Starting phenix.real_space_refine
on Wed Mar 12 00:48:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ij5_60616/03_2025/9ij5_60616.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ij5_60616/03_2025/9ij5_60616.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ij5_60616/03_2025/9ij5_60616.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ij5_60616/03_2025/9ij5_60616.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ij5_60616/03_2025/9ij5_60616.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ij5_60616/03_2025/9ij5_60616.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.043
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: 6
    Type Number    sf(0)   Gaussians
     P      51      5.49       5
     Mg      1      5.21       5
     S      44      5.16       5
     C    4368      2.51       5
     N    1236      2.21       5
     O    1439      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7139
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 755, 6057
          Classifications: {'peptide': 755}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 717}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 550
          Classifications: {'RNA': 26}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 1, 'rna3p': 24}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "C"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 531
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 22}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.57, per 1000 atoms: 0.64
  Number of scatterers: 7139
  At special positions: 0
  Unit cell: (77.52, 86.64, 106.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P      51     15.00
     Mg      1     11.99
     O    1439      8.00
     N    1236      7.00
     C    4368      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: 2.14
  Conformation dependent library (CDL) restraints added in 719.6 milliseconds
  

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 8 sheets defined
      33.2% alpha, 24.9% beta
      23 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 2.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 251 through 261
    Processing helix  chain 'A' and resid 262 through 267
    Processing helix  chain 'A' and resid 314 through 316
      No H-bonds generated for 'chain 'A' and resid 314 through 316'
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 388 through 399
    Processing helix  chain 'A' and resid 402 through 412
    Processing helix  chain 'A' and resid 450 through 456
    Processing helix  chain 'A' and resid 508 through 520
      removed outlier: 3.666A  pdb=" N   MET A 512 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 540
    Processing helix  chain 'A' and resid 540 through 549
    Processing helix  chain 'A' and resid 612 through 631
      removed outlier: 3.790A  pdb=" N   ALA A 616 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLY A 628 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
      Proline residue:  A 629  - end of helix
    Processing helix  chain 'A' and resid 646 through 661
      removed outlier: 3.771A  pdb=" N   TYR A 650 " --> pdb=" O   ARG A 646 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   ARG A 652 " --> pdb=" O   GLU A 648 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 660 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 686
      removed outlier: 3.970A  pdb=" N   TYR A 679 " --> pdb=" O   ARG A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 723
      removed outlier: 4.127A  pdb=" N   VAL A 711 " --> pdb=" O   ARG A 707 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 723 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 801
      removed outlier: 4.092A  pdb=" N   LEU A 788 " --> pdb=" O   ASP A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 818
      No H-bonds generated for 'chain 'A' and resid 816 through 818'
    Processing helix  chain 'A' and resid 819 through 826
    Processing helix  chain 'A' and resid 826 through 835
    Processing helix  chain 'A' and resid 836 through 838
      No H-bonds generated for 'chain 'A' and resid 836 through 838'
    Processing helix  chain 'A' and resid 916 through 928
    Processing helix  chain 'A' and resid 939 through 955
    Processing helix  chain 'A' and resid 961 through 965
    Processing sheet with id=AA1, first strand: chain 'A' and resid 769 through 774
      removed outlier: 3.726A  pdb=" N   ASP A 743 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   VAL A 739 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   MET A 845 " --> pdb=" O   ASN A 909 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ASN A 909 " --> pdb=" O   MET A 845 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL A 847 " --> pdb=" O   VAL A 907 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A 887 " --> pdb=" O   TYR A 904 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   VAL A 885 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   SER A 223 " --> pdb=" O   ALA A 861 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   TYR A 859 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337
