Starting phenix.real_space_refine
on Thu Jul 24 18:08:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k6p_62131/07_2025/9k6p_62131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k6p_62131/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2025/9k6p_62131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2025/9k6p_62131.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2025/9k6p_62131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2025/9k6p_62131.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.027
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.64, per 1000 atoms: 0.71
  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: 1.68
  Conformation dependent library (CDL) restraints added in 951.5 milliseconds
  

  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: 1.96
  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: 2.13

  Time building geometry restraints manager: 1.94 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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.960
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.660
-------------------------------------------------------------------------------
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 : 9.99
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.002   TRP A 199 
 HIS   0.018   0.002   HIS A  56 
 PHE   0.030   0.003   PHE A 442 
 TYR   0.040   0.004   TYR A 749 
 ARG   0.013   0.001   ARG A 423 

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

*********************** 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  : 0.705 
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: 0.2707
  time to fit residues: 30.4665
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  : 0.628 
-------------------------------------------------------------------------------
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 65 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 70 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 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 = 0.5115 r_free = 0.5115 target = 0.270913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.239885 restraints weight = 8609.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.4910 rms_B_bonded: 2.67
r_work: 0.4775 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.4775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5261
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6763  Z= 0.138
  Angle     :  0.692   8.362   9237  Z= 0.361
  Chirality :  0.047   0.229   1041
  Planarity :  0.006   0.067   1121
  Dihedral  : 17.642 179.300   1146
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 30.00 %
    Favored  : 65.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.28), residues: 764
  helix: -1.29 (0.32), residues: 223
  sheet: -2.16 (0.42), residues: 134
  loop : -2.04 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 199 
 HIS   0.004   0.001   HIS A 742 
 PHE   0.035   0.002   PHE A 811 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.005   0.001   ARG A 814 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  242)
  hydrogen bonds       : angle       6.37808 (  678)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.66542 (    2)
  covalent geometry    : bond        0.00321 ( 6762)
  covalent geometry    : angle       0.69159 ( 9235)

*********************** 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  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.6141 (mtt) cc_final: 0.5770 (mtp)
REVERT: A  477 ILE cc_start: 0.5265 (OUTLIER) cc_final: 0.4580 (tt)
REVERT: A  537 ASP cc_start: 0.4803 (m-30) cc_final: 0.4534 (m-30)
REVERT: A  780 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5780 (pp30)
REVERT: A  807 HIS cc_start: 0.4995 (OUTLIER) cc_final: 0.4592 (m-70)
  outliers start: 30
  outliers final: 11
  residues processed: 102
  average time/residue: 0.2081
  time to fit residues: 27.8080
Evaluate side-chains
  82 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  209 SER
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  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  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 36 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:   20.0000
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.5118 r_free = 0.5118 target = 0.267857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.235589 restraints weight = 8845.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.4925 rms_B_bonded: 2.63
r_work: 0.4775 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5469
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6763  Z= 0.171
  Angle     :  0.695   8.479   9237  Z= 0.357
  Chirality :  0.048   0.217   1041
  Planarity :  0.005   0.056   1121
  Dihedral  : 17.281 177.621   1140
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 28.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.30), residues: 764
  helix: -0.84 (0.33), residues: 225
  sheet: -2.22 (0.42), residues: 134
  loop : -1.78 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 199 
 HIS   0.007   0.001   HIS A 816 
 PHE   0.012   0.002   PHE A  45 
 TYR   0.012   0.002   TYR A 667 
 ARG   0.003   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (  242)
  hydrogen bonds       : angle       6.10219 (  678)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       1.13044 (    2)
  covalent geometry    : bond        0.00401 ( 6762)
  covalent geometry    : angle       0.69530 ( 9235)

