Starting phenix.real_space_refine
on Tue Mar  3 20:52:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w64_21552/03_2026/6w64_21552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w64_21552/03_2026/6w64_21552.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w64_21552/03_2026/6w64_21552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w64_21552/03_2026/6w64_21552.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w64_21552/03_2026/6w64_21552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w64_21552/03_2026/6w64_21552.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      56      5.49       5
     S      34      5.16       5
     C    5213      2.51       5
     N    1474      2.21       5
     O    1728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8505
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 928, 7331
          Classifications: {'peptide': 928}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 32, 'TRANS': 895}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 192
          Unresolved non-hydrogen angles: 233
          Unresolved non-hydrogen dihedrals: 159
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 97
    Chain: "B"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 805
          Classifications: {'RNA': 38}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 13, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 11, 'rna3p': 26}
    Chain: "C"
      Number of atoms: 369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 369
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
  Time building chain proxies: 1.96, per 1000 atoms: 0.23
  Number of scatterers: 8505
  At special positions: 0
  Unit cell: (85.05, 128.1, 108.15, 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      34     16.00
     P      56     15.00
     O    1728      8.00
     N    1474      7.00
     C    5213      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 420.0 milliseconds
  

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      55.7% alpha, 7.2% beta
      13 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 54
      Proline residue:  A  42  - end of helix
    Processing helix  chain 'A' and resid 70 through 80
    Processing helix  chain 'A' and resid 96 through 104
      removed outlier: 3.630A  pdb=" N   LEU A 100 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 118
    Processing helix  chain 'A' and resid 132 through 143
    Processing helix  chain 'A' and resid 145 through 159
    Processing helix  chain 'A' and resid 168 through 176
    Processing helix  chain 'A' and resid 282 through 293
    Processing helix  chain 'A' and resid 297 through 332
      Proline residue:  A 311  - end of helix
    Processing helix  chain 'A' and resid 337 through 346
    Processing helix  chain 'A' and resid 364 through 368
    Processing helix  chain 'A' and resid 371 through 393
      removed outlier: 4.539A  pdb=" N   THR A 375 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 422
    Processing helix  chain 'A' and resid 429 through 439
    Processing helix  chain 'A' and resid 444 through 463
    Processing helix  chain 'A' and resid 490 through 501
    Processing helix  chain 'A' and resid 533 through 540
    Processing helix  chain 'A' and resid 571 through 581
    Processing helix  chain 'A' and resid 585 through 601
    Processing helix  chain 'A' and resid 708 through 721
      removed outlier: 3.804A  pdb=" N   LYS A 721 " --> pdb=" O   SER A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 747
      removed outlier: 3.531A  pdb=" N   ILE A 746 " --> pdb=" O   ASP A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 771
    Processing helix  chain 'A' and resid 772 through 777
      removed outlier: 3.569A  pdb=" N   ALA A 775 " --> pdb=" O   SER A 772 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   LYS A 776 " --> pdb=" O   SER A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 787
    Processing helix  chain 'A' and resid 800 through 822
    Processing helix  chain 'A' and resid 838 through 846
    Processing helix  chain 'A' and resid 846 through 886
    Processing helix  chain 'A' and resid 905 through 914
      removed outlier: 3.638A  pdb=" N   ASP A 914 " --> pdb=" O   SER A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 929
    Processing helix  chain 'A' and resid 967 through 971
    Processing helix  chain 'A' and resid 972 through 984
    Processing helix  chain 'A' and resid 990 through 1008
    Processing helix  chain 'A' and resid 1010 through 1015