      removed outlier: 3.773A  pdb=" N   PHE A 341 " --> pdb=" O   TYR A 361 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG A 384 " --> pdb=" O   MET A 498 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   MET A 498 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   ASP A 386 " --> pdb=" O   SER A 496 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   SER A 496 " --> pdb=" O   ASP A 386 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A 499 " --> pdb=" O   ILE A 415 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   ILE A 415 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272
      removed outlier: 6.321A  pdb=" N   HIS A 242 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   LEU A 306 " --> pdb=" O   HIS A 242 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   THR A 244 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ILE A 304 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   SER A 246 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   ILE A 302 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 431
    Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 441
    Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 572
    Processing sheet with id=AA8, first strand: chain 'A' and resid 638 through 641
      removed outlier: 6.302A  pdb=" N   ALA A 605 " --> pdb=" O   VAL A 668 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ILE A 670 " --> pdb=" O   ALA A 605 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   PHE A 607 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   VAL A 667 " --> pdb=" O   GLN A 695 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   ILE A 697 " --> pdb=" O   VAL A 667 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   CYS A 669 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    774 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      56 hydrogen bonds
      112 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1805
        1.33 -     1.46: 1901
        1.46 -     1.58: 3524
        1.58 -     1.70: 101
        1.70 -     1.83: 69
  Bond restraints: 7400
  Sorted by residual:
  bond pdb=" C   ALA A 862 "
       pdb=" N   PRO A 863 "
    ideal  model  delta    sigma   weight residual
    1.336  1.370 -0.034 1.08e-02 8.57e+03 1.01e+01
  bond pdb=" CB  PRO A 221 "
       pdb=" CG  PRO A 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.642 -0.150 5.00e-02 4.00e+02 9.02e+00
  bond pdb=" CG  GLN A 830 "
       pdb=" CD  GLN A 830 "
    ideal  model  delta    sigma   weight residual
    1.516  1.445  0.071 2.50e-02 1.60e+03 8.01e+00
  bond pdb=" CG  LEU A 372 "
       pdb=" CD2 LEU A 372 "
    ideal  model  delta    sigma   weight residual
    1.521  1.442  0.079 3.30e-02 9.18e+02 5.74e+00
  bond pdb=" CB  LYS A 290 "
       pdb=" CG  LYS A 290 "
    ideal  model  delta    sigma   weight residual
    1.520  1.586 -0.066 3.00e-02 1.11e+03 4.81e+00
  ... (remaining 7395 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 9935
        2.91 -     5.82: 279
        5.82 -     8.72: 32
        8.72 -    11.63: 13
       11.63 -    14.54: 4
  Bond angle restraints: 10263
  Sorted by residual:
  angle pdb=" CA  PRO A 221 "
        pdb=" N   PRO A 221 "
        pdb=" CD  PRO A 221 "
      ideal   model   delta    sigma   weight residual
     112.00   97.46   14.54 1.40e+00 5.10e-01 1.08e+02
  angle pdb=" CA  MET A 329 "
        pdb=" CB  MET A 329 "
        pdb=" CG  MET A 329 "
      ideal   model   delta    sigma   weight residual
     114.10  126.01  -11.91 2.00e+00 2.50e-01 3.55e+01
  angle pdb=" C   ILE A 782 "
        pdb=" CA  ILE A 782 "
        pdb=" CB  ILE A 782 "
      ideal   model   delta    sigma   weight residual
     111.29  120.47   -9.18 1.64e+00 3.72e-01 3.13e+01
  angle pdb=" CA  LYS A 290 "
        pdb=" CB  LYS A 290 "
        pdb=" CG  LYS A 290 "
      ideal   model   delta    sigma   weight residual
     114.10  125.05  -10.95 2.00e+00 2.50e-01 3.00e+01
  angle pdb=" CA  PRO A 468 "
        pdb=" N   PRO A 468 "
        pdb=" CD  PRO A 468 "
      ideal   model   delta    sigma   weight residual
     112.00  104.72    7.28 1.40e+00 5.10e-01 2.71e+01
  ... (remaining 10258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3697
       17.83 -    35.66: 551
       35.66 -    53.48: 169
       53.48 -    71.31: 83
       71.31 -    89.14: 21
  Dihedral angle restraints: 4521
    sinusoidal: 2311
      harmonic: 2210
  Sorted by residual:
  dihedral pdb=" CA  ILE A 231 "
           pdb=" C   ILE A 231 "
           pdb=" N   GLN A 232 "
           pdb=" CA  GLN A 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.18   25.82     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  MET A 329 "
           pdb=" C   MET A 329 "
           pdb=" N   LYS A 330 "
           pdb=" CA  LYS A 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.42   22.58     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" C   ILE A 782 "
           pdb=" N   ILE A 782 "
           pdb=" CA  ILE A 782 "