*********************** 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
  124 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 86
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.6536 (ttp-170)
REVERT: A  418 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5179 (pp)
REVERT: A  477 ILE cc_start: 0.5503 (OUTLIER) cc_final: 0.4914 (tt)
REVERT: A  549 MET cc_start: 0.5653 (mpp) cc_final: 0.5418 (mpp)
REVERT: A  662 THR cc_start: 0.5483 (OUTLIER) cc_final: 0.4834 (t)
REVERT: A  780 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6201 (pp30)
REVERT: A  807 HIS cc_start: 0.5678 (OUTLIER) cc_final: 0.5219 (t70)
  outliers start: 38
  outliers final: 20
  residues processed: 119
  average time/residue: 0.2106
  time to fit residues: 32.7971
Evaluate side-chains
  101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
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  418 ILE
Chi-restraints excluded: chain A residue  463 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  560 LEU
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  680 LEU
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  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 69 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0980
   chunk 74 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0570
   chunk 19 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 510 ASN
A 548 GLN
** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 757 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5173 r_free = 0.5173 target = 0.273141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4955 r_free = 0.4955 target = 0.244499 restraints weight = 8613.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.4994 rms_B_bonded: 2.46
r_work: 0.4860 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5272
moved from start:          0.2506

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= 0.114
  Angle     :  0.623   8.528   9237  Z= 0.317
  Chirality :  0.045   0.229   1041
  Planarity :  0.005   0.043   1121
  Dihedral  : 17.068 179.312   1140
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 29.71 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.30), residues: 764
  helix: -0.50 (0.34), residues: 225
  sheet: -2.25 (0.42), residues: 139
  loop : -1.59 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 753 
 PHE   0.015   0.001   PHE A 748 
 TYR   0.014   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  242)
  hydrogen bonds       : angle       5.66089 (  678)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       0.73741 (    2)
  covalent geometry    : bond        0.00264 ( 6762)
  covalent geometry    : angle       0.62293 ( 9235)

*********************** 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: 29
    poor density    : 80
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  248 LYS cc_start: 0.5596 (mmmt) cc_final: 0.5352 (mmtp)
REVERT: A  418 ILE cc_start: 0.5346 (OUTLIER) cc_final: 0.5136 (pp)
REVERT: A  662 THR cc_start: 0.5402 (OUTLIER) cc_final: 0.4775 (t)
REVERT: A  695 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.5127 (pm20)
REVERT: A  780 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.6063 (pp30)
REVERT: A  807 HIS cc_start: 0.5478 (OUTLIER) cc_final: 0.4981 (t70)
  outliers start: 29
  outliers final: 14
  residues processed: 105
  average time/residue: 0.2188
  time to fit residues: 30.9876
Evaluate side-chains
  97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   52 ILE
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  222 THR
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  518 VAL
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  752 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 44 optimal weight:    0.0470
   chunk 74 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    0.5478

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5174 r_free = 0.5174 target = 0.274207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.243530 restraints weight = 8756.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.4985 rms_B_bonded: 2.59
r_work: 0.4852 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.4852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5296
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6763  Z= 0.117
  Angle     :  0.616   8.198   9237  Z= 0.314
  Chirality :  0.045   0.230   1041
  Planarity :  0.005   0.056   1121
  Dihedral  : 16.949 179.481   1140
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.41 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.31), residues: 764
  helix: -0.32 (0.34), residues: 225
  sheet: -2.21 (0.42), residues: 139
  loop : -1.54 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 199 
 HIS   0.010   0.001   HIS A 203 
 PHE   0.017   0.001   PHE A 748 
 TYR   0.011   0.001   TYR A 749 
 ARG   0.005   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03277 (  242)
  hydrogen bonds       : angle       5.56544 (  678)
  SS BOND              : bond        0.00386 (    1)
  SS BOND              : angle       1.38381 (    2)
  covalent geometry    : bond        0.00275 ( 6762)
  covalent geometry    : angle       0.61619 ( 9235)

*********************** 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
  115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7019 (mmm-85) cc_final: 0.6567 (ttp-170)
REVERT: A  181 PHE cc_start: 0.6566 (m-80) cc_final: 0.6350 (m-10)
REVERT: A  248 LYS cc_start: 0.5698 (mmmt) cc_final: 0.5472 (mmtp)
REVERT: A  418 ILE cc_start: 0.5332 (OUTLIER) cc_final: 0.5113 (pp)
REVERT: A  477 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.4696 (tt)
REVERT: A  662 THR cc_start: 0.5391 (OUTLIER) cc_final: 0.4770 (t)
REVERT: A  807 HIS cc_start: 0.5646 (OUTLIER) cc_final: 0.5170 (t70)
  outliers start: 31
  outliers final: 17
  residues processed: 111
  average time/residue: 0.2336
  time to fit residues: 34.0645
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  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   40 LEU
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  418 ILE
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  555 THR
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  779 LEU
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 65 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0170
   chunk 28 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.8022

