Starting phenix.real_space_refine
on Wed Sep 17 14:09:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z0p_39710/09_2025/8z0p_39710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z0p_39710/09_2025/8z0p_39710.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z0p_39710/09_2025/8z0p_39710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z0p_39710/09_2025/8z0p_39710.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z0p_39710/09_2025/8z0p_39710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z0p_39710/09_2025/8z0p_39710.map"
  }
  resolution = 3.1
  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=  -0.001 sd=   0.020
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      2      6.06       5
     P       1      5.49       5
     S      34      5.16       5
     C    2944      2.51       5
     N     800      2.21       5
     O     838      1.98       5
     H    4627      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9246
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 9239
          Classifications: {'peptide': 586}
          Link IDs: {'PTRANS': 34, 'TRANS': 551}
          Chain breaks: 6
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 7
          Unusual residues: {' ZN': 2, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.62, per 1000 atoms: 0.18
  Number of scatterers: 9246
  At special positions: 0
  Unit cell: (67.854, 74.166, 93.628, 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      2     29.99
     S      34     16.00
     P       1     15.00
     O     838      8.00
     N     800      7.00
     C    2944      6.00
     H    4627      1.00
    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: 0.59
  Conformation dependent library (CDL) restraints added in 293.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" ND1 HIS A 548 "
      pdb="  ZN A 902 "
        pdb="ZN    ZN A 902 " - pdb=" NE2 HIS A 551 "
        pdb="ZN    ZN A 902 " - pdb=" NE2 HIS A 724 "


  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1110

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 7 sheets defined
      32.9% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 114 through 119
    Processing helix  chain 'A' and resid 120 through 130
      removed outlier: 3.890A  pdb=" N   LEU A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 156
      removed outlier: 4.267A  pdb=" N   ILE A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   PHE A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLY A 156 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 315
      No H-bonds generated for 'chain 'A' and resid 313 through 315'
    Processing helix  chain 'A' and resid 316 through 322
    Processing helix  chain 'A' and resid 324 through 329
      removed outlier: 3.848A  pdb=" N   ARG A 328 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 351
      removed outlier: 4.428A  pdb=" N   VAL A 350 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ASP A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 391
    Processing helix  chain 'A' and resid 442 through 451
    Processing helix  chain 'A' and resid 455 through 467
    Processing helix  chain 'A' and resid 519 through 529
    Processing helix  chain 'A' and resid 531 through 536
    Processing helix  chain 'A' and resid 554 through 569
    Processing helix  chain 'A' and resid 583 through 595
      removed outlier: 4.302A  pdb=" N   TRP A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 600
      No H-bonds generated for 'chain 'A' and resid 598 through 600'
    Processing helix  chain 'A' and resid 608 through 611
      removed outlier: 3.739A  pdb=" N   GLN A 611 " --> pdb=" O   LYS A 608 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 608 through 611'
    Processing helix  chain 'A' and resid 620 through 632
      removed outlier: 3.713A  pdb=" N   LEU A 624 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   CYS A 632 " --> pdb=" O   LEU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 676
      removed outlier: 3.643A  pdb=" N   ARG A 675 " --> pdb=" O   GLU A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 700
    Processing helix  chain 'A' and resid 704 through 715
    Processing helix  chain 'A' and resid 755 through 757
      No H-bonds generated for 'chain 'A' and resid 755 through 757'
    Processing helix  chain 'A' and resid 759 through 762
    Processing helix  chain 'A' and resid 763 through 771
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 75
      removed outlier: 6.468A  pdb=" N   ALA A  73 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   LEU A  60 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LYS A 424 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109
    Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 185
    Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 310
      removed outlier: 6.210A  pdb=" N   VAL A 340 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   HIS A 367 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 510 through 512
      removed outlier: 6.455A  pdb=" N   THR A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ALA A 501 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   MET A 750 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 543
