Starting phenix.real_space_refine
on Sat May  2 09:10:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yhq_33836/05_2026/7yhq_33836.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yhq_33836/05_2026/7yhq_33836.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/7yhq_33836/05_2026/7yhq_33836.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yhq_33836/05_2026/7yhq_33836.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yhq_33836/05_2026/7yhq_33836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yhq_33836/05_2026/7yhq_33836.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=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      43      5.49       5
     S      23      5.16       5
     C    2461      2.51       5
     N     726      2.21       5
     O     808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4065
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3182
          Classifications: {'peptide': 393}
          Link IDs: {'PTRANS': 25, 'TRANS': 367}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 539
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "C"
      Number of atoms: 181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 181
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "C"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 155
          Unusual residues: {'PED': 1}
          Classifications: {'DNA': 7, 'undetermined': 1}
          Link IDs: {'rna3p': 6, None: 1}
            Not linked:
              pdbres="PED C  26 "
              pdbres=" DG C  27 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1949  SG  CYS A1045      55.589  28.918  53.222  1.00 76.27           S
  ATOM   1897  SG  CYS A1038      52.380  29.895  47.604  1.00 69.77           S
  ATOM   1968  SG  CYS A1048      52.542  24.215  49.877  1.00 71.00           S
  ATOM   2011  SG  CYS A1054      57.449  28.416  49.055  1.00 77.53           S

  Time building chain proxies: 1.01, per 1000 atoms: 0.25
  Number of scatterers: 4065
  At special positions: 0
  Unit cell: (86.43, 72.36, 86.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S      23     16.00
     P      43     15.00
     O     808      8.00
     N     726      7.00
     C    2461      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 96.0 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1401 "
        pdb="FE2  SF4 A1401 " - pdb=" SG  CYS A1038 "
        pdb="FE3  SF4 A1401 " - pdb=" SG  CYS A1048 "
        pdb="FE4  SF4 A1401 " - pdb=" SG  CYS A1054 "
        pdb="FE1  SF4 A1401 " - pdb=" SG  CYS A1045 "
      Number of angles added : 12


  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      55.7% alpha, 3.8% beta
      13 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 560 through 580
    Processing helix  chain 'A' and resid 581 through 583
      No H-bonds generated for 'chain 'A' and resid 581 through 583'
    Processing helix  chain 'A' and resid 595 through 606
      removed outlier: 3.960A  pdb=" N   SER A 599 " --> pdb=" O   SER A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 625
    Processing helix  chain 'A' and resid 884 through 891
      removed outlier: 3.626A  pdb=" N   ILE A 888 " --> pdb=" O   ASP A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 900
    Processing helix  chain 'A' and resid 905 through 925
    Processing helix  chain 'A' and resid 929 through 934
    Processing helix  chain 'A' and resid 936 through 946
    Processing helix  chain 'A' and resid 951 through 964
      removed outlier: 4.180A  pdb=" N   VAL A 955 " --> pdb=" O   GLY A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 981
    Processing helix  chain 'A' and resid 1007 through 1012
    Processing helix  chain 'A' and resid 1013 through 1016
      removed outlier: 3.977A  pdb=" N   CYS A1016 " --> pdb=" O   PRO A1013 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1013 through 1016'
    Processing helix  chain 'A' and resid 1019 through 1037
    Processing helix  chain 'A' and resid 1044 through 1053
      Proline residue:  A1049  - end of helix
      removed outlier: 4.182A  pdb=" N   GLY A1052 " --> pdb=" O   PRO A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1059
      removed outlier: 3.536A  pdb=" N   ALA A1058 " --> pdb=" O   CYS A1054 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER A1059 " --> pdb=" O   ARG A1055 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1054 through 1059'
    Processing helix  chain 'A' and resid 1212 through 1216
    Processing helix  chain 'A' and resid 1286 through 1291
    Processing helix  chain 'A' and resid 1294 through 1299
      removed outlier: 3.509A  pdb=" N   ASN A1297 " --> pdb=" O   PHE A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1309 through 1315
    Processing helix  chain 'A' and resid 1337 through 1343
      removed outlier: 3.614A  pdb=" N   ILE A1341 " --> pdb=" O   SER A1337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1346 through 1356
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1306 through 1308
      removed outlier: 3.956A  pdb=" N   TYR A1229 " --> pdb=" O   LEU A1208 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TYR A1206 " --> pdb=" O   LEU A1231 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1363 through 1364
      removed outlier: 3.723A  pdb=" N   GLY A1363 " --> pdb=" O   LYS A1372 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS A1372 " --> pdb=" O   GLY A1363 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    135 hydrogen bonds defined for protein.
