Starting phenix.real_space_refine
on Tue Feb  3 19:07:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s1z_24813/02_2026/7s1z_24813.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s1z_24813/02_2026/7s1z_24813.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2026/7s1z_24813.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2026/7s1z_24813.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2026/7s1z_24813.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2026/7s1z_24813.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.010 sd=   0.150
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      34      5.16       5
     C    4224      2.51       5
     N    1034      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6416
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3208
          Classifications: {'peptide': 472}
          Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83}
          Link IDs: {'PTRANS': 15, 'TRANS': 456}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 392
          Unresolved non-hydrogen angles: 507
          Unresolved non-hydrogen dihedrals: 302
          Unresolved non-hydrogen chiralities: 52
          Planarities with less than four sites: {'ASN:plan1': 10, 'PHE:plan': 6, 'ARG:plan': 5, 'TYR:plan': 4, 'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 208
    Chain: "B"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3208
          Classifications: {'peptide': 472}
          Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83}
          Link IDs: {'PTRANS': 15, 'TRANS': 456}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 392
          Unresolved non-hydrogen angles: 507
          Unresolved non-hydrogen dihedrals: 302
          Unresolved non-hydrogen chiralities: 52
          Planarities with less than four sites: {'ASN:plan1': 10, 'PHE:plan': 6, 'ARG:plan': 5, 'TYR:plan': 4, 'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 208
  Time building chain proxies: 1.72, per 1000 atoms: 0.27
  Number of scatterers: 6416
  At special positions: 0
  Unit cell: (104.94, 83.74, 87.98, 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      34     16.00
     O    1124      8.00
     N    1034      7.00
     C    4224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 563 " - pdb=" SG  CYS A 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 577 " - pdb=" SG  CYS A 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 563 " - pdb=" SG  CYS B 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 577 " - pdb=" SG  CYS B 582 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 289.3 milliseconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1640

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      71.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 288 through 300
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 4.532A  pdb=" N   PHE A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 315
      removed outlier: 4.532A  pdb=" N   TRP A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 344
      removed outlier: 4.115A  pdb=" N   LEU A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 398
      removed outlier: 4.508A  pdb=" N   GLY A 365 " --> pdb=" O   GLY A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 3.502A  pdb=" N   ILE A 411 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   VAL A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 454
      removed outlier: 3.650A  pdb=" N   ALA A 432 " --> pdb=" O   MET A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.651A  pdb=" N   LYS A 460 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS A 461 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 461'
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 486 through 495
    Processing helix  chain 'A' and resid 496 through 499
    Processing helix  chain 'A' and resid 500 through 506
      removed outlier: 4.358A  pdb=" N   GLY A 504 " --> pdb=" O   GLY A 500 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 511
    Processing helix  chain 'A' and resid 516 through 542
    Processing helix  chain 'A' and resid 565 through 570
      removed outlier: 3.599A  pdb=" N   CYS A 568 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A 570 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 597
      removed outlier: 3.562A  pdb=" N   SER A 597 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 630
      removed outlier: 3.647A  pdb=" N   ILE A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
    Processing helix  chain 'A' and resid 654 through 667
      removed outlier: 4.131A  pdb=" N   THR A 658 " --> pdb=" O   GLY A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 699
      removed outlier: 4.242A  pdb=" N   ILE A 677 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 730
    Processing helix  chain 'A' and resid 731 through 753
    Processing helix  chain 'B' and resid 288 through 300
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 4.441A  pdb=" N   PHE B 305 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 4.511A  pdb=" N   TRP B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 344
      removed outlier: 4.170A  pdb=" N   LEU B 322 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 398
      removed outlier: 4.482A  pdb=" N   GLY B 365 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 425
      removed outlier: 3.654A  pdb=" N   ILE B 411 " --> pdb=" O   ASN B 407 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 454
      removed outlier: 3.639A  pdb=" N   ALA B 432 " --> pdb=" O   MET B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 461
      removed outlier: 3.646A  pdb=" N   LYS B 460 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LYS B 461 " --> pdb=" O   GLU B 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 457 through 461'
    Processing helix  chain 'B' and resid 469 through 477
    Processing helix  chain 'B' and resid 486 through 495
    Processing helix  chain 'B' and resid 496 through 500
      removed outlier: 5.936A  pdb=" N   GLY B 500 " --> pdb=" O   ALA B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 506
      removed outlier: 3.585A  pdb=" N   ALA B 505 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 511
    Processing helix  chain 'B' and resid 516 through 542
    Processing helix  chain 'B' and resid 565 through 570
      removed outlier: 3.598A  pdb=" N   CYS B 568 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU B 570 " --> pdb=" O   ALA B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 597
      removed outlier: 3.529A  pdb=" N   SER B 597 " --> pdb=" O   MET B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 630
      removed outlier: 3.526A  pdb=" N   ILE B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      Proline residue:  B 623  - end of helix
    Processing helix  chain 'B' and resid 654 through 667
      removed outlier: 3.964A  pdb=" N   THR B 658 " --> pdb=" O   GLY B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 673 through 699
      removed outlier: 3.924A  pdb=" N   ILE B 677 " --> pdb=" O   VAL B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 730
      removed outlier: 3.505A  pdb=" N   SER B 716 " --> pdb=" O   ASN B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 753

    473 hydrogen bonds defined for protein.