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 510 ASN
** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 621 HIS
** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5105 r_free = 0.5105 target = 0.265040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.231956 restraints weight = 8773.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.4887 rms_B_bonded: 2.60
r_work: 0.4743 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.4743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5584
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   6763  Z= 0.211
  Angle     :  0.731   7.465   9237  Z= 0.374
  Chirality :  0.049   0.214   1041
  Planarity :  0.006   0.063   1121
  Dihedral  : 16.919 176.985   1140
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 22.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 27.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.30), residues: 764
  helix: -0.60 (0.33), residues: 227
  sheet: -2.37 (0.39), residues: 151
  loop : -1.70 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 435 
 HIS   0.009   0.001   HIS A 816 
 PHE   0.017   0.002   PHE A 748 
 TYR   0.017   0.003   TYR A 749 
 ARG   0.008   0.001   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  242)
  hydrogen bonds       : angle       6.01598 (  678)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       1.05029 (    2)
  covalent geometry    : bond        0.00500 ( 6762)
  covalent geometry    : angle       0.73120 ( 9235)

*********************** 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
  126 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 89
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.7133 (mpp) cc_final: 0.6115 (mtt)
REVERT: A  280 ARG cc_start: 0.1202 (OUTLIER) cc_final: 0.0644 (mpp-170)
REVERT: A  477 ILE cc_start: 0.5679 (OUTLIER) cc_final: 0.5102 (tt)
REVERT: A  618 MET cc_start: 0.4822 (mmm) cc_final: 0.4501 (mtp)
REVERT: A  662 THR cc_start: 0.5542 (OUTLIER) cc_final: 0.4983 (t)
  outliers start: 37
  outliers final: 26
  residues processed: 120
  average time/residue: 0.3773
  time to fit residues: 61.0452
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  : 3.117 
-------------------------------------------------------------------------------
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  169 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  280 ARG
Chi-restraints excluded: chain A residue  463 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  560 LEU
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  629 VAL
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  779 LEU
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  807 HIS
Chi-restraints excluded: chain A residue  812 ARG
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  856 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 71 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 621 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5087 r_free = 0.5087 target = 0.267379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4840 r_free = 0.4840 target = 0.234543 restraints weight = 8638.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.4873 rms_B_bonded: 2.69
r_work: 0.4733 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.4733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5409
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6763  Z= 0.134
  Angle     :  0.646   8.428   9237  Z= 0.332
  Chirality :  0.046   0.216   1041
  Planarity :  0.005   0.060   1121
  Dihedral  : 16.831 177.102   1140
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 16.28
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.31), residues: 764
  helix: -0.25 (0.35), residues: 219
  sheet: -2.56 (0.40), residues: 139
  loop : -1.59 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 168 
 PHE   0.016   0.001   PHE A 182 
 TYR   0.016   0.002   TYR A 494 
 ARG   0.006   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 (  242)
  hydrogen bonds       : angle       5.66145 (  678)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       1.36645 (    2)
  covalent geometry    : bond        0.00321 ( 6762)
  covalent geometry    : angle       0.64540 ( 9235)