      removed outlier: 6.367A  pdb=" N   VAL A 542 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   LEU A 576 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ILE A 605 " --> pdb=" O   LEU A 576 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL A 578 " --> pdb=" O   ILE A 605 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 634 through 641
      removed outlier: 7.165A  pdb=" N   VAL A 654 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   PHE A 637 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ALA A 652 " --> pdb=" O   PHE A 637 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   THR A 639 " --> pdb=" O   GLY A 650 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   GLY A 650 " --> pdb=" O   THR A 639 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LYS A 660 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   ILE A 684 " --> pdb=" O   LYS A 660 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL A 662 " --> pdb=" O   ILE A 684 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   GLU A 686 " --> pdb=" O   VAL A 662 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    387 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4609
        1.03 -     1.22: 18
        1.22 -     1.42: 1940
        1.42 -     1.61: 2730
        1.61 -     1.81: 50
  Bond restraints: 9347
  Sorted by residual:
  bond pdb=" N   THR A  57 "
       pdb=" CA  THR A  57 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   THR A  57 "
       pdb=" H   THR A  57 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.37e+00
  bond pdb=" N   HIS A 644 "
       pdb=" CA  HIS A 644 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.14e+00
  bond pdb=" CA  THR A 701 "
       pdb=" C   THR A 701 "
    ideal  model  delta    sigma   weight residual
    1.530  1.518  0.012 1.10e-02 8.26e+03 1.14e+00
  bond pdb=" CA  GLU A 174 "
       pdb=" C   GLU A 174 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.009 9.60e-03 1.09e+04 8.93e-01
  ... (remaining 9342 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 16463
        1.55 -     3.11: 417
        3.11 -     4.66: 39
        4.66 -     6.22: 3
        6.22 -     7.77: 1
  Bond angle restraints: 16923
  Sorted by residual:
  angle pdb=" N   GLU A 176 "
        pdb=" CA  GLU A 176 "
        pdb=" CB  GLU A 176 "
      ideal   model   delta    sigma   weight residual
     114.17  109.02    5.15 1.14e+00 7.69e-01 2.04e+01
  angle pdb=" C   LEU A 514 "
        pdb=" CA  LEU A 514 "
        pdb=" CB  LEU A 514 "
      ideal   model   delta    sigma   weight residual
     116.34  110.86    5.48 1.40e+00 5.10e-01 1.53e+01
  angle pdb=" N   SER A 352 "
        pdb=" CA  SER A 352 "
        pdb=" C   SER A 352 "
      ideal   model   delta    sigma   weight residual
     113.18  108.81    4.37 1.33e+00 5.65e-01 1.08e+01
  angle pdb=" C   LYS A 495 "
        pdb=" N   ILE A 496 "
        pdb=" CA  ILE A 496 "
      ideal   model   delta    sigma   weight residual
     123.16  119.84    3.32 1.06e+00 8.90e-01 9.83e+00
  angle pdb=" N   LYS A 146 "
        pdb=" CA  LYS A 146 "
        pdb=" C   LYS A 146 "
      ideal   model   delta    sigma   weight residual
     113.41  109.59    3.82 1.22e+00 6.72e-01 9.80e+00
  ... (remaining 16918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3949
       17.95 -    35.91: 322
       35.91 -    53.86: 114
       53.86 -    71.81: 23
       71.81 -    89.77: 7
  Dihedral angle restraints: 4415
    sinusoidal: 2409
      harmonic: 2006
  Sorted by residual:
  dihedral pdb=" CA  MET A 178 "
           pdb=" C   MET A 178 "
           pdb=" N   THR A 179 "
           pdb=" CA  THR A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.69   25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  LYS A 146 "
           pdb=" C   LYS A 146 "
           pdb=" N   TYR A 147 "
           pdb=" CA  TYR A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.29   23.71     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  THR A 177 "
           pdb=" C   THR A 177 "
           pdb=" N   MET A 178 "
           pdb=" CA  MET A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.10   21.90     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 4412 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 427
       0.028 -    0.056: 181
       0.056 -    0.084: 56
       0.084 -    0.112: 48
       0.112 -    0.140: 16
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  VAL A 732 "
            pdb=" N   VAL A 732 "
            pdb=" C   VAL A 732 "
            pdb=" CB  VAL A 732 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  ILE A 605 "
            pdb=" N   ILE A 605 "
            pdb=" C   ILE A 605 "
            pdb=" CB  ILE A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  VAL A  76 "
            pdb=" N   VAL A  76 "
            pdb=" C   VAL A  76 "
            pdb=" CB  VAL A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 725 not shown)

  Planarity restraints: 1367
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 145 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   GLU A 145 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLU A 145 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS A 146 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 764 "   -0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO A 765 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 765 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 765 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 133 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.81e+00
