Starting phenix.real_space_refine
on Tue Feb 11 16:09:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyo_60574/02_2025/8zyo_60574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyo_60574/02_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_60574/02_2025/8zyo_60574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyo_60574/02_2025/8zyo_60574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyo_60574/02_2025/8zyo_60574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyo_60574/02_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-5592/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: 5.21, per 1000 atoms: 0.84
  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: 1.63
  Conformation dependent library (CDL) restraints added in 942.3 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: 0.68
  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: 1.81

  Time building geometry restraints manager: 1.85 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:             1.930
  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:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.130
  Find NCS groups from input model:        0.240
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.600
-------------------------------------------------------------------------------
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  : 0.666 
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: 0.2405
  time to fit residues: 37.7982
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  : 0.747 
-------------------------------------------------------------------------------
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 = 16520.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 3.40
r_work: 0.3339 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    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 = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
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  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 ARG cc_start: 0.8410 (ptm160) cc_final: 0.8116 (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: 0.7877 (mtt180)
  outliers start: 30
  outliers final: 16
  residues processed: 141
  average time/residue: 0.2179
  time to fit residues: 38.7695
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  : 0.715 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   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 = 0.4004 r_free = 0.4004 target = 0.175601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.130883 restraints weight = 9121.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.36
r_work: 0.3268 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6389  Z= 0.195
  Angle     :  0.517   6.192   8670  Z= 0.268
  Chirality :  0.037   0.144   1022
  Planarity :  0.003   0.031   1017
  Dihedral  :  8.071  99.739    864
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 25.85 %
    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:  1.92 (0.32), residues: 741
  helix:  1.46 (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   0.001   HIS A 492 
 PHE   0.014   0.001   PHE D 656 
 TYR   0.018   0.002   TYR A 616 
 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
  152 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  574 MET cc_start: 0.8285 (mmm) cc_final: 0.7941 (mmm)
REVERT: B  554 MET cc_start: 0.8620 (tpp) cc_final: 0.8306 (mmp)
REVERT: B  557 PHE cc_start: 0.8705 (t80) cc_final: 0.8496 (t80)
REVERT: C  528 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7913 (mtt180)
REVERT: C  597 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8447 (m-80)
  outliers start: 33
  outliers final: 22
  residues processed: 139
  average time/residue: 0.2207
  time to fit residues: 38.6381
Evaluate side-chains
  139 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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  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  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 D residue  416 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0570
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.8300

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.175458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.125211 restraints weight = 9503.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.98
r_work: 0.3262 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6389  Z= 0.191
  Angle     :  0.506   6.094   8670  Z= 0.262
  Chirality :  0.037   0.145   1022
  Planarity :  0.003   0.031   1017
  Dihedral  :  7.834  96.016    862
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 25.70 %
    Favored  : 69.50 %
  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:  1.95 (0.32), residues: 741
  helix:  1.48 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.87 (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   0.018   0.002   TYR A 616 
 ARG   0.004   0.000   ARG A 534 

*********************** 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
  148 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  554 MET cc_start: 0.8628 (tpp) cc_final: 0.8338 (mmp)
REVERT: C  528 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7927 (mtt180)
REVERT: C  597 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8367 (m-80)
REVERT: D  597 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7893 (t80)
  outliers start: 31
  outliers final: 24
  residues processed: 137
  average time/residue: 0.2199
  time to fit residues: 38.0341
Evaluate side-chains
  141 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
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  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  597 TYR
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:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0470
   chunk 52 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0870
   chunk 34 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.4256