    1395 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: 1.01

  Time building geometry restraints manager: 0.91 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: 2004
        1.34 -     1.46: 1560
        1.46 -     1.58: 2948
        1.58 -     1.70: 0
        1.70 -     1.81: 48
  Bond restraints: 6560
  Sorted by residual:
  bond pdb=" CG1 ILE B 747 "
       pdb=" CD1 ILE B 747 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.44e+00
  bond pdb=" CG1 ILE A 747 "
       pdb=" CD1 ILE A 747 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.22e+00
  bond pdb=" C   ALA B 675 "
       pdb=" N   PRO B 676 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 1.51e-02 4.39e+03 1.91e+00
  bond pdb=" C   ALA A 675 "
       pdb=" N   PRO A 676 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 1.51e-02 4.39e+03 1.76e+00
  bond pdb=" C   PHE A 495 "
       pdb=" N   PRO A 496 "
    ideal  model  delta    sigma   weight residual
    1.333  1.351 -0.018 1.44e-02 4.82e+03 1.59e+00
  ... (remaining 6555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 8568
        1.45 -     2.91: 318
        2.91 -     4.36: 68
        4.36 -     5.81: 16
        5.81 -     7.27: 10
  Bond angle restraints: 8980
  Sorted by residual:
  angle pdb=" N   ILE A 507 "
        pdb=" CA  ILE A 507 "
        pdb=" C   ILE A 507 "
      ideal   model   delta    sigma   weight residual
     112.80  106.16    6.64 1.15e+00 7.56e-01 3.33e+01
  angle pdb=" N   ILE B 507 "
        pdb=" CA  ILE B 507 "
        pdb=" C   ILE B 507 "
      ideal   model   delta    sigma   weight residual
     113.07  107.03    6.04 1.36e+00 5.41e-01 1.97e+01
  angle pdb=" N   ILE B 556 "
        pdb=" CA  ILE B 556 "
        pdb=" C   ILE B 556 "
      ideal   model   delta    sigma   weight residual
     111.91  108.72    3.19 8.90e-01 1.26e+00 1.28e+01
  angle pdb=" N   ILE A 556 "
        pdb=" CA  ILE A 556 "
        pdb=" C   ILE A 556 "
      ideal   model   delta    sigma   weight residual
     111.91  108.85    3.06 8.90e-01 1.26e+00 1.18e+01
  angle pdb=" N   SER A 516 "
        pdb=" CA  SER A 516 "
        pdb=" C   SER A 516 "
      ideal   model   delta    sigma   weight residual
     112.72  109.19    3.53 1.28e+00 6.10e-01 7.60e+00
  ... (remaining 8975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.22: 3350
       16.22 -    32.45: 255
       32.45 -    48.67: 50
       48.67 -    64.89: 3
       64.89 -    81.12: 4
  Dihedral angle restraints: 3662
    sinusoidal: 1056
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CB  CYS B 577 "
           pdb=" SG  CYS B 577 "
           pdb=" SG  CYS B 582 "
           pdb=" CB  CYS B 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   21.59   71.41     1      1.00e+01 1.00e-02 6.54e+01
  dihedral pdb=" CB  CYS A 577 "
           pdb=" SG  CYS A 577 "
           pdb=" SG  CYS A 582 "
           pdb=" CB  CYS A 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   21.64   71.36     1      1.00e+01 1.00e-02 6.53e+01
  dihedral pdb=" CA  GLY A 286 "
           pdb=" C   GLY A 286 "
           pdb=" N   TRP A 287 "
           pdb=" CA  TRP A 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.96   21.04     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 3659 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 555
       0.026 -    0.052: 309
       0.052 -    0.079: 162
       0.079 -    0.105: 58
       0.105 -    0.131: 10
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CG  LEU B 743 "
            pdb=" CB  LEU B 743 "
            pdb=" CD1 LEU B 743 "
            pdb=" CD2 LEU B 743 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CG  LEU A 743 "
            pdb=" CB  LEU A 743 "
            pdb=" CD1 LEU A 743 "
            pdb=" CD2 LEU A 743 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE B 507 "
            pdb=" N   ILE B 507 "
            pdb=" C   ILE B 507 "
            pdb=" CB  ILE B 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1091 not shown)

  Planarity restraints: 1126
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 705 "   -0.065 5.00e-02 4.00e+02   9.77e-02 1.53e+01
        pdb=" N   PRO B 706 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO B 706 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 706 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 675 "    0.059 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO B 676 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO B 676 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 676 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 675 "   -0.054 5.00e-02 4.00e+02   8.22e-02 1.08e+01
        pdb=" N   PRO A 676 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 676 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 676 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 1123 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1424
        2.78 -     3.31: 6932
        3.31 -     3.84: 10887
        3.84 -     4.37: 11091
