Starting phenix.real_space_refine
on Sat May  2 15:21:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v9i_64873/05_2026/9v9i_64873.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v9i_64873/05_2026/9v9i_64873.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v9i_64873/05_2026/9v9i_64873.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v9i_64873/05_2026/9v9i_64873.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v9i_64873/05_2026/9v9i_64873.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v9i_64873/05_2026/9v9i_64873.map"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.035
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      33      5.49       5
     Mg      2      5.21       5
     S      15      5.16       5
     C    4116      2.51       5
     N    1219      2.21       5
     O    1331      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6716
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 756, 6015
          Classifications: {'peptide': 756}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 42, 'TRANS': 713}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    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: 332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 332
          Classifications: {'RNA': 16}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 1, 'rna3p': 14}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2, 'water': 6}
          Link IDs: {None: 7}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.88, per 1000 atoms: 0.28
  Number of scatterers: 6716
  At special positions: 0
  Unit cell: (79.143, 99.567, 101.269, 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      15     16.00
     P      33     15.00
     Mg      2     11.99
     O    1331      8.00
     N    1219      7.00
     C    4116      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 329.5 milliseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      32.0% alpha, 22.0% beta
      4 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 54
      removed outlier: 3.755A  pdb=" N   ARG A  41 " --> pdb=" O   GLN A  37 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LEU A  42 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 131
      removed outlier: 3.667A  pdb=" N   ALA A 116 " --> pdb=" O   GLU A 112 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP A 126 " --> pdb=" O   ARG A 122 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASN A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 202
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 299 through 304
    Processing helix  chain 'A' and resid 312 through 324
    Processing helix  chain 'A' and resid 325 through 327
      No H-bonds generated for 'chain 'A' and resid 325 through 327'
    Processing helix  chain 'A' and resid 360 through 362
      No H-bonds generated for 'chain 'A' and resid 360 through 362'
    Processing helix  chain 'A' and resid 372 through 392
      removed outlier: 4.412A  pdb=" N   MET A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 431
      removed outlier: 3.673A  pdb=" N   GLY A 423 " --> pdb=" O   ARG A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 464
    Processing helix  chain 'A' and resid 482 through 491
      removed outlier: 3.806A  pdb=" N   LEU A 486 " --> pdb=" O   HIS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 516 through 531
    Processing helix  chain 'A' and resid 587 through 606
    Processing helix  chain 'A' and resid 621 through 639
    Processing helix  chain 'A' and resid 723 through 734
    Processing helix  chain 'A' and resid 735 through 737
      No H-bonds generated for 'chain 'A' and resid 735 through 737'
    Processing helix  chain 'A' and resid 749 through 754
    Processing helix  chain 'A' and resid 755 through 757
      No H-bonds generated for 'chain 'A' and resid 755 through 757'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346
      removed outlier: 3.594A  pdb=" N   PHE A 344 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139
      removed outlier: 6.664A  pdb=" N   LEU A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   ARG A 162 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   VAL A 330 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60
      removed outlier: 3.625A  pdb=" N   THR A  60 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA A  67 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A  68 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR A  70 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LEU A  23 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   GLU A  99 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   VAL A  25 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 230
    Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 239
      removed outlier: 6.657A  pdb=" N   PHE A 274 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   SER A 235 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ALA A 272 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246
    Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 365
    Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.987A  pdb=" N   LEU A 402 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   GLN A 439 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU A 404 " --> pdb=" O   GLN A 439 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   ASP A 401 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 472 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   VAL A 403 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   VAL A 474 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU A 405 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 575
      removed outlier: 3.543A  pdb=" N   ASP A 550 " --> pdb=" O   ILE A 557 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   PHE A 545 " --> pdb=" O   VAL A 613 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   HIS A 615 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   MET A 547 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ASP A 617 " --> pdb=" O   MET A 547 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   VAL A 549 " --> pdb=" O   ASP A 617 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL A 649 " --> pdb=" O   THR A 714 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   GLU A 687 " --> pdb=" O   LEU A 683 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   SER A 679 " --> pdb=" O   THR A 691 " (cutoff:3.500A)

    252 hydrogen bonds defined for protein.
