Starting phenix.real_space_refine
on Wed Sep 17 07:07:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k6p_62131/09_2025/9k6p_62131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k6p_62131/09_2025/9k6p_62131.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k6p_62131/09_2025/9k6p_62131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k6p_62131/09_2025/9k6p_62131.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k6p_62131/09_2025/9k6p_62131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k6p_62131/09_2025/9k6p_62131.map"
  }
  resolution = 3.2
  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=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     P      19      5.49       5
     S      40      5.16       5
     C    4107      2.51       5
     N    1177      2.21       5
     O    1233      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 6576
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 772, 6172
          Classifications: {'peptide': 772}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 726}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 215
          Classifications: {'RNA': 10}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 2, 'rna3p': 7}
    Chain: "C"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 189
          Classifications: {'RNA': 9}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 2, 'rna3p': 6}
  Time building chain proxies: 1.72, per 1000 atoms: 0.26
  Number of scatterers: 6576
  At special positions: 0
  Unit cell: (70.68, 91.2, 106.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P      19     15.00
     O    1233      8.00
     N    1177      7.00
     C    4107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 455 " - pdb=" SG  CYS A 462 " distance=2.03

  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: 0.55
  Conformation dependent library (CDL) restraints added in 297.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1454

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      32.8% alpha, 15.5% beta
      6 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 82 through 87
      removed outlier: 3.645A  pdb=" N   ILE A  86 " --> pdb=" O   PHE A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 156 through 166
      removed outlier: 4.151A  pdb=" N   MET A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 174
      removed outlier: 3.662A  pdb=" N   MET A 172 " --> pdb=" O   HIS A 168 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ARG A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 251 through 262
      removed outlier: 4.415A  pdb=" N   ARG A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 369
      removed outlier: 4.183A  pdb=" N   THR A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 386
    Processing helix  chain 'A' and resid 391 through 397
    Processing helix  chain 'A' and resid 463 through 481
    Processing helix  chain 'A' and resid 501 through 512
      removed outlier: 3.510A  pdb=" N   PHE A 505 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   TYR A 512 " --> pdb=" O   LEU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 539
      removed outlier: 3.858A  pdb=" N   ALA A 530 " --> pdb=" O   THR A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 572
      removed outlier: 3.965A  pdb=" N   LEU A 563 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL A 569 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LEU A 571 " --> pdb=" O   ILE A 567 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 658
      removed outlier: 3.701A  pdb=" N   MET A 645 " --> pdb=" O   ASP A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 674
      No H-bonds generated for 'chain 'A' and resid 672 through 674'
    Processing helix  chain 'A' and resid 675 through 695
      removed outlier: 3.875A  pdb=" N   LEU A 685 " --> pdb=" O   HIS A 681 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ALA A 686 " --> pdb=" O   HIS A 682 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ILE A 687 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS A 693 " --> pdb=" O   GLU A 689 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A 695 " --> pdb=" O   CYS A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 721
      removed outlier: 3.767A  pdb=" N   LYS A 720 " --> pdb=" O   CYS A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 788
      removed outlier: 3.575A  pdb=" N   ILE A 781 " --> pdb=" O   ASP A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 816
      removed outlier: 3.841A  pdb=" N   TYR A 804 " --> pdb=" O   PRO A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 844
    Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 412
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48
      removed outlier: 3.750A  pdb=" N   GLU A  46 " --> pdb=" O   LYS A 402 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   MET A 400 " --> pdb=" O   ASP A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94
      removed outlier: 6.234A  pdb=" N   ILE A  54 " --> pdb=" O   CYS A 137 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   CYS A 137 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   HIS A  56 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A 113 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 199
