Starting phenix.real_space_refine
on Tue Jul 29 02:54:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xjx_38409/07_2025/8xjx_38409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xjx_38409/07_2025/8xjx_38409.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xjx_38409/07_2025/8xjx_38409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xjx_38409/07_2025/8xjx_38409.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xjx_38409/07_2025/8xjx_38409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xjx_38409/07_2025/8xjx_38409.cif"
  }
  resolution = 2.78
  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=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5737 atoms to isotropic.
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
     Mn      1      7.51       5
     P      32      5.49       5
     S      29      5.16       5
     C    3914      2.51       5
     N    1120      2.21       5
     O    1215      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6311
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 693, 5626
          Classifications: {'peptide': 693}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 23, 'TRANS': 669}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 25
    Chain: "B"
      Number of atoms: 359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 359
          Classifications: {'DNA': 17}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 16}
    Chain: "C"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 298
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1, 'water': 18}
          Link IDs: {None: 18}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.15, per 1000 atoms: 0.82
  Number of scatterers: 6311
  At special positions: 0
  Unit cell: (75.739, 91.908, 107.226, 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)
     Mn      1     24.99
     S      29     16.00
     P      32     15.00
     O    1215      8.00
     N    1120      7.00
     C    3914      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: 1.64
  Conformation dependent library (CDL) restraints added in 941.5 milliseconds
  

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1322

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 7 sheets defined
      36.9% alpha, 18.5% beta
      11 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 2.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 48
    Processing helix  chain 'A' and resid 84 through 108
      removed outlier: 3.686A  pdb=" N   HIS A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 166
      removed outlier: 3.856A  pdb=" N   MET A 163 " --> pdb=" O   THR A 159 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN A 166 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.544A  pdb=" N   LEU A 262 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ASN A 263 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 288
      removed outlier: 3.606A  pdb=" N   TRP A 282 " --> pdb=" O   CYS A 278 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 333
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 358 through 375
    Processing helix  chain 'A' and resid 394 through 400
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 408 through 413
    Processing helix  chain 'A' and resid 422 through 428
    Processing helix  chain 'A' and resid 432 through 445
      removed outlier: 3.601A  pdb=" N   GLY A 443 " --> pdb=" O   GLN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 467
      removed outlier: 3.643A  pdb=" N   ILE A 457 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 489
      removed outlier: 3.514A  pdb=" N   LYS A 488 " --> pdb=" O   ILE A 484 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   ASN A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 507
      removed outlier: 3.974A  pdb=" N   THR A 495 " --> pdb=" O   SER A 491 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS A 506 " --> pdb=" O   GLY A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 585
    Processing helix  chain 'A' and resid 602 through 613
      removed outlier: 3.649A  pdb=" N   VAL A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   HIS A 612 " --> pdb=" O   LYS A 608 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   TYR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 692
      removed outlier: 3.530A  pdb=" N   ILE A 685 " --> pdb=" O   PRO A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 695
      No H-bonds generated for 'chain 'A' and resid 693 through 695'
    Processing helix  chain 'A' and resid 706 through 721
      removed outlier: 3.644A  pdb=" N   ALA A 712 " --> pdb=" O   THR A 708 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13
      removed outlier: 4.891A  pdb=" N   ILE A 144 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL A 127 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   GLN A 122 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   ILE A 129 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   GLN A 120 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   GLU A 131 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311
      removed outlier: 3.637A  pdb=" N   THR A 646 " --> pdb=" O   CYS A 657 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   CYS A 522 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   HIS A 594 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE A 524 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   ASP A 596 " --> pdb=" O   ILE A 524 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   ILE A 526 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 382
      removed outlier: 9.119A  pdb=" N   THR A 416 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LYS A 342 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   LEU A 418 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   SER A 344 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL A 417 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)

    242 hydrogen bonds defined for protein.