    720 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      8 hydrogen bonds
      16 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 0.81 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: 1858
        1.33 -     1.45: 1300
        1.45 -     1.57: 3674
        1.57 -     1.69: 64
        1.69 -     1.81: 23
  Bond restraints: 6919
  Sorted by residual:
  bond pdb=" C   GLU A 673 "
       pdb=" N   ASN A 674 "
    ideal  model  delta    sigma   weight residual
    1.330  1.416 -0.086 1.47e-02 4.63e+03 3.44e+01
  bond pdb=" N   MET A 311 "
       pdb=" CA  MET A 311 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.033 1.18e-02 7.18e+03 7.85e+00
  bond pdb=" N   ASP A 408 "
       pdb=" CA  ASP A 408 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.30e-02 5.92e+03 7.25e+00
  bond pdb=" N   SER A 109 "
       pdb=" CA  SER A 109 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.34e-02 5.57e+03 5.84e+00
  bond pdb=" N   VAL A 308 "
       pdb=" CA  VAL A 308 "
    ideal  model  delta    sigma   weight residual
    1.461  1.489 -0.028 1.23e-02 6.61e+03 5.24e+00
  ... (remaining 6914 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 9190
        1.64 -     3.28: 296
        3.28 -     4.91: 46
        4.91 -     6.55: 6
        6.55 -     8.19: 3
  Bond angle restraints: 9541
  Sorted by residual:
  angle pdb=" N   PRO A 309 "
        pdb=" CA  PRO A 309 "
        pdb=" CB  PRO A 309 "
      ideal   model   delta    sigma   weight residual
     103.51  100.11    3.40 9.60e-01 1.09e+00 1.26e+01
  angle pdb=" N   GLN A 310 "
        pdb=" CA  GLN A 310 "
        pdb=" CB  GLN A 310 "
      ideal   model   delta    sigma   weight residual
     110.23  104.61    5.62 1.62e+00 3.81e-01 1.20e+01
  angle pdb=" C   GLU A 673 "
        pdb=" N   ASN A 674 "
        pdb=" CA  ASN A 674 "
      ideal   model   delta    sigma   weight residual
     120.68  125.84   -5.16 1.52e+00 4.33e-01 1.15e+01
  angle pdb=" CA  ASP A 408 "
        pdb=" CB  ASP A 408 "
        pdb=" CG  ASP A 408 "
      ideal   model   delta    sigma   weight residual
     112.60  115.92   -3.32 1.00e+00 1.00e+00 1.10e+01
  angle pdb=" C   MET A 311 "
        pdb=" N   PRO A 312 "
        pdb=" CA  PRO A 312 "
      ideal   model   delta    sigma   weight residual
     120.38  123.71   -3.33 1.03e+00 9.43e-01 1.05e+01
  ... (remaining 9536 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.99: 3917
       27.99 -    55.97: 185
       55.97 -    83.96: 21
       83.96 -   111.95: 0
      111.95 -   139.94: 1
  Dihedral angle restraints: 4124
    sinusoidal: 1944
      harmonic: 2180
  Sorted by residual:
  dihedral pdb=" C4'  DG B  12 "
           pdb=" C3'  DG B  12 "
           pdb=" O3'  DG B  12 "
           pdb=" P    DT B  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   80.06  139.94     1      3.50e+01 8.16e-04 1.38e+01
  dihedral pdb=" CA  HIS A 206 "
           pdb=" C   HIS A 206 "
           pdb=" N   VAL A 207 "
           pdb=" CA  VAL A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.67  -18.33     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  TYR A 543 "
           pdb=" C   TYR A 543 "
           pdb=" N   ASP A 544 "
           pdb=" CA  ASP A 544 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.95  -18.05     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 864
       0.047 -    0.095: 139
       0.095 -    0.142: 58
       0.142 -    0.189: 5
       0.189 -    0.236: 1
  Chirality restraints: 1067
  Sorted by residual:
  chirality pdb=" CA  GLN A 310 "
            pdb=" N   GLN A 310 "
            pdb=" C   GLN A 310 "
            pdb=" CB  GLN A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  LEU A 405 "
            pdb=" N   LEU A 405 "
            pdb=" C   LEU A 405 "
            pdb=" CB  LEU A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" CA  GLU A 634 "
            pdb=" N   GLU A 634 "
            pdb=" C   GLU A 634 "
            pdb=" CB  GLU A 634 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.49e-01
  ... (remaining 1064 not shown)

  Planarity restraints: 1133
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 284 "    0.043 5.00e-02 4.00e+02   6.57e-02 6.91e+00
        pdb=" N   PRO A 285 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 716 "    0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO A 717 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 717 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 717 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 107 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   SER A 107 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER A 107 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A 108 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1130 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 91