      removed outlier: 3.557A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 199 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 206
    Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 268
    Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 428
    Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 494
      removed outlier: 3.877A  pdb=" N   ILE A 521 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 625 through 632
      removed outlier: 3.581A  pdb=" N   VAL A 614 " --> pdb=" O   THR A 628 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE A 593 " --> pdb=" O   SER A 617 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG A 668 " --> pdb=" O   ILE A 705 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   VAL A 706 " --> pdb=" O   VAL A 767 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL A 767 " --> pdb=" O   VAL A 706 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    648 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      15 hydrogen bonds
      30 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1009
        1.28 -     1.41: 1756
        1.41 -     1.55: 3876
        1.55 -     1.69: 61
        1.69 -     1.83: 60
  Bond restraints: 6762
  Sorted by residual:
  bond pdb=" CG  PRO A 527 "
       pdb=" CD  PRO A 527 "
    ideal  model  delta    sigma   weight residual
    1.503  1.138  0.365 3.40e-02 8.65e+02 1.15e+02
  bond pdb=" CB  PRO A 527 "
       pdb=" CG  PRO A 527 "
    ideal  model  delta    sigma   weight residual
    1.492  1.189  0.303 5.00e-02 4.00e+02 3.68e+01
  bond pdb=" CG  PRO A  92 "
       pdb=" CD  PRO A  92 "
    ideal  model  delta    sigma   weight residual
    1.503  1.303  0.200 3.40e-02 8.65e+02 3.47e+01
  bond pdb=" CA  PHE A 200 "
       pdb=" CB  PHE A 200 "
    ideal  model  delta    sigma   weight residual
    1.524  1.580 -0.056 1.30e-02 5.92e+03 1.84e+01
  bond pdb=" N   PRO A 527 "
       pdb=" CD  PRO A 527 "
    ideal  model  delta    sigma   weight residual
    1.473  1.531 -0.058 1.40e-02 5.10e+03 1.73e+01
  ... (remaining 6757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.81: 9204
        7.81 -    15.61: 27
       15.61 -    23.42: 1
       23.42 -    31.23: 2
       31.23 -    39.03: 1
  Bond angle restraints: 9235
  Sorted by residual:
  angle pdb=" N   PRO A 527 "
        pdb=" CD  PRO A 527 "
        pdb=" CG  PRO A 527 "
      ideal   model   delta    sigma   weight residual
     103.20   75.97   27.23 1.50e+00 4.44e-01 3.30e+02
  angle pdb=" CA  PRO A 527 "
        pdb=" N   PRO A 527 "
        pdb=" CD  PRO A 527 "
      ideal   model   delta    sigma   weight residual
     112.00   92.39   19.61 1.40e+00 5.10e-01 1.96e+02
  angle pdb=" CA  PRO A 527 "
        pdb=" CB  PRO A 527 "
        pdb=" CG  PRO A 527 "
      ideal   model   delta    sigma   weight residual
     104.50   78.31   26.19 1.90e+00 2.77e-01 1.90e+02
  angle pdb=" CB  PRO A 527 "
        pdb=" CG  PRO A 527 "
        pdb=" CD  PRO A 527 "
      ideal   model   delta    sigma   weight residual
     106.10  145.13  -39.03 3.20e+00 9.77e-02 1.49e+02
  angle pdb=" CA  PRO A 762 "
        pdb=" N   PRO A 762 "
        pdb=" CD  PRO A 762 "
      ideal   model   delta    sigma   weight residual
     112.00   96.79   15.21 1.40e+00 5.10e-01 1.18e+02
  ... (remaining 9230 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.73: 3901
       35.73 -    71.45: 217
       71.45 -   107.17: 16
      107.17 -   142.90: 1
      142.90 -   178.62: 2
  Dihedral angle restraints: 4137
    sinusoidal: 1890
      harmonic: 2247
  Sorted by residual:
  dihedral pdb=" CD  ARG A 812 "
           pdb=" NE  ARG A 812 "
           pdb=" CZ  ARG A 812 "
           pdb=" NH1 ARG A 812 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.51   82.51     1      1.00e+01 1.00e-02 8.35e+01
  dihedral pdb=" O4'   U C  18 "
           pdb=" C1'   U C  18 "
           pdb=" N1    U C  18 "
           pdb=" C2    U C  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.62 -178.62     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CD  ARG A 814 "
           pdb=" NE  ARG A 814 "
           pdb=" CZ  ARG A 814 "
           pdb=" NH1 ARG A 814 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   70.95  -70.95     1      1.00e+01 1.00e-02 6.47e+01
  ... (remaining 4134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 914
       0.099 -    0.197: 105
       0.197 -    0.296: 14
       0.296 -    0.395: 3
       0.395 -    0.493: 5
  Chirality restraints: 1041
  Sorted by residual:
  chirality pdb=" CB  ILE A 592 "
            pdb=" CA  ILE A 592 "
            pdb=" CG1 ILE A 592 "
            pdb=" CG2 ILE A 592 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.15    0.49 2.00e-01 2.50e+01 6.09e+00
  chirality pdb=" CB  ILE A  74 "
            pdb=" CA  ILE A  74 "
            pdb=" CG1 ILE A  74 "
            pdb=" CG2 ILE A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.47 2.00e-01 2.50e+01 5.41e+00
  chirality pdb=" CB  ILE A 651 "
            pdb=" CA  ILE A 651 "
            pdb=" CG1 ILE A 651 "