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.177852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.132156 restraints weight = 10029.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.19
r_work: 0.3324 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6389  Z= 0.147
  Angle     :  0.497   7.545   8670  Z= 0.252
  Chirality :  0.036   0.141   1022
  Planarity :  0.003   0.031   1017
  Dihedral  :  7.335  88.651    862
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 26.47 %
    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:  2.10 (0.32), residues: 741
  helix:  1.57 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.99 (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   0.015   0.001   PHE D 656 
 TYR   0.014   0.001   TYR A 616 
 ARG   0.003   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: 28
    poor density    : 117
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  574 MET cc_start: 0.8225 (mmm) cc_final: 0.7956 (mmm)
REVERT: A  616 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8325 (t80)
REVERT: B  539 LEU cc_start: 0.8922 (tt) cc_final: 0.8619 (tp)
REVERT: B  554 MET cc_start: 0.8616 (tpp) cc_final: 0.8409 (mmp)
REVERT: C  528 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7889 (mtt180)
REVERT: C  597 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8127 (m-80)
REVERT: D  597 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7932 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 135
  average time/residue: 0.2146
  time to fit residues: 36.5951
Evaluate side-chains
  133 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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  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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0020
   overall best weight:    0.8990

-------------------------------------------------------------------------------
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 = 0.175528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125743 restraints weight = 9109.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.92
r_work: 0.3276 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1384

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= 0.211
  Angle     :  0.518   6.087   8670  Z= 0.269
  Chirality :  0.038   0.145   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.906  85.597    862
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 25.85 %
    Favored  : 69.50 %
  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:  1.98 (0.32), residues: 741
  helix:  1.49 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.94 (0.59), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   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   0.004   0.000   ARG B 541 

*********************** 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
  146 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.5083 (p90)
REVERT: A  616 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8502 (t80)
REVERT: B  539 LEU cc_start: 0.8838 (tt) cc_final: 0.8555 (tp)
REVERT: B  554 MET cc_start: 0.8767 (tpp) cc_final: 0.8543 (mmp)
REVERT: C  597 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8205 (m-80)
REVERT: D  597 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7908 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 136
  average time/residue: 0.2104
  time to fit residues: 36.2487
Evaluate side-chains
  140 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  493 TYR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  589 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 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:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 23 optimal weight:    0.4980
   chunk 58 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   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 = 0.4010 r_free = 0.4010 target = 0.176182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.131803 restraints weight = 9220.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.18
r_work: 0.3291 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6389  Z= 0.184
  Angle     :  0.515   7.211   8670  Z= 0.268
  Chirality :  0.037   0.143   1022
  Planarity :  0.003   0.029   1017
  Dihedral  :  5.954  87.589    862
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 25.85 %
    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:  2.01 (0.32), residues: 741
  helix:  1.52 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.91 (0.58), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 585 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.014   0.001   PHE D 656 
 TYR   0.016   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
  151 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 116
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.5003 (p90)
REVERT: A  574 MET cc_start: 0.8471 (mmm) cc_final: 0.8205 (mmm)
REVERT: A  616 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8411 (t80)
REVERT: B  457 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5464 (mt)
REVERT: B  539 LEU cc_start: 0.8826 (tt) cc_final: 0.8531 (tp)
REVERT: B  554 MET cc_start: 0.8729 (tpp) cc_final: 0.8525 (mmp)
REVERT: C  597 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8190 (m-80)
REVERT: D  597 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7922 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 140
  average time/residue: 0.2200
  time to fit residues: 38.9194
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  : 0.718 
-------------------------------------------------------------------------------
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  419 ILE
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  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:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 53 optimal weight:    0.3980
   chunk 48 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   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 = 0.4012 r_free = 0.4012 target = 0.176173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.132495 restraints weight = 9215.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.34
r_work: 0.3283 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3281
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    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 = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6389  Z= 0.185
  Angle     :  0.516   6.522   8670  Z= 0.270
  Chirality :  0.038   0.144   1022
  Planarity :  0.003   0.030   1017
  Dihedral  :  5.930  87.527    862
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 26.16 %
    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:  2.05 (0.32), residues: 741
  helix:  1.54 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop :  0.97 (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 A 557 
 TYR   0.017   0.002   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
  149 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7459 (mtmm)
REVERT: A  493 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.5034 (p90)
REVERT: A  574 MET cc_start: 0.8284 (mmm) cc_final: 0.8059 (mmm)
REVERT: A  616 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8456 (t80)
REVERT: B  457 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5454 (mt)
REVERT: B  539 LEU cc_start: 0.8814 (tt) cc_final: 0.8481 (tp)
REVERT: B  554 MET cc_start: 0.8656 (tpp) cc_final: 0.8446 (mmp)
REVERT: C  597 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8136 (m-80)
REVERT: D  597 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7984 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 140
  average time/residue: 0.2280
  time to fit residues: 40.3924
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  : 0.684 
-------------------------------------------------------------------------------
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  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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.175257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.125429 restraints weight = 9439.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.96
r_work: 0.3270 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1572