        4.37 -     4.90: 19946
  Nonbonded interactions: 50280
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 476 "
            pdb=" NH1 ARG A 546 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   ILE B 356 "
            pdb=" OG  SER B 692 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   ILE A 356 "
            pdb=" OG  SER A 692 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL B 450 "
            pdb=" OG1 THR B 453 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   VAL A 450 "
            pdb=" OG1 THR A 453 "
     model   vdw
     2.305 3.040
  ... (remaining 50275 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.760
  Find NCS groups from input model:        0.060
  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:             0.000
  Load rotamer database and sin/cos tables:0.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4670
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      :  0.003   0.061   6564  Z= 0.153
  Angle     :  0.702   7.266   8988  Z= 0.397
  Chirality :  0.041   0.131   1094
  Planarity :  0.007   0.098   1126
  Dihedral  : 12.332  81.117   2010
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.18 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.27), residues: 940
  helix:  1.26 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -3.30 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 294 
 TYR   0.011   0.001   TYR A 533 
 PHE   0.021   0.001   PHE B 364 
 TRP   0.011   0.001   TRP A 300 
 HIS   0.005   0.001   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6560)
  covalent geometry    : angle       0.70213 ( 8980)
  SS BOND              : bond        0.00214 (    4)
  SS BOND              : angle       0.88471 (    8)
  hydrogen bonds       : bond        0.12045 (  473)
  hydrogen bonds       : angle       5.60206 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  428 MET cc_start: 0.4302 (tpp) cc_final: 0.3394 (ttp)
REVERT: A  469 LYS cc_start: 0.6823 (mmmt) cc_final: 0.6396 (mmtt)
REVERT: A  713 MET cc_start: 0.5462 (ptp) cc_final: 0.5207 (ptm)
REVERT: B  428 MET cc_start: 0.4383 (tpp) cc_final: 0.3450 (ttp)
REVERT: B  469 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6809 (mmtp)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0554
  time to fit residues: 5.0469
Evaluate side-chains
  45 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4357 r_free = 0.4357 target = 0.204925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.163502 restraints weight = 7102.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.56
r_work: 0.3821 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6384
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6564  Z= 0.157
  Angle     :  0.616   5.208   8988  Z= 0.324
  Chirality :  0.043   0.131   1094
  Planarity :  0.006   0.074   1126
  Dihedral  :  4.588  23.155    974
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.03 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.28), residues: 940
  helix:  1.24 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.26 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 294 
 TYR   0.006   0.001   TYR A 584 
 PHE   0.017   0.002   PHE B 364 
 TRP   0.015   0.002   TRP A 732 
 HIS   0.002   0.001   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6560)
  covalent geometry    : angle       0.61593 ( 8980)
  SS BOND              : bond        0.00319 (    4)
  SS BOND              : angle       0.72703 (    8)
  hydrogen bonds       : bond        0.03989 (  473)
  hydrogen bonds       : angle       4.59423 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  428 MET cc_start: 0.4908 (tpp) cc_final: 0.3712 (ttp)
REVERT: A  469 LYS cc_start: 0.7460 (mmmt) cc_final: 0.7175 (mmtp)
REVERT: B  428 MET cc_start: 0.5280 (tpp) cc_final: 0.3997 (ttp)
  outliers start: 6
  outliers final: 2
  residues processed: 55
  average time/residue: 0.0577
  time to fit residues: 4.9047
Evaluate side-chains
  47 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  715 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0030
   chunk 34 optimal weight:    0.0270
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.2646

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.208314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.167483 restraints weight = 7003.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 2.57
r_work: 0.3868 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6309
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6564  Z= 0.115
  Angle     :  0.550   5.209   8988  Z= 0.285
  Chirality :  0.040   0.117   1094
  Planarity :  0.005   0.062   1126
  Dihedral  :  4.348  21.996    974
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 15.12 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.28), residues: 940
  helix:  1.56 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.24 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 294 
 TYR   0.003   0.001   TYR A 746 
 PHE   0.010   0.001   PHE B 681 
