Starting phenix.real_space_refine
on Fri Aug 22 17:29:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dvu_27745/08_2025/8dvu_27745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dvu_27745/08_2025/8dvu_27745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dvu_27745/08_2025/8dvu_27745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dvu_27745/08_2025/8dvu_27745.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dvu_27745/08_2025/8dvu_27745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dvu_27745/08_2025/8dvu_27745.map"
  }
  resolution = 2.9
  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=   0.015
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      38      5.49       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    3784      2.51       5
     N    1059      2.21       5
     O    1254      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6170
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 669, 5375
          Classifications: {'peptide': 669}
          Link IDs: {'PTRANS': 25, 'TRANS': 643}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 766
          Classifications: {'RNA': 36}
          Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18}
          Link IDs: {'rna3p': 35}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4570  SG  CYS A 810      36.881  19.714  31.150  1.00  7.69           S
  ATOM   4596  SG  CYS A 813      34.935  16.553  31.282  1.00 10.45           S
  ATOM   4899  SG  CYS A 864      36.768  16.868  27.740  1.00 13.54           S
  ATOM   4938  SG  CYS A 869      33.961  19.186  29.142  1.00 16.27           S

  Time building chain proxies: 1.49, per 1000 atoms: 0.24
  Number of scatterers: 6170
  At special positions: 0
  Unit cell: (94.218, 94.218, 71.238, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      33     16.00
     P      38     15.00
     Mg      1     11.99
     O    1254      8.00
     N    1059      7.00
     C    3784      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: 0.49
  Conformation dependent library (CDL) restraints added in 435.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 813 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 869 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 810 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
      Number of angles added : 6


  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1274

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 6 sheets defined
      49.2% alpha, 9.1% beta
      18 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 251
    Processing helix  chain 'A' and resid 253 through 257
    Processing helix  chain 'A' and resid 269 through 284
    Processing helix  chain 'A' and resid 299 through 315
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 3.673A  pdb=" N   GLU A 339 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.629A  pdb=" N   LEU A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.792A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 377
    Processing helix  chain 'A' and resid 381 through 395
    Processing helix  chain 'A' and resid 419 through 434
    Processing helix  chain 'A' and resid 445 through 450
    Processing helix  chain 'A' and resid 469 through 491
    Processing helix  chain 'A' and resid 492 through 496
    Processing helix  chain 'A' and resid 506 through 522
      removed outlier: 3.705A  pdb=" N   VAL A 522 " --> pdb=" O   LYS A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 558
      removed outlier: 3.650A  pdb=" N   GLU A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   HIS A 557 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 578
      removed outlier: 3.632A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA A 577 " --> pdb=" O   ASN A 573 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLY A 578 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 602
      removed outlier: 3.929A  pdb=" N   LYS A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 649
    Processing helix  chain 'A' and resid 674 through 685
    Processing helix  chain 'A' and resid 720 through 729
    Processing helix  chain 'A' and resid 746 through 769
    Processing helix  chain 'A' and resid 772 through 792
    Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261
      removed outlier: 6.750A  pdb=" N   THR A 260 " --> pdb=" O   GLY A 407 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   VAL A 294 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   ASP A 372 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   PHE A 296 " --> pdb=" O   ASP A 372 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   THR A 322 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462
    Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 661
      removed outlier: 6.381A  pdb=" N   GLY A 659 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819
      removed outlier: 6.821A  pdb=" N   LEU A 816 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   CYS A 810 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 833
      removed outlier: 4.532A  pdb=" N   ILE A 916 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 844
      removed outlier: 6.277A  pdb=" N   CYS A 864 " --> pdb=" O   ASP A 872 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASP A 872 " --> pdb=" O   CYS A 864 " (cutoff:3.500A)

    258 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      92 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 0.69 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: 1358
        1.33 -     1.45: 1471
        1.45 -     1.57: 3416
        1.57 -     1.69: 73
        1.69 -     1.81: 46
  Bond restraints: 6364
  Sorted by residual:
  bond pdb=" C   GLU A 716 "
       pdb=" O   GLU A 716 "
    ideal  model  delta    sigma   weight residual
    1.233  1.212  0.021 1.30e-02 5.92e+03 2.59e+00
  bond pdb=" C   ASN A 625 "
       pdb=" O   ASN A 625 "
    ideal  model  delta    sigma   weight residual
    1.249  1.239  0.010 8.50e-03 1.38e+04 1.26e+00
  bond pdb=" C4  ADP A1003 "
       pdb=" C5  ADP A1003 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 9.69e-01
  bond pdb=" N   GLU A 716 "
       pdb=" CA  GLU A 716 "
    ideal  model  delta    sigma   weight residual
    1.462  1.475 -0.013 1.46e-02 4.69e+03 7.81e-01
  bond pdb=" CB  PRO A 797 "
       pdb=" CG  PRO A 797 "
    ideal  model  delta    sigma   weight residual
    1.492  1.535 -0.043 5.00e-02 4.00e+02 7.35e-01
  ... (remaining 6359 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 8539
        1.35 -     2.70: 176
        2.70 -     4.06: 30
        4.06 -     5.41: 12
        5.41 -     6.76: 3
  Bond angle restraints: 8760
  Sorted by residual:
  angle pdb=" C   GLY A 689 "
        pdb=" N   ASP A 690 "
        pdb=" CA  ASP A 690 "
      ideal   model   delta    sigma   weight residual
     121.54  128.30   -6.76 1.91e+00 2.74e-01 1.25e+01
  angle pdb=" C   GLU A 716 "
        pdb=" CA  GLU A 716 "
        pdb=" CB  GLU A 716 "
      ideal   model   delta    sigma   weight residual
     111.86  108.41    3.45 1.34e+00 5.57e-01 6.62e+00
  angle pdb=" N   ALA A 440 "
        pdb=" CA  ALA A 440 "
        pdb=" C   ALA A 440 "
      ideal   model   delta    sigma   weight residual
     110.64  114.09   -3.45 1.48e+00 4.57e-01 5.44e+00
  angle pdb=" CA  PRO A 797 "
        pdb=" C   PRO A 797 "
        pdb=" O   PRO A 797 "
      ideal   model   delta    sigma   weight residual
     121.38  119.63    1.75 7.70e-01 1.69e+00 5.17e+00
  angle pdb=" CA  VAL A 332 "
        pdb=" CB  VAL A 332 "
        pdb=" CG1 VAL A 332 "
      ideal   model   delta    sigma   weight residual
     110.40  114.15   -3.75 1.70e+00 3.46e-01 4.87e+00
  ... (remaining 8755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 3497
       16.62 -    33.23: 250
       33.23 -    49.85: 99
       49.85 -    66.46: 59
       66.46 -    83.08: 21
  Dihedral angle restraints: 3926
    sinusoidal: 1964
      harmonic: 1962
  Sorted by residual:
  dihedral pdb=" O2A ADP A1003 "
           pdb=" O3A ADP A1003 "
           pdb=" PA  ADP A1003 "
           pdb=" PB  ADP A1003 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00    7.39  -67.39     1      2.00e+01 2.50e-03 1.48e+01
  dihedral pdb=" CA  LEU A 346 "
           pdb=" C   LEU A 346 "
           pdb=" N   THR A 347 "
           pdb=" CA  THR A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.92   19.08     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ASP A 492 "
           pdb=" CB  ASP A 492 "
           pdb=" CG  ASP A 492 "
           pdb=" OD1 ASP A 492 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.59   57.59     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 3923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 683
       0.032 -    0.064: 227
       0.064 -    0.096: 64
       0.096 -    0.128: 30
       0.128 -    0.160: 4
  Chirality restraints: 1008
  Sorted by residual:
  chirality pdb=" CA  GLU A 716 "
            pdb=" N   GLU A 716 "
            pdb=" C   GLU A 716 "
            pdb=" CB  GLU A 716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CB  VAL A 332 "
            pdb=" CA  VAL A 332 "
            pdb=" CG1 VAL A 332 "
            pdb=" CG2 VAL A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CB  ILE A 439 "
            pdb=" CA  ILE A 439 "
            pdb=" CG1 ILE A 439 "
            pdb=" CG2 ILE A 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 1005 not shown)