    Processing helix  chain 'A' and resid 1018 through 1033
    Processing helix  chain 'A' and resid 1072 through 1082
    Processing helix  chain 'A' and resid 1085 through 1090
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13
      removed outlier: 7.423A  pdb=" N   ASN A 477 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLY A 486 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLY A 479 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   ILE A 488 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   LEU A 485 " --> pdb=" O   LYS A 515 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG A 523 " --> pdb=" O   ASN A 518 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ALA A 530 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84
      removed outlier: 3.595A  pdb=" N   LYS A  81 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 683
      removed outlier: 6.268A  pdb=" N   GLU A 660 " --> pdb=" O   PRO A 678 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLU A 680 " --> pdb=" O   ALA A 658 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 669 through 670
    Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689
    Processing sheet with id=AA6, first strand: chain 'A' and resid 893 through 894
      removed outlier: 7.012A  pdb=" N   GLY A 893 " --> pdb=" O   VAL A 939 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050

    406 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      33 hydrogen bonds
      66 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1268
        1.28 -     1.41: 2320
        1.41 -     1.54: 5026
        1.54 -     1.68: 118
        1.68 -     1.81: 58
  Bond restraints: 8790
  Sorted by residual:
  bond pdb=" C   PHE A  80 "
       pdb=" O   PHE A  80 "
    ideal  model  delta    sigma   weight residual
    1.233  1.148  0.084 1.12e-02 7.97e+03 5.68e+01
  bond pdb=" N   ARG A 962 "
       pdb=" CA  ARG A 962 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.038 1.17e-02 7.31e+03 1.07e+01
  bond pdb=" N   LYS A  81 "
       pdb=" CA  LYS A  81 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.040 1.23e-02 6.61e+03 1.03e+01
  bond pdb=" C   ASN A1064 "
       pdb=" N   GLY A1065 "
    ideal  model  delta    sigma   weight residual
    1.331  1.376 -0.046 1.46e-02 4.69e+03 9.74e+00
  bond pdb=" N   GLY A 682 "
       pdb=" CA  GLY A 682 "
    ideal  model  delta    sigma   weight residual
    1.448  1.480 -0.031 1.00e-02 1.00e+04 9.62e+00
  ... (remaining 8785 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 11873
        1.75 -     3.50: 193
        3.50 -     5.25: 38
        5.25 -     6.99: 2
        6.99 -     8.74: 3
  Bond angle restraints: 12109
  Sorted by residual:
  angle pdb=" N   PRO A 987 "
        pdb=" CA  PRO A 987 "
        pdb=" CB  PRO A 987 "
      ideal   model   delta    sigma   weight residual
     103.36  110.25   -6.89 8.80e-01 1.29e+00 6.14e+01
  angle pdb=" CA  PHE A  80 "
        pdb=" C   PHE A  80 "
        pdb=" O   PHE A  80 "
      ideal   model   delta    sigma   weight residual
     120.89  112.15    8.74 1.27e+00 6.20e-01 4.74e+01
  angle pdb=" CA  PHE A  80 "
        pdb=" C   PHE A  80 "
        pdb=" N   LYS A  81 "
      ideal   model   delta    sigma   weight residual
     115.75  123.12   -7.37 1.08e+00 8.57e-01 4.66e+01
  angle pdb=" C   ASN A1064 "
        pdb=" N   GLY A1065 "
        pdb=" CA  GLY A1065 "
      ideal   model   delta    sigma   weight residual
     121.41  129.72   -8.31 1.96e+00 2.60e-01 1.80e+01
  angle pdb=" O   SER A  95 "
        pdb=" C   SER A  95 "
        pdb=" N   ASN A  96 "
      ideal   model   delta    sigma   weight residual
     122.07  125.89   -3.82 1.03e+00 9.43e-01 1.37e+01
  ... (remaining 12104 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.97: 5153
       34.97 -    69.93: 195
       69.93 -   104.90: 17
      104.90 -   139.86: 0
      139.86 -   174.83: 3
  Dihedral angle restraints: 5368
    sinusoidal: 2635
      harmonic: 2733
  Sorted by residual:
  dihedral pdb=" O4'   U B  11 "
           pdb=" C1'   U B  11 "
           pdb=" N1    U B  11 "
           pdb=" C2    U B  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -7.34 -152.66     1      1.50e+01 4.44e-03 8.06e+01
  dihedral pdb=" O4'   U B  -6 "
           pdb=" C1'   U B  -6 "
           pdb=" N1    U B  -6 "
           pdb=" C2    U B  -6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   46.83 -174.83     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" CA  LYS A 487 "
           pdb=" C   LYS A 487 "
           pdb=" N   ILE A 488 "