 TRP   0.009   0.001   TRP B 430 
 HIS   0.001   0.000   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6560)
  covalent geometry    : angle       0.55005 ( 8980)
  SS BOND              : bond        0.00228 (    4)
  SS BOND              : angle       0.45150 (    8)
  hydrogen bonds       : bond        0.03539 (  473)
  hydrogen bonds       : angle       4.28794 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  428 MET cc_start: 0.5075 (tpp) cc_final: 0.3842 (ttp)
REVERT: B  428 MET cc_start: 0.5396 (tpp) cc_final: 0.4131 (ttp)
REVERT: B  492 GLU cc_start: 0.7900 (tt0) cc_final: 0.7663 (tt0)
  outliers start: 9
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0517
  time to fit residues: 4.3109
Evaluate side-chains
  41 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 36 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0000
   chunk 88 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0070
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.3602

-------------------------------------------------------------------------------
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 = 0.4378 r_free = 0.4378 target = 0.206888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.165744 restraints weight = 7061.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 2.60
r_work: 0.3853 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.116
  Angle     :  0.538   5.190   8988  Z= 0.279
  Chirality :  0.040   0.119   1094
  Planarity :  0.005   0.059   1126
  Dihedral  :  4.228  20.936    974
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.73 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.28), residues: 940
  helix:  1.72 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.20 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 705 
 TYR   0.004   0.001   TYR A 655 
 PHE   0.009   0.001   PHE B 681 
 TRP   0.007   0.001   TRP A 714 
 HIS   0.001   0.000   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6560)
  covalent geometry    : angle       0.53745 ( 8980)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       0.60219 (    8)
  hydrogen bonds       : bond        0.03452 (  473)
  hydrogen bonds       : angle       4.15916 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  428 MET cc_start: 0.5224 (tpp) cc_final: 0.4039 (ttm)
REVERT: B  428 MET cc_start: 0.5284 (tpp) cc_final: 0.3981 (ttp)
  outliers start: 9
  outliers final: 2
  residues processed: 50
  average time/residue: 0.0498
  time to fit residues: 4.0402
Evaluate side-chains
  42 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain B residue  747 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 83 optimal weight:    0.2980
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.200709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.158978 restraints weight = 7197.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 2.59
r_work: 0.3784 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6440
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6564  Z= 0.143
  Angle     :  0.564   6.353   8988  Z= 0.293
  Chirality :  0.041   0.122   1094
  Planarity :  0.005   0.059   1126
  Dihedral  :  4.302  20.642    974
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.97 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.28), residues: 940
  helix:  1.59 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -3.29 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 546 
 TYR   0.005   0.001   TYR A 584 
 PHE   0.014   0.001   PHE A 364 
 TRP   0.011   0.001   TRP B 714 
 HIS   0.002   0.001   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6560)
  covalent geometry    : angle       0.56375 ( 8980)
  SS BOND              : bond        0.00172 (    4)
  SS BOND              : angle       0.62102 (    8)
  hydrogen bonds       : bond        0.03755 (  473)
  hydrogen bonds       : angle       4.27447 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  428 MET cc_start: 0.5404 (tpp) cc_final: 0.4237 (ttm)
REVERT: B  428 MET cc_start: 0.5555 (tpp) cc_final: 0.4292 (ttp)
  outliers start: 13
  outliers final: 3
  residues processed: 59
  average time/residue: 0.0468
  time to fit residues: 4.5141
Evaluate side-chains
  47 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  697 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 85 optimal weight:    0.0670
   chunk 59 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0030
   chunk 50 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:   30.0000
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.4128

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.203221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.161466 restraints weight = 7075.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 2.59
r_work: 0.3816 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.118
  Angle     :  0.542   6.511   8988  Z= 0.278
  Chirality :  0.040   0.115   1094
  Planarity :  0.005   0.057   1126
  Dihedral  :  4.192  19.860    974
