Starting phenix.real_space_refine
on Tue Mar 11 15:34:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyo_60574/03_2025/8zyo_60574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyo_60574/03_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_60574/03_2025/8zyo_60574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyo_60574/03_2025/8zyo_60574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyo_60574/03_2025/8zyo_60574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyo_60574/03_2025/8zyo_60574.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.18, per 1000 atoms: 0.83
  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: 1.69
  Conformation dependent library (CDL) restraints added in 920.0 milliseconds
  

  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: 0.58
  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: 1.75

  Time building geometry restraints manager: 1.97 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:             2.150
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.510
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.260
-------------------------------------------------------------------------------
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= 0.320
  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 : 8.41
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (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
 TRP   0.011   0.001   TRP D 585 
 HIS   0.005   0.001   HIS A 492 
 PHE   0.013   0.001   PHE D 656 
 TYR   0.016   0.002   TYR A 616 
 ARG   0.004   0.000   ARG D 541 

*********************** 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  : 0.702 
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: 0.2288
  time to fit residues: 36.2330
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  : 0.629 
-------------------------------------------------------------------------------
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 65 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.185356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.131176 restraints weight = 16520.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 3.40
r_work: 0.3338 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.0711

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= 0.175
  Angle     :  0.515   6.530   8670  Z= 0.269
  Chirality :  0.037   0.145   1022
  Planarity :  0.003   0.035   1017
  Dihedral  :  8.161 102.808    864
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 25.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.32), residues: 741
  helix:  1.49 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.66 (0.56), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 568 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.013   0.001   PHE D 656 
 TYR   0.017   0.002   TYR A 616 
 ARG   0.003   0.000   ARG C 541 

*********************** 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: 30
    poor density    : 120
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 ARG cc_start: 0.8412 (ptm160) cc_final: 0.8117 (ptt180)
REVERT: A  616 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8420 (t80)
REVERT: C  528 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7875 (mtt180)
  outliers start: 30
  outliers final: 16
  residues processed: 141
  average time/residue: 0.2133
  time to fit residues: 38.1795
Evaluate side-chains
  134 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  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 D residue  416 LEU
Chi-restraints excluded: chain D residue  465 VAL
Chi-restraints excluded: chain D residue  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.177069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137549 restraints weight = 9110.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.70
r_work: 0.3246 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3246
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.0952

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= 0.163
  Angle     :  0.498   6.354   8670  Z= 0.257
  Chirality :  0.036   0.143   1022
  Planarity :  0.003   0.031   1017
  Dihedral  :  8.025  99.742    864
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 24.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.32), residues: 741
  helix:  1.52 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.86 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 568 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.013   0.001   PHE D 656 
 TYR   0.017   0.002   TYR D 597 
 ARG   0.003   0.000   ARG C 541 

*********************** 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
  155 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 120
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  574 MET cc_start: 0.8345 (mmm) cc_final: 0.7987 (mmm)
REVERT: B  554 MET cc_start: 0.8689 (tpp) cc_final: 0.8393 (mmp)
REVERT: C  528 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7897 (mtt180)
REVERT: C  597 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8324 (m-80)
  outliers start: 35
  outliers final: 24
  residues processed: 140
  average time/residue: 0.2039
  time to fit residues: 36.3373
Evaluate side-chains
  142 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
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  469 ILE
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  591 ASP
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  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 D residue  416 LEU
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  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 41 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.173661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.122794 restraints weight = 9266.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.98
r_work: 0.3229 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3217
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1196

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= 0.262
  Angle     :  0.547   5.876   8670  Z= 0.286
  Chirality :  0.039   0.152   1022
  Planarity :  0.004   0.031   1017
  Dihedral  :  8.008  97.972    862
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 25.39 %
    Favored  : 69.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.32), residues: 741
  helix:  1.36 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.74 (0.57), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 568 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.014   0.001   PHE D 656 
 TYR   0.021   0.002   TYR A 616 
 ARG   0.002   0.000   ARG D 582 

*********************** 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
  156 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 ARG cc_start: 0.8679 (ptt180) cc_final: 0.8477 (ptt180)
REVERT: B  539 LEU cc_start: 0.8956 (tp) cc_final: 0.8752 (tt)
REVERT: B  554 MET cc_start: 0.8686 (tpp) cc_final: 0.8376 (mmp)
REVERT: B  557 PHE cc_start: 0.8732 (t80) cc_final: 0.8530 (t80)
REVERT: C  597 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8544 (m-80)
REVERT: D  597 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8001 (t80)
  outliers start: 36
  outliers final: 26
  residues processed: 144
  average time/residue: 0.2227
  time to fit residues: 40.3714
Evaluate side-chains
  146 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  591 ASP
Chi-restraints excluded: chain B residue  414 ILE
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 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  597 TYR
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 75 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 53 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0270
   chunk 61 optimal weight:    9.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.176642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.127150 restraints weight = 10214.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.02
r_work: 0.3297 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    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 = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6389  Z= 0.164
  Angle     :  0.507   6.723   8670  Z= 0.258
  Chirality :  0.037   0.142   1022
  Planarity :  0.003   0.032   1017
  Dihedral  :  7.596  90.686    862
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 26.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.32), residues: 741
  helix:  1.52 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.97 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 585 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.014   0.001   PHE D 656 
 TYR   0.015   0.001   TYR D 616 
 ARG   0.004   0.000   ARG A 534 