           pdb=" CA  ILE A 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.19   22.81     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 5365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1077
       0.038 -    0.076: 212
       0.076 -    0.114: 61
       0.114 -    0.153: 13
       0.153 -    0.191: 4
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" C2'   A B -10 "
            pdb=" C3'   A B -10 "
            pdb=" O2'   A B -10 "
            pdb=" C1'   A B -10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.56   -0.19 2.00e-01 2.50e+01 9.09e-01
  chirality pdb=" CA  PRO A 987 "
            pdb=" N   PRO A 987 "
            pdb=" C   PRO A 987 "
            pdb=" CB  PRO A 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.04e-01
  chirality pdb=" C3'   C B  -8 "
            pdb=" C4'   C B  -8 "
            pdb=" O3'   C B  -8 "
            pdb=" C2'   C B  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.56   -0.18 2.00e-01 2.50e+01 8.15e-01
  ... (remaining 1364 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 681 "   -0.017 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   SER A 681 "    0.055 2.00e-02 2.50e+03
        pdb=" O   SER A 681 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLY A 682 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  80 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   PHE A  80 "    0.036 2.00e-02 2.50e+03
        pdb=" O   PHE A  80 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A  81 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  96 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.23e+00
        pdb=" C   ASN A  96 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ASN A  96 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A  97 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 830
        2.74 -     3.28: 8889
        3.28 -     3.82: 14483
        3.82 -     4.36: 16738
        4.36 -     4.90: 28352
  Nonbonded interactions: 69292
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  57 "
            pdb=" OD1 ASP A  72 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   SER A 981 "
            pdb=" OG  SER A 984 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NH1 ARG A 853 "
            pdb=" OE2 GLU A 857 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   ASN A  96 "
            pdb=" ND2 ASN A  96 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   TYR A 104 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.216 3.040
  ... (remaining 69287 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 group one per residue
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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.820
  Find NCS groups from input model:        0.040
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   8790  Z= 0.197
  Angle     :  0.577   8.742  12109  Z= 0.371
  Chirality :  0.037   0.191   1367
  Planarity :  0.003   0.032   1338
  Dihedral  : 16.240 174.826   3600
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.99 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  3.10 %
    Favored  : 95.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.29), residues: 916
  helix:  2.21 (0.24), residues: 501
  sheet: -2.20 (0.54), residues: 74
  loop : -2.47 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 918 
 TYR   0.024   0.001   TYR A 695 
 PHE   0.007   0.001   PHE A 911 
 TRP   0.010   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8790)
  covalent geometry    : angle       0.57655 (12109)
  hydrogen bonds       : bond        0.15680 (  439)
  hydrogen bonds       : angle       5.75751 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 248
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 PRO cc_start: 0.8928 (Cg_endo) cc_final: 0.8659 (Cg_exo)
REVERT: A  539 GLU cc_start: 0.4957 (tp30) cc_final: 0.3806 (tp30)
REVERT: A  806 MET cc_start: 0.7081 (ttp) cc_final: 0.6737 (ptp)
REVERT: A  850 PHE cc_start: 0.8922 (t80) cc_final: 0.8486 (t80)
REVERT: A  918 ARG cc_start: 0.6123 (mmm-85) cc_final: 0.5806 (mmm-85)
REVERT: A  929 MET cc_start: 0.7474 (mtt) cc_final: 0.7214 (mtp)
REVERT: A  940 ASN cc_start: 0.7558 (t0) cc_final: 0.6847 (p0)
REVERT: A 1074 ASP cc_start: 0.6321 (p0) cc_final: 0.5871 (p0)
  outliers start: 10
  outliers final: 4
  residues processed: 256
  average time/residue: 0.0999
  time to fit residues: 34.0175
Evaluate side-chains
  145 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 141
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  533 SER