        pdb=" N   PRO A 134 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 134 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 134 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1364 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.17: 427
        2.17 -     2.78: 18029
        2.78 -     3.39: 24986
        3.39 -     3.99: 32269
        3.99 -     4.60: 50580
  Nonbonded interactions: 126291
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 344 "
            pdb="HD21 ASN A 371 "
     model   vdw
     1.566 2.450
  nonbonded pdb=" OE1 GLU A  89 "
            pdb=" HG  SER A 557 "
     model   vdw
     1.618 2.450
  nonbonded pdb="HE21 GLN A 318 "
            pdb=" OE1 GLU A 322 "
     model   vdw
     1.619 2.450
  nonbonded pdb=" OD1 ASN A  86 "
            pdb="HD21 ASN A 117 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" O   GLU A 130 "
            pdb=" HG1 THR A 131 "
     model   vdw
     1.642 2.450
  ... (remaining 126286 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.960
  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:             0.060
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.530
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
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      :  0.010   0.620   4723  Z= 0.349
  Angle     :  0.677   7.771   6399  Z= 0.394
  Chirality :  0.043   0.140    728
  Planarity :  0.004   0.035    820
  Dihedral  : 15.657  89.767   1739
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  7.52 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 12.50 %
    Favored  : 86.33 %
  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: -1.15 (0.36), residues: 572
  helix: -0.16 (0.43), residues: 169
  sheet:  0.14 (0.45), residues: 121
  loop : -1.55 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 465 
 TYR   0.010   0.002   TYR A 329 
 PHE   0.016   0.002   PHE A 397 
 TRP   0.012   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 644 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4720)
  covalent geometry    : angle       0.67717 ( 6399)
  hydrogen bonds       : bond        0.19398 (  136)
  hydrogen bonds       : angle       7.40235 (  387)
  metal coordination   : bond        0.37142 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 PHE cc_start: 0.7915 (m-10) cc_final: 0.7584 (m-10)
REVERT: A  623 ARG cc_start: 0.4130 (OUTLIER) cc_final: 0.3554 (ptm-80)
  outliers start: 6
  outliers final: 5
  residues processed: 70
  average time/residue: 0.1821
  time to fit residues: 15.5352
Evaluate side-chains
  69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  623 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 707 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.207774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.189679 restraints weight = 15265.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 2.00
r_work: 0.4123 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3995 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.0792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4723  Z= 0.105
  Angle     :  0.567   7.492   6399  Z= 0.298
  Chirality :  0.043   0.155    728
  Planarity :  0.004   0.033    820
  Dihedral  :  5.992  40.692    633
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  7.34 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 13.28 %
    Favored  : 86.13 %
  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: -0.88 (0.37), residues: 572
  helix:  0.42 (0.44), residues: 165
  sheet:  0.13 (0.46), residues: 119
  loop : -1.51 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  68 
 TYR   0.007   0.001   TYR A 329 
 PHE   0.011   0.001   PHE A 306 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4720)
  covalent geometry    : angle       0.56748 ( 6399)
  hydrogen bonds       : bond        0.03942 (  136)
  hydrogen bonds       : angle       5.65254 (  387)
  metal coordination   : bond        0.00996 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.7491 (p0) cc_final: 0.7222 (p0)
REVERT: A  397 PHE cc_start: 0.7961 (m-80) cc_final: 0.7591 (m-10)
REVERT: A  630 ARG cc_start: 0.7097 (tmm-80) cc_final: 0.6599 (ttp80)
  outliers start: 3
  outliers final: 1
  residues processed: 69
  average time/residue: 0.1692
  time to fit residues: 14.7069
Evaluate side-chains
  62 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 56 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.199434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.181933 restraints weight = 15729.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 1.98
r_work: 0.4052 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4723  Z= 0.147
  Angle     :  0.595   7.848   6399  Z= 0.314
  Chirality :  0.045   0.145    728
  Planarity :  0.004   0.037    820
  Dihedral  :  5.457  26.278    622
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  9.27 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.28 %
    Favored  : 84.77 %