*********************** 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
  118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 1.656 
Fit side-chains
REVERT: A  150 ARG cc_start: 0.4544 (ptt180) cc_final: 0.3930 (ptp-170)
REVERT: A  280 ARG cc_start: 0.1069 (OUTLIER) cc_final: 0.0691 (mmp80)
REVERT: A  355 LYS cc_start: 0.0586 (OUTLIER) cc_final: -0.0921 (tptp)
REVERT: A  477 ILE cc_start: 0.5628 (OUTLIER) cc_final: 0.5021 (tt)
REVERT: A  570 LYS cc_start: 0.6124 (mmtm) cc_final: 0.5590 (mmtm)
REVERT: A  618 MET cc_start: 0.4312 (mmm) cc_final: 0.4036 (mtp)
REVERT: A  640 GLN cc_start: 0.6727 (pm20) cc_final: 0.4782 (mt0)
REVERT: A  662 THR cc_start: 0.5531 (OUTLIER) cc_final: 0.4966 (t)
REVERT: A  807 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.5203 (t70)
  outliers start: 33
  outliers final: 21
  residues processed: 113
  average time/residue: 0.3248
  time to fit residues: 49.2175
Evaluate side-chains
  106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
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  222 THR
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  463 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  555 THR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain A residue  629 VAL
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  779 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.265872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.232642 restraints weight = 8734.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.4858 rms_B_bonded: 2.71
r_work: 0.4715 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.4715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5444
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6763  Z= 0.143
  Angle     :  0.663   8.284   9237  Z= 0.338
  Chirality :  0.047   0.230   1041
  Planarity :  0.006   0.122   1121
  Dihedral  : 16.804 177.153   1140
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 29.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.31), residues: 764
  helix: -0.27 (0.34), residues: 222
  sheet: -2.55 (0.39), residues: 139
  loop : -1.58 (0.33), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 199 
 HIS   0.006   0.001   HIS A 203 
 PHE   0.015   0.001   PHE A 748 
 TYR   0.016   0.002   TYR A 494 
 ARG   0.007   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  242)
  hydrogen bonds       : angle       5.63523 (  678)
  SS BOND              : bond        0.00198 (    1)
  SS BOND              : angle       1.38634 (    2)
  covalent geometry    : bond        0.00344 ( 6762)
  covalent geometry    : angle       0.66324 ( 9235)

*********************** 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
  113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A  104 MET cc_start: 0.7159 (mpp) cc_final: 0.5951 (mtt)
REVERT: A  150 ARG cc_start: 0.4658 (ptt180) cc_final: 0.4081 (ptp-170)
REVERT: A  280 ARG cc_start: 0.1141 (OUTLIER) cc_final: 0.0781 (mmp80)
REVERT: A  355 LYS cc_start: 0.0602 (OUTLIER) cc_final: -0.0909 (tptp)
REVERT: A  477 ILE cc_start: 0.5762 (OUTLIER) cc_final: 0.5194 (tt)
REVERT: A  570 LYS cc_start: 0.6135 (mmtm) cc_final: 0.5399 (mmtm)
REVERT: A  640 GLN cc_start: 0.6676 (pm20) cc_final: 0.4684 (mt0)
REVERT: A  662 THR cc_start: 0.5459 (OUTLIER) cc_final: 0.4907 (t)
REVERT: A  807 HIS cc_start: 0.5713 (OUTLIER) cc_final: 0.5268 (t70)
  outliers start: 30
  outliers final: 21
  residues processed: 109
  average time/residue: 0.2658
  time to fit residues: 36.9296
Evaluate side-chains
  106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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  209 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  463 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  555 THR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain A residue  629 VAL
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  779 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 50 optimal weight:    0.1980
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5090 r_free = 0.5090 target = 0.268104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.235766 restraints weight = 8696.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.4884 rms_B_bonded: 2.70
r_work: 0.4743 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.4743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5379
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6763  Z= 0.129
  Angle     :  0.654   8.259   9237  Z= 0.332
  Chirality :  0.046   0.218   1041
  Planarity :  0.006   0.120   1121
  Dihedral  : 16.809 177.656   1140
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.31), residues: 764
  helix: -0.18 (0.34), residues: 219
  sheet: -2.41 (0.43), residues: 122
  loop : -1.51 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 764 
 PHE   0.013   0.001   PHE A 748 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.008   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  242)
  hydrogen bonds       : angle       5.49078 (  678)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       1.42796 (    2)
  covalent geometry    : bond        0.00310 ( 6762)
  covalent geometry    : angle       0.65373 ( 9235)