        2.64 -     3.21: 5647
        3.21 -     3.77: 9923
        3.77 -     4.34: 14568
        4.34 -     4.90: 23271
  Nonbonded interactions: 53500
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 497 "
            pdb="MG    MG A 801 "
     model   vdw
     2.080 2.170
  nonbonded pdb=" OD2 ASP A 550 "
            pdb="MG    MG A 802 "
     model   vdw
     2.120 2.170
  nonbonded pdb=" OP2  DT B   1 "
            pdb="MG    MG A 801 "
     model   vdw
     2.234 2.170
  nonbonded pdb=" OD1 ASP A 550 "
            pdb="MG    MG A 802 "
     model   vdw
     2.287 2.170
  nonbonded pdb=" OH  TYR A 546 "
            pdb=" OD2 ASP A 730 "
     model   vdw
     2.305 3.040
  ... (remaining 53495 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:             1.330
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.040
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
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      :  0.004   0.086   6919  Z= 0.219
  Angle     :  0.674   8.190   9541  Z= 0.383
  Chirality :  0.043   0.236   1067
  Planarity :  0.006   0.066   1133
  Dihedral  : 15.241 139.936   2720
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  0.93 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.30), residues: 754
  helix:  0.79 (0.36), residues: 218
  sheet: -0.07 (0.38), residues: 202
  loop : -0.05 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 490 
 TYR   0.014   0.002   TYR A 257 
 PHE   0.017   0.002   PHE A 159 
 TRP   0.010   0.001   TRP A 620 
 HIS   0.006   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 6919)
  covalent geometry    : angle       0.67367 ( 9541)
  hydrogen bonds       : bond        0.21922 (  260)
  hydrogen bonds       : angle       8.16204 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  484 TYR cc_start: 0.6933 (t80) cc_final: 0.6647 (t80)
REVERT: A  654 LYS cc_start: 0.7451 (tptt) cc_final: 0.6812 (mttt)
  outliers start: 3
  outliers final: 0
  residues processed: 90
  average time/residue: 0.7740
  time to fit residues: 72.3916
Evaluate side-chains
  56 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 521 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.192895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148770 restraints weight = 7603.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.01
r_work: 0.3401 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6919  Z= 0.133
  Angle     :  0.563   6.834   9541  Z= 0.301
  Chirality :  0.041   0.154   1067
  Planarity :  0.005   0.067   1133
  Dihedral  : 14.731 140.833   1256
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.86 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.31), residues: 754
  helix:  1.32 (0.36), residues: 224
  sheet:  0.02 (0.40), residues: 188
  loop : -0.17 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 490 
 TYR   0.012   0.001   TYR A 380 
 PHE   0.011   0.001   PHE A 232 
 TRP   0.012   0.001   TRP A 570 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6919)
  covalent geometry    : angle       0.56269 ( 9541)
  hydrogen bonds       : bond        0.04133 (  260)
  hydrogen bonds       : angle       5.33284 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  255 ARG cc_start: 0.6856 (ttt-90) cc_final: 0.6567 (tpt-90)
REVERT: A  326 ASP cc_start: 0.7862 (m-30) cc_final: 0.7603 (m-30)
REVERT: A  484 TYR cc_start: 0.6909 (t80) cc_final: 0.6345 (t80)
REVERT: A  485 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7207 (m-30)
REVERT: A  490 ARG cc_start: 0.6978 (mtp85) cc_final: 0.6658 (mtp85)
REVERT: A  654 LYS cc_start: 0.7313 (tptt) cc_final: 0.6621 (mttt)
REVERT: A  665 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7520 (mt)
  outliers start: 9
  outliers final: 1
  residues processed: 74
  average time/residue: 0.6907
  time to fit residues: 53.4326
Evaluate side-chains
  63 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0570
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.8900

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.194320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.150277 restraints weight = 7568.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.90
r_work: 0.3437 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6919  Z= 0.123
  Angle     :  0.520   6.947   9541  Z= 0.276
  Chirality :  0.040   0.144   1067
  Planarity :  0.005   0.057   1133
  Dihedral  : 14.752 140.798   1256
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.89 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.31), residues: 754
  helix:  1.63 (0.35), residues: 224
  sheet: -0.03 (0.40), residues: 188
  loop : -0.10 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 490 
 TYR   0.012   0.001   TYR A 380 