           pdb=" CB  ILE A 782 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.96   10.96     0      2.50e+00 1.60e-01 1.92e+01
  ... (remaining 4518 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1016
       0.086 -    0.173: 174
       0.173 -    0.259: 10
       0.259 -    0.346: 2
       0.346 -    0.432: 2
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" CB  VAL A 791 "
            pdb=" CA  VAL A 791 "
            pdb=" CG1 VAL A 791 "
            pdb=" CG2 VAL A 791 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.66e+00
  chirality pdb=" CB  ILE A 854 "
            pdb=" CA  ILE A 854 "
            pdb=" CG1 ILE A 854 "
            pdb=" CG2 ILE A 854 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.21e+00
  chirality pdb=" CB  ILE A 229 "
            pdb=" CA  ILE A 229 "
            pdb=" CG1 ILE A 229 "
            pdb=" CG2 ILE A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 1201 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 220 "    0.116 5.00e-02 4.00e+02   1.63e-01 4.25e+01
        pdb=" N   PRO A 221 "   -0.281 5.00e-02 4.00e+02
        pdb=" CA  PRO A 221 "    0.085 5.00e-02 4.00e+02
        pdb=" CD  PRO A 221 "    0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 652 "   -0.209 9.50e-02 1.11e+02   9.44e-02 7.16e+00
        pdb=" NE  ARG A 652 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 652 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 652 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 652 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 467 "   -0.044 5.00e-02 4.00e+02   6.41e-02 6.57e+00
        pdb=" N   PRO A 468 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 468 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 468 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1641
        2.79 -     3.32: 5991
        3.32 -     3.85: 13389
        3.85 -     4.37: 15385
        4.37 -     4.90: 24752
  Nonbonded interactions: 61158
  Sorted by model distance:
  nonbonded pdb=" O   THR A 649 "
            pdb=" OG1 THR A 653 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   SER A 544 "
            pdb=" OG1 THR A 548 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   PRO A 312 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" ND2 ASN A 322 "
            pdb=" O3'   C C  12 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   GLY A 338 "
            pdb=" ND2 ASN A 422 "
     model   vdw
     2.350 3.120
  ... (remaining 61153 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.170
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:10.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
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      :  0.008   0.150   7400  Z= 0.498
  Angle     :  1.161  14.538  10263  Z= 0.607
  Chirality :  0.064   0.432   1204
  Planarity :  0.010   0.163   1111
  Dihedral  : 19.966  89.140   3091
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 31.92 %
    Favored  : 67.06 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -2.72 (0.27), residues: 751
  helix: -1.94 (0.28), residues: 215
  sheet: -0.83 (0.40), residues: 167
  loop : -2.16 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP A 639 
 HIS   0.013   0.002   HIS A 946 
 PHE   0.032   0.004   PHE A 838 
 TYR   0.018   0.003   TYR A 361 
 ARG   0.023   0.001   ARG A 652 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  769 TRP cc_start: 0.7081 (m100) cc_final: 0.6821 (m100)
REVERT: A  845 MET cc_start: 0.8302 (ttt) cc_final: 0.7968 (ttt)
  outliers start: 7
  outliers final: 3
  residues processed: 105
  average time/residue: 0.9134
  time to fit residues: 102.9960
Evaluate side-chains
  95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  504 LYS
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  936 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 353 HIS
A 555 HIS
** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.211965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.176943 restraints weight = 8355.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.4262 rms_B_bonded: 2.13
r_work: 0.4181 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.4069 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7400  Z= 0.190
  Angle     :  0.615   7.731  10263  Z= 0.318
  Chirality :  0.043   0.183   1204
  Planarity :  0.005   0.079   1111
  Dihedral  : 17.624  82.068   1590
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 31.48 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 (0.28), residues: 751
  helix: -0.55 (0.32), residues: 221
  sheet: -0.90 (0.38), residues: 176
  loop : -1.89 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 639 
 HIS   0.003   0.001   HIS A 903 
 PHE   0.019   0.002   PHE A 325 
 TYR   0.011   0.001   TYR A 241 
 ARG   0.009   0.000   ARG A 652 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  327 ARG cc_start: 0.5322 (OUTLIER) cc_final: 0.4823 (mtt-85)
REVERT: A  330 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5985 (tptt)
REVERT: A  348 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6727 (pmm)