  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: -1.04 (0.37), residues: 572
  helix:  0.45 (0.44), residues: 160
  sheet: -0.23 (0.48), residues: 112
  loop : -1.53 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 623 
 TYR   0.009   0.002   TYR A 480 
 PHE   0.016   0.002   PHE A 306 
 TRP   0.009   0.002   TRP A 659 
 HIS   0.006   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4720)
  covalent geometry    : angle       0.59539 ( 6399)
  hydrogen bonds       : bond        0.03928 (  136)
  hydrogen bonds       : angle       5.24792 (  387)
  metal coordination   : bond        0.00500 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.7432 (p0) cc_final: 0.7192 (p0)
REVERT: A  143 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.6140 (mp10)
REVERT: A  306 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6548 (m-80)
REVERT: A  416 MET cc_start: 0.7211 (tmm) cc_final: 0.6824 (ttt)
REVERT: A  623 ARG cc_start: 0.4551 (OUTLIER) cc_final: 0.3903 (ptm-80)
REVERT: A  630 ARG cc_start: 0.7131 (tmm-80) cc_final: 0.6753 (ttp80)
  outliers start: 10
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1738
  time to fit residues: 16.4945
Evaluate side-chains
  70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  306 PHE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  654 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.201564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.184296 restraints weight = 15731.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4159 rms_B_bonded: 1.97
r_work: 0.4076 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3949 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4723  Z= 0.100
  Angle     :  0.539   7.125   6399  Z= 0.281
  Chirality :  0.043   0.144    728
  Planarity :  0.004   0.036    820
  Dihedral  :  5.063  22.021    621
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  7.87 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 15.23 %
    Favored  : 83.59 %
  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: -0.83 (0.37), residues: 572
  helix:  0.79 (0.45), residues: 159
  sheet: -0.10 (0.48), residues: 112
  loop : -1.51 (0.39), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 623 
 TYR   0.006   0.001   TYR A  75 
 PHE   0.012   0.001   PHE A 306 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 4720)
  covalent geometry    : angle       0.53854 ( 6399)
  hydrogen bonds       : bond        0.03016 (  136)
  hydrogen bonds       : angle       4.97311 (  387)
  metal coordination   : bond        0.00077 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  416 MET cc_start: 0.7061 (tmm) cc_final: 0.6788 (ttt)
REVERT: A  465 ARG cc_start: 0.5565 (mtm-85) cc_final: 0.5346 (mtm180)
REVERT: A  495 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7419 (ptpt)
REVERT: A  630 ARG cc_start: 0.7081 (tmm-80) cc_final: 0.6721 (ttp80)
  outliers start: 6
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1848
  time to fit residues: 14.5535
Evaluate side-chains
  63 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  667 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.4292 r_free = 0.4292 target = 0.197665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.180712 restraints weight = 15769.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 1.96
r_work: 0.4042 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3916 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4723  Z= 0.121
  Angle     :  0.555   7.686   6399  Z= 0.289
  Chirality :  0.044   0.141    728
  Planarity :  0.004   0.037    820
  Dihedral  :  5.062  24.288    621
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  9.62 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.45 %
    Favored  : 83.59 %
  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: -0.90 (0.37), residues: 572
  helix:  0.89 (0.44), residues: 160
  sheet: -0.26 (0.48), residues: 114
  loop : -1.61 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  68 
 TYR   0.007   0.001   TYR A 480 
 PHE   0.014   0.001   PHE A 306 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.006   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4720)
  covalent geometry    : angle       0.55465 ( 6399)
  hydrogen bonds       : bond        0.03252 (  136)
  hydrogen bonds       : angle       4.87957 (  387)
  metal coordination   : bond        0.00115 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.7434 (p0) cc_final: 0.7206 (p0)
REVERT: A  116 SER cc_start: 0.8372 (t) cc_final: 0.8158 (p)
REVERT: A  465 ARG cc_start: 0.5657 (mtm-85) cc_final: 0.5436 (mtm-85)
REVERT: A  495 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7360 (ptpt)
REVERT: A  623 ARG cc_start: 0.4804 (OUTLIER) cc_final: 0.4214 (ptt90)
REVERT: A  630 ARG cc_start: 0.7051 (tmm-80) cc_final: 0.6722 (ttp80)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 0.1667
  time to fit residues: 14.9098
Evaluate side-chains
  72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  667 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 25 optimal weight:    0.3980
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.201574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.184478 restraints weight = 15548.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 1.93