    369 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 0.41

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.21 -     1.43: 1865
        1.43 -     1.64: 2351
        1.64 -     1.85: 28
        1.85 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 4256
  Sorted by residual:
  bond pdb=" O1P PED C  26 "
       pdb=" P   PED C  26 "
    ideal  model  delta    sigma   weight residual
    1.679  1.469  0.210 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" CA  ASN A1044 "
       pdb=" C   ASN A1044 "
    ideal  model  delta    sigma   weight residual
    1.531  1.474  0.057 1.12e-02 7.97e+03 2.57e+01
  bond pdb=" N   THR A 962 "
       pdb=" CA  THR A 962 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.031 1.17e-02 7.31e+03 7.22e+00
  bond pdb=" C   TRP A 562 "
       pdb=" O   TRP A 562 "
    ideal  model  delta    sigma   weight residual
    1.237  1.267 -0.030 1.17e-02 7.31e+03 6.70e+00
  bond pdb=" C   PHE A 625 "
       pdb=" N   PRO A 626 "
    ideal  model  delta    sigma   weight residual
    1.329  1.361 -0.032 1.25e-02 6.40e+03 6.55e+00
  ... (remaining 4251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 5728
        2.20 -     4.39: 183
        4.39 -     6.59: 26
        6.59 -     8.78: 6
        8.78 -    10.98: 4
  Bond angle restraints: 5947
  Sorted by residual:
  angle pdb=" N   ASN A1044 "
        pdb=" CA  ASN A1044 "
        pdb=" C   ASN A1044 "
      ideal   model   delta    sigma   weight residual
     110.70  100.96    9.74 1.55e+00 4.16e-01 3.95e+01
  angle pdb=" C   PHE A 625 "
        pdb=" N   PRO A 626 "
        pdb=" CA  PRO A 626 "
      ideal   model   delta    sigma   weight residual
     120.14  113.74    6.40 1.06e+00 8.90e-01 3.65e+01
  angle pdb=" N   TRP A 561 "
        pdb=" CA  TRP A 561 "
        pdb=" C   TRP A 561 "
      ideal   model   delta    sigma   weight residual
     111.82  106.16    5.66 1.16e+00 7.43e-01 2.38e+01
  angle pdb=" N   ASN A1046 "
        pdb=" CA  ASN A1046 "
        pdb=" C   ASN A1046 "
      ideal   model   delta    sigma   weight residual
     111.82  106.35    5.47 1.16e+00 7.43e-01 2.22e+01
  angle pdb=" C3'  DT B   5 "
        pdb=" O3'  DT B   5 "
        pdb=" P    DG B   6 "
      ideal   model   delta    sigma   weight residual
     120.20  113.50    6.70 1.50e+00 4.44e-01 2.00e+01
  ... (remaining 5942 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.85: 2176
       35.85 -    71.69: 239
       71.69 -   107.53: 10
      107.53 -   143.38: 0
      143.38 -   179.22: 2
  Dihedral angle restraints: 2427
    sinusoidal: 1285
      harmonic: 1142
  Sorted by residual:
  dihedral pdb=" CA  TYR A1001 "
           pdb=" C   TYR A1001 "
           pdb=" N   PRO A1002 "
           pdb=" CA  PRO A1002 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.52  -20.48     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" C4'  DT C  17 "
           pdb=" C3'  DT C  17 "
           pdb=" O3'  DT C  17 "
           pdb=" P    DT C  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.22 -179.22     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT B  12 "
           pdb=" C3'  DT B  12 "
           pdb=" O3'  DT B  12 "
           pdb=" P    DC B  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.30  168.70     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 2424 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 624
       0.102 -    0.203: 25
       0.203 -    0.305: 3
       0.305 -    0.406: 1
       0.406 -    0.508: 3
  Chirality restraints: 656
  Sorted by residual:
  chirality pdb=" P    DG B   6 "
            pdb=" OP1  DG B   6 "
            pdb=" OP2  DG B   6 "
            pdb=" O5'  DG B   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.85   -0.51 2.00e-01 2.50e+01 6.45e+00
  chirality pdb=" P    DT B   5 "
            pdb=" OP1  DT B   5 "
            pdb=" OP2  DT B   5 "
            pdb=" O5'  DT B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.83   -0.48 2.00e-01 2.50e+01 5.76e+00
  chirality pdb=" P    DG B   3 "
            pdb=" OP1  DG B   3 "
            pdb=" OP2  DG B   3 "
            pdb=" O5'  DG B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.82   -0.47 2.00e-01 2.50e+01 5.62e+00
  ... (remaining 653 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 561 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.76e+00
        pdb=" C   TRP A 561 "    0.034 2.00e-02 2.50e+03