REVERT: A  456 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.5271 (tptt)
REVERT: A  473 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6992 (ptp90)
REVERT: A  505 MET cc_start: 0.7264 (ttt) cc_final: 0.6968 (ttt)
REVERT: A  736 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.6205 (mm110)
REVERT: A  777 MET cc_start: 0.2881 (mmp) cc_final: 0.2577 (mmt)
REVERT: A  801 ASN cc_start: 0.5503 (t0) cc_final: 0.5166 (t0)
REVERT: A  845 MET cc_start: 0.8483 (ttt) cc_final: 0.8092 (ttt)
  outliers start: 32
  outliers final: 7
  residues processed: 119
  average time/residue: 1.0187
  time to fit residues: 129.5526
Evaluate side-chains
  101 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  910 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 353 HIS
A 559 HIS
A 746 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.197839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.159998 restraints weight = 8404.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 2.26
r_work: 0.3954 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3832 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   7400  Z= 0.378
  Angle     :  0.745   7.389  10263  Z= 0.382
  Chirality :  0.048   0.213   1204
  Planarity :  0.005   0.039   1111
  Dihedral  : 17.511  81.534   1580
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 30.01 %
    Favored  : 63.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.74 (0.29), residues: 751
  helix: -0.19 (0.33), residues: 215
  sheet: -0.96 (0.38), residues: 178
  loop : -1.84 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 932 
 HIS   0.008   0.001   HIS A 946 
 PHE   0.032   0.003   PHE A 950 
 TYR   0.016   0.002   TYR A 361 
 ARG   0.006   0.001   ARG A 646 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 98
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.4890 (OUTLIER) cc_final: 0.4231 (ptpp)
REVERT: A  231 ILE cc_start: 0.3545 (OUTLIER) cc_final: 0.3158 (mt)
REVERT: A  290 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7732 (mppt)
REVERT: A  305 GLN cc_start: 0.7106 (tp40) cc_final: 0.6531 (tp40)
REVERT: A  327 ARG cc_start: 0.5389 (OUTLIER) cc_final: 0.4886 (mtt-85)
REVERT: A  329 MET cc_start: 0.8248 (tmt) cc_final: 0.7974 (tmt)
REVERT: A  456 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.5245 (tptt)
REVERT: A  503 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6121 (pm20)
REVERT: A  505 MET cc_start: 0.7165 (ttt) cc_final: 0.6915 (ttt)
REVERT: A  646 ARG cc_start: 0.5612 (mtm110) cc_final: 0.5075 (mtm110)
REVERT: A  666 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6396 (tpp)
REVERT: A  670 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7051 (mp)
REVERT: A  682 ILE cc_start: 0.6531 (mp) cc_final: 0.6298 (mp)
REVERT: A  736 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6661 (tp-100)
REVERT: A  801 ASN cc_start: 0.5545 (t0) cc_final: 0.4850 (t0)
  outliers start: 41
  outliers final: 21
  residues processed: 128
  average time/residue: 0.9322
  time to fit residues: 128.0775
Evaluate side-chains
  117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  666 MET
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  883 GLU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 22 optimal weight:    0.3980
   chunk 0 optimal weight:   30.0000
   chunk 54 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
A 353 HIS
** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.205016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.170673 restraints weight = 8544.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 2.01
r_work: 0.4109 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3987 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7400  Z= 0.307
  Angle     :  0.682   8.766  10263  Z= 0.351
  Chirality :  0.046   0.202   1204
  Planarity :  0.005   0.040   1111
  Dihedral  : 17.504  83.872   1580
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 28.55 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.53 (0.29), residues: 751
  helix:  0.11 (0.33), residues: 215
  sheet: -0.96 (0.39), residues: 166
  loop : -1.70 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 639 
 HIS   0.004   0.001   HIS A 865 
 PHE   0.019   0.002   PHE A 950 
 TYR   0.012   0.002   TYR A 770 
 ARG   0.004   0.000   ARG A 652 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 103
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.4747 (OUTLIER) cc_final: 0.4107 (ptpp)
REVERT: A  231 ILE cc_start: 0.2572 (OUTLIER) cc_final: 0.2218 (mt)
REVERT: A  305 GLN cc_start: 0.7469 (tp40) cc_final: 0.6960 (tp40)
REVERT: A  327 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4883 (mtt-85)
REVERT: A  486 LYS cc_start: 0.5441 (OUTLIER) cc_final: 0.4202 (ttpt)
REVERT: A  503 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5949 (pm20)
REVERT: A  670 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7154 (mp)
REVERT: A  736 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6771 (tp-100)
REVERT: A  777 MET cc_start: 0.3086 (mmp) cc_final: 0.2647 (mmt)