    684 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 2.87

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1650
        1.33 -     1.45: 1324
        1.45 -     1.57: 3404
        1.57 -     1.69: 63
        1.69 -     1.81: 51
  Bond restraints: 6492
  Sorted by residual:
  bond pdb=" P    DT B   1 "
       pdb=" OP3  DT B   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.599 -0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" N   VAL A 606 "
       pdb=" CA  VAL A 606 "
    ideal  model  delta    sigma   weight residual
    1.461  1.502 -0.041 1.17e-02 7.31e+03 1.21e+01
  bond pdb=" N   GLU A 607 "
       pdb=" CA  GLU A 607 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.23e-02 6.61e+03 3.37e+00
  bond pdb=" CA  GLU A 607 "
       pdb=" C   GLU A 607 "
    ideal  model  delta    sigma   weight residual
    1.524  1.539 -0.016 1.29e-02 6.01e+03 1.45e+00
  bond pdb=" C   GLU A 607 "
       pdb=" O   GLU A 607 "
    ideal  model  delta    sigma   weight residual
    1.237  1.223  0.013 1.19e-02 7.06e+03 1.27e+00
  ... (remaining 6487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 8715
        1.72 -     3.43: 167
        3.43 -     5.15: 28
        5.15 -     6.87: 4
        6.87 -     8.58: 3
  Bond angle restraints: 8917
  Sorted by residual:
  angle pdb=" N   PRO A 474 "
        pdb=" CA  PRO A 474 "
        pdb=" CB  PRO A 474 "
      ideal   model   delta    sigma   weight residual
     103.33  110.58   -7.25 9.30e-01 1.16e+00 6.07e+01
  angle pdb=" C   GLU A 607 "
        pdb=" CA  GLU A 607 "
        pdb=" CB  GLU A 607 "
      ideal   model   delta    sigma   weight residual
     110.85  119.43   -8.58 1.70e+00 3.46e-01 2.55e+01
  angle pdb=" N   VAL A 606 "
        pdb=" CA  VAL A 606 "
        pdb=" CB  VAL A 606 "
      ideal   model   delta    sigma   weight residual
     110.55  115.67   -5.12 1.17e+00 7.31e-01 1.92e+01
  angle pdb=" C   GLU A 607 "
        pdb=" N   LYS A 608 "
        pdb=" CA  LYS A 608 "
      ideal   model   delta    sigma   weight residual
     120.38  115.29    5.09 1.37e+00 5.33e-01 1.38e+01
  angle pdb=" C   GLY A 167 "
        pdb=" N   LYS A 168 "
        pdb=" CA  LYS A 168 "
      ideal   model   delta    sigma   weight residual
     121.54  128.08   -6.54 1.91e+00 2.74e-01 1.17e+01
  ... (remaining 8912 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.50: 3529
       26.50 -    53.00: 240
       53.00 -    79.51: 25
       79.51 -   106.01: 1
      106.01 -   132.51: 1
  Dihedral angle restraints: 3796
    sinusoidal: 1751
      harmonic: 2045
  Sorted by residual:
  dihedral pdb=" CA  MET A 610 "
           pdb=" C   MET A 610 "
           pdb=" N   SER A 611 "
           pdb=" CA  SER A 611 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.06   18.94     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  GLY A 547 "
           pdb=" C   GLY A 547 "
           pdb=" N   HIS A 548 "
           pdb=" CA  HIS A 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.34   18.66     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" C4'  DT B  13 "
           pdb=" C3'  DT B  13 "
           pdb=" O3'  DT B  13 "
           pdb=" P    DT B  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   87.49  132.51     1      3.50e+01 8.16e-04 1.31e+01
  ... (remaining 3793 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 876
       0.064 -    0.127: 108
       0.127 -    0.191: 8
       0.191 -    0.254: 1
       0.254 -    0.318: 2
  Chirality restraints: 995
  Sorted by residual:
  chirality pdb=" P    DT B   1 "
            pdb=" OP1  DT B   1 "
            pdb=" OP2  DT B   1 "
            pdb=" O5'  DT B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.66   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CB  VAL A 606 "
            pdb=" CA  VAL A 606 "
            pdb=" CG1 VAL A 606 "
            pdb=" CG2 VAL A 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  PRO A 474 "
            pdb=" N   PRO A 474 "
            pdb=" C   PRO A 474 "
            pdb=" CB  PRO A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 992 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 125 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.40e+00
        pdb=" C   ARG A 125 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ARG A 125 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLN A 126 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  43 "    0.012 2.00e-02 2.50e+03   8.90e-03 1.98e+00
        pdb=" CG  TRP A  43 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  43 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  43 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  43 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  43 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  43 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  43 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  43 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  43 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 510 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.92e+00
        pdb=" N   PRO A 511 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 511 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 511 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.37: 12
        2.37 -     3.00: 3106
        3.00 -     3.64: 9087
        3.64 -     4.27: 14789
        4.27 -     4.90: 24417
  Nonbonded interactions: 51411
  Sorted by model distance:
  nonbonded pdb=" OXT VAL A 737 "
            pdb="MN    MN A 801 "
     model   vdw
     1.742 2.320