 PHE   0.010   0.001   PHE A 323 
 TRP   0.012   0.001   TRP A  65 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6919)
  covalent geometry    : angle       0.52014 ( 9541)
  hydrogen bonds       : bond        0.03718 (  260)
  hydrogen bonds       : angle       4.85968 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7414 (m90)
REVERT: A  193 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7587 (tm-30)
REVERT: A  255 ARG cc_start: 0.6969 (ttt-90) cc_final: 0.6624 (tpt-90)
REVERT: A  326 ASP cc_start: 0.7872 (m-30) cc_final: 0.7633 (m-30)
REVERT: A  387 MET cc_start: 0.8160 (mmp) cc_final: 0.7884 (mmm)
REVERT: A  421 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7795 (mtt-85)
REVERT: A  484 TYR cc_start: 0.6916 (t80) cc_final: 0.6247 (t80)
REVERT: A  485 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7052 (m-30)
REVERT: A  654 LYS cc_start: 0.7247 (tptt) cc_final: 0.6633 (mptt)
REVERT: A  665 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7531 (mt)
REVERT: A  758 ARG cc_start: 0.6617 (mmm160) cc_final: 0.5712 (mmt90)
  outliers start: 10
  outliers final: 3
  residues processed: 72
  average time/residue: 0.7041
  time to fit residues: 53.0897
Evaluate side-chains
  68 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0370
   chunk 45 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    2.2066

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.188436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.145537 restraints weight = 7685.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.10
r_work: 0.3368 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6919  Z= 0.226
  Angle     :  0.627   7.365   9541  Z= 0.329
  Chirality :  0.044   0.154   1067
  Planarity :  0.005   0.052   1133
  Dihedral  : 14.986 140.554   1256
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.44 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.31), residues: 754
  helix:  1.35 (0.35), residues: 225
  sheet: -0.17 (0.39), residues: 196
  loop : -0.19 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 490 
 TYR   0.014   0.002   TYR A 258 
 PHE   0.015   0.002   PHE A 323 
 TRP   0.013   0.002   TRP A 136 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 6919)
  covalent geometry    : angle       0.62656 ( 9541)
  hydrogen bonds       : bond        0.04820 (  260)
  hydrogen bonds       : angle       5.11787 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6736 (tpt-90)
REVERT: A  654 LYS cc_start: 0.7491 (tptt) cc_final: 0.6791 (mptt)
REVERT: A  665 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7604 (mt)
  outliers start: 15
  outliers final: 3
  residues processed: 68
  average time/residue: 0.7247
  time to fit residues: 51.3333
Evaluate side-chains
  57 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 646 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.193719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150669 restraints weight = 7675.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.06
r_work: 0.3445 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6919  Z= 0.116
  Angle     :  0.516   6.994   9541  Z= 0.274
  Chirality :  0.040   0.145   1067
  Planarity :  0.004   0.042   1133
  Dihedral  : 14.700 140.409   1256
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.09 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.31), residues: 754
  helix:  1.66 (0.35), residues: 225
  sheet: -0.13 (0.39), residues: 196
  loop : -0.14 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 509 
 TYR   0.013   0.001   TYR A 484 
 PHE   0.009   0.001   PHE A 545 
 TRP   0.013   0.001   TRP A 136 
 HIS   0.002   0.001   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6919)
  covalent geometry    : angle       0.51573 ( 9541)
  hydrogen bonds       : bond        0.03413 (  260)
  hydrogen bonds       : angle       4.70353 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7517 (m90)
REVERT: A  255 ARG cc_start: 0.7142 (ttt-90) cc_final: 0.6785 (tpt-90)
REVERT: A  318 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7110 (mp0)
REVERT: A  387 MET cc_start: 0.8165 (mmp) cc_final: 0.7901 (mmm)
REVERT: A  654 LYS cc_start: 0.7247 (tptt) cc_final: 0.6614 (mptt)
REVERT: A  665 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7565 (mt)
REVERT: A  758 ARG cc_start: 0.6727 (mmm160) cc_final: 0.5768 (mmt90)
  outliers start: 8
  outliers final: 1
  residues processed: 60
  average time/residue: 0.7341
  time to fit residues: 46.0254
Evaluate side-chains
  58 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 43 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.192950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.148851 restraints weight = 7688.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.02