*********************** 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
  145 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  574 MET cc_start: 0.8266 (mmm) cc_final: 0.8024 (mmm)
REVERT: A  616 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8299 (t80)
REVERT: B  554 MET cc_start: 0.8634 (tpp) cc_final: 0.8401 (mmp)
REVERT: C  597 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8263 (m-80)
REVERT: D  462 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7694 (mmm)
REVERT: D  597 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7988 (t80)
  outliers start: 30
  outliers final: 19
  residues processed: 133
  average time/residue: 0.2328
  time to fit residues: 39.7745
Evaluate side-chains
  137 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
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  469 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  466 ASP
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  597 TYR
Chi-restraints excluded: chain D residue  416 LEU
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  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
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 17 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.175282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.125503 restraints weight = 9118.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.92
r_work: 0.3265 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1391

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= 0.199
  Angle     :  0.517   6.346   8670  Z= 0.267
  Chirality :  0.038   0.145   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.932  85.764    862
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 25.54 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.32), residues: 741
  helix:  1.50 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.95 (0.59), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 568 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.013   0.001   PHE D 656 
 TYR   0.018   0.002   TYR A 616 
 ARG   0.003   0.000   ARG A 534 

*********************** 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
  149 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.4973 (p90)
REVERT: A  616 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8453 (t80)
REVERT: B  457 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5325 (mt)
REVERT: B  554 MET cc_start: 0.8681 (tpp) cc_final: 0.8408 (mmp)
REVERT: C  597 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8247 (m-80)
REVERT: D  462 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7718 (mmm)
REVERT: D  597 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7985 (t80)
  outliers start: 33
  outliers final: 24
  residues processed: 139
  average time/residue: 0.2156
  time to fit residues: 37.8600
Evaluate side-chains
  146 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  589 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  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 D residue  416 LEU
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  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
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 10 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.176133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.126595 restraints weight = 9234.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.92
r_work: 0.3301 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6389  Z= 0.182
  Angle     :  0.520   7.850   8670  Z= 0.268
  Chirality :  0.037   0.143   1022
  Planarity :  0.003   0.030   1017
  Dihedral  :  5.941  87.760    862
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 26.01 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.32), residues: 741
  helix:  1.52 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.98 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 585 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.014   0.001   PHE D 656 
 TYR   0.017   0.002   TYR A 616 
 ARG   0.003   0.000   ARG A 534 

*********************** 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
  153 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7435 (mtmm)
REVERT: A  493 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.4934 (p90)
REVERT: A  574 MET cc_start: 0.8536 (mmm) cc_final: 0.8238 (mmm)
REVERT: A  616 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8399 (t80)
REVERT: A  656 PHE cc_start: 0.8315 (m-80) cc_final: 0.8074 (m-80)
REVERT: B  457 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5446 (mt)
REVERT: B  539 LEU cc_start: 0.8901 (tt) cc_final: 0.8597 (tp)
REVERT: B  554 MET cc_start: 0.8781 (tpp) cc_final: 0.8535 (mmp)
REVERT: C  597 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8208 (m-80)
REVERT: D  462 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7689 (mmm)
REVERT: D  597 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7954 (t80)
  outliers start: 34
  outliers final: 24
  residues processed: 140
  average time/residue: 0.2165
  time to fit residues: 38.4235
Evaluate side-chains
  150 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
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  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  616 TYR
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  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  597 TYR
Chi-restraints excluded: chain C residue  650 LEU
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  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0060
   chunk 48 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4974

-------------------------------------------------------------------------------
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 = 0.177467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137542 restraints weight = 9213.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.72
r_work: 0.3248 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6389  Z= 0.160
  Angle     :  0.508   7.328   8670  Z= 0.262
  Chirality :  0.037   0.142   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.892  88.895    862
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 26.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.32), residues: 741
  helix:  1.62 (0.22), residues: 588
  sheet:  None (None), residues: 0
  loop :  1.03 (0.58), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 585 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.014   0.001   PHE A 557 
 TYR   0.015   0.001   TYR A 616 
 ARG   0.003   0.000   ARG A 534 

