Starting phenix.real_space_refine
on Fri Aug 22 17:02:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyo_60574/08_2025/8zyo_60574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyo_60574/08_2025/8zyo_60574.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyo_60574/08_2025/8zyo_60574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyo_60574/08_2025/8zyo_60574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyo_60574/08_2025/8zyo_60574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyo_60574/08_2025/8zyo_60574.cif"
  }
  resolution = 3.29
  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=   0.001 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4189      2.51       5
     N    1003      2.21       5
     O    1013      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6238
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1658
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 1561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1561
          Classifications: {'peptide': 199}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 192}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 1309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1309
          Classifications: {'peptide': 166}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 160}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "D"
      Number of atoms: 1642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1642
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "D"
      Number of atoms: 68
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 34
          Unusual residues: {'XB7': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 34
          Unusual residues: {'XB7': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1 AXB7 D1101 " occ=0.30
      ... (66 atoms not shown)
      pdb=" O1 BXB7 D1101 " occ=0.70
  Time building chain proxies: 2.08, per 1000 atoms: 0.33
  Number of scatterers: 6238
  At special positions: 0
  Unit cell: (103.75, 115.37, 72.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     F       2      9.00
     O    1013      8.00
     N    1003      7.00
     C    4189      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.58
  Conformation dependent library (CDL) restraints added in 403.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1466

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      81.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 409 through 432
      Proline residue:  A 426  - end of helix
    Processing helix  chain 'A' and resid 453 through 470
    Processing helix  chain 'A' and resid 489 through 495
      removed outlier: 3.705A  pdb=" N   TYR A 493 " --> pdb=" O   ILE A 489 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LYS A 495 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 504
    Processing helix  chain 'A' and resid 521 through 525
    Processing helix  chain 'A' and resid 526 through 530
    Processing helix  chain 'A' and resid 531 through 538
      removed outlier: 4.154A  pdb=" N   VAL A 535 " --> pdb=" O   ARG A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 543
      removed outlier: 3.722A  pdb=" N   SER A 543 " --> pdb=" O   ASP A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 575
    Processing helix  chain 'A' and resid 584 through 593
    Processing helix  chain 'A' and resid 606 through 624
    Processing helix  chain 'A' and resid 634 through 656
    Processing helix  chain 'A' and resid 658 through 665
    Processing helix  chain 'B' and resid 408 through 431
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 453 through 471
      removed outlier: 4.052A  pdb=" N   PHE B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 505
      removed outlier: 3.727A  pdb=" N   ALA B 504 " --> pdb=" O   ILE B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 525
    Processing helix  chain 'B' and resid 526 through 530
    Processing helix  chain 'B' and resid 531 through 538
      removed outlier: 3.670A  pdb=" N   VAL B 535 " --> pdb=" O   ARG B 531 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS B 538 " --> pdb=" O   ARG B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 543
      removed outlier: 4.084A  pdb=" N   TYR B 542 " --> pdb=" O   LYS B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 575
      removed outlier: 3.697A  pdb=" N   GLU B 575 " --> pdb=" O   ILE B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 593
    Processing helix  chain 'B' and resid 606 through 623
    Processing helix  chain 'B' and resid 634 through 663
      removed outlier: 3.726A  pdb=" N   SER B 660 " --> pdb=" O   PHE B 656 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 432
      removed outlier: 3.636A  pdb=" N   TRP C 412 " --> pdb=" O   ALA C 408 " (cutoff:3.500A)
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 521 through 526
    Processing helix  chain 'C' and resid 527 through 531
    Processing helix  chain 'C' and resid 532 through 538
    Processing helix  chain 'C' and resid 539 through 541
      No H-bonds generated for 'chain 'C' and resid 539 through 541'
    Processing helix  chain 'C' and resid 545 through 576
