERT: B  509 MET cc_start: 0.8288 (ppp) cc_final: 0.7303 (ppp)
REVERT: B  556 TRP cc_start: 0.9096 (p90) cc_final: 0.8770 (p90)
  outliers start: 23
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1279
  time to fit residues: 15.6834
Evaluate side-chains
  88 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 21 optimal weight:    0.0570
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.108178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.074920 restraints weight = 10798.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.076705 restraints weight = 5762.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.077724 restraints weight = 4324.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3588  Z= 0.197
  Angle     :  0.671   9.399   4884  Z= 0.323
  Chirality :  0.046   0.238    572
  Planarity :  0.004   0.044    614
  Dihedral  :  5.694  52.210    515
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 26.91 %
    Favored  : 67.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.22 (0.41), residues: 433
  helix:  1.84 (0.51), residues: 110
  sheet:  0.17 (0.51), residues: 102
  loop : -1.39 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 447 
 HIS   0.002   0.001   HIS B 465 
 PHE   0.009   0.002   PHE B 568 
 TYR   0.012   0.001   TYR B 605 
 ARG   0.002   0.000   ARG B 613 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5854 (OUTLIER) cc_final: 0.5277 (t)
REVERT: A  417 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5718 (t-90)
REVERT: B  447 TRP cc_start: 0.8401 (p-90) cc_final: 0.7400 (p-90)
REVERT: B  504 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8564 (tt)
REVERT: B  509 MET cc_start: 0.8256 (ppp) cc_final: 0.7211 (ppp)
REVERT: B  530 ASP cc_start: 0.8545 (t70) cc_final: 0.8257 (t70)
REVERT: B  556 TRP cc_start: 0.9030 (p90) cc_final: 0.8533 (p90)
REVERT: B  623 TRP cc_start: 0.8044 (m100) cc_final: 0.7335 (m100)
  outliers start: 23
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1230
  time to fit residues: 15.3058
Evaluate side-chains
  92 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    1 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0570
   chunk 30 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.108071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.074463 restraints weight = 11035.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.076278 restraints weight = 5844.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.077246 restraints weight = 4363.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3588  Z= 0.212
  Angle     :  0.671   9.381   4884  Z= 0.327
  Chirality :  0.046   0.238    572
  Planarity :  0.004   0.044    614
  Dihedral  :  5.679  51.955    515
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 28.40 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.29 (0.40), residues: 433
  helix:  1.72 (0.50), residues: 110
  sheet:  0.16 (0.52), residues: 102
  loop : -1.40 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 620 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.009   0.002   PHE B 568 
 TYR   0.012   0.001   TYR A 409 
 ARG   0.004   0.000   ARG B 610 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5516 (t)
REVERT: A  409 TYR cc_start: 0.5812 (m-80) cc_final: 0.5605 (m-80)
REVERT: A  417 HIS cc_start: 0.6051 (OUTLIER) cc_final: 0.5816 (t-90)
REVERT: B  447 TRP cc_start: 0.8369 (p-90) cc_final: 0.7264 (p-90)
REVERT: B  470 TYR cc_start: 0.6772 (m-10) cc_final: 0.6421 (m-10)
REVERT: B  504 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8395 (tt)
REVERT: B  556 TRP cc_start: 0.9059 (p90) cc_final: 0.8495 (p90)
REVERT: B  623 TRP cc_start: 0.8013 (m100) cc_final: 0.7138 (m100)
  outliers start: 25
  outliers final: 18
  residues processed: 98
  average time/residue: 0.1351
  time to fit residues: 16.7179
Evaluate side-chains
  98 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    1 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.108306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.074883 restraints weight = 10985.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.076637 restraints weight = 5845.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.077653 restraints weight = 4386.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3588  Z= 0.237
  Angle     :  0.687   9.333   4884  Z= 0.332
  Chirality :  0.045   0.238    572
  Planarity :  0.004   0.042    614
  Dihedral  :  5.677  51.701    515
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.38 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.32 (0.40), residues: 433
  helix:  1.70 (0.50), residues: 110
  sheet:  0.34 (0.53), residues: 97
  loop : -1.51 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 620 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.009   0.001   PHE C  92 
 TYR   0.011   0.001   TYR A 405 
 ARG   0.003   0.000   ARG B 613 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5903 (OUTLIER) cc_final: 0.5352 (t)
REVERT: A  417 HIS cc_start: 0.6120 (OUTLIER) cc_final: 0.5872 (t-90)
REVERT: B  504 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8398 (tt)
REVERT: B  556 TRP cc_start: 0.9042 (p90) cc_final: 0.8405 (p90)
  outliers start: 21
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1381
  time to fit residues: 16.3461
Evaluate side-chains
  94 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    1 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.108398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.074896 restraints weight = 10805.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.076642 restraints weight = 5861.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.077609 restraints weight = 4408.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3588  Z= 0.232
  Angle     :  0.682   9.398   4884  Z= 0.331
  Chirality :  0.045   0.238    572
  Planarity :  0.004   0.042    614
  Dihedral  :  5.663  51.882    515
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 27.65 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.34 (0.41), residues: 433
  helix:  1.71 (0.50), residues: 110
  sheet:  0.34 (0.54), residues: 92
  loop : -1.50 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.009   0.002   PHE A 403 
 TYR   0.013   0.002   TYR A 409 
 ARG   0.003   0.000   ARG A 368 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5377 (t)
REVERT: A  409 TYR cc_start: 0.5828 (m-80) cc_final: 0.5595 (m-80)
REVERT: B  447 TRP cc_start: 0.8516 (p-90) cc_final: 0.7379 (p-90)