  Planarity restraints: 984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 716 "    0.008 2.00e-02 2.50e+03   1.51e-02 2.29e+00
        pdb=" C   GLU A 716 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   GLU A 716 "    0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 717 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 381 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.14e+00
        pdb=" N   PRO A 382 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 382 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 382 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   8 "   -0.009 2.00e-02 2.50e+03   6.30e-03 8.92e-01
        pdb=" N1    U B   8 "    0.016 2.00e-02 2.50e+03
        pdb=" C2    U B   8 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2    U B   8 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U B   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U B   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4    U B   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    U B   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U B   8 "    0.000 2.00e-02 2.50e+03
  ... (remaining 981 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 211
        2.71 -     3.26: 5844
        3.26 -     3.81: 10420
        3.81 -     4.35: 13704
        4.35 -     4.90: 21731
  Nonbonded interactions: 51910
  Sorted by model distance:
  nonbonded pdb="MG    MG A1002 "
            pdb=" O2B ADP A1003 "
     model   vdw
     2.164 2.170
  nonbonded pdb=" O   CYS A 829 "
            pdb=" O2'   G B  10 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   SER A 378 "
            pdb=" ND2 ASN A 384 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NZ  LYS A 814 "
            pdb=" OE1 GLN A 902 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NZ  LYS A 458 "
            pdb=" OE2 GLU A 751 "
     model   vdw
     2.342 3.120
  ... (remaining 51905 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.860
  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:7.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
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   0.092   6368  Z= 0.130
  Angle     :  0.618  24.590   8766  Z= 0.297
  Chirality :  0.038   0.160   1008
  Planarity :  0.003   0.027    984
  Dihedral  : 16.456  83.078   2652
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.55 %
    Favored  : 88.44 %
  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 aren not related in a simple way.
  whole: -2.23 (0.28), residues: 665
  helix: -0.12 (0.27), residues: 316
  sheet: -2.08 (0.47), residues: 92
  loop : -2.99 (0.27), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 811 
 TYR   0.008   0.001   TYR A 390 
 PHE   0.008   0.001   PHE A 842 
 TRP   0.003   0.001   TRP A 908 
 HIS   0.002   0.000   HIS A 876 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 6364)
  covalent geometry    : angle       0.51497 ( 8760)
  hydrogen bonds       : bond        0.13589 (  304)
  hydrogen bonds       : angle       5.01460 (  842)
  metal coordination   : bond        0.07012 (    4)
  metal coordination   : angle      13.08373 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  369 MET cc_start: 0.9111 (mtm) cc_final: 0.8792 (mtm)
REVERT: A  385 MET cc_start: 0.8671 (mmm) cc_final: 0.8470 (mmp)
REVERT: A  492 ASP cc_start: 0.7216 (t70) cc_final: 0.6800 (t0)
REVERT: A  498 GLN cc_start: 0.7766 (mm110) cc_final: 0.7544 (mp10)
REVERT: A  560 MET cc_start: 0.8845 (mtt) cc_final: 0.8369 (mtt)
REVERT: A  761 MET cc_start: 0.8748 (ttp) cc_final: 0.8516 (ttm)
REVERT: A  786 HIS cc_start: 0.8184 (t70) cc_final: 0.7883 (t70)
  outliers start: 6
  outliers final: 4
  residues processed: 114
  average time/residue: 0.6185
  time to fit residues: 73.4569
Evaluate side-chains
  84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  457 GLN
Chi-restraints excluded: chain A residue  691 HIS
Chi-restraints excluded: chain A residue  800 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0770
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
A 393 GLN
A 517 GLN
A 588 GLN
A 708 GLN
A 769 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.129714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.109208 restraints weight = 6454.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.13
r_work: 0.3010 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6368  Z= 0.114
  Angle     :  0.509   6.223   8766  Z= 0.257
  Chirality :  0.039   0.155   1008
  Planarity :  0.003   0.030    984
  Dihedral  : 15.117  73.947   1292
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.23 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.30), residues: 665
  helix:  1.01 (0.28), residues: 321
  sheet: -1.66 (0.49), residues: 93