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  890 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 459 HIS
A 471 GLN
A 616 ASN
A 672 ASN
A 895 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.144406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.117611 restraints weight = 18563.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.119321 restraints weight = 15960.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.120243 restraints weight = 11099.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.120371 restraints weight = 9279.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.120459 restraints weight = 8901.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8790  Z= 0.240
  Angle     :  0.734  13.175  12109  Z= 0.380
  Chirality :  0.043   0.177   1367
  Planarity :  0.004   0.031   1338
  Dihedral  : 19.851 179.226   1816
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.68 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.29), residues: 916
  helix:  1.63 (0.23), residues: 511
  sheet: -2.54 (0.50), residues: 89
  loop : -2.67 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  22 
 TYR   0.026   0.002   TYR A 406 
 PHE   0.021   0.003   PHE A 743 
 TRP   0.018   0.003   TRP A  79 
 HIS   0.016   0.002   HIS A 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 8790)
  covalent geometry    : angle       0.73429 (12109)
  hydrogen bonds       : bond        0.05556 (  439)
  hydrogen bonds       : angle       4.87645 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6274 (tpt) cc_final: 0.5859 (tpt)
REVERT: A   37 LEU cc_start: 0.8373 (mt) cc_final: 0.8137 (mt)
REVERT: A  159 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7014 (tp30)
REVERT: A  460 LYS cc_start: 0.8557 (tttm) cc_final: 0.8348 (ttmt)
REVERT: A  641 LYS cc_start: 0.7874 (mmtp) cc_final: 0.7673 (ttmm)
REVERT: A  806 MET cc_start: 0.7660 (ttp) cc_final: 0.7404 (ttp)
REVERT: A  940 ASN cc_start: 0.7901 (t0) cc_final: 0.7207 (p0)
REVERT: A  959 PHE cc_start: 0.7635 (m-10) cc_final: 0.7401 (m-80)
  outliers start: 19
  outliers final: 10
  residues processed: 157
  average time/residue: 0.0940
  time to fit residues: 20.4067
Evaluate side-chains
  129 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    0.3980
   chunk 78 optimal weight:    0.2980
   chunk 51 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 82 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 711 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.145165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.118090 restraints weight = 18469.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.119787 restraints weight = 13737.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.121250 restraints weight = 9851.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.121153 restraints weight = 7661.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.121305 restraints weight = 7860.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8790  Z= 0.165
  Angle     :  0.645  11.703  12109  Z= 0.332
  Chirality :  0.041   0.160   1367
  Planarity :  0.004   0.064   1338
  Dihedral  : 19.891 176.684   1811
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.10 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.28), residues: 916
  helix:  1.83 (0.23), residues: 498
  sheet: -2.57 (0.51), residues: 85
  loop : -2.60 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  22 
 TYR   0.022   0.002   TYR A 406 
 PHE   0.030   0.002   PHE A  80 
 TRP   0.024   0.002   TRP A 915 
 HIS   0.003   0.001   HIS A 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8790)
  covalent geometry    : angle       0.64527 (12109)
  hydrogen bonds       : bond        0.04715 (  439)
  hydrogen bonds       : angle       4.60755 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6238 (tpt) cc_final: 0.5880 (tpt)
REVERT: A   86 ASN cc_start: 0.8625 (p0) cc_final: 0.8376 (p0)
REVERT: A  159 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6907 (tp30)
REVERT: A  460 LYS cc_start: 0.8523 (tttm) cc_final: 0.8276 (ttmt)
REVERT: A  595 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7716 (pp)
REVERT: A  940 ASN cc_start: 0.7942 (t0) cc_final: 0.7274 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 149
  average time/residue: 0.0792
  time to fit residues: 16.8153
Evaluate side-chains
  134 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 87 optimal weight:   30.0000