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= 0.200
  Angle     :  0.531   6.376   8670  Z= 0.277
  Chirality :  0.038   0.144   1022
  Planarity :  0.003   0.030   1017
  Dihedral  :  5.940  87.347    862
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 26.01 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.01 (0.32), residues: 741
  helix:  1.51 (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   0.010   0.001   TRP D 585 
 HIS   0.003   0.000   HIS A 492 
 PHE   0.013   0.001   PHE A 557 
 TYR   0.017   0.002   TYR A 616 
 ARG   0.004   0.000   ARG A 537 

*********************** 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
  154 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7470 (mtmm)
REVERT: A  493 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.4984 (p90)
REVERT: A  574 MET cc_start: 0.8325 (mmm) cc_final: 0.8085 (mmm)
REVERT: A  616 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8460 (t80)
REVERT: B  457 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5556 (mt)
REVERT: B  539 LEU cc_start: 0.8840 (tt) cc_final: 0.8489 (tp)
REVERT: B  554 MET cc_start: 0.8660 (tpp) cc_final: 0.8456 (mmp)
REVERT: C  597 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8120 (m-80)
REVERT: D  597 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7970 (t80)
  outliers start: 33
  outliers final: 24
  residues processed: 143
  average time/residue: 0.2134
  time to fit residues: 38.5264
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  : 0.710 
-------------------------------------------------------------------------------
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  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  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  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:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.176400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.132420 restraints weight = 9112.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.30
r_work: 0.3300 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6389  Z= 0.179
  Angle     :  0.517   6.283   8670  Z= 0.269
  Chirality :  0.037   0.149   1022
  Planarity :  0.003   0.030   1017
  Dihedral  :  5.872  88.967    862
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 26.78 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.13 (0.32), residues: 741
  helix:  1.60 (0.22), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.98 (0.59), 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   0.020   0.001   PHE B 557 
 TYR   0.016   0.001   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
  145 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7476 (mtmm)
REVERT: A  493 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.4903 (p90)
REVERT: A  574 MET cc_start: 0.8495 (mmm) cc_final: 0.8214 (mmm)
REVERT: A  616 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8484 (t80)
REVERT: B  457 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5595 (mt)
REVERT: B  539 LEU cc_start: 0.8808 (tt) cc_final: 0.8423 (tp)
REVERT: C  597 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7955 (m-80)
REVERT: D  597 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7934 (t80)
  outliers start: 28
  outliers final: 21
  residues processed: 137
  average time/residue: 0.2143
  time to fit residues: 37.2535
Evaluate side-chains
  144 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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  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 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 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:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.7986

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.175400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.125058 restraints weight = 9889.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.02
r_work: 0.3271 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1658

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= 0.200
  Angle     :  0.529   6.192   8670  Z= 0.276
  Chirality :  0.038   0.147   1022
  Planarity :  0.003   0.030   1017
  Dihedral  :  5.881  87.647    862
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 26.47 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 :  0.95 (0.59), 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   0.017   0.002   TYR A 616 
 ARG   0.002   0.000   ARG A 537 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3794.65 seconds
wall clock time: 68 minutes 5.91 seconds (4085.91 seconds total)