r_work: 0.3425 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6919  Z= 0.126
  Angle     :  0.516   6.965   9541  Z= 0.273
  Chirality :  0.040   0.142   1067
  Planarity :  0.005   0.067   1133
  Dihedral  : 14.657 140.695   1256
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.71 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.31), residues: 754
  helix:  1.79 (0.35), residues: 225
  sheet: -0.02 (0.40), residues: 196
  loop : -0.17 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 276 
 TYR   0.011   0.001   TYR A 377 
 PHE   0.010   0.001   PHE A 232 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.002   0.001   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6919)
  covalent geometry    : angle       0.51565 ( 9541)
  hydrogen bonds       : bond        0.03516 (  260)
  hydrogen bonds       : angle       4.62447 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 HIS cc_start: 0.7880 (OUTLIER) cc_final: 0.7627 (m90)
REVERT: A  255 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6752 (tpt-90)
REVERT: A  318 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7105 (mp0)
REVERT: A  387 MET cc_start: 0.8194 (mmp) cc_final: 0.7851 (mmm)
REVERT: A  654 LYS cc_start: 0.7256 (tptt) cc_final: 0.6637 (mptt)
REVERT: A  665 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7571 (mt)
REVERT: A  758 ARG cc_start: 0.6709 (mmm160) cc_final: 0.5756 (mmt90)
  outliers start: 9
  outliers final: 2
  residues processed: 60
  average time/residue: 0.7531
  time to fit residues: 47.2193
Evaluate side-chains
  59 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    2.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.189151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.145612 restraints weight = 7669.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.05
r_work: 0.3367 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6919  Z= 0.260
  Angle     :  0.647   7.003   9541  Z= 0.340
  Chirality :  0.046   0.157   1067
  Planarity :  0.006   0.062   1133
  Dihedral  : 14.945 140.349   1256
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.71 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.31), residues: 754
  helix:  1.32 (0.35), residues: 225
  sheet: -0.03 (0.40), residues: 185
  loop : -0.46 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 567 
 TYR   0.020   0.002   TYR A 258 
 PHE   0.016   0.002   PHE A 323 
 TRP   0.014   0.002   TRP A 136 
 HIS   0.004   0.001   HIS A 680 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 6919)
  covalent geometry    : angle       0.64726 ( 9541)
  hydrogen bonds       : bond        0.04956 (  260)
  hydrogen bonds       : angle       5.02854 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 ARG cc_start: 0.7152 (ttt-90) cc_final: 0.6705 (tpt-90)
REVERT: A  318 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7285 (mp0)
REVERT: A  665 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7622 (mt)
  outliers start: 11
  outliers final: 5
  residues processed: 66
  average time/residue: 0.8573
  time to fit residues: 58.7163
Evaluate side-chains
  61 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.190574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.146234 restraints weight = 7709.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.02
r_work: 0.3405 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6919  Z= 0.154
  Angle     :  0.559   6.898   9541  Z= 0.296
  Chirality :  0.041   0.148   1067
  Planarity :  0.005   0.056   1133
  Dihedral  : 14.697 140.260   1256
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.64 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.31), residues: 754
  helix:  1.51 (0.35), residues: 225
  sheet: -0.17 (0.40), residues: 196
  loop : -0.34 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 509 
 TYR   0.016   0.002   TYR A 258 
 PHE   0.011   0.001   PHE A 323 
 TRP   0.015   0.001   TRP A 136 
 HIS   0.002   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6919)
  covalent geometry    : angle       0.55945 ( 9541)
  hydrogen bonds       : bond        0.03866 (  260)
  hydrogen bonds       : angle       4.79983 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6653 (tpt-90)
REVERT: A  318 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7192 (mp0)
REVERT: A  665 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7603 (mt)
REVERT: A  758 ARG cc_start: 0.6815 (mmm160) cc_final: 0.5785 (mmt90)
  outliers start: 11
  outliers final: 5
  residues processed: 63
  average time/residue: 0.7844
  time to fit residues: 51.5126
Evaluate side-chains
  63 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 63 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0270
   chunk 32 optimal weight:    0.0670