            pdb=" CG2 ILE A 651 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.41 2.00e-01 2.50e+01 4.22e+00
  ... (remaining 1038 not shown)

  Planarity restraints: 1121
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 812 "   -1.096 9.50e-02 1.11e+02   4.91e-01 1.46e+02
        pdb=" NE  ARG A 812 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 812 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 812 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 812 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 814 "   -1.044 9.50e-02 1.11e+02   4.68e-01 1.32e+02
        pdb=" NE  ARG A 814 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 814 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 814 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 814 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 742 "    0.074 5.00e-02 4.00e+02   1.13e-01 2.05e+01
        pdb=" N   PRO A 743 "   -0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO A 743 "    0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A 743 "    0.061 5.00e-02 4.00e+02
  ... (remaining 1118 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1335
        2.78 -     3.31: 5908
        3.31 -     3.84: 11859
        3.84 -     4.37: 13148
        4.37 -     4.90: 21993
  Nonbonded interactions: 54243
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 765 "
            pdb=" O   SER A 798 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OH  TYR A 804 "
            pdb=" OP2   A B   5 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   ARG A 534 "
            pdb=" OG1 THR A 538 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   PRO A 152 "
            pdb=" OG1 THR A 744 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   THR A 703 "
            pdb=" OG1 THR A 703 "
     model   vdw
     2.302 3.040
  ... (remaining 54238 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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.060
  Find NCS groups from input model:        0.020
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5247
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   0.365   6763  Z= 0.385
  Angle     :  1.430  39.033   9237  Z= 0.772
  Chirality :  0.072   0.493   1041
  Planarity :  0.023   0.491   1121
  Dihedral  : 20.780 178.623   2680
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 32.79 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    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: -3.66 (0.25), residues: 764
  helix: -2.58 (0.26), residues: 223
  sheet: -2.32 (0.43), residues: 108
  loop : -2.40 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 423 
 TYR   0.040   0.004   TYR A 749 
 PHE   0.030   0.003   PHE A 442 
 TRP   0.018   0.002   TRP A 199 
 HIS   0.018   0.002   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00970 ( 6762)
  covalent geometry    : angle       1.42935 ( 9235)
  SS BOND              : bond        0.00520 (    1)
  SS BOND              : angle       2.25442 (    2)
  hydrogen bonds       : bond        0.18260 (  242)
  hydrogen bonds       : angle       8.94774 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.6412 (ttp-170)
REVERT: A  807 HIS cc_start: 0.4560 (OUTLIER) cc_final: 0.4303 (t70)
  outliers start: 8
  outliers final: 4
  residues processed: 90
  average time/residue: 0.1259
  time to fit residues: 14.1112
Evaluate side-chains
  80 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  811 PHE
Chi-restraints excluded: chain A residue  817 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 466 HIS
A 551 ASN
A 553 GLN
A 711 HIS
** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5118 r_free = 0.5118 target = 0.271326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.240246 restraints weight = 8759.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.4912 rms_B_bonded: 2.69
r_work: 0.4777 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.4777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5252
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6763  Z= 0.134
  Angle     :  0.685   8.193   9237  Z= 0.357
  Chirality :  0.047   0.229   1041
  Planarity :  0.006   0.068   1121
  Dihedral  : 17.628 179.208   1146
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 30.15 %
    Favored  : 65.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -2.74 (0.28), residues: 764
  helix: -1.25 (0.32), residues: 223
  sheet: -2.23 (0.43), residues: 128
  loop : -2.00 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 167 
 TYR   0.008   0.001   TYR A 174 
 PHE   0.033   0.001   PHE A 811 
 TRP   0.006   0.001   TRP A 199 
 HIS   0.004   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6762)
  covalent geometry    : angle       0.68541 ( 9235)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.70986 (    2)
  hydrogen bonds       : bond        0.04002 (  242)
  hydrogen bonds       : angle       6.32873 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  214 MET cc_start: 0.6134 (mtt) cc_final: 0.5886 (mtp)
REVERT: A  477 ILE cc_start: 0.5261 (OUTLIER) cc_final: 0.4579 (tt)
REVERT: A  537 ASP cc_start: 0.4785 (m-30) cc_final: 0.4518 (m-30)