r_work: 0.4068 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3944 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4723  Z= 0.109
  Angle     :  0.543   9.601   6399  Z= 0.280
  Chirality :  0.043   0.146    728
  Planarity :  0.004   0.036    820
  Dihedral  :  4.944  20.670    621
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  7.87 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.65 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.96 (0.37), residues: 572
  helix:  0.79 (0.44), residues: 165
  sheet: -0.29 (0.48), residues: 113
  loop : -1.66 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 623 
 TYR   0.006   0.001   TYR A  75 
 PHE   0.012   0.001   PHE A 306 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4720)
  covalent geometry    : angle       0.54321 ( 6399)
  hydrogen bonds       : bond        0.02983 (  136)
  hydrogen bonds       : angle       4.75624 (  387)
  metal coordination   : bond        0.00154 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 SER cc_start: 0.8403 (t) cc_final: 0.8200 (p)
REVERT: A  465 ARG cc_start: 0.5703 (mtm-85) cc_final: 0.5498 (mtm-85)
REVERT: A  495 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7334 (ptmm)
REVERT: A  623 ARG cc_start: 0.4829 (OUTLIER) cc_final: 0.4242 (ptt90)
REVERT: A  630 ARG cc_start: 0.7000 (tmm-80) cc_final: 0.6675 (ttp80)
  outliers start: 11
  outliers final: 7
  residues processed: 66
  average time/residue: 0.1873
  time to fit residues: 15.2093
Evaluate side-chains
  65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  667 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0670
   chunk 16 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.197762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.180961 restraints weight = 15731.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.4122 rms_B_bonded: 1.91
r_work: 0.4036 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3910 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4723  Z= 0.139
  Angle     :  0.570   8.327   6399  Z= 0.297
  Chirality :  0.044   0.144    728
  Planarity :  0.004   0.037    820
  Dihedral  :  5.122  23.695    621
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  9.44 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.45 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.14 (0.37), residues: 572
  helix:  0.61 (0.44), residues: 166
  sheet: -0.62 (0.49), residues: 119
  loop : -1.66 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 623 
 TYR   0.007   0.001   TYR A 480 
 PHE   0.015   0.001   PHE A 306 
 TRP   0.009   0.001   TRP A 659 
 HIS   0.006   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4720)
  covalent geometry    : angle       0.56972 ( 6399)
  hydrogen bonds       : bond        0.03437 (  136)
  hydrogen bonds       : angle       4.86366 (  387)
  metal coordination   : bond        0.00158 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 ARG cc_start: 0.5778 (mtm-85) cc_final: 0.5573 (mtm-85)
REVERT: A  495 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7317 (ptmm)
REVERT: A  623 ARG cc_start: 0.5107 (OUTLIER) cc_final: 0.4484 (ptt90)
REVERT: A  630 ARG cc_start: 0.6989 (tmm-80) cc_final: 0.6685 (ttp80)
  outliers start: 14
  outliers final: 10
  residues processed: 73
  average time/residue: 0.2091
  time to fit residues: 18.3220
Evaluate side-chains
  78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  667 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4317 r_free = 0.4317 target = 0.200446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.183481 restraints weight = 15649.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.4142 rms_B_bonded: 1.92
r_work: 0.4058 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3932 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4723  Z= 0.101
  Angle     :  0.536   8.076   6399  Z= 0.277
  Chirality :  0.043   0.142    728
  Planarity :  0.004   0.036    820
  Dihedral  :  4.908  20.661    621
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  7.87 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.84 %
    Favored  : 83.01 %
  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: -1.00 (0.37), residues: 572
  helix:  0.80 (0.44), residues: 166
  sheet: -0.61 (0.47), residues: 123
  loop : -1.60 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 328 
 TYR   0.009   0.001   TYR A 329 
 PHE   0.011   0.001   PHE A 306 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 4720)
  covalent geometry    : angle       0.53626 ( 6399)
  hydrogen bonds       : bond        0.02903 (  136)
  hydrogen bonds       : angle       4.69310 (  387)
  metal coordination   : bond        0.00079 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6977 (mp10)
REVERT: A  465 ARG cc_start: 0.5785 (mtm-85) cc_final: 0.5583 (mtm-85)
REVERT: A  495 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7290 (ptmm)
REVERT: A  623 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.4450 (ptt90)
REVERT: A  630 ARG cc_start: 0.6960 (tmm-80) cc_final: 0.6658 (ttp80)
  outliers start: 11
  outliers final: 7
  residues processed: 69
  average time/residue: 0.2168
  time to fit residues: 18.0748
Evaluate side-chains
  67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  667 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
A 418 GLN