  loop : -2.52 (0.30), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 502 
 TYR   0.011   0.001   TYR A 390 
 PHE   0.008   0.001   PHE A 842 
 TRP   0.012   0.001   TRP A 771 
 HIS   0.003   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6364)
  covalent geometry    : angle       0.50047 ( 8760)
  hydrogen bonds       : bond        0.03699 (  304)
  hydrogen bonds       : angle       3.62151 (  842)
  metal coordination   : bond        0.00738 (    4)
  metal coordination   : angle       3.61945 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  369 MET cc_start: 0.9264 (mtm) cc_final: 0.8990 (mtm)
REVERT: A  385 MET cc_start: 0.8909 (mmm) cc_final: 0.8708 (mmp)
REVERT: A  425 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7923 (m-30)
REVERT: A  479 MET cc_start: 0.9262 (mtp) cc_final: 0.8884 (mtp)
REVERT: A  492 ASP cc_start: 0.7202 (t70) cc_final: 0.6662 (t0)
REVERT: A  498 GLN cc_start: 0.7993 (mm110) cc_final: 0.7519 (mp10)
REVERT: A  560 MET cc_start: 0.9009 (mtt) cc_final: 0.8517 (mtt)
REVERT: A  717 TYR cc_start: 0.8901 (t80) cc_final: 0.8691 (t80)
REVERT: A  761 MET cc_start: 0.8766 (ttp) cc_final: 0.8441 (ttm)
REVERT: A  786 HIS cc_start: 0.8352 (t70) cc_final: 0.8033 (t70)
REVERT: A  883 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6335 (tm-30)
REVERT: A  914 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7458 (tm-30)
  outliers start: 20
  outliers final: 8
  residues processed: 93
  average time/residue: 0.5389
  time to fit residues: 52.3783
Evaluate side-chains
  88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  883 GLU
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0000
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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 = 0.3331 r_free = 0.3331 target = 0.127057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.105957 restraints weight = 6449.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.16
r_work: 0.2968 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6368  Z= 0.146
  Angle     :  0.540   5.989   8766  Z= 0.271
  Chirality :  0.041   0.137   1008
  Planarity :  0.003   0.032    984
  Dihedral  : 15.053  77.509   1286
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 14.24 %
    Favored  : 82.08 %
  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 aren not related in a simple way.
  whole: -0.60 (0.31), residues: 665
  helix:  1.39 (0.29), residues: 321
  sheet: -1.46 (0.48), residues: 89
  loop : -2.42 (0.31), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 732 
 TYR   0.013   0.002   TYR A 390 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.013   0.002   TRP A 771 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6364)
  covalent geometry    : angle       0.53269 ( 8760)
  hydrogen bonds       : bond        0.03995 (  304)
  hydrogen bonds       : angle       3.62625 (  842)
  metal coordination   : bond        0.00622 (    4)
  metal coordination   : angle       3.42138 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  369 MET cc_start: 0.9195 (mtm) cc_final: 0.8908 (mtm)
REVERT: A  425 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8018 (m-30)
REVERT: A  492 ASP cc_start: 0.7211 (t70) cc_final: 0.6632 (t70)
REVERT: A  498 GLN cc_start: 0.7981 (mm110) cc_final: 0.7523 (mp10)
REVERT: A  560 MET cc_start: 0.9049 (mtt) cc_final: 0.8556 (mtt)
REVERT: A  679 LYS cc_start: 0.8542 (tttt) cc_final: 0.7539 (mttp)
REVERT: A  708 GLN cc_start: 0.8444 (mt0) cc_final: 0.8174 (mt0)
REVERT: A  761 MET cc_start: 0.8928 (ttp) cc_final: 0.8534 (ttm)
REVERT: A  786 HIS cc_start: 0.8357 (t70) cc_final: 0.8043 (t70)
REVERT: A  906 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8727 (p)
REVERT: A  914 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7515 (tm-30)
  outliers start: 22
  outliers final: 9
  residues processed: 87
  average time/residue: 0.5424
  time to fit residues: 49.3360
Evaluate side-chains
  86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  457 GLN
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 41 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.1180

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.127193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.106990 restraints weight = 6393.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.18
r_work: 0.2954 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6368  Z= 0.139
  Angle     :  0.532   5.913   8766  Z= 0.267
  Chirality :  0.040   0.145   1008
  Planarity :  0.003   0.034    984
  Dihedral  : 15.085  79.799   1286
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 13.90 %
    Favored  : 82.24 %
  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 aren not related in a simple way.