REVERT: A  780 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.5703 (pp30)
REVERT: A  807 HIS cc_start: 0.4980 (OUTLIER) cc_final: 0.4574 (m-70)
  outliers start: 30
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0986
  time to fit residues: 13.1139
Evaluate side-chains
  81 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  856 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 1 optimal weight:    0.1980
   chunk 66 optimal weight:    3.9990
   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 486 GLN
** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 757 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5149 r_free = 0.5149 target = 0.271742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.240350 restraints weight = 8846.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.4964 rms_B_bonded: 2.62
r_work: 0.4817 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5371
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6763  Z= 0.142
  Angle     :  0.661   8.445   9237  Z= 0.339
  Chirality :  0.046   0.217   1041
  Planarity :  0.005   0.057   1121
  Dihedral  : 17.302 178.300   1142
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 28.38 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -2.27 (0.30), residues: 764
  helix: -0.73 (0.33), residues: 224
  sheet: -2.13 (0.42), residues: 134
  loop : -1.71 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  28 
 TYR   0.010   0.002   TYR A 804 
 PHE   0.011   0.001   PHE A 200 
 TRP   0.006   0.001   TRP A 199 
 HIS   0.005   0.001   HIS A 816 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6762)
  covalent geometry    : angle       0.66097 ( 9235)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       0.50644 (    2)
  hydrogen bonds       : bond        0.03738 (  242)
  hydrogen bonds       : angle       5.92287 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 85
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6534 (ttp-170)
REVERT: A  477 ILE cc_start: 0.5442 (OUTLIER) cc_final: 0.4816 (tt)
REVERT: A  662 THR cc_start: 0.5459 (OUTLIER) cc_final: 0.4807 (t)
REVERT: A  780 GLN cc_start: 0.6486 (OUTLIER) cc_final: 0.6044 (pp30)
REVERT: A  807 HIS cc_start: 0.5498 (OUTLIER) cc_final: 0.5019 (t70)
  outliers start: 36
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0983
  time to fit residues: 14.7853
Evaluate side-chains
  94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  856 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.0970
   chunk 76 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 34 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 271 HIS
** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5169 r_free = 0.5169 target = 0.273586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4932 r_free = 0.4932 target = 0.242493 restraints weight = 8821.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.4985 rms_B_bonded: 2.61
r_work: 0.4840 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5325
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6763  Z= 0.122
  Angle     :  0.631   8.402   9237  Z= 0.321
  Chirality :  0.046   0.235   1041
  Planarity :  0.005   0.047   1121
  Dihedral  : 17.109 179.190   1140
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 29.41 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -2.11 (0.30), residues: 764
  helix: -0.44 (0.34), residues: 224
  sheet: -2.34 (0.42), residues: 133
  loop : -1.59 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 506 
 TYR   0.011   0.001   TYR A 494 
 PHE   0.016   0.001   PHE A 748 
 TRP   0.006   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 816 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6762)
  covalent geometry    : angle       0.63091 ( 9235)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       0.67731 (    2)
  hydrogen bonds       : bond        0.03422 (  242)
  hydrogen bonds       : angle       5.71959 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.6015 (mtt) cc_final: 0.5669 (mtp)
REVERT: A  248 LYS cc_start: 0.5521 (mmmt) cc_final: 0.5293 (mmtp)
REVERT: A  477 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.4757 (tt)
REVERT: A  662 THR cc_start: 0.5359 (OUTLIER) cc_final: 0.4701 (t)
REVERT: A  780 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.6047 (pp30)
REVERT: A  807 HIS cc_start: 0.5493 (OUTLIER) cc_final: 0.5026 (t70)
  outliers start: 30
  outliers final: 15
  residues processed: 106
  average time/residue: 0.0896
  time to fit residues: 12.6131
Evaluate side-chains
  93 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  203 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  807 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    0.2980
   chunk 71 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 75 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0970
   chunk 73 optimal weight:    0.0980
   chunk 6 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN
A 548 GLN
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5186 r_free = 0.5186 target = 0.276317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4951 r_free = 0.4951 target = 0.245302 restraints weight = 8946.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.5000 rms_B_bonded: 2.65