      removed outlier: 3.647A  pdb=" N   GLU C 575 " --> pdb=" O   ILE C 571 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 585 through 594
    Processing helix  chain 'C' and resid 606 through 623
    Processing helix  chain 'C' and resid 634 through 665
      removed outlier: 3.511A  pdb=" N   LEU C 646 " --> pdb=" O   ILE C 642 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLN C 664 " --> pdb=" O   SER C 660 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG C 665 " --> pdb=" O   ALA C 661 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 431
      removed outlier: 4.338A  pdb=" N   TRP D 412 " --> pdb=" O   ALA D 408 " (cutoff:3.500A)
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 453 through 470
    Processing helix  chain 'D' and resid 489 through 494
    Processing helix  chain 'D' and resid 498 through 503
    Processing helix  chain 'D' and resid 521 through 526
    Processing helix  chain 'D' and resid 527 through 530
    Processing helix  chain 'D' and resid 531 through 538
      removed outlier: 3.958A  pdb=" N   VAL D 535 " --> pdb=" O   ARG D 531 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LYS D 538 " --> pdb=" O   ARG D 534 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 543
      removed outlier: 3.546A  pdb=" N   TYR D 542 " --> pdb=" O   LYS D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 545 through 575
      removed outlier: 3.697A  pdb=" N   GLU D 575 " --> pdb=" O   ILE D 571 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 584 through 593
    Processing helix  chain 'D' and resid 606 through 623
    Processing helix  chain 'D' and resid 634 through 665
      removed outlier: 4.207A  pdb=" N   GLN D 664 " --> pdb=" O   SER D 660 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG D 665 " --> pdb=" O   ALA D 661 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1266 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: 0.91

  Time building geometry restraints manager: 0.76 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: 1829
        1.34 -     1.46: 1628
        1.46 -     1.58: 2882
        1.58 -     1.70: 0
        1.70 -     1.81: 50
  Bond restraints: 6389
  Sorted by residual:
  bond pdb=" C20BXB7 D1101 "
       pdb=" C21BXB7 D1101 "
    ideal  model  delta    sigma   weight residual
    1.511  1.386  0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" C5 BXB7 D1101 "
       pdb=" C6 BXB7 D1101 "
    ideal  model  delta    sigma   weight residual
    1.503  1.380  0.123 2.00e-02 2.50e+03 3.78e+01
  bond pdb=" C20AXB7 D1101 "
       pdb=" C21AXB7 D1101 "
    ideal  model  delta    sigma   weight residual
    1.511  1.389  0.122 2.00e-02 2.50e+03 3.75e+01
  bond pdb=" C5 AXB7 D1101 "
       pdb=" C6 AXB7 D1101 "
    ideal  model  delta    sigma   weight residual
    1.503  1.381  0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" C14AXB7 D1101 "
       pdb=" C19AXB7 D1101 "
    ideal  model  delta    sigma   weight residual
    1.406  1.332  0.074 2.00e-02 2.50e+03 1.35e+01
  ... (remaining 6384 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 8486
        2.04 -     4.08: 137
        4.08 -     6.12: 37
        6.12 -     8.16: 7
        8.16 -    10.20: 3
  Bond angle restraints: 8670
  Sorted by residual:
  angle pdb=" CB  LYS D 434 "
        pdb=" CG  LYS D 434 "
        pdb=" CD  LYS D 434 "
      ideal   model   delta    sigma   weight residual
     111.30  121.50  -10.20 2.30e+00 1.89e-01 1.97e+01
  angle pdb=" N   ASN D 629 "
        pdb=" CA  ASN D 629 "
        pdb=" C   ASN D 629 "
      ideal   model   delta    sigma   weight residual
     110.97  106.46    4.51 1.09e+00 8.42e-01 1.71e+01
  angle pdb=" CA  PHE D 627 "
        pdb=" C   PHE D 627 "
        pdb=" O   PHE D 627 "
      ideal   model   delta    sigma   weight residual
     120.20  115.66    4.54 1.12e+00 7.97e-01 1.64e+01
  angle pdb=" C   LEU D 524 "
        pdb=" N   LYS D 525 "
        pdb=" CA  LYS D 525 "
      ideal   model   delta    sigma   weight residual
     121.94  114.50    7.44 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" N   PHE A 627 "
        pdb=" CA  PHE A 627 "
        pdb=" CB  PHE A 627 "
      ideal   model   delta    sigma   weight residual
     110.28  104.58    5.70 1.55e+00 4.16e-01 1.35e+01
  ... (remaining 8665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.65: 3370
       25.65 -    51.30: 268
       51.30 -    76.95: 15
       76.95 -   102.60: 2
      102.60 -   128.25: 2
  Dihedral angle restraints: 3657
    sinusoidal: 1391
      harmonic: 2266
  Sorted by residual:
  dihedral pdb=" C10BXB7 D1101 "
           pdb=" C8 BXB7 D1101 "
           pdb=" C9 BXB7 D1101 "
           pdb=" N1 BXB7 D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.72   71.53 -128.25     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" CA  PHE B 656 "
           pdb=" C   PHE B 656 "
           pdb=" N   GLY B 657 "
           pdb=" CA  GLY B 657 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.27   18.73     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" C12BXB7 D1101 "
           pdb=" C8 BXB7 D1101 "
           pdb=" N1 BXB7 D1101 "
           pdb=" C9 BXB7 D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.79  -45.51  105.30     1      3.00e+01 1.11e-03 1.35e+01