  whole: -0.32 (0.31), residues: 665
  helix:  1.61 (0.29), residues: 321
  sheet: -1.18 (0.51), residues: 89
  loop : -2.32 (0.31), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 533 
 TYR   0.014   0.002   TYR A 390 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.009   0.001   TRP A 771 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6364)
  covalent geometry    : angle       0.52563 ( 8760)
  hydrogen bonds       : bond        0.03859 (  304)
  hydrogen bonds       : angle       3.58094 (  842)
  metal coordination   : bond        0.00562 (    4)
  metal coordination   : angle       3.11128 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7726 (mtmm)
REVERT: A  369 MET cc_start: 0.9212 (mtm) cc_final: 0.8940 (mtm)
REVERT: A  425 ASP cc_start: 0.8329 (m-30) cc_final: 0.8028 (m-30)
REVERT: A  479 MET cc_start: 0.9231 (mtp) cc_final: 0.8889 (mtp)
REVERT: A  492 ASP cc_start: 0.7248 (t70) cc_final: 0.6633 (t70)
REVERT: A  498 GLN cc_start: 0.8096 (mm110) cc_final: 0.7579 (mp10)
REVERT: A  560 MET cc_start: 0.9070 (mtt) cc_final: 0.8564 (mtt)
REVERT: A  679 LYS cc_start: 0.8543 (tttt) cc_final: 0.7538 (mttp)
REVERT: A  708 GLN cc_start: 0.8407 (mt0) cc_final: 0.8139 (mt0)
REVERT: A  761 MET cc_start: 0.8919 (ttp) cc_final: 0.8492 (ttm)
REVERT: A  786 HIS cc_start: 0.8367 (t70) cc_final: 0.8061 (t70)
REVERT: A  906 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8770 (p)
REVERT: A  914 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7551 (tm-30)
  outliers start: 23
  outliers final: 11
  residues processed: 88
  average time/residue: 0.5197
  time to fit residues: 48.0276
Evaluate side-chains
  87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  457 GLN
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 44 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
A 867 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.125762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.106223 restraints weight = 6539.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 1.11
r_work: 0.2947 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6368  Z= 0.125
  Angle     :  0.519   6.461   8766  Z= 0.260
  Chirality :  0.040   0.139   1008
  Planarity :  0.003   0.035    984
  Dihedral  : 15.092  78.987   1286
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 13.90 %
    Favored  : 82.24 %
  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 aren not related in a simple way.
  whole: -0.02 (0.32), residues: 665
  helix:  1.83 (0.29), residues: 321
  sheet: -1.00 (0.50), residues: 101
  loop : -2.20 (0.33), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.015   0.001   TYR A 717 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.007   0.001   TRP A 771 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6364)
  covalent geometry    : angle       0.51321 ( 8760)
  hydrogen bonds       : bond        0.03675 (  304)
  hydrogen bonds       : angle       3.50170 (  842)
  metal coordination   : bond        0.00537 (    4)
  metal coordination   : angle       2.91886 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7719 (mtmm)
REVERT: A  425 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8029 (m-30)
REVERT: A  479 MET cc_start: 0.9226 (mtp) cc_final: 0.8895 (mtp)
REVERT: A  492 ASP cc_start: 0.7196 (t70) cc_final: 0.6328 (t0)
REVERT: A  560 MET cc_start: 0.9084 (mtt) cc_final: 0.8592 (mtt)
REVERT: A  679 LYS cc_start: 0.8579 (tttt) cc_final: 0.7590 (mttp)
REVERT: A  708 GLN cc_start: 0.8389 (mt0) cc_final: 0.8147 (mt0)
REVERT: A  761 MET cc_start: 0.8939 (ttp) cc_final: 0.8510 (ttm)
REVERT: A  786 HIS cc_start: 0.8385 (t70) cc_final: 0.8092 (t70)
REVERT: A  906 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8781 (p)
REVERT: A  914 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7524 (tm-30)
  outliers start: 23
  outliers final: 12
  residues processed: 92
  average time/residue: 0.5857
  time to fit residues: 56.4739
Evaluate side-chains
  90 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  457 GLN
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  899 THR
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   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 289 GLN
A 588 GLN
A 867 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.125296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.104295 restraints weight = 6475.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 1.15
r_work: 0.2930 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6368  Z= 0.161
  Angle     :  0.567   7.915   8766  Z= 0.282
  Chirality :  0.042   0.214   1008
  Planarity :  0.003   0.034    984
  Dihedral  : 15.146  85.360   1286
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.24 %
    Favored  : 81.41 %
  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 aren not related in a simple way.