  nonbonded pdb=" OP1  DA B   3 "
            pdb="MN    MN A 801 "
     model   vdw
     1.797 2.320
  nonbonded pdb=" O   SER A 313 "
            pdb=" O   HOH A 901 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   ALA A 668 "
            pdb=" O   HOH A 902 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER A 265 "
            pdb=" O   HOH A 903 "
     model   vdw
     2.263 3.040
  ... (remaining 51406 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:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.580
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:16.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.119   6492  Z= 0.160
  Angle     :  0.601   8.585   8917  Z= 0.352
  Chirality :  0.044   0.318    995
  Planarity :  0.004   0.035   1020
  Dihedral  : 16.486 132.512   2474
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.51 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.49 %
    Favored  : 99.34 %
  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: -0.23 (0.31), residues: 687
  helix:  0.76 (0.33), residues: 240
  sheet:  1.12 (0.43), residues: 130
  loop : -1.47 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  43 
 HIS   0.003   0.001   HIS A 710 
 PHE   0.017   0.001   PHE A 351 
 TYR   0.009   0.001   TYR A  53 
 ARG   0.004   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12717 (  267)
  hydrogen bonds       : angle       6.37829 (  734)
  covalent geometry    : bond        0.00320 ( 6492)
  covalent geometry    : angle       0.60124 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  400 HIS cc_start: 0.7151 (m90) cc_final: 0.6834 (m90)
  outliers start: 1
  outliers final: 2
  residues processed: 112
  average time/residue: 1.1956
  time to fit residues: 140.7511
Evaluate side-chains
  76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  575 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0670
   chunk 18 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.9322

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 376 GLN
A 435 GLN
A 552 GLN
A 583 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.204407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.187646 restraints weight = 5708.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 1.26
r_work: 0.3792 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3551 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6492  Z= 0.142
  Angle     :  0.559   5.798   8917  Z= 0.316
  Chirality :  0.042   0.154    995
  Planarity :  0.004   0.048   1020
  Dihedral  : 16.286 135.365   1117
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.53 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.84 %
    Favored  : 85.53 %
  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: -0.12 (0.31), residues: 687
  helix:  0.87 (0.33), residues: 255
  sheet:  1.01 (0.43), residues: 122
  loop : -1.37 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  43 
 HIS   0.004   0.001   HIS A 590 
 PHE   0.016   0.002   PHE A 351 
 TYR   0.008   0.001   TYR A  53 
 ARG   0.005   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  267)
  hydrogen bonds       : angle       4.90747 (  734)
  covalent geometry    : bond        0.00314 ( 6492)
  covalent geometry    : angle       0.55897 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A  122 GLN cc_start: 0.6025 (tt0) cc_final: 0.5743 (mt0)
REVERT: A  155 GLU cc_start: 0.6864 (tt0) cc_final: 0.6422 (tp30)
REVERT: A  400 HIS cc_start: 0.7417 (m90) cc_final: 0.7153 (m90)
REVERT: A  411 ILE cc_start: 0.8479 (mm) cc_final: 0.8266 (mp)
REVERT: A  532 ASN cc_start: 0.7655 (m-40) cc_final: 0.7379 (m-40)
REVERT: A  667 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7425 (ttt)
  outliers start: 16
  outliers final: 3
  residues processed: 84
  average time/residue: 1.1153
  time to fit residues: 99.1095
Evaluate side-chains
  67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  575 GLN
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  724 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 370 GLN
A 435 GLN
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 556 ASN
A 627 ASN
A 663 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.195508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.179260 restraints weight = 5715.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 1.25
r_work: 0.3695 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   6492  Z= 0.289
  Angle     :  0.734   8.347   8917  Z= 0.403
  Chirality :  0.048   0.182    995
  Planarity :  0.005   0.064   1020
  Dihedral  : 16.839 141.167   1114
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.84 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 11.02 %
    Favored  : 83.39 %
  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: -0.67 (0.30), residues: 687
  helix:  0.34 (0.31), residues: 254
  sheet:  0.67 (0.42), residues: 122
  loop : -1.58 (0.32), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A  43 
 HIS   0.006   0.001   HIS A 320 
 PHE   0.020   0.003   PHE A 101 
 TYR   0.014   0.002   TYR A 440 
 ARG   0.007   0.001   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05979 (  267)
  hydrogen bonds       : angle       5.31314 (  734)
  covalent geometry    : bond        0.00680 ( 6492)
  covalent geometry    : angle       0.73425 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7872 (ptm160) cc_final: 0.7662 (mtm180)
REVERT: A  126 GLN cc_start: 0.7402 (tt0) cc_final: 0.6845 (tm-30)
REVERT: A  400 HIS cc_start: 0.7352 (m90) cc_final: 0.7053 (m90)
REVERT: A  411 ILE cc_start: 0.8549 (mm) cc_final: 0.8345 (mp)