REVERT: A  801 ASN cc_start: 0.5442 (t0) cc_final: 0.4816 (t0)
  outliers start: 52
  outliers final: 21
  residues processed: 138
  average time/residue: 0.8971
  time to fit residues: 132.6934
Evaluate side-chains
  124 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  883 GLU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0970
   chunk 77 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 64 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
A 353 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.207383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.173774 restraints weight = 8418.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.4226 rms_B_bonded: 1.98
r_work: 0.4143 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.4034 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7400  Z= 0.248
  Angle     :  0.656   6.938  10263  Z= 0.337
  Chirality :  0.045   0.182   1204
  Planarity :  0.005   0.041   1111
  Dihedral  : 17.476  84.418   1580
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 31.33 %
    Favored  : 62.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.38 (0.30), residues: 751
  helix:  0.26 (0.34), residues: 220
  sheet: -0.95 (0.39), residues: 169
  loop : -1.63 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 639 
 HIS   0.006   0.001   HIS A 946 
 PHE   0.022   0.002   PHE A 341 
 TYR   0.012   0.002   TYR A 770 
 ARG   0.009   0.000   ARG A 564 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  288 GLU cc_start: 0.7206 (mp0) cc_final: 0.6768 (tp30)
REVERT: A  305 GLN cc_start: 0.7427 (tp40) cc_final: 0.6896 (tp40)
REVERT: A  348 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6949 (pmm)
REVERT: A  486 LYS cc_start: 0.5478 (OUTLIER) cc_final: 0.4212 (ttpt)
REVERT: A  503 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5957 (pm20)
REVERT: A  512 MET cc_start: 0.7803 (mmm) cc_final: 0.7503 (mmm)
REVERT: A  670 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7314 (mp)
REVERT: A  736 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6620 (tp-100)
REVERT: A  801 ASN cc_start: 0.5640 (t0) cc_final: 0.5012 (t0)
REVERT: A  852 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6461 (ttmm)
REVERT: A  878 THR cc_start: 0.8304 (m) cc_final: 0.8022 (m)
  outliers start: 42
  outliers final: 22
  residues processed: 131
  average time/residue: 0.9107
  time to fit residues: 127.9563
Evaluate side-chains
  125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0970
   chunk 41 optimal weight:    8.9990
   chunk 74 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 47 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
A 353 HIS
A 385 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.211951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.179185 restraints weight = 8390.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.4343 rms_B_bonded: 1.98
r_work: 0.4269 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.4165 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6727
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7400  Z= 0.185
  Angle     :  0.618   8.165  10263  Z= 0.316
  Chirality :  0.044   0.275   1204
  Planarity :  0.005   0.053   1111
  Dihedral  : 17.408  84.210   1580
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 32.21 %
    Favored  : 62.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.08 (0.30), residues: 751
  helix:  0.73 (0.35), residues: 214
  sheet: -0.77 (0.39), residues: 165
  loop : -1.55 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 639 
 HIS   0.005   0.001   HIS A 353 
 PHE   0.014   0.002   PHE A 950 
 TYR   0.013   0.001   TYR A 770 
 ARG   0.010   0.000   ARG A 564 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 108
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.4436 (OUTLIER) cc_final: 0.3405 (ptpp)
REVERT: A  254 MET cc_start: 0.5685 (pmm) cc_final: 0.5461 (pmt)
REVERT: A  288 GLU cc_start: 0.7118 (mp0) cc_final: 0.6758 (tp30)
REVERT: A  305 GLN cc_start: 0.7419 (tp40) cc_final: 0.6919 (tp40)
REVERT: A  348 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7052 (pmm)
REVERT: A  473 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6886 (ptp90)
REVERT: A  599 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7331 (pt)
REVERT: A  670 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7263 (mp)
REVERT: A  736 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6356 (mm110)
REVERT: A  777 MET cc_start: 0.2980 (mmp) cc_final: 0.2473 (mmt)
REVERT: A  801 ASN cc_start: 0.5728 (t0) cc_final: 0.5092 (t0)
REVERT: A  852 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6348 (ttmm)
REVERT: A  878 THR cc_start: 0.8184 (m) cc_final: 0.7886 (m)
  outliers start: 38
  outliers final: 18
  residues processed: 135
  average time/residue: 0.9067
  time to fit residues: 131.4386
Evaluate side-chains
  121 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  883 GLU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 52 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0070