r_work: 0.4863 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5258
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6763  Z= 0.111
  Angle     :  0.613   8.218   9237  Z= 0.312
  Chirality :  0.045   0.220   1041
  Planarity :  0.005   0.057   1121
  Dihedral  : 17.070 179.877   1140
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 29.26 %
    Favored  : 66.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.96 (0.31), residues: 764
  helix: -0.27 (0.34), residues: 225
  sheet: -2.13 (0.42), residues: 139
  loop : -1.56 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 411 
 TYR   0.011   0.001   TYR A 494 
 PHE   0.016   0.001   PHE A 748 
 TRP   0.007   0.001   TRP A 199 
 HIS   0.006   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6762)
  covalent geometry    : angle       0.61319 ( 9235)
  SS BOND              : bond        0.00369 (    1)
  SS BOND              : angle       1.22382 (    2)
  hydrogen bonds       : bond        0.03223 (  242)
  hydrogen bonds       : angle       5.53927 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6547 (ttp-170)
REVERT: A  248 LYS cc_start: 0.5689 (mmmt) cc_final: 0.5455 (mmtp)
REVERT: A  402 LYS cc_start: 0.7784 (tttp) cc_final: 0.6972 (tptp)
REVERT: A  477 ILE cc_start: 0.5386 (OUTLIER) cc_final: 0.4767 (tt)
REVERT: A  662 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.4714 (t)
REVERT: A  695 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.5237 (pm20)
REVERT: A  753 HIS cc_start: 0.5114 (OUTLIER) cc_final: 0.4868 (m90)
REVERT: A  780 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5882 (pp30)
REVERT: A  807 HIS cc_start: 0.5576 (OUTLIER) cc_final: 0.5116 (t70)
  outliers start: 28
  outliers final: 15
  residues processed: 108
  average time/residue: 0.0989
  time to fit residues: 13.9147
Evaluate side-chains
  99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  753 HIS
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  852 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 58 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 38 optimal weight:    0.2980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 510 ASN
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5178 r_free = 0.5178 target = 0.275152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4936 r_free = 0.4936 target = 0.243716 restraints weight = 8872.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.4993 rms_B_bonded: 2.63
r_work: 0.4846 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5301
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6763  Z= 0.119
  Angle     :  0.617   8.021   9237  Z= 0.313
  Chirality :  0.045   0.205   1041
  Planarity :  0.005   0.060   1121
  Dihedral  : 17.092 179.848   1140
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 29.26 %
    Favored  : 65.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.92 (0.31), residues: 764
  helix: -0.20 (0.34), residues: 225
  sheet: -2.22 (0.42), residues: 139
  loop : -1.51 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 411 
 TYR   0.010   0.001   TYR A 494 
 PHE   0.015   0.001   PHE A 748 
 TRP   0.007   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 764 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6762)
  covalent geometry    : angle       0.61709 ( 9235)
  SS BOND              : bond        0.00239 (    1)
  SS BOND              : angle       1.09230 (    2)
  hydrogen bonds       : bond        0.03213 (  242)
  hydrogen bonds       : angle       5.44330 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.6899 (mpp) cc_final: 0.5719 (mtt)
REVERT: A  248 LYS cc_start: 0.5746 (mmmt) cc_final: 0.5517 (mmtp)
REVERT: A  402 LYS cc_start: 0.7812 (tttp) cc_final: 0.6910 (tptp)
REVERT: A  477 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.4969 (tt)
REVERT: A  640 GLN cc_start: 0.6767 (pm20) cc_final: 0.4840 (mt0)
REVERT: A  662 THR cc_start: 0.5333 (OUTLIER) cc_final: 0.4728 (t)
REVERT: A  695 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.5126 (pm20)
REVERT: A  780 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6033 (pp30)
REVERT: A  807 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.5190 (t70)
  outliers start: 33
  outliers final: 21
  residues processed: 110
  average time/residue: 0.0978
  time to fit residues: 14.1075
Evaluate side-chains
  103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  203 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  792 ARG
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  852 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0040
   chunk 51 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 510 ASN
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5175 r_free = 0.5175 target = 0.274826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.243014 restraints weight = 8735.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.4985 rms_B_bonded: 2.61
r_work: 0.4837 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5323
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6763  Z= 0.123
  Angle     :  0.616   7.856   9237  Z= 0.313
  Chirality :  0.045   0.184   1041