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   overall best weight:    2.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.142071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.114508 restraints weight = 19145.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.115735 restraints weight = 15535.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.116738 restraints weight = 11801.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.117621 restraints weight = 9690.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.117642 restraints weight = 9428.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8790  Z= 0.212
  Angle     :  0.676  13.166  12109  Z= 0.352
  Chirality :  0.043   0.154   1367
  Planarity :  0.004   0.034   1338
  Dihedral  : 20.006 176.936   1811
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.52 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.28), residues: 916
  helix:  1.54 (0.23), residues: 499
  sheet: -2.43 (0.49), residues: 94
  loop : -2.71 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 535 
 TYR   0.026   0.002   TYR A 406 
 PHE   0.044   0.002   PHE A  80 
 TRP   0.027   0.002   TRP A 915 
 HIS   0.006   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 8790)
  covalent geometry    : angle       0.67550 (12109)
  hydrogen bonds       : bond        0.04839 (  439)
  hydrogen bonds       : angle       4.72746 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6151 (tpt) cc_final: 0.5788 (tpt)
REVERT: A   37 LEU cc_start: 0.8290 (mt) cc_final: 0.8069 (mt)
REVERT: A  159 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7005 (tp30)
REVERT: A  539 GLU cc_start: 0.4553 (tp30) cc_final: 0.3278 (tp30)
REVERT: A  940 ASN cc_start: 0.7934 (t0) cc_final: 0.7351 (p0)
REVERT: A  948 ASP cc_start: 0.7426 (t0) cc_final: 0.7146 (t0)
REVERT: A 1053 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7121 (ptpp)
  outliers start: 26
  outliers final: 18
  residues processed: 144
  average time/residue: 0.0823
  time to fit residues: 16.8399
Evaluate side-chains
  135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  951 VAL
Chi-restraints excluded: chain A residue 1053 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   chunk 87 optimal weight:    6.9990
   chunk 85 optimal weight:   50.0000
   chunk 53 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.143923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.116777 restraints weight = 18784.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.118128 restraints weight = 15005.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.119378 restraints weight = 11298.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.119433 restraints weight = 9144.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.119542 restraints weight = 9023.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8790  Z= 0.163
  Angle     :  0.622  12.728  12109  Z= 0.324
  Chirality :  0.041   0.177   1367
  Planarity :  0.004   0.031   1338
  Dihedral  : 19.978 178.389   1811
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.04 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.28), residues: 916
  helix:  1.62 (0.23), residues: 498
  sheet: -2.67 (0.46), residues: 95
  loop : -2.64 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.021   0.002   TYR A 406 
 PHE   0.041   0.002   PHE A  80 
 TRP   0.028   0.002   TRP A 915 
 HIS   0.003   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8790)
  covalent geometry    : angle       0.62199 (12109)
  hydrogen bonds       : bond        0.04390 (  439)
  hydrogen bonds       : angle       4.60891 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6167 (tpt) cc_final: 0.5796 (tpt)
REVERT: A  159 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6931 (tp30)
REVERT: A  315 MET cc_start: 0.7692 (mmt) cc_final: 0.7443 (mmt)
REVERT: A  335 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.6349 (m-10)
REVERT: A  539 GLU cc_start: 0.4767 (tp30) cc_final: 0.3552 (tp30)
REVERT: A  585 LEU cc_start: 0.7442 (tp) cc_final: 0.7237 (tp)
REVERT: A  753 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7772 (tt)
REVERT: A  915 TRP cc_start: 0.7607 (t60) cc_final: 0.7377 (t60)
REVERT: A  940 ASN cc_start: 0.7969 (t0) cc_final: 0.7354 (p0)
REVERT: A  948 ASP cc_start: 0.7295 (t0) cc_final: 0.7007 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 140
  average time/residue: 0.0781
  time to fit residues: 15.9165
Evaluate side-chains
  135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 ASN
A 477 ASN