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.40 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.28), residues: 940
  helix:  1.70 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.23 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 546 
 TYR   0.009   0.001   TYR A 739 
 PHE   0.008   0.001   PHE A 364 
 TRP   0.007   0.001   TRP B 430 
 HIS   0.001   0.000   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6560)
  covalent geometry    : angle       0.54156 ( 8980)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.56332 (    8)
  hydrogen bonds       : bond        0.03507 (  473)
  hydrogen bonds       : angle       4.14771 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B  468 TYR cc_start: 0.5016 (OUTLIER) cc_final: 0.3961 (m-10)
  outliers start: 13
  outliers final: 2
  residues processed: 59
  average time/residue: 0.0515
  time to fit residues: 4.9116
Evaluate side-chains
  49 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain B residue  468 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0370
   chunk 14 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5258

-------------------------------------------------------------------------------
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 = 0.4337 r_free = 0.4337 target = 0.201477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.159391 restraints weight = 6978.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.61
r_work: 0.3798 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6564  Z= 0.128
  Angle     :  0.551   5.531   8988  Z= 0.283
  Chirality :  0.041   0.118   1094
  Planarity :  0.005   0.057   1126
  Dihedral  :  4.154  19.436    974
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.75 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.28), residues: 940
  helix:  1.68 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop : -3.25 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 546 
 TYR   0.009   0.001   TYR A 739 
 PHE   0.010   0.001   PHE A 488 
 TRP   0.008   0.001   TRP B 714 
 HIS   0.001   0.000   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6560)
  covalent geometry    : angle       0.55060 ( 8980)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       0.61903 (    8)
  hydrogen bonds       : bond        0.03613 (  473)
  hydrogen bonds       : angle       4.13688 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.140 
Fit side-chains
REVERT: B  454 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7126 (t80)
REVERT: B  468 TYR cc_start: 0.5117 (OUTLIER) cc_final: 0.4136 (m-10)
  outliers start: 10
  outliers final: 4
  residues processed: 59
  average time/residue: 0.0496
  time to fit residues: 4.5751
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  468 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0060
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.4351 r_free = 0.4351 target = 0.203028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.160606 restraints weight = 7014.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 2.65
r_work: 0.3808 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6376
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6564  Z= 0.118
  Angle     :  0.538   5.214   8988  Z= 0.275
  Chirality :  0.040   0.115   1094
  Planarity :  0.005   0.056   1126
  Dihedral  :  4.094  18.999    974
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.28 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.28), residues: 940
  helix:  1.76 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.22 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 546 
 TYR   0.007   0.001   TYR A 739 
 PHE   0.009   0.001   PHE A 488 
 TRP   0.007   0.001   TRP B 733 
 HIS   0.001   0.000   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6560)
  covalent geometry    : angle       0.53761 ( 8980)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       0.66941 (    8)
  hydrogen bonds       : bond        0.03489 (  473)
  hydrogen bonds       : angle       4.08860 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.220 
Fit side-chains
REVERT: B  454 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7204 (t80)
REVERT: B  468 TYR cc_start: 0.5126 (OUTLIER) cc_final: 0.4222 (m-10)
REVERT: B  499 THR cc_start: 0.8734 (p) cc_final: 0.8435 (p)
  outliers start: 10
  outliers final: 7
  residues processed: 57
  average time/residue: 0.0491
  time to fit residues: 4.3329
Evaluate side-chains
  56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  468 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 42 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0370
   chunk 48 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 45 optimal weight:    0.1980
   chunk 79 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0570
   overall best weight:    0.2376

-------------------------------------------------------------------------------