  ... (remaining 3654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 797
       0.046 -    0.093: 196
       0.093 -    0.139: 21
       0.139 -    0.185: 6
       0.185 -    0.231: 2
  Chirality restraints: 1022
  Sorted by residual:
  chirality pdb=" CA  VAL D 630 "
            pdb=" N   VAL D 630 "
            pdb=" C   VAL D 630 "
            pdb=" CB  VAL D 630 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  PHE C 656 "
            pdb=" N   PHE C 656 "
            pdb=" C   PHE C 656 "
            pdb=" CB  PHE C 656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.95e-01
  chirality pdb=" CA  PHE D 627 "
            pdb=" N   PHE D 627 "
            pdb=" C   PHE D 627 "
            pdb=" CB  PHE D 627 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.80e-01
  ... (remaining 1019 not shown)

  Planarity restraints: 1017
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 649 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.01e+00
        pdb=" C   SER D 649 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER D 649 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU D 650 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 625 "   -0.008 2.00e-02 2.50e+03   1.70e-02 2.90e+00
        pdb=" C   VAL D 625 "    0.029 2.00e-02 2.50e+03
        pdb=" O   VAL D 625 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY D 626 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 506 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 507 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 507 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 507 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1014 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1169
        2.76 -     3.30: 6120
        3.30 -     3.83: 10587
        3.83 -     4.37: 11494
        4.37 -     4.90: 20166
  Nonbonded interactions: 49536
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 539 "
            pdb=" OG  SER B 543 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   LEU C 523 "
            pdb=" OG1 THR C 526 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PHE D 619 "
            pdb=" OG1 THR D 623 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   PRO A 632 "
            pdb=" ND2 ASN B 629 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   SER D 624 "
            pdb=" OG  SER D 624 "
     model   vdw
     2.269 3.040
  ... (remaining 49531 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 407 through 471 or (resid 498 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 499 through 665))
  selection = chain 'B'
  selection = (chain 'D' and (resid 407 through 471 or (resid 498 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 499 through 665))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 max=1.00 mean=0.99
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:             3.540
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.310
  Find NCS groups from input model:        0.090
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
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      :  0.005   0.125   6389  Z= 0.269
  Angle     :  0.675  10.197   8670  Z= 0.354
  Chirality :  0.040   0.231   1022
  Planarity :  0.004   0.039   1017
  Dihedral  : 17.016 128.249   2191
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 31.11 %
    Favored  : 68.42 %
  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 aren not related in a simple way.
  whole:  1.70 (0.31), residues: 741
  helix:  1.47 (0.22), residues: 580
  sheet:  None (None), residues: 0
  loop :  0.09 (0.52), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 541 
 TYR   0.016   0.002   TYR A 616 
 PHE   0.013   0.001   PHE D 656 
 TRP   0.011   0.001   TRP D 585 
 HIS   0.005   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 6389)
  covalent geometry    : angle       0.67509 ( 8670)
  hydrogen bonds       : bond        0.10422 (  430)
  hydrogen bonds       : angle       4.18439 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 ARG cc_start: 0.8393 (ptm160) cc_final: 0.8071 (ptt180)
REVERT: A  574 MET cc_start: 0.8365 (mmm) cc_final: 0.8071 (mmm)
REVERT: A  616 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8473 (t80)
REVERT: C  608 LYS cc_start: 0.9083 (tttt) cc_final: 0.8684 (tttp)
  outliers start: 3
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1095
  time to fit residues: 17.2990
Evaluate side-chains
  123 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0770
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
C 633 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.189516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.137170 restraints weight = 11429.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.47
r_work: 0.3441 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.0742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6389  Z= 0.108
  Angle     :  0.499   6.559   8670  Z= 0.259
  Chirality :  0.036   0.143   1022
  Planarity :  0.003   0.034   1017
  Dihedral  :  8.159 103.321    864
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 25.70 %
    Favored  : 70.12 %
  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 aren not related in a simple way.