  whole:  0.05 (0.32), residues: 665
  helix:  1.84 (0.29), residues: 321
  sheet: -0.80 (0.54), residues: 84
  loop : -2.09 (0.32), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.019   0.002   TYR A 717 
 PHE   0.010   0.001   PHE A 842 
 TRP   0.005   0.001   TRP A 771 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6364)
  covalent geometry    : angle       0.56149 ( 8760)
  hydrogen bonds       : bond        0.04108 (  304)
  hydrogen bonds       : angle       3.57087 (  842)
  metal coordination   : bond        0.00648 (    4)
  metal coordination   : angle       3.10390 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7774 (mtmm)
REVERT: A  425 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8026 (m-30)
REVERT: A  479 MET cc_start: 0.9190 (mtp) cc_final: 0.8855 (mtp)
REVERT: A  492 ASP cc_start: 0.7188 (t70) cc_final: 0.6311 (t0)
REVERT: A  560 MET cc_start: 0.9084 (mtt) cc_final: 0.8571 (mtt)
REVERT: A  679 LYS cc_start: 0.8525 (tttt) cc_final: 0.7541 (mttp)
REVERT: A  708 GLN cc_start: 0.8424 (mt0) cc_final: 0.8181 (mt0)
REVERT: A  761 MET cc_start: 0.8962 (ttp) cc_final: 0.8544 (ttm)
REVERT: A  786 HIS cc_start: 0.8348 (t70) cc_final: 0.8049 (t70)
REVERT: A  906 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8798 (p)
REVERT: A  914 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7440 (tm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 81
  average time/residue: 0.5291
  time to fit residues: 44.9604
Evaluate side-chains
  84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  899 THR
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0770
   chunk 37 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.5744

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 588 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.123756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.103090 restraints weight = 6469.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.14
r_work: 0.2960 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6368  Z= 0.176
  Angle     :  0.582   7.628   8766  Z= 0.289
  Chirality :  0.042   0.223   1008
  Planarity :  0.004   0.034    984
  Dihedral  : 15.213  92.579   1286
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.75 %
    Favored  : 80.90 %
  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 aren not related in a simple way.
  whole: -0.01 (0.32), residues: 665
  helix:  1.79 (0.29), residues: 321
  sheet: -0.88 (0.52), residues: 89
  loop : -2.12 (0.33), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 811 
 TYR   0.019   0.002   TYR A 717 
 PHE   0.010   0.001   PHE A 842 
 TRP   0.006   0.001   TRP A 908 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6364)
  covalent geometry    : angle       0.57590 ( 8760)
  hydrogen bonds       : bond        0.04267 (  304)
  hydrogen bonds       : angle       3.61396 (  842)
  metal coordination   : bond        0.00638 (    4)
  metal coordination   : angle       3.15486 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7748 (mtmm)
REVERT: A  425 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8033 (m-30)
REVERT: A  479 MET cc_start: 0.9192 (mtp) cc_final: 0.8891 (mtp)
REVERT: A  492 ASP cc_start: 0.7236 (t70) cc_final: 0.6368 (t0)
REVERT: A  560 MET cc_start: 0.9094 (mtt) cc_final: 0.8607 (mtt)
REVERT: A  679 LYS cc_start: 0.8565 (tttt) cc_final: 0.7615 (mttp)
REVERT: A  708 GLN cc_start: 0.8406 (mt0) cc_final: 0.8155 (mt0)
REVERT: A  761 MET cc_start: 0.8995 (ttp) cc_final: 0.8514 (ttm)
REVERT: A  786 HIS cc_start: 0.8370 (t70) cc_final: 0.8074 (t70)
REVERT: A  906 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8800 (p)
REVERT: A  914 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7373 (tm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 83
  average time/residue: 0.5609
  time to fit residues: 48.8397
Evaluate side-chains
  81 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  899 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    0.0770
   chunk 65 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 588 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.126295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.106900 restraints weight = 6507.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 1.06
r_work: 0.2954 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6368  Z= 0.109
  Angle     :  0.518   7.762   8766  Z= 0.258
  Chirality :  0.039   0.205   1008
  Planarity :  0.003   0.036    984
  Dihedral  : 15.142  84.626   1285
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.75 %
    Favored  : 81.07 %
  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 aren not related in a simple way.