REVERT: B  556 TRP cc_start: 0.9095 (p90) cc_final: 0.8461 (p90)
REVERT: B  610 ARG cc_start: 0.6429 (ptt90) cc_final: 0.6156 (ptt90)
REVERT: C    9 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8119 (t0)
  outliers start: 27
  outliers final: 16
  residues processed: 97
  average time/residue: 0.1259
  time to fit residues: 15.5851
Evaluate side-chains
  91 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 478 HIS
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.107871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.074260 restraints weight = 10885.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.076025 restraints weight = 5876.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.077005 restraints weight = 4414.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3588  Z= 0.230
  Angle     :  0.714  12.402   4884  Z= 0.339
  Chirality :  0.045   0.237    572
  Planarity :  0.004   0.041    614
  Dihedral  :  5.625  52.049    515
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 27.41 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.36 (0.41), residues: 433
  helix:  1.71 (0.51), residues: 110
  sheet:  0.31 (0.54), residues: 92
  loop : -1.52 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 447 
 HIS   0.004   0.001   HIS B 478 
 PHE   0.008   0.002   PHE C  92 
 TYR   0.012   0.001   TYR A 409 
 ARG   0.003   0.000   ARG B 613 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5502 (t)
REVERT: A  409 TYR cc_start: 0.5955 (m-80) cc_final: 0.5598 (m-80)
REVERT: B  447 TRP cc_start: 0.8553 (p-90) cc_final: 0.7450 (p-90)
REVERT: B  556 TRP cc_start: 0.9100 (p90) cc_final: 0.8462 (p90)
REVERT: B  610 ARG cc_start: 0.6518 (ptt90) cc_final: 0.6243 (ptt90)
REVERT: C    9 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7999 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 97
  average time/residue: 0.1372
  time to fit residues: 16.8781
Evaluate side-chains
  94 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0970
   chunk 27 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 349 HIS
B 478 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.108628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.074831 restraints weight = 10495.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.076590 restraints weight = 5636.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.077568 restraints weight = 4225.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3588  Z= 0.208
  Angle     :  0.710  10.190   4884  Z= 0.338
  Chirality :  0.047   0.270    572
  Planarity :  0.004   0.041    614
  Dihedral  :  5.588  52.524    515
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 29.14 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.30 (0.41), residues: 433
  helix:  1.79 (0.51), residues: 110
  sheet:  0.17 (0.54), residues: 95
  loop : -1.42 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 366 
 HIS   0.004   0.001   HIS B 478 
 PHE   0.008   0.001   PHE B 502 
 TYR   0.010   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 368 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5609 (OUTLIER) cc_final: 0.5153 (t)
REVERT: B  556 TRP cc_start: 0.9083 (p90) cc_final: 0.8452 (p90)
REVERT: B  610 ARG cc_start: 0.6553 (ptt90) cc_final: 0.6279 (ptt90)
REVERT: C    9 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7975 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 93
  average time/residue: 0.1348
  time to fit residues: 15.7268
Evaluate side-chains
  91 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 22 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 478 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.109018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.074977 restraints weight = 10573.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.076775 restraints weight = 5647.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.077745 restraints weight = 4219.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3588  Z= 0.211
  Angle     :  0.721   9.392   4884  Z= 0.344
  Chirality :  0.046   0.238    572
  Planarity :  0.004   0.040    614
  Dihedral  :  5.594  52.528    515
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 28.64 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.20 (0.41), residues: 433
  helix:  1.77 (0.51), residues: 110
  sheet:  0.37 (0.54), residues: 92
  loop : -1.35 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 366 
 HIS   0.006   0.001   HIS A 349 
 PHE   0.008   0.001   PHE C  92 
 TYR   0.046   0.002   TYR A 409 
 ARG   0.003   0.000   ARG A 368 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5611 (OUTLIER) cc_final: 0.5197 (t)
REVERT: B  447 TRP cc_start: 0.8545 (p-90) cc_final: 0.7409 (p-90)
REVERT: B  556 TRP cc_start: 0.9073 (p90) cc_final: 0.8444 (p90)
REVERT: B  563 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8437 (mt-10)
REVERT: B  610 ARG cc_start: 0.6596 (ptt90) cc_final: 0.6327 (ptt90)
REVERT: C    9 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7928 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1401
  time to fit residues: 16.0314
Evaluate side-chains
  90 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 25 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 37 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 478 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.108154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.074369 restraints weight = 10585.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.076127 restraints weight = 5679.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.077052 restraints weight = 4253.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3588  Z= 0.220
  Angle     :  0.725  10.150   4884  Z= 0.346
  Chirality :  0.046   0.237    572
  Planarity :  0.004   0.041    614
  Dihedral  :  5.582  52.135    515
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 29.14 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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: -0.22 (0.41), residues: 433
  helix:  1.79 (0.51), residues: 110
  sheet:  0.25 (0.54), residues: 92
  loop : -1.34 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 366 
 HIS   0.005   0.001   HIS A 349 
 PHE   0.008   0.002   PHE C  92 
 TYR   0.040   0.002   TYR A 409 
 ARG   0.003   0.000   ARG A 368 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1682.38 seconds
wall clock time: 29 minutes 44.48 seconds (1784.48 seconds total)