   chunk 3 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    1.9604

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 ASN
A 353 HIS
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 840 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.204016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.168883 restraints weight = 8345.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.4194 rms_B_bonded: 2.06
r_work: 0.4111 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.4001 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7400  Z= 0.275
  Angle     :  0.693   9.997  10263  Z= 0.352
  Chirality :  0.046   0.227   1204
  Planarity :  0.005   0.047   1111
  Dihedral  : 17.387  82.570   1580
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 33.09 %
    Favored  : 60.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.18 (0.30), residues: 751
  helix:  0.57 (0.35), residues: 215
  sheet: -0.86 (0.38), residues: 169
  loop : -1.57 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 639 
 HIS   0.006   0.001   HIS A 946 
 PHE   0.023   0.002   PHE A 950 
 TYR   0.010   0.002   TYR A 888 
 ARG   0.011   0.001   ARG A 564 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 99
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A  288 GLU cc_start: 0.7103 (mp0) cc_final: 0.6658 (tp30)
REVERT: A  305 GLN cc_start: 0.7330 (tp40) cc_final: 0.6763 (tp40)
REVERT: A  348 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7111 (pmm)
REVERT: A  486 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.3956 (ttpt)
REVERT: A  503 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.6084 (pm20)
REVERT: A  512 MET cc_start: 0.7851 (mmm) cc_final: 0.7507 (mmm)
REVERT: A  670 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7220 (mp)
REVERT: A  777 MET cc_start: 0.2989 (mmp) cc_final: 0.2593 (mmt)
REVERT: A  801 ASN cc_start: 0.5717 (t0) cc_final: 0.5123 (t0)
REVERT: A  852 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6329 (ttmm)
REVERT: A  878 THR cc_start: 0.8379 (m) cc_final: 0.8102 (m)
REVERT: A  942 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8369 (m)
  outliers start: 43
  outliers final: 24
  residues processed: 129
  average time/residue: 0.9788
  time to fit residues: 136.6022
Evaluate side-chains
  127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  883 GLU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue  942 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0670
   chunk 31 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    2.6124

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 353 HIS
** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 GLN
A 840 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.200993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.165669 restraints weight = 8515.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 2.08
r_work: 0.4077 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3968 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7400  Z= 0.341
  Angle     :  0.761  13.562  10263  Z= 0.387
  Chirality :  0.048   0.208   1204
  Planarity :  0.005   0.049   1111
  Dihedral  : 17.417  83.240   1580
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 32.94 %
    Favored  : 60.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.40 (0.30), residues: 751
  helix:  0.35 (0.34), residues: 214
  sheet: -1.08 (0.38), residues: 171
  loop : -1.61 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 639 
 HIS   0.007   0.001   HIS A 946 
 PHE   0.026   0.002   PHE A 950 
 TYR   0.011   0.002   TYR A 361 
 ARG   0.012   0.001   ARG A 564 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 100
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.4705 (OUTLIER) cc_final: 0.3129 (ptpp)
REVERT: A  288 GLU cc_start: 0.7163 (mp0) cc_final: 0.6824 (pm20)
REVERT: A  305 GLN cc_start: 0.7354 (tp40) cc_final: 0.6787 (tp40)
REVERT: A  486 LYS cc_start: 0.5354 (OUTLIER) cc_final: 0.3983 (ttpt)
REVERT: A  503 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5942 (pm20)
REVERT: A  512 MET cc_start: 0.7862 (mmm) cc_final: 0.7479 (mmm)
REVERT: A  613 MET cc_start: 0.5560 (mmp) cc_final: 0.5119 (mpt)
REVERT: A  670 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7230 (mp)
REVERT: A  682 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6616 (mp)
REVERT: A  736 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6728 (tp-100)
REVERT: A  801 ASN cc_start: 0.5735 (t0) cc_final: 0.5065 (t0)
REVERT: A  852 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6474 (ttmm)
REVERT: A  878 THR cc_start: 0.8367 (m) cc_final: 0.8139 (m)
  outliers start: 46
  outliers final: 27
  residues processed: 133
  average time/residue: 0.8186
  time to fit residues: 117.6707
Evaluate side-chains
  128 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  688 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  817 ASP
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  883 GLU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 74 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 353 HIS
A 457 ASN
A 736 GLN