  whole:  2.00 (0.32), residues: 741
  helix:  1.57 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.63 (0.56), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 541 
 TYR   0.014   0.001   TYR A 616 
 PHE   0.013   0.001   PHE D 656 
 TRP   0.009   0.001   TRP B 568 
 HIS   0.004   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6389)
  covalent geometry    : angle       0.49934 ( 8670)
  hydrogen bonds       : bond        0.03701 (  430)
  hydrogen bonds       : angle       3.79424 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 ARG cc_start: 0.8326 (ptm160) cc_final: 0.8084 (ptt180)
REVERT: A  616 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8399 (t80)
REVERT: C  528 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7974 (mtt180)
  outliers start: 27
  outliers final: 14
  residues processed: 141
  average time/residue: 0.1036
  time to fit residues: 18.4723
Evaluate side-chains
  133 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  616 TYR
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 21 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0970
   chunk 62 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0030
   chunk 30 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.4588

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.187052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135929 restraints weight = 9439.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.19
r_work: 0.3464 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6389  Z= 0.106
  Angle     :  0.484   6.301   8670  Z= 0.248
  Chirality :  0.036   0.142   1022
  Planarity :  0.003   0.031   1017
  Dihedral  :  7.940  99.568    864
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 25.23 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.32), residues: 741
  helix:  1.61 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.78 (0.57), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 541 
 TYR   0.016   0.001   TYR D 597 
 PHE   0.013   0.001   PHE D 656 
 TRP   0.009   0.001   TRP B 568 
 HIS   0.003   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6389)
  covalent geometry    : angle       0.48403 ( 8670)
  hydrogen bonds       : bond        0.03528 (  430)
  hydrogen bonds       : angle       3.68670 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  574 MET cc_start: 0.8398 (mmm) cc_final: 0.8022 (mmm)
REVERT: A  656 PHE cc_start: 0.8055 (m-80) cc_final: 0.7806 (m-80)
REVERT: B  554 MET cc_start: 0.8644 (tpp) cc_final: 0.8335 (mmp)
REVERT: C  528 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7980 (mtt180)
REVERT: C  597 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8153 (m-80)
  outliers start: 32
  outliers final: 15
  residues processed: 136
  average time/residue: 0.0974
  time to fit residues: 16.7960
Evaluate side-chains
  132 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LYS
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain C residue  650 LEU
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  530 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0070
   chunk 58 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.6200

-------------------------------------------------------------------------------
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 = 0.4023 r_free = 0.4023 target = 0.177495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.128039 restraints weight = 9250.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.93
r_work: 0.3316 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6389  Z= 0.115
  Angle     :  0.489   6.056   8670  Z= 0.251
  Chirality :  0.036   0.143   1022
  Planarity :  0.003   0.031   1017
  Dihedral  :  7.771  98.018    862
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 25.08 %
    Favored  : 70.28 %
  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 aren not related in a simple way.