  Planarity :  0.005   0.059   1121
  Dihedral  : 17.080 179.737   1140
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 28.68 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.81 (0.31), residues: 764
  helix: -0.06 (0.34), residues: 222
  sheet: -2.04 (0.42), residues: 135
  loop : -1.53 (0.33), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 411 
 TYR   0.010   0.001   TYR A 804 
 PHE   0.014   0.001   PHE A 748 
 TRP   0.007   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6762)
  covalent geometry    : angle       0.61599 ( 9235)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       1.15052 (    2)
  hydrogen bonds       : bond        0.03249 (  242)
  hydrogen bonds       : angle       5.40420 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 80
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.6843 (mpp) cc_final: 0.5850 (mtt)
REVERT: A  402 LYS cc_start: 0.7870 (tttp) cc_final: 0.6944 (tptp)
REVERT: A  477 ILE cc_start: 0.5611 (OUTLIER) cc_final: 0.5000 (tt)
REVERT: A  640 GLN cc_start: 0.6813 (pm20) cc_final: 0.4897 (mt0)
REVERT: A  662 THR cc_start: 0.5372 (OUTLIER) cc_final: 0.4778 (t)
REVERT: A  695 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5138 (pm20)
REVERT: A  780 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6041 (pp30)
REVERT: A  807 HIS cc_start: 0.5798 (OUTLIER) cc_final: 0.5305 (t70)
  outliers start: 35
  outliers final: 22
  residues processed: 109
  average time/residue: 0.0984
  time to fit residues: 14.0271
Evaluate side-chains
  105 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  203 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  792 ARG
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  852 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    0.2980
   chunk 62 optimal weight:    0.0980
   chunk 18 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 510 ASN
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5181 r_free = 0.5181 target = 0.275326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4941 r_free = 0.4941 target = 0.243819 restraints weight = 8821.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.4996 rms_B_bonded: 2.60
r_work: 0.4848 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5305
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6763  Z= 0.118
  Angle     :  0.610   7.876   9237  Z= 0.310
  Chirality :  0.045   0.174   1041
  Planarity :  0.005   0.059   1121
  Dihedral  : 17.077 179.920   1140
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 29.12 %
    Favored  : 66.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.79 (0.31), residues: 764
  helix: -0.01 (0.34), residues: 222
  sheet: -2.09 (0.43), residues: 133
  loop : -1.52 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 411 
 TYR   0.010   0.001   TYR A 804 
 PHE   0.013   0.001   PHE A 748 
 TRP   0.008   0.001   TRP A 199 
 HIS   0.005   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6762)
  covalent geometry    : angle       0.60941 ( 9235)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       1.15169 (    2)
  hydrogen bonds       : bond        0.03173 (  242)
  hydrogen bonds       : angle       5.34826 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.6570 (mpp) cc_final: 0.5448 (mtt)
REVERT: A  402 LYS cc_start: 0.7829 (tttp) cc_final: 0.6927 (tptp)
REVERT: A  477 ILE cc_start: 0.5756 (OUTLIER) cc_final: 0.5182 (tt)
REVERT: A  662 THR cc_start: 0.5343 (OUTLIER) cc_final: 0.4770 (t)
REVERT: A  695 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.5152 (pm20)
REVERT: A  780 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.5920 (pp30)
REVERT: A  807 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.5285 (t70)
  outliers start: 30
  outliers final: 21
  residues processed: 102
  average time/residue: 0.0963
  time to fit residues: 12.9298
Evaluate side-chains
  100 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  203 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  792 ARG
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  852 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 510 ASN
** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5163 r_free = 0.5163 target = 0.273100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4915 r_free = 0.4915 target = 0.240922 restraints weight = 8764.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.4968 rms_B_bonded: 2.63
r_work: 0.4824 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5352
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6763  Z= 0.135
  Angle     :  0.632   8.003   9237  Z= 0.321
  Chirality :  0.046   0.212   1041
  Planarity :  0.005   0.058   1121
  Dihedral  : 17.124 179.421   1140
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 28.97 %
    Favored  : 66.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.84 (0.31), residues: 764
  helix: -0.03 (0.34), residues: 222
  sheet: -2.23 (0.42), residues: 133
  loop : -1.52 (0.33), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 366 
 TYR   0.012   0.002   TYR A 804 
 PHE   0.014   0.001   PHE A 181 
 TRP   0.009   0.001   TRP A 199 
 HIS   0.005   0.001   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6762)