A 616 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.143585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.116668 restraints weight = 18538.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.118137 restraints weight = 15121.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.119236 restraints weight = 11281.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.119385 restraints weight = 9109.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.119556 restraints weight = 8994.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8790  Z= 0.160
  Angle     :  0.619  12.797  12109  Z= 0.321
  Chirality :  0.041   0.176   1367
  Planarity :  0.004   0.030   1338
  Dihedral  : 19.988 178.386   1811
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.95 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.28), residues: 916
  helix:  1.70 (0.23), residues: 499
  sheet: -2.32 (0.50), residues: 85
  loop : -2.65 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.018   0.002   TYR A 406 
 PHE   0.021   0.002   PHE A 743 
 TRP   0.019   0.002   TRP A 915 
 HIS   0.003   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8790)
  covalent geometry    : angle       0.61914 (12109)
  hydrogen bonds       : bond        0.04297 (  439)
  hydrogen bonds       : angle       4.59241 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6202 (tpt) cc_final: 0.5746 (tpt)
REVERT: A  159 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6916 (tp30)
REVERT: A  335 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.6136 (m-10)
REVERT: A  539 GLU cc_start: 0.4717 (tp30) cc_final: 0.3469 (tp30)
REVERT: A  585 LEU cc_start: 0.7502 (tp) cc_final: 0.7281 (tp)
REVERT: A  940 ASN cc_start: 0.7817 (t0) cc_final: 0.7260 (p0)
REVERT: A  948 ASP cc_start: 0.7255 (t0) cc_final: 0.6974 (t0)
REVERT: A 1043 ARG cc_start: 0.6016 (mmt180) cc_final: 0.5488 (tpp80)
  outliers start: 26
  outliers final: 21
  residues processed: 139
  average time/residue: 0.0811
  time to fit residues: 16.4732
Evaluate side-chains
  135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  709 LYS
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0060
   chunk 25 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 93 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.8800

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.142852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.115544 restraints weight = 18886.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.116740 restraints weight = 15365.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.117992 restraints weight = 11580.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.118092 restraints weight = 9564.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.118279 restraints weight = 9254.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8790  Z= 0.175
  Angle     :  0.649  12.604  12109  Z= 0.336
  Chirality :  0.042   0.168   1367
  Planarity :  0.004   0.030   1338
  Dihedral  : 20.003 178.700   1811
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.21 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.28), residues: 916
  helix:  1.65 (0.23), residues: 500
  sheet: -2.19 (0.51), residues: 85
  loop : -2.71 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.016   0.002   TYR A 406 
 PHE   0.023   0.002   PHE A 476 
 TRP   0.036   0.002   TRP A 915 
 HIS   0.004   0.001   HIS A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8790)
  covalent geometry    : angle       0.64947 (12109)
  hydrogen bonds       : bond        0.04385 (  439)
  hydrogen bonds       : angle       4.66076 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6203 (tpt) cc_final: 0.5758 (tpt)
REVERT: A   75 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7562 (mt)
REVERT: A  159 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6861 (tp30)
REVERT: A  335 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.6258 (m-80)
REVERT: A  539 GLU cc_start: 0.4618 (tp30) cc_final: 0.3302 (tp30)
REVERT: A  585 LEU cc_start: 0.7609 (tp) cc_final: 0.7379 (tp)
REVERT: A  780 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7534 (pm20)
REVERT: A  915 TRP cc_start: 0.7557 (t60) cc_final: 0.7331 (t60)
REVERT: A  940 ASN cc_start: 0.7892 (t0) cc_final: 0.7402 (p0)
REVERT: A  948 ASP cc_start: 0.7317 (t0) cc_final: 0.7050 (t0)
REVERT: A 1043 ARG cc_start: 0.6381 (mmt180) cc_final: 0.5887 (tpp80)
  outliers start: 26
  outliers final: 19
  residues processed: 142
  average time/residue: 0.0748
  time to fit residues: 15.5337
Evaluate side-chains
  136 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 480 ASN