  whole:  2.11 (0.32), residues: 741
  helix:  1.61 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.87 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 541 
 TYR   0.016   0.002   TYR A 616 
 PHE   0.013   0.001   PHE D 656 
 TRP   0.010   0.001   TRP B 568 
 HIS   0.003   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6389)
  covalent geometry    : angle       0.48913 ( 8670)
  hydrogen bonds       : bond        0.03574 (  430)
  hydrogen bonds       : angle       3.68585 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.4895 (p90)
REVERT: A  616 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8383 (t80)
REVERT: A  656 PHE cc_start: 0.8052 (m-80) cc_final: 0.7777 (m-80)
REVERT: B  554 MET cc_start: 0.8638 (tpp) cc_final: 0.8362 (mmp)
REVERT: B  557 PHE cc_start: 0.8675 (t80) cc_final: 0.8464 (t80)
REVERT: C  528 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7903 (mtt180)
REVERT: C  597 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8229 (m-80)
  outliers start: 30
  outliers final: 20
  residues processed: 139
  average time/residue: 0.0973
  time to fit residues: 17.1841
Evaluate side-chains
  138 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LYS
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  493 TYR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  616 TYR
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  521 ILE
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  465 VAL
Chi-restraints excluded: chain D residue  526 THR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 5 optimal weight:    0.5980
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.174666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.127411 restraints weight = 9583.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.19
r_work: 0.3256 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6389  Z= 0.155
  Angle     :  0.527   5.839   8670  Z= 0.273
  Chirality :  0.038   0.146   1022
  Planarity :  0.003   0.031   1017
  Dihedral  :  7.931  99.584    862
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 25.85 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.32), residues: 741
  helix:  1.49 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.86 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 541 
 TYR   0.019   0.002   TYR A 616 
 PHE   0.013   0.001   PHE D 656 
 TRP   0.010   0.001   TRP B 568 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6389)
  covalent geometry    : angle       0.52683 ( 8670)
  hydrogen bonds       : bond        0.03879 (  430)
  hydrogen bonds       : angle       3.82648 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.5010 (p90)
REVERT: A  574 MET cc_start: 0.8334 (mmm) cc_final: 0.8048 (mmm)
REVERT: B  554 MET cc_start: 0.8654 (tpp) cc_final: 0.8360 (mmp)
REVERT: C  597 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8458 (m-80)
REVERT: C  651 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5513 (mtt)
  outliers start: 32
  outliers final: 25
  residues processed: 138
  average time/residue: 0.0946
  time to fit residues: 16.5037
Evaluate side-chains
  143 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LYS
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  493 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  466 ASP
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain C residue  521 ILE
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  575 GLU
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain C residue  651 MET
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  461 ILE
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  465 VAL
Chi-restraints excluded: chain D residue  526 THR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 54 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.173491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.122466 restraints weight = 9459.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.99
r_work: 0.3232 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6389  Z= 0.182
  Angle     :  0.571   8.214   8670  Z= 0.295
  Chirality :  0.039   0.153   1022
  Planarity :  0.004   0.028   1017
  Dihedral  :  8.165 103.423    862
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 26.63 %
    Favored  : 68.11 %
  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 aren not related in a simple way.
  whole:  1.67 (0.32), residues: 741
  helix:  1.33 (0.22), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.56 (0.57), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 534 
 TYR   0.021   0.002   TYR D 616 
 PHE   0.013   0.001   PHE D 656 
 TRP   0.011   0.001   TRP B 568 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 6389)
  covalent geometry    : angle       0.57077 ( 8670)
  hydrogen bonds       : bond        0.04117 (  430)
  hydrogen bonds       : angle       3.96483 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.4964 (p90)
REVERT: A  574 MET cc_start: 0.8437 (mmm) cc_final: 0.8097 (mmm)
REVERT: B  539 LEU cc_start: 0.8918 (tt) cc_final: 0.8548 (tp)
REVERT: B  554 MET cc_start: 0.8669 (tpp) cc_final: 0.8389 (mmp)
REVERT: C  597 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8420 (m-80)
REVERT: C  651 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5475 (mtt)
REVERT: D  462 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7664 (mmm)
  outliers start: 34
  outliers final: 24
  residues processed: 141
  average time/residue: 0.0895
  time to fit residues: 15.8198
Evaluate side-chains
  144 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  493 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  466 ASP
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain C residue  419 ILE
Chi-restraints excluded: chain C residue  521 ILE
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  575 GLU
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain C residue  651 MET
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  461 ILE
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  465 VAL
Chi-restraints excluded: chain D residue  526 THR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0020
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   chunk 28 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 73 optimal weight:    0.3980
   chunk 56 optimal weight:    6.9990
   overall best weight:    0.3788

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.177558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.126818 restraints weight = 12088.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.53
r_work: 0.3268 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   6389  Z= 0.108
  Angle     :  0.511   7.000   8670  Z= 0.261
  Chirality :  0.036   0.142   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  7.786  98.586    862
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 27.55 %
    Favored  : 68.58 %
  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 aren not related in a simple way.