  whole:  0.41 (0.33), residues: 665
  helix:  2.10 (0.29), residues: 321
  sheet: -0.57 (0.53), residues: 96
  loop : -1.92 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.014   0.001   TYR A 717 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.006   0.001   TRP A 771 
 HIS   0.002   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6364)
  covalent geometry    : angle       0.51275 ( 8760)
  hydrogen bonds       : bond        0.03482 (  304)
  hydrogen bonds       : angle       3.46154 (  842)
  metal coordination   : bond        0.00483 (    4)
  metal coordination   : angle       2.87289 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7755 (mtmm)
REVERT: A  425 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8016 (m-30)
REVERT: A  479 MET cc_start: 0.9237 (mtp) cc_final: 0.8874 (mtp)
REVERT: A  491 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6941 (tppt)
REVERT: A  492 ASP cc_start: 0.7127 (t70) cc_final: 0.6232 (t0)
REVERT: A  560 MET cc_start: 0.9075 (mtt) cc_final: 0.8603 (mtt)
REVERT: A  679 LYS cc_start: 0.8544 (tttt) cc_final: 0.7564 (mttp)
REVERT: A  708 GLN cc_start: 0.8390 (mt0) cc_final: 0.8155 (mt0)
REVERT: A  761 MET cc_start: 0.8936 (ttp) cc_final: 0.8552 (ttm)
REVERT: A  786 HIS cc_start: 0.8373 (t70) cc_final: 0.8042 (t70)
REVERT: A  906 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8778 (p)
REVERT: A  914 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7190 (tt0)
  outliers start: 19
  outliers final: 10
  residues processed: 84
  average time/residue: 0.5902
  time to fit residues: 51.9833
Evaluate side-chains
  84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  899 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0770
   chunk 67 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 588 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.126820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.106170 restraints weight = 6424.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.14
r_work: 0.2975 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6368  Z= 0.128
  Angle     :  0.538   8.106   8766  Z= 0.267
  Chirality :  0.040   0.204   1008
  Planarity :  0.003   0.035    984
  Dihedral  : 15.149  85.845   1285
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.58 %
    Favored  : 80.90 %
  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 aren not related in a simple way.