A 840 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.200011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.164567 restraints weight = 8542.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.4113 rms_B_bonded: 2.08
r_work: 0.4027 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3914 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   7400  Z= 0.372
  Angle     :  0.790  12.790  10263  Z= 0.402
  Chirality :  0.049   0.215   1204
  Planarity :  0.005   0.054   1111
  Dihedral  : 17.413  83.114   1580
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 33.38 %
    Favored  : 60.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.60 (0.29), residues: 751
  helix:  0.05 (0.34), residues: 219
  sheet: -1.08 (0.38), residues: 166
  loop : -1.72 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 639 
 HIS   0.007   0.001   HIS A 946 
 PHE   0.036   0.003   PHE A 950 
 TYR   0.014   0.002   TYR A 458 
 ARG   0.012   0.001   ARG A 564 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 99
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.4834 (OUTLIER) cc_final: 0.3507 (ptpp)
REVERT: A  305 GLN cc_start: 0.7317 (tp40) cc_final: 0.6723 (tp40)
REVERT: A  486 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.3979 (ttpt)
REVERT: A  503 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5951 (pm20)
REVERT: A  512 MET cc_start: 0.7825 (mmm) cc_final: 0.7376 (mmm)
REVERT: A  670 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7189 (mp)
REVERT: A  746 HIS cc_start: 0.5523 (m-70) cc_final: 0.5308 (m-70)
REVERT: A  801 ASN cc_start: 0.5679 (t0) cc_final: 0.5033 (t0)
REVERT: A  852 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6467 (ttmm)
  outliers start: 44
  outliers final: 27
  residues processed: 132
  average time/residue: 0.8618
  time to fit residues: 122.6769
Evaluate side-chains
  126 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  817 ASP
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  883 GLU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 353 HIS
A 736 GLN
A 840 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.207648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.172626 restraints weight = 8519.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.4189 rms_B_bonded: 2.19
r_work: 0.4101 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3989 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7400  Z= 0.210
  Angle     :  0.697  12.930  10263  Z= 0.354
  Chirality :  0.045   0.214   1204
  Planarity :  0.005   0.055   1111
  Dihedral  : 17.396  84.705   1580
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 35.72 %
    Favored  : 60.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.29 (0.30), residues: 751
  helix:  0.41 (0.35), residues: 217
  sheet: -0.86 (0.38), residues: 165
  loop : -1.62 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 604 
 HIS   0.006   0.001   HIS A 946 
 PHE   0.037   0.002   PHE A 950 
 TYR   0.011   0.001   TYR A 770 
 ARG   0.013   0.001   ARG A 564 

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A  288 GLU cc_start: 0.7263 (mp0) cc_final: 0.6738 (tp30)
REVERT: A  305 GLN cc_start: 0.7393 (tp40) cc_final: 0.6792 (tp40)
REVERT: A  348 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7002 (pmm)
REVERT: A  512 MET cc_start: 0.7932 (mmm) cc_final: 0.7497 (mmm)
REVERT: A  670 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7179 (mp)
REVERT: A  736 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6929 (tp-100)
REVERT: A  777 MET cc_start: 0.2786 (mmp) cc_final: 0.2321 (mmt)
REVERT: A  801 ASN cc_start: 0.5877 (t0) cc_final: 0.5127 (t0)
  outliers start: 29
  outliers final: 18
  residues processed: 122
  average time/residue: 0.8477
  time to fit residues: 111.6800
Evaluate side-chains
  114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  917 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 48 optimal weight:    0.4980
   chunk 74 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 353 HIS
A 840 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.207289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.172674 restraints weight = 8319.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 2.15
r_work: 0.4075 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3961 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.121   7400  Z= 0.277
  Angle     :  1.050  59.093  10263  Z= 0.601
  Chirality :  0.051   0.850   1204
  Planarity :  0.005   0.051   1111
  Dihedral  : 17.391  84.642   1580
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 35.43 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.27 (0.30), residues: 751
  helix:  0.43 (0.35), residues: 217
  sheet: -0.85 (0.38), residues: 165
  loop : -1.61 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 639 
 HIS   0.005   0.001   HIS A 353 
 PHE   0.034   0.002   PHE A 950 
 TYR   0.011   0.001   TYR A 770 
 ARG   0.011   0.001   ARG A 646 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5286.06 seconds
wall clock time: 90 minutes 57.89 seconds (5457.89 seconds total)