  covalent geometry    : angle       0.63187 ( 9235)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       1.21330 (    2)
  hydrogen bonds       : bond        0.03269 (  242)
  hydrogen bonds       : angle       5.45455 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.6710 (mpp) cc_final: 0.5734 (mtt)
REVERT: A  280 ARG cc_start: 0.1251 (OUTLIER) cc_final: 0.0918 (mmp80)
REVERT: A  402 LYS cc_start: 0.7846 (tttp) cc_final: 0.6951 (tptp)
REVERT: A  477 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5204 (tt)
REVERT: A  640 GLN cc_start: 0.6852 (pm20) cc_final: 0.4801 (mt0)
REVERT: A  662 THR cc_start: 0.5345 (OUTLIER) cc_final: 0.4779 (t)
REVERT: A  780 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6257 (pp30)
REVERT: A  807 HIS cc_start: 0.5782 (OUTLIER) cc_final: 0.5280 (t70)
  outliers start: 29
  outliers final: 21
  residues processed: 104
  average time/residue: 0.1010
  time to fit residues: 13.6789
Evaluate side-chains
  105 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  203 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  792 ARG
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  852 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0170
   chunk 61 optimal weight:    0.0770
   chunk 66 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 510 ASN
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5195 r_free = 0.5195 target = 0.277163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.245385 restraints weight = 8740.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.5009 rms_B_bonded: 2.64
r_work: 0.4861 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.4861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5272
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6763  Z= 0.117
  Angle     :  0.628   8.003   9237  Z= 0.319
  Chirality :  0.045   0.190   1041
  Planarity :  0.005   0.055   1121
  Dihedral  : 17.136 179.789   1140
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 29.85 %
    Favored  : 66.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.75 (0.31), residues: 764
  helix:  0.09 (0.34), residues: 222
  sheet: -2.17 (0.42), residues: 133
  loop : -1.50 (0.33), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 411 
 TYR   0.013   0.001   TYR A 494 
 PHE   0.014   0.001   PHE A 200 
 TRP   0.011   0.001   TRP A 199 
 HIS   0.004   0.001   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6762)
  covalent geometry    : angle       0.62805 ( 9235)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       1.22183 (    2)
  hydrogen bonds       : bond        0.03126 (  242)
  hydrogen bonds       : angle       5.39276 (  678)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.6376 (mpp) cc_final: 0.5368 (mtp)
REVERT: A  366 ARG cc_start: 0.6401 (tpt90) cc_final: 0.6107 (tpp-160)
REVERT: A  402 LYS cc_start: 0.7824 (tttp) cc_final: 0.6920 (tptp)
REVERT: A  477 ILE cc_start: 0.5735 (OUTLIER) cc_final: 0.5238 (tt)
REVERT: A  640 GLN cc_start: 0.6816 (pm20) cc_final: 0.4894 (mt0)
REVERT: A  662 THR cc_start: 0.5362 (OUTLIER) cc_final: 0.4809 (t)
REVERT: A  780 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.5932 (pp30)
REVERT: A  807 HIS cc_start: 0.5680 (OUTLIER) cc_final: 0.5198 (t70)
  outliers start: 25
  outliers final: 19
  residues processed: 100
  average time/residue: 0.0972
  time to fit residues: 12.7818
Evaluate side-chains
  99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  203 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  757 GLN
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  792 ARG
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  852 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0170
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 757 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5186 r_free = 0.5186 target = 0.276104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4941 r_free = 0.4941 target = 0.243890 restraints weight = 8763.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.4993 rms_B_bonded: 2.66
r_work: 0.4849 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5292
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6763  Z= 0.121
  Angle     :  0.628   7.903   9237  Z= 0.318
  Chirality :  0.046   0.229   1041
  Planarity :  0.005   0.054   1121
  Dihedral  : 17.136 179.658   1140
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 29.71 %
    Favored  : 66.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.74 (0.31), residues: 764
  helix:  0.09 (0.34), residues: 222
  sheet: -2.15 (0.42), residues: 133
  loop : -1.49 (0.33), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 506 
 TYR   0.016   0.001   TYR A 494 
 PHE   0.013   0.001   PHE A 748 
 TRP   0.013   0.001   TRP A 199 
 HIS   0.005   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6762)
  covalent geometry    : angle       0.62799 ( 9235)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       1.28801 (    2)
  hydrogen bonds       : bond        0.03166 (  242)
  hydrogen bonds       : angle       5.40185 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1761.95 seconds
wall clock time: 31 minutes 5.48 seconds (1865.48 seconds total)