  whole:  0.42 (0.32), residues: 665
  helix:  2.08 (0.29), residues: 321
  sheet: -0.53 (0.53), residues: 96
  loop : -1.88 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.017   0.002   TYR A 717 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.005   0.001   TRP A 771 
 HIS   0.002   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6364)
  covalent geometry    : angle       0.53288 ( 8760)
  hydrogen bonds       : bond        0.03686 (  304)
  hydrogen bonds       : angle       3.46279 (  842)
  metal coordination   : bond        0.00534 (    4)
  metal coordination   : angle       2.91646 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7305 (mmtm)
REVERT: A  425 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7999 (m-30)
REVERT: A  479 MET cc_start: 0.9208 (mtp) cc_final: 0.8840 (mtp)
REVERT: A  491 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6742 (mppt)
REVERT: A  492 ASP cc_start: 0.7118 (t70) cc_final: 0.6221 (t0)
REVERT: A  560 MET cc_start: 0.9071 (mtt) cc_final: 0.8560 (mtt)
REVERT: A  679 LYS cc_start: 0.8518 (tttt) cc_final: 0.7511 (mttp)
REVERT: A  708 GLN cc_start: 0.8425 (mt0) cc_final: 0.8178 (mt0)
REVERT: A  761 MET cc_start: 0.8934 (ttp) cc_final: 0.8540 (ttm)
REVERT: A  786 HIS cc_start: 0.8348 (t70) cc_final: 0.8013 (t70)
REVERT: A  906 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8770 (p)
REVERT: A  914 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7144 (tt0)
  outliers start: 21
  outliers final: 12
  residues processed: 83
  average time/residue: 0.5500
  time to fit residues: 47.8922
Evaluate side-chains
  86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  488 ARG
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  899 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0670
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 595 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.129697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.110350 restraints weight = 6452.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.13
r_work: 0.2972 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6368  Z= 0.106
  Angle     :  0.519   8.222   8766  Z= 0.258
  Chirality :  0.039   0.202   1008
  Planarity :  0.003   0.036    984
  Dihedral  : 15.123  80.973   1285
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.42 %
    Favored  : 80.90 %
  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 aren not related in a simple way.
  whole:  0.56 (0.32), residues: 665
  helix:  2.19 (0.29), residues: 322
  sheet: -0.49 (0.53), residues: 96
  loop : -1.83 (0.34), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.017   0.001   TYR A 717 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.006   0.001   TRP A 771 
 HIS   0.002   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6364)
  covalent geometry    : angle       0.51394 ( 8760)
  hydrogen bonds       : bond        0.03373 (  304)
  hydrogen bonds       : angle       3.40128 (  842)
  metal coordination   : bond        0.00437 (    4)
  metal coordination   : angle       2.71933 (    6)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7283 (mmtm)
REVERT: A  425 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8015 (m-30)
REVERT: A  479 MET cc_start: 0.9226 (mtp) cc_final: 0.8852 (mtp)
REVERT: A  491 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6920 (mppt)
REVERT: A  492 ASP cc_start: 0.7023 (t70) cc_final: 0.6095 (t0)
REVERT: A  560 MET cc_start: 0.9072 (mtt) cc_final: 0.8604 (mtt)
REVERT: A  679 LYS cc_start: 0.8506 (tttt) cc_final: 0.7497 (mttp)
REVERT: A  708 GLN cc_start: 0.8377 (mt0) cc_final: 0.8130 (mt0)
REVERT: A  761 MET cc_start: 0.8889 (ttp) cc_final: 0.8547 (ttm)
REVERT: A  786 HIS cc_start: 0.8345 (t70) cc_final: 0.8011 (t70)
REVERT: A  906 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8766 (p)
REVERT: A  914 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7185 (tt0)
  outliers start: 16
  outliers final: 10
  residues processed: 81
  average time/residue: 0.5498
  time to fit residues: 46.6582
Evaluate side-chains
  86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  645 ASN
Chi-restraints excluded: chain A residue  671 THR
Chi-restraints excluded: chain A residue  697 THR
Chi-restraints excluded: chain A residue  899 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  914 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0020
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
A 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.126183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.107016 restraints weight = 6451.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.09
r_work: 0.2960 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6368  Z= 0.125
  Angle     :  0.537   8.152   8766  Z= 0.266
  Chirality :  0.040   0.199   1008
  Planarity :  0.003   0.035    984
  Dihedral  : 15.121  82.331   1285
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.75 %
    Favored  : 80.40 %
  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 aren not related in a simple way.
  whole:  0.52 (0.32), residues: 665
  helix:  2.14 (0.28), residues: 322
  sheet: -0.51 (0.53), residues: 96
  loop : -1.83 (0.34), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.020   0.002   TYR A 717 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.005   0.001   TRP A 771 
 HIS   0.002   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6364)
  covalent geometry    : angle       0.53231 ( 8760)
  hydrogen bonds       : bond        0.03611 (  304)
  hydrogen bonds       : angle       3.42686 (  842)
  metal coordination   : bond        0.00506 (    4)
  metal coordination   : angle       2.64412 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1984.26 seconds
wall clock time: 34 minutes 35.26 seconds (2075.26 seconds total)