  whole:  2.04 (0.32), residues: 741
  helix:  1.55 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.86 (0.57), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 534 
 TYR   0.014   0.001   TYR A 616 
 PHE   0.014   0.001   PHE D 656 
 TRP   0.011   0.001   TRP D 585 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6389)
  covalent geometry    : angle       0.51060 ( 8670)
  hydrogen bonds       : bond        0.03522 (  430)
  hydrogen bonds       : angle       3.80710 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.4851 (p90)
REVERT: A  574 MET cc_start: 0.8449 (mmm) cc_final: 0.8133 (mmm)
REVERT: A  616 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8500 (t80)
REVERT: A  656 PHE cc_start: 0.8316 (m-80) cc_final: 0.8100 (m-80)
REVERT: B  539 LEU cc_start: 0.8889 (tt) cc_final: 0.8587 (tp)
REVERT: B  554 MET cc_start: 0.8713 (tpp) cc_final: 0.8504 (mmp)
REVERT: C  597 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8092 (m-80)
REVERT: C  651 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.5277 (mtt)
REVERT: D  462 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7670 (mmm)
  outliers start: 25
  outliers final: 16
  residues processed: 137
  average time/residue: 0.0954
  time to fit residues: 16.5143
Evaluate side-chains
  142 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  493 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  616 TYR
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  466 ASP
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  521 ILE
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain C residue  651 MET
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  465 VAL
Chi-restraints excluded: chain D residue  530 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0870
   chunk 49 optimal weight:    0.0770
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.5516

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.176962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.133938 restraints weight = 9136.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.27
r_work: 0.3304 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6389  Z= 0.116
  Angle     :  0.523   6.927   8670  Z= 0.266
  Chirality :  0.037   0.142   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  7.383  89.242    862
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 27.86 %
    Favored  : 68.58 %
  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 aren not related in a simple way.
  whole:  2.10 (0.32), residues: 741
  helix:  1.60 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.89 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.015   0.001   TYR A 616 
 PHE   0.013   0.001   PHE D 656 
 TRP   0.010   0.001   TRP B 568 
 HIS   0.003   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6389)
  covalent geometry    : angle       0.52256 ( 8670)
  hydrogen bonds       : bond        0.03572 (  430)
  hydrogen bonds       : angle       3.80134 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  574 MET cc_start: 0.8535 (mmm) cc_final: 0.8162 (mmm)
REVERT: A  616 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8519 (t80)
REVERT: B  539 LEU cc_start: 0.8834 (tt) cc_final: 0.8524 (tp)
REVERT: B  554 MET cc_start: 0.8764 (tpp) cc_final: 0.8559 (mmp)
REVERT: B  651 MET cc_start: 0.7634 (mmt) cc_final: 0.7292 (mmt)
REVERT: C  597 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8063 (m-80)
REVERT: C  651 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.5272 (mtt)
REVERT: D  462 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7622 (mmm)
  outliers start: 23
  outliers final: 17
  residues processed: 136
  average time/residue: 0.0831
  time to fit residues: 14.2659
Evaluate side-chains
  140 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  616 TYR
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  466 ASP
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  521 ILE
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain C residue  651 MET
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  465 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 71 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0170
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0050
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.4232

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.178555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.133652 restraints weight = 9867.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.33
r_work: 0.3326 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.057   6389  Z= 0.109
  Angle     :  0.508   6.724   8670  Z= 0.262
  Chirality :  0.037   0.142   1022
  Planarity :  0.003   0.030   1017
  Dihedral  :  5.753  89.962    862
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 27.55 %
    Favored  : 68.73 %
  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 aren not related in a simple way.