** A 616 ASN ** 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 = 0.4104 r_free = 0.4104 target = 0.141517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.114679 restraints weight = 18634.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.115782 restraints weight = 15459.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.116867 restraints weight = 11460.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.117026 restraints weight = 9706.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.117302 restraints weight = 9120.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.4987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8790  Z= 0.193
  Angle     :  0.672  12.508  12109  Z= 0.347
  Chirality :  0.042   0.183   1367
  Planarity :  0.004   0.031   1338
  Dihedral  : 20.050 178.893   1811
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.21 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.28), residues: 916
  helix:  1.57 (0.23), residues: 500
  sheet: -2.25 (0.52), residues: 85
  loop : -2.85 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 652 
 TYR   0.020   0.002   TYR A 116 
 PHE   0.022   0.002   PHE A 743 
 TRP   0.023   0.002   TRP A 915 
 HIS   0.005   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8790)
  covalent geometry    : angle       0.67184 (12109)
  hydrogen bonds       : bond        0.04419 (  439)
  hydrogen bonds       : angle       4.78781 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6191 (tpt) cc_final: 0.5751 (tpt)
REVERT: A   75 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7622 (mt)
REVERT: A  159 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6874 (tp30)
REVERT: A  335 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.6153 (m-80)
REVERT: A  539 GLU cc_start: 0.4667 (tp30) cc_final: 0.3287 (tp30)
REVERT: A  780 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7504 (pm20)
REVERT: A  940 ASN cc_start: 0.7814 (t0) cc_final: 0.7300 (p0)
REVERT: A  996 TYR cc_start: 0.5736 (m-10) cc_final: 0.5406 (m-10)
REVERT: A 1043 ARG cc_start: 0.6579 (mmt180) cc_final: 0.5999 (tpp80)
  outliers start: 30
  outliers final: 20
  residues processed: 139
  average time/residue: 0.0800
  time to fit residues: 16.2314
Evaluate side-chains
  141 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  709 LYS
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0980
   chunk 94 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 86 optimal weight:   30.0000
   chunk 73 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 616 ASN
** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.144275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.116929 restraints weight = 18621.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.117961 restraints weight = 16265.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.118988 restraints weight = 12500.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.119303 restraints weight = 9890.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.119402 restraints weight = 9510.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8790  Z= 0.146
  Angle     :  0.649  12.534  12109  Z= 0.332
  Chirality :  0.041   0.182   1367
  Planarity :  0.003   0.028   1338
  Dihedral  : 19.989 177.966   1811
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.85 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.28), residues: 916
  helix:  1.67 (0.23), residues: 499
  sheet: -2.15 (0.53), residues: 75
  loop : -2.85 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 960 
 TYR   0.035   0.002   TYR A1007 
 PHE   0.022   0.002   PHE A 743 
 TRP   0.042   0.002   TRP A 915 
 HIS   0.002   0.001   HIS A 820 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8790)
  covalent geometry    : angle       0.64865 (12109)
  hydrogen bonds       : bond        0.04117 (  439)
  hydrogen bonds       : angle       4.62496 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6148 (tpt) cc_final: 0.5723 (tpt)
REVERT: A   75 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7524 (mt)
REVERT: A  159 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7100 (tp30)
REVERT: A  585 LEU cc_start: 0.7516 (tp) cc_final: 0.7276 (tp)
REVERT: A  780 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7424 (mp0)
REVERT: A  786 LEU cc_start: 0.7467 (mt) cc_final: 0.7120 (mt)
REVERT: A  915 TRP cc_start: 0.7576 (t60) cc_final: 0.7375 (t60)
REVERT: A  918 ARG cc_start: 0.6762 (mmm-85) cc_final: 0.6460 (mmm-85)
REVERT: A  940 ASN cc_start: 0.7779 (t0) cc_final: 0.7243 (p0)
REVERT: A 1043 ARG cc_start: 0.6731 (mmt180) cc_final: 0.6158 (tpp80)
  outliers start: 25
  outliers final: 16
  residues processed: 144
  average time/residue: 0.0914