REVERT: A  464 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6663 (mp)
REVERT: A  532 ASN cc_start: 0.7881 (m-40) cc_final: 0.7592 (m-40)
  outliers start: 34
  outliers final: 11
  residues processed: 95
  average time/residue: 1.1040
  time to fit residues: 110.9389
Evaluate side-chains
  74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  575 GLN
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  724 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 50 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.2980
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A  97 ASN
A 435 GLN
A 510 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.203045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.180044 restraints weight = 5848.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 1.50
r_work: 0.3753 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6492  Z= 0.126
  Angle     :  0.550   7.071   8917  Z= 0.309
  Chirality :  0.041   0.147    995
  Planarity :  0.004   0.044   1020
  Dihedral  : 16.074 124.186   1114
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.39 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.94 %
    Favored  : 79.93 %
  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: -0.16 (0.31), residues: 687
  helix:  0.83 (0.33), residues: 257
  sheet:  1.02 (0.43), residues: 122
  loop : -1.42 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  43 
 HIS   0.004   0.001   HIS A 590 
 PHE   0.020   0.001   PHE A 351 
 TYR   0.009   0.001   TYR A 158 
 ARG   0.005   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  267)
  hydrogen bonds       : angle       4.85056 (  734)
  covalent geometry    : bond        0.00277 ( 6492)
  covalent geometry    : angle       0.54992 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  126 GLN cc_start: 0.7127 (tt0) cc_final: 0.6790 (tm-30)
REVERT: A  464 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7061 (mp)
  outliers start: 19
  outliers final: 7
  residues processed: 79
  average time/residue: 0.9988
  time to fit residues: 84.1118
Evaluate side-chains
  69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  575 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 42 optimal weight:    0.0570
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 7 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.4904

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 510 GLN
A 541 ASN
A 575 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.199593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.175623 restraints weight = 5773.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 1.54
r_work: 0.3704 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6492  Z= 0.175
  Angle     :  0.604   8.191   8917  Z= 0.335
  Chirality :  0.043   0.169    995
  Planarity :  0.004   0.051   1020
  Dihedral  : 16.319 130.088   1114
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.26 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 16.28 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.18 (0.31), residues: 687
  helix:  0.88 (0.33), residues: 253
  sheet:  0.93 (0.43), residues: 125
  loop : -1.44 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  43 
 HIS   0.003   0.001   HIS A 320 
 PHE   0.017   0.002   PHE A 351 
 TYR   0.010   0.001   TYR A  20 
 ARG   0.005   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  267)
  hydrogen bonds       : angle       4.96002 (  734)
  covalent geometry    : bond        0.00403 ( 6492)
  covalent geometry    : angle       0.60357 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A   82 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7081 (mp)
REVERT: A  111 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7652 (mtm180)
REVERT: A  126 GLN cc_start: 0.7407 (tt0) cc_final: 0.6676 (tm-30)
REVERT: A  155 GLU cc_start: 0.6381 (tp30) cc_final: 0.6078 (tt0)
REVERT: A  464 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6761 (mp)
REVERT: A  575 GLN cc_start: 0.7341 (pp30) cc_final: 0.7000 (pp30)
  outliers start: 27
  outliers final: 10
  residues processed: 80
  average time/residue: 1.0404
  time to fit residues: 88.3284
Evaluate side-chains
  71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  105 ARG
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  685 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 510 GLN
A 541 ASN
A 575 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.200437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.175704 restraints weight = 5726.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.4107 rms_B_bonded: 1.58
r_work: 0.3701 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6492  Z= 0.160
  Angle     :  0.589   8.535   8917  Z= 0.328
  Chirality :  0.042   0.162    995
  Planarity :  0.004   0.047   1020
  Dihedral  : 16.280 131.423   1111
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.68 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 17.60 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.23 (0.31), residues: 687
  helix:  0.84 (0.33), residues: 255
  sheet:  1.11 (0.45), residues: 108
  loop : -1.45 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  43 
 HIS   0.003   0.001   HIS A 710 
 PHE   0.013   0.002   PHE A 148 
 TYR   0.008   0.001   TYR A 690 
 ARG   0.005   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  267)
  hydrogen bonds       : angle       4.95422 (  734)
  covalent geometry    : bond        0.00364 ( 6492)
  covalent geometry    : angle       0.58876 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 59