   chunk 50 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.198166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.155362 restraints weight = 7661.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 1.99
r_work: 0.3514 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6919  Z= 0.096
  Angle     :  0.492   7.521   9541  Z= 0.263
  Chirality :  0.038   0.142   1067
  Planarity :  0.004   0.055   1133
  Dihedral  : 14.482 140.035   1256
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.26 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.31), residues: 754
  helix:  1.92 (0.35), residues: 225
  sheet:  0.03 (0.40), residues: 188
  loop : -0.21 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 490 
 TYR   0.014   0.001   TYR A 380 
 PHE   0.007   0.001   PHE A 232 
 TRP   0.016   0.001   TRP A 570 
 HIS   0.003   0.000   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 6919)
  covalent geometry    : angle       0.49213 ( 9541)
  hydrogen bonds       : bond        0.02870 (  260)
  hydrogen bonds       : angle       4.42744 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7288 (tmm-80)
REVERT: A  189 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7488 (m90)
REVERT: A  255 ARG cc_start: 0.7182 (ttt-90) cc_final: 0.6752 (tpt-90)
REVERT: A  318 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7218 (mp0)
REVERT: A  424 GLU cc_start: 0.6778 (tp30) cc_final: 0.6477 (tp30)
REVERT: A  654 LYS cc_start: 0.7072 (tptt) cc_final: 0.6612 (mptt)
REVERT: A  758 ARG cc_start: 0.6731 (mmm160) cc_final: 0.5757 (mmt90)
  outliers start: 9
  outliers final: 5
  residues processed: 69
  average time/residue: 0.6959
  time to fit residues: 50.2401
Evaluate side-chains
  64 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  640 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 69 optimal weight:    0.2980
   chunk 45 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.193366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.149002 restraints weight = 7693.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.04
r_work: 0.3426 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6919  Z= 0.145
  Angle     :  0.547   8.064   9541  Z= 0.289
  Chirality :  0.040   0.144   1067
  Planarity :  0.005   0.054   1133
  Dihedral  : 14.592 140.250   1256
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 17.73 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.31), residues: 754
  helix:  1.81 (0.35), residues: 225
  sheet:  0.01 (0.40), residues: 196
  loop : -0.23 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 490 
 TYR   0.014   0.001   TYR A 258 
 PHE   0.010   0.001   PHE A 323 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6919)
  covalent geometry    : angle       0.54676 ( 9541)
  hydrogen bonds       : bond        0.03571 (  260)
  hydrogen bonds       : angle       4.55894 (  736)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6638 (tpt-90)
REVERT: A  318 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7190 (mp0)
REVERT: A  573 ARG cc_start: 0.7823 (mmt180) cc_final: 0.7553 (tpt-90)
REVERT: A  654 LYS cc_start: 0.7347 (tptt) cc_final: 0.6676 (mptt)
REVERT: A  665 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7481 (mt)
REVERT: A  758 ARG cc_start: 0.6781 (mmm160) cc_final: 0.5773 (mmt90)
  outliers start: 8
  outliers final: 5
  residues processed: 58
  average time/residue: 0.7906
  time to fit residues: 47.7935
Evaluate side-chains
  61 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  665 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 53 optimal weight:    0.0870
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 74 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.196461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.151842 restraints weight = 7617.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 1.97
r_work: 0.3472 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6919  Z= 0.102
  Angle     :  0.506   7.754   9541  Z= 0.269
  Chirality :  0.039   0.141   1067
  Planarity :  0.004   0.052   1133
  Dihedral  : 14.468 140.050   1256
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 18.20 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.31), residues: 754
  helix:  2.00 (0.34), residues: 225
  sheet:  0.12 (0.40), residues: 188
  loop : -0.13 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 490 
 TYR   0.017   0.001   TYR A 484 
 PHE   0.007   0.001   PHE A 545 
 TRP   0.014   0.001   TRP A 570 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6919)
  covalent geometry    : angle       0.50583 ( 9541)
  hydrogen bonds       : bond        0.02944 (  260)
  hydrogen bonds       : angle       4.37854 (  736)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2478.83 seconds
wall clock time: 42 minutes 58.55 seconds (2578.55 seconds total)