  time to fit residues: 18.7021
Evaluate side-chains
  135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  709 LYS
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 39 optimal weight:    8.9990
   chunk 73 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0030
   chunk 84 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 90 optimal weight:    7.9990
   chunk 52 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:   50.0000
   overall best weight:    2.3596

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.140974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.114019 restraints weight = 18530.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.114952 restraints weight = 15537.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.116205 restraints weight = 11947.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.116376 restraints weight = 9513.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.116537 restraints weight = 9402.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.5382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8790  Z= 0.205
  Angle     :  0.709  12.484  12109  Z= 0.367
  Chirality :  0.044   0.190   1367
  Planarity :  0.004   0.043   1338
  Dihedral  : 20.040 177.815   1811
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 18.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.63 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.28), residues: 916
  helix:  1.46 (0.23), residues: 500
  sheet: -2.10 (0.55), residues: 75
  loop : -2.95 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 535 
 TYR   0.018   0.002   TYR A 640 
 PHE   0.023   0.002   PHE A 743 
 TRP   0.030   0.002   TRP A 915 
 HIS   0.005   0.001   HIS A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 8790)
  covalent geometry    : angle       0.70878 (12109)
  hydrogen bonds       : bond        0.04467 (  439)
  hydrogen bonds       : angle       4.81331 ( 1254)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6214 (tpt) cc_final: 0.5779 (tpt)
REVERT: A   75 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7552 (mt)
REVERT: A  159 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6984 (tp30)
REVERT: A  709 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7436 (ptpp)
REVERT: A  780 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7550 (pm20)
REVERT: A  940 ASN cc_start: 0.7842 (t0) cc_final: 0.7261 (p0)
REVERT: A  996 TYR cc_start: 0.5545 (m-10) cc_final: 0.5136 (m-10)
REVERT: A 1038 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5647 (mp)
REVERT: A 1043 ARG cc_start: 0.6560 (mmt180) cc_final: 0.6021 (tpp80)
  outliers start: 23
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0804
  time to fit residues: 15.7391
Evaluate side-chains
  132 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  709 LYS
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  854 LEU
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  951 VAL
Chi-restraints excluded: chain A residue 1038 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6640

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.145065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.117848 restraints weight = 18196.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.118884 restraints weight = 15347.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.119960 restraints weight = 11784.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.120290 restraints weight = 9726.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.120454 restraints weight = 9228.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.5519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8790  Z= 0.138
  Angle     :  0.685  12.621  12109  Z= 0.345
  Chirality :  0.041   0.196   1367
  Planarity :  0.004   0.040   1338
  Dihedral  : 19.942 176.640   1811
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.02 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.28), residues: 916
  helix:  1.57 (0.23), residues: 500
  sheet: -2.00 (0.52), residues: 86
  loop : -3.00 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 620 
 TYR   0.031   0.002   TYR A 995 
 PHE   0.024   0.002   PHE A 743 
 TRP   0.045   0.002   TRP A 915 
 HIS   0.003   0.001   HIS A 820 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8790)
  covalent geometry    : angle       0.68529 (12109)
  hydrogen bonds       : bond        0.04059 (  439)
  hydrogen bonds       : angle       4.66688 ( 1254)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1316.65 seconds
wall clock time: 23 minutes 36.96 seconds (1416.96 seconds total)