  whole:  2.24 (0.32), residues: 741
  helix:  1.68 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.98 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.014   0.001   TYR A 616 
 PHE   0.016   0.001   PHE A 557 
 TRP   0.011   0.001   TRP D 585 
 HIS   0.003   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6389)
  covalent geometry    : angle       0.50835 ( 8670)
  hydrogen bonds       : bond        0.03452 (  430)
  hydrogen bonds       : angle       3.75370 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.4793 (p90)
REVERT: A  531 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7877 (mtm-85)
REVERT: A  574 MET cc_start: 0.8476 (mmm) cc_final: 0.8186 (mmm)
REVERT: A  616 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8484 (t80)
REVERT: B  457 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5572 (mt)
REVERT: B  539 LEU cc_start: 0.8857 (tt) cc_final: 0.8541 (tp)
REVERT: B  554 MET cc_start: 0.8625 (tpp) cc_final: 0.8417 (mmp)
REVERT: B  651 MET cc_start: 0.7451 (mmt) cc_final: 0.7096 (mmt)
REVERT: C  597 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7845 (m-80)
REVERT: C  651 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.5298 (mtt)
REVERT: D  462 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7712 (mmm)
  outliers start: 24
  outliers final: 17
  residues processed: 138
  average time/residue: 0.0937
  time to fit residues: 16.4177
Evaluate side-chains
  145 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  493 TYR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  616 TYR
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  466 ASP
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  521 ILE
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain C residue  650 LEU
Chi-restraints excluded: chain C residue  651 MET
Chi-restraints excluded: chain D residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    0.0000
   chunk 65 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.4019 r_free = 0.4019 target = 0.177052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.134475 restraints weight = 9231.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.34
r_work: 0.3304 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6389  Z= 0.117
  Angle     :  0.516   6.580   8670  Z= 0.267
  Chirality :  0.037   0.144   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.801  88.265    862
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 27.24 %
    Favored  : 68.89 %
  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 aren not related in a simple way.
  whole:  2.23 (0.32), residues: 741
  helix:  1.67 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.99 (0.59), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.015   0.001   TYR A 616 
 PHE   0.020   0.001   PHE B 557 
 TRP   0.010   0.001   TRP B 568 
 HIS   0.003   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6389)
  covalent geometry    : angle       0.51569 ( 8670)
  hydrogen bonds       : bond        0.03537 (  430)
  hydrogen bonds       : angle       3.78619 ( 1266)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7454 (mtmm)
REVERT: A  493 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.4803 (p90)
REVERT: A  574 MET cc_start: 0.8349 (mmm) cc_final: 0.8078 (mmm)
REVERT: A  616 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8472 (t80)
REVERT: B  457 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5512 (mt)
REVERT: B  539 LEU cc_start: 0.8824 (tt) cc_final: 0.8488 (tp)
REVERT: B  554 MET cc_start: 0.8652 (tpp) cc_final: 0.8431 (mmp)
REVERT: B  651 MET cc_start: 0.7465 (mmt) cc_final: 0.7061 (mmt)
REVERT: C  597 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7976 (m-80)
REVERT: C  651 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5286 (mtt)
REVERT: D  462 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7683 (mmm)
  outliers start: 25
  outliers final: 16
  residues processed: 140
  average time/residue: 0.0972
  time to fit residues: 17.1827
Evaluate side-chains
  144 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  493 TYR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  616 TYR
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  466 ASP
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  521 ILE
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  597 TYR
Chi-restraints excluded: chain C residue  650 LEU
Chi-restraints excluded: chain C residue  651 MET
Chi-restraints excluded: chain D residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0980
   chunk 76 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 53 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4012 r_free = 0.4012 target = 0.176356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.132449 restraints weight = 9190.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.31
r_work: 0.3275 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6389  Z= 0.123
  Angle     :  0.524   6.532   8670  Z= 0.271
  Chirality :  0.038   0.148   1022
  Planarity :  0.003   0.044   1017
  Dihedral  :  5.815  87.932    862
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 27.24 %
    Favored  : 68.73 %
  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 aren not related in a simple way.
  whole:  2.19 (0.32), residues: 741
  helix:  1.64 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.99 (0.59), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.016   0.001   TYR A 616 
 PHE   0.015   0.001   PHE A 557 
 TRP   0.010   0.001   TRP B 568 
 HIS   0.003   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6389)
  covalent geometry    : angle       0.52424 ( 8670)
  hydrogen bonds       : bond        0.03611 (  430)
  hydrogen bonds       : angle       3.81010 ( 1266)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1838.55 seconds
wall clock time: 32 minutes 6.85 seconds (1926.85 seconds total)