*********************** 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: 28
    poor density    : 82
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  104 MET cc_start: 0.6911 (mpp) cc_final: 0.5892 (mtp)
REVERT: A  280 ARG cc_start: 0.1286 (OUTLIER) cc_final: 0.0972 (mmp80)
REVERT: A  355 LYS cc_start: 0.0738 (OUTLIER) cc_final: -0.0753 (tptp)
REVERT: A  366 ARG cc_start: 0.6567 (tpt90) cc_final: 0.5705 (tpp80)
REVERT: A  402 LYS cc_start: 0.7825 (tttp) cc_final: 0.6936 (tptp)
REVERT: A  477 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5423 (tt)
REVERT: A  640 GLN cc_start: 0.6571 (pm20) cc_final: 0.4686 (mt0)
REVERT: A  662 THR cc_start: 0.5433 (OUTLIER) cc_final: 0.4878 (t)
REVERT: A  807 HIS cc_start: 0.5586 (OUTLIER) cc_final: 0.5226 (t70)
  outliers start: 28
  outliers final: 20
  residues processed: 105
  average time/residue: 0.2703
  time to fit residues: 38.1675
Evaluate side-chains
  99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 1.883 
-------------------------------------------------------------------------------
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  222 THR
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  463 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  565 LEU
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain A residue  629 VAL
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  767 VAL
Chi-restraints excluded: chain A residue  779 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5003 r_free = 0.5003 target = 0.256468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.220965 restraints weight = 8839.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.4761 rms_B_bonded: 2.72
r_work: 0.4615 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.4615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5679
moved from start:          0.4179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.108   6763  Z= 0.255
  Angle     :  0.813   9.164   9237  Z= 0.417
  Chirality :  0.053   0.351   1041
  Planarity :  0.007   0.118   1121
  Dihedral  : 16.991 174.489   1140
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 24.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 28.97 %
    Favored  : 66.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.30), residues: 764
  helix: -0.56 (0.33), residues: 221
  sheet: -2.67 (0.37), residues: 149
  loop : -1.84 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 435 
 HIS   0.011   0.002   HIS A 168 
 PHE   0.048   0.003   PHE A 202 
 TYR   0.025   0.003   TYR A 494 
 ARG   0.006   0.001   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04471 (  242)
  hydrogen bonds       : angle       6.18398 (  678)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       1.26217 (    2)
  covalent geometry    : bond        0.00609 ( 6762)
  covalent geometry    : angle       0.81328 ( 9235)

********************** 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
  115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.912 
Fit side-chains
REVERT: A  104 MET cc_start: 0.7328 (mpp) cc_final: 0.6509 (mtt)
REVERT: A  150 ARG cc_start: 0.5136 (ptt180) cc_final: 0.4579 (ptp-170)
REVERT: A  355 LYS cc_start: 0.0781 (OUTLIER) cc_final: -0.0909 (tptp)
REVERT: A  411 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.5303 (mtt90)
REVERT: A  477 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5579 (tt)
REVERT: A  618 MET cc_start: 0.5134 (mmm) cc_final: 0.4719 (mtp)
REVERT: A  662 THR cc_start: 0.5342 (OUTLIER) cc_final: 0.4800 (t)
  outliers start: 28
  outliers final: 20
  residues processed: 108
  average time/residue: 0.3397
  time to fit residues: 48.5663
Evaluate side-chains
  103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
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  355 LYS
Chi-restraints excluded: chain A residue  463 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  560 LEU
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  629 VAL
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  767 VAL
Chi-restraints excluded: chain A residue  779 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 49 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   chunk 36 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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5080 r_free = 0.5080 target = 0.266500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.233190 restraints weight = 8788.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.4867 rms_B_bonded: 2.73
r_work: 0.4726 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.4726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5426
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6763  Z= 0.140
  Angle     :  0.688   8.215   9237  Z= 0.350
  Chirality :  0.047   0.223   1041
  Planarity :  0.006   0.112   1121
  Dihedral  : 16.953 175.837   1140
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 29.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.31), residues: 764
  helix: -0.33 (0.34), residues: 219
  sheet: -2.69 (0.40), residues: 127
  loop : -1.59 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 199 
 HIS   0.013   0.001   HIS A 168 
 PHE   0.013   0.001   PHE A 182 
 TYR   0.017   0.001   TYR A 494 
 ARG   0.008   0.001   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03424 (  242)
  hydrogen bonds       : angle       5.65176 (  678)
  SS BOND              : bond        0.00299 (    1)
  SS BOND              : angle       0.78091 (    2)
  covalent geometry    : bond        0.00335 ( 6762)
  covalent geometry    : angle       0.68777 ( 9235)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4389.52 seconds
wall clock time: 82 minutes 35.30 seconds (4955.30 seconds total)