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A   82 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7122 (mp)
REVERT: A  126 GLN cc_start: 0.7174 (tt0) cc_final: 0.6750 (tm-30)
REVERT: A  464 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7067 (mp)
REVERT: A  667 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7611 (ttt)
  outliers start: 25
  outliers final: 12
  residues processed: 75
  average time/residue: 1.0570
  time to fit residues: 84.2855
Evaluate side-chains
  72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  105 ARG
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  575 GLN
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  724 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 510 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.196656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.171524 restraints weight = 5746.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 1.59
r_work: 0.3692 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6492  Z= 0.252
  Angle     :  0.686   9.403   8917  Z= 0.378
  Chirality :  0.047   0.184    995
  Planarity :  0.005   0.057   1020
  Dihedral  : 16.718 138.351   1111
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.99 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 17.60 %
    Favored  : 77.63 %
  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: -0.54 (0.31), residues: 687
  helix:  0.52 (0.33), residues: 252
  sheet:  0.86 (0.47), residues: 105
  loop : -1.49 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A  43 
 HIS   0.004   0.001   HIS A 320 
 PHE   0.018   0.002   PHE A 101 
 TYR   0.012   0.002   TYR A 440 
 ARG   0.006   0.001   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05488 (  267)
  hydrogen bonds       : angle       5.20019 (  734)
  covalent geometry    : bond        0.00591 ( 6492)
  covalent geometry    : angle       0.68604 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.623 
Fit side-chains
REVERT: A   82 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7181 (mp)
REVERT: A  111 ARG cc_start: 0.7697 (ptm160) cc_final: 0.7497 (mtm180)
REVERT: A  124 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6111 (pp)
REVERT: A  126 GLN cc_start: 0.7278 (tt0) cc_final: 0.6872 (tm-30)
REVERT: A  133 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7011 (tt)
REVERT: A  464 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7164 (mp)
REVERT: A  575 GLN cc_start: 0.7230 (pp30) cc_final: 0.6958 (pp30)
REVERT: A  721 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7628 (mtt-85)
  outliers start: 29
  outliers final: 14
  residues processed: 82
  average time/residue: 0.9644
  time to fit residues: 84.3555
Evaluate side-chains
  83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  105 ARG
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  724 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 400 HIS
A 510 GLN
A 638 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.199069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.179278 restraints weight = 5743.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 1.30
r_work: 0.3764 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6492  Z= 0.178
  Angle     :  0.609   9.101   8917  Z= 0.338
  Chirality :  0.043   0.167    995
  Planarity :  0.004   0.047   1020
  Dihedral  : 16.473 136.816   1111
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.40 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 18.75 %
    Favored  : 76.97 %
  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: -0.41 (0.31), residues: 687
  helix:  0.62 (0.33), residues: 255
  sheet:  0.93 (0.47), residues: 105
  loop : -1.44 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  43 
 HIS   0.003   0.001   HIS A 320 
 PHE   0.013   0.002   PHE A 148 
 TYR   0.009   0.001   TYR A 440 
 ARG   0.005   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04539 (  267)
  hydrogen bonds       : angle       5.01664 (  734)
  covalent geometry    : bond        0.00408 ( 6492)
  covalent geometry    : angle       0.60897 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.623 
Fit side-chains
REVERT: A   82 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7221 (mp)
REVERT: A  126 GLN cc_start: 0.7045 (tt0) cc_final: 0.6792 (tm-30)
REVERT: A  128 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.6070 (mt)
REVERT: A  133 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7030 (tt)
REVERT: A  174 MET cc_start: 0.6529 (OUTLIER) cc_final: 0.5717 (ttm)
REVERT: A  464 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7167 (mp)
REVERT: A  575 GLN cc_start: 0.7105 (pp30) cc_final: 0.6831 (pp30)
  outliers start: 26
  outliers final: 16
  residues processed: 81
  average time/residue: 0.9226
  time to fit residues: 79.8780
Evaluate side-chains
  79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  105 ARG
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  148 PHE
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  724 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A  79 HIS
A 510 GLN
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.183180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.143965 restraints weight = 5552.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.88
r_work: 0.3438 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   6492  Z= 0.275
  Angle     :  0.724   8.602   8917  Z= 0.398
  Chirality :  0.048   0.191    995
  Planarity :  0.005   0.056   1020
  Dihedral  : 16.963 142.762   1111
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.42 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 17.93 %