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 = 0.4388 r_free = 0.4388 target = 0.207296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.165536 restraints weight = 7081.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.4032 rms_B_bonded: 2.60
r_work: 0.3862 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6564  Z= 0.106
  Angle     :  0.527   5.203   8988  Z= 0.268
  Chirality :  0.039   0.111   1094
  Planarity :  0.005   0.056   1126
  Dihedral  :  3.942  18.110    974
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 20.64 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.28), residues: 940
  helix:  1.88 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.19 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 546 
 TYR   0.006   0.000   TYR A 739 
 PHE   0.007   0.001   PHE A 488 
 TRP   0.008   0.001   TRP A 732 
 HIS   0.001   0.000   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 6560)
  covalent geometry    : angle       0.52695 ( 8980)
  SS BOND              : bond        0.00150 (    4)
  SS BOND              : angle       0.63888 (    8)
  hydrogen bonds       : bond        0.03280 (  473)
  hydrogen bonds       : angle       3.96324 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.212 
Fit side-chains
REVERT: B  296 MET cc_start: 0.5831 (ttm) cc_final: 0.5627 (ttp)
REVERT: B  454 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.7075 (t80)
REVERT: B  468 TYR cc_start: 0.5057 (OUTLIER) cc_final: 0.4069 (m-10)
  outliers start: 8
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0591
  time to fit residues: 4.6607
Evaluate side-chains
  49 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  468 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0050
   chunk 14 optimal weight:    0.0370
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 89 optimal weight:    0.0670
   overall best weight:    0.2610

-------------------------------------------------------------------------------
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 = 0.4389 r_free = 0.4389 target = 0.207246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.164943 restraints weight = 6962.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.4025 rms_B_bonded: 2.68
r_work: 0.3853 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6312
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6564  Z= 0.107
  Angle     :  0.524   5.659   8988  Z= 0.266
  Chirality :  0.039   0.120   1094
  Planarity :  0.005   0.056   1126
  Dihedral  :  3.906  18.273    974
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 21.17 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.28), residues: 940
  helix:  1.93 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.16 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 705 
 TYR   0.003   0.000   TYR A 711 
 PHE   0.009   0.001   PHE A 488 
 TRP   0.009   0.001   TRP B 714 
 HIS   0.001   0.000   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6560)
  covalent geometry    : angle       0.52389 ( 8980)
  SS BOND              : bond        0.00170 (    4)
  SS BOND              : angle       0.69056 (    8)
  hydrogen bonds       : bond        0.03259 (  473)
  hydrogen bonds       : angle       3.94975 ( 1395)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.216 
Fit side-chains
REVERT: B  296 MET cc_start: 0.5830 (ttm) cc_final: 0.5616 (ttp)
REVERT: B  468 TYR cc_start: 0.5017 (OUTLIER) cc_final: 0.4129 (m-10)
  outliers start: 6
  outliers final: 4
  residues processed: 49
  average time/residue: 0.0553
  time to fit residues: 4.1533
Evaluate side-chains
  48 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  468 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 90 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4651 r_free = 0.4651 target = 0.233353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.191353 restraints weight = 7194.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.4314 rms_B_bonded: 2.57
r_work: 0.4089 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6564  Z= 0.147
  Angle     :  0.567   6.927   8988  Z= 0.292
  Chirality :  0.041   0.125   1094
  Planarity :  0.005   0.056   1126
  Dihedral  :  4.099  18.348    974
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 21.00 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.28), residues: 940
  helix:  1.75 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.13 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 546 
 TYR   0.006   0.001   TYR B 584 
 PHE   0.011   0.001   PHE A 488 
 TRP   0.012   0.001   TRP A 733 
 HIS   0.001   0.001   HIS B 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6560)
  covalent geometry    : angle       0.56652 ( 8980)
  SS BOND              : bond        0.00187 (    4)
  SS BOND              : angle       0.67418 (    8)
  hydrogen bonds       : bond        0.03759 (  473)
  hydrogen bonds       : angle       4.16132 ( 1395)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1392.24 seconds
wall clock time: 24 minutes 35.85 seconds (1475.85 seconds total)