A 596 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.201321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.184193 restraints weight = 15740.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 1.94
r_work: 0.4071 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3943 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4723  Z= 0.094
  Angle     :  0.533   7.965   6399  Z= 0.273
  Chirality :  0.043   0.141    728
  Planarity :  0.004   0.036    820
  Dihedral  :  4.808  21.870    621
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  8.39 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.23 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.89 (0.38), residues: 572
  helix:  0.93 (0.45), residues: 166
  sheet: -0.54 (0.48), residues: 123
  loop : -1.56 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 328 
 TYR   0.007   0.001   TYR A  75 
 PHE   0.010   0.001   PHE A 306 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.003   0.001   HIS A 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 4720)
  covalent geometry    : angle       0.53305 ( 6399)
  hydrogen bonds       : bond        0.02684 (  136)
  hydrogen bonds       : angle       4.58441 (  387)
  metal coordination   : bond        0.00079 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6911 (mp10)
REVERT: A  495 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7257 (ptmm)
REVERT: A  623 ARG cc_start: 0.5081 (OUTLIER) cc_final: 0.4477 (ptt90)
REVERT: A  630 ARG cc_start: 0.6955 (tmm-80) cc_final: 0.6664 (ttp80)
  outliers start: 10
  outliers final: 6
  residues processed: 68
  average time/residue: 0.2148
  time to fit residues: 17.7334
Evaluate side-chains
  71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  667 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 434 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.195173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.178578 restraints weight = 15596.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.4092 rms_B_bonded: 1.88
r_work: 0.4010 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3883 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4723  Z= 0.173
  Angle     :  0.611   7.908   6399  Z= 0.320
  Chirality :  0.045   0.154    728
  Planarity :  0.004   0.037    820
  Dihedral  :  5.247  21.755    621
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  8.92 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.23 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.32 (0.37), residues: 572
  helix:  0.35 (0.43), residues: 173
  sheet: -0.63 (0.49), residues: 119
  loop : -1.78 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 328 
 TYR   0.009   0.002   TYR A 591 
 PHE   0.016   0.002   PHE A 306 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.006   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4720)
  covalent geometry    : angle       0.61060 ( 6399)
  hydrogen bonds       : bond        0.03757 (  136)
  hydrogen bonds       : angle       4.87922 (  387)
  metal coordination   : bond        0.00351 (    3)

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

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

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1144 Ramachandran restraints generated.
    572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6973 (mp10)
REVERT: A  495 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7338 (ptmm)
REVERT: A  623 ARG cc_start: 0.5341 (OUTLIER) cc_final: 0.4711 (ptt90)
REVERT: A  630 ARG cc_start: 0.6982 (tmm-80) cc_final: 0.6680 (ttp80)
REVERT: A  699 GLU cc_start: 0.7694 (tt0) cc_final: 0.7287 (tt0)
  outliers start: 10
  outliers final: 7
  residues processed: 68
  average time/residue: 0.2092
  time to fit residues: 17.1162
Evaluate side-chains
  72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  667 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 596 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.196586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.180515 restraints weight = 15492.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.4114 rms_B_bonded: 1.78
r_work: 0.4029 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3909 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4723  Z= 0.137
  Angle     :  0.577   8.027   6399  Z= 0.301
  Chirality :  0.044   0.143    728
  Planarity :  0.004   0.037    820
  Dihedral  :  5.202  22.731    621
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  9.62 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.62 %
    Favored  : 82.23 %
  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 aren not related in a simple way.
  whole: -1.49 (0.36), residues: 572
  helix:  0.19 (0.42), residues: 179
  sheet: -0.66 (0.49), residues: 119
  loop : -1.96 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 328 
 TYR   0.007   0.001   TYR A  75 
 PHE   0.014   0.001   PHE A 306 
 TRP   0.009   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4720)
  covalent geometry    : angle       0.57729 ( 6399)
  hydrogen bonds       : bond        0.03405 (  136)
  hydrogen bonds       : angle       4.81774 (  387)
  metal coordination   : bond        0.00128 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2647.64 seconds
wall clock time: 45 minutes 36.82 seconds (2736.82 seconds total)