    Favored  : 76.81 %
  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: -0.76 (0.30), residues: 687
  helix:  0.30 (0.32), residues: 253
  sheet:  0.82 (0.47), residues: 104
  loop : -1.62 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A  43 
 HIS   0.004   0.001   HIS A 320 
 PHE   0.019   0.003   PHE A 351 
 TYR   0.013   0.002   TYR A 440 
 ARG   0.006   0.001   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05785 (  267)
  hydrogen bonds       : angle       5.25479 (  734)
  covalent geometry    : bond        0.00647 ( 6492)
  covalent geometry    : angle       0.72366 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 62
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A   82 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7164 (mp)
REVERT: A  124 ILE cc_start: 0.6205 (OUTLIER) cc_final: 0.5777 (pp)
REVERT: A  128 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.6100 (mt)
REVERT: A  133 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7043 (tt)
REVERT: A  155 GLU cc_start: 0.6876 (tt0) cc_final: 0.6307 (tp30)
REVERT: A  174 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.4899 (ttm)
REVERT: A  274 LYS cc_start: 0.7413 (mppt) cc_final: 0.7069 (mptp)
REVERT: A  414 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7999 (mp10)
REVERT: A  464 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6433 (mp)
REVERT: A  575 GLN cc_start: 0.7129 (pp30) cc_final: 0.6817 (pp30)
REVERT: A  721 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7666 (mtt-85)
  outliers start: 32
  outliers final: 18
  residues processed: 85
  average time/residue: 0.9908
  time to fit residues: 89.4720
Evaluate side-chains
  87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  105 ARG
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  148 PHE
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  724 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 178 HIS
A 510 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.199092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.173386 restraints weight = 5852.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 1.63
r_work: 0.3710 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6492  Z= 0.171
  Angle     :  0.620   8.408   8917  Z= 0.345
  Chirality :  0.043   0.165    995
  Planarity :  0.004   0.044   1020
  Dihedral  : 16.559 139.843   1111
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.70 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 19.41 %
    Favored  : 76.32 %
  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: -0.47 (0.31), residues: 687
  helix:  0.53 (0.33), residues: 255
  sheet:  0.78 (0.45), residues: 122
  loop : -1.49 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  43 
 HIS   0.003   0.001   HIS A 590 
 PHE   0.013   0.002   PHE A 351 
 TYR   0.017   0.001   TYR A 158 
 ARG   0.005   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04490 (  267)
  hydrogen bonds       : angle       5.01610 (  734)
  covalent geometry    : bond        0.00390 ( 6492)
  covalent geometry    : angle       0.61990 ( 8917)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 58
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A   82 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7127 (mp)
REVERT: A  124 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5886 (pp)
REVERT: A  126 GLN cc_start: 0.7421 (tt0) cc_final: 0.6852 (tm-30)
REVERT: A  128 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.6105 (mt)
REVERT: A  133 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.6992 (tt)
REVERT: A  174 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.5562 (ttm)
REVERT: A  464 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7040 (mp)
REVERT: A  575 GLN cc_start: 0.7222 (pp30) cc_final: 0.6887 (pp30)
  outliers start: 26
  outliers final: 16
  residues processed: 76
  average time/residue: 0.8959
  time to fit residues: 73.0628
Evaluate side-chains
  79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  105 ARG
Chi-restraints excluded: chain A residue  110 LYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  148 PHE
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  724 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 510 GLN
A 575 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.202153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.178173 restraints weight = 5869.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.4135 rms_B_bonded: 1.56
r_work: 0.3727 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6492  Z= 0.134
  Angle     :  0.572   7.838   8917  Z= 0.321
  Chirality :  0.042   0.154    995
  Planarity :  0.004   0.038   1020
  Dihedral  : 16.356 136.319   1111
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.70 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.23 %
    Favored  : 75.99 %
  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: -0.24 (0.32), residues: 687
  helix:  0.75 (0.33), residues: 254
  sheet:  0.86 (0.44), residues: 127
  loop : -1.41 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A  43 
 HIS   0.003   0.001   HIS A 590 
 PHE   0.011   0.001   PHE A 351 
 TYR   0.013   0.001   TYR A 158 
 ARG   0.004   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  267)
  hydrogen bonds       : angle       4.85630 (  734)
  covalent geometry    : bond        0.00300 ( 6492)
  covalent geometry    : angle       0.57233 ( 8917)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4453.37 seconds
wall clock time: 76 minutes 33.80 seconds (4593.80 seconds total)