*********************** 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
  154 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7460 (mtmm)
REVERT: A  493 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.4902 (p90)
REVERT: A  574 MET cc_start: 0.8372 (mmm) cc_final: 0.8126 (mmm)
REVERT: A  616 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8392 (t80)
REVERT: B  457 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5543 (mt)
REVERT: B  539 LEU cc_start: 0.8851 (tt) cc_final: 0.8536 (tp)
REVERT: B  554 MET cc_start: 0.8691 (tpp) cc_final: 0.8480 (mmp)
REVERT: C  597 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8094 (m-80)
REVERT: D  462 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7642 (mmm)
REVERT: D  597 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7924 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 145
  average time/residue: 0.2125
  time to fit residues: 39.1791
Evaluate side-chains
  147 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
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  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  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  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  416 LEU
Chi-restraints excluded: chain D residue  461 ILE
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.175592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125854 restraints weight = 9399.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.94
r_work: 0.3276 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    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 = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1582

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= 0.199
  Angle     :  0.536   7.106   8670  Z= 0.279
  Chirality :  0.038   0.144   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.908  86.986    862
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 26.47 %
    Favored  : 69.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.32), residues: 741
  helix:  1.56 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.99 (0.59), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 568 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.013   0.001   PHE D 656 
 TYR   0.018   0.002   TYR A 616 
 ARG   0.003   0.000   ARG A 534 

*********************** 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
  148 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7472 (mtmm)
REVERT: A  493 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.4973 (p90)
REVERT: A  574 MET cc_start: 0.8336 (mmm) cc_final: 0.8093 (mmm)
REVERT: A  616 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8451 (t80)
REVERT: B  457 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5431 (mt)
REVERT: B  539 LEU cc_start: 0.8825 (tt) cc_final: 0.8498 (tp)
REVERT: B  554 MET cc_start: 0.8653 (tpp) cc_final: 0.8435 (mmp)
REVERT: C  597 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8136 (m-80)
REVERT: D  462 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7690 (mmm)
REVERT: D  597 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7962 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 139
  average time/residue: 0.2120
  time to fit residues: 37.2614
Evaluate side-chains
  145 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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  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  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  416 LEU
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  465 VAL
Chi-restraints excluded: chain D residue  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4004 r_free = 0.4004 target = 0.175596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.128217 restraints weight = 9133.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.27
r_work: 0.3268 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3236
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6389  Z= 0.198
  Angle     :  0.536   7.027   8670  Z= 0.278
  Chirality :  0.038   0.148   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.913  87.601    862
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 26.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.32), residues: 741
  helix:  1.56 (0.22), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.94 (0.58), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 585 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.021   0.001   PHE B 557 
 TYR   0.017   0.002   TYR A 616 
 ARG   0.003   0.000   ARG A 534 

********************** 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
  149 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7469 (mtmm)
REVERT: A  493 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.4859 (p90)
REVERT: A  574 MET cc_start: 0.8362 (mmm) cc_final: 0.8110 (mmm)
REVERT: A  616 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8454 (t80)
REVERT: B  457 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5486 (mt)
REVERT: B  539 LEU cc_start: 0.8837 (tt) cc_final: 0.8500 (tp)
REVERT: B  554 MET cc_start: 0.8665 (tpp) cc_final: 0.8446 (mmp)
REVERT: C  597 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8105 (m-80)
REVERT: D  462 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7664 (mmm)
REVERT: D  597 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7980 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 139
  average time/residue: 0.2234
  time to fit residues: 39.3169
Evaluate side-chains
  146 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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  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  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  416 LEU
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  465 VAL
Chi-restraints excluded: chain D residue  530 LEU
Chi-restraints excluded: chain D residue  597 TYR
Chi-restraints excluded: chain D residue  606 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 43 optimal weight:    0.0030
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0870
   chunk 36 optimal weight:    0.2980
   chunk 42 optimal weight:    0.0980
   chunk 13 optimal weight:    0.3980
   chunk 40 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.1768

-------------------------------------------------------------------------------
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 = 0.4073 r_free = 0.4073 target = 0.182320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.143419 restraints weight = 9520.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.78
r_work: 0.3341 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053   6389  Z= 0.138
  Angle     :  0.497   7.009   8670  Z= 0.255
  Chirality :  0.036   0.140   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.622  85.768    862
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 28.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.32), residues: 741
  helix:  1.78 (0.22), residues: 589
  sheet:  None (None), residues: 0
  loop :  0.98 (0.57), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 585 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.017   0.001   PHE A 557 
 TYR   0.011   0.001   TYR D 652 
 ARG   0.003   0.000   ARG A 534 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3832.07 seconds
wall clock time: 66 minutes 14.73 seconds (3974.73 seconds total)