        pdb=" O   TRP A 561 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   TRP A 562 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C  27 "    0.018 2.00e-02 2.50e+03   1.02e-02 3.11e+00
        pdb=" N9   DG C  27 "   -0.008 2.00e-02 2.50e+03
        pdb=" C8   DG C  27 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DG C  27 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG C  27 "   -0.020 2.00e-02 2.50e+03
        pdb=" C6   DG C  27 "    0.015 2.00e-02 2.50e+03
        pdb=" O6   DG C  27 "    0.002 2.00e-02 2.50e+03
        pdb=" N1   DG C  27 "    0.009 2.00e-02 2.50e+03
        pdb=" C2   DG C  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG C  27 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG C  27 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG C  27 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 627 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO A 628 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 628 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 628 "    0.024 5.00e-02 4.00e+02
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 851
        2.78 -     3.31: 3854
        3.31 -     3.84: 7214
        3.84 -     4.37: 8241
        4.37 -     4.90: 12622
  Nonbonded interactions: 32782
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 943 "
            pdb=" OG  SER A 946 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OH  TYR A1024 "
            pdb=" OD1 ASN A1297 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   MET A1050 "
            pdb=" N   CYS A1054 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG  SER A 623 "
            pdb=" O   THR A1368 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OE1 GLN A 987 "
            pdb=" N   SER A 992 "
     model   vdw
     2.341 3.120
  ... (remaining 32777 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:             4.420
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.720
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
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      :  0.007   0.210   4263  Z= 0.376
  Angle     :  1.457  54.076   5959  Z= 0.546
  Chirality :  0.060   0.508    656
  Planarity :  0.005   0.041    604
  Dihedral  : 24.124 179.224   1683
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  1.71 %
    Favored  : 96.29 %
  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: -0.58 (0.46), residues: 383
  helix:  1.04 (0.43), residues: 170
  sheet: -2.96 (0.87), residues: 20
  loop : -1.43 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1221 
 TYR   0.022   0.002   TYR A1001 
 PHE   0.012   0.002   PHE A1354 
 TRP   0.014   0.001   TRP A1355 
 HIS   0.003   0.001   HIS A1212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 4256)
  covalent geometry    : angle       0.92647 ( 5947)
  hydrogen bonds       : bond        0.20386 (  167)
  hydrogen bonds       : angle       9.05802 (  433)
  metal coordination   : bond        0.05504 (    4)
  metal coordination   : angle      25.08588 (   12)
  Misc. bond           : bond        0.06755 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A  566 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6823 (mtt-85)
REVERT: A  901 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8328 (ptpt)
REVERT: A  929 LEU cc_start: 0.8896 (mt) cc_final: 0.8632 (mp)
REVERT: A 1378 LEU cc_start: 0.7059 (mt) cc_final: 0.6671 (mp)
  outliers start: 7
  outliers final: 3
  residues processed: 72
  average time/residue: 0.0867
  time to fit residues: 7.5389
Evaluate side-chains
  50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  566 ARG
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue 1038 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 973 ASN
A1008 GLN
** A1029 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 = 0.4125 r_free = 0.4125 target = 0.130222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.106048 restraints weight = 12087.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.108530 restraints weight = 7152.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.110333 restraints weight = 5056.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.111594 restraints weight = 4024.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.112350 restraints weight = 3437.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4263  Z= 0.166
  Angle     :  1.148  43.050   5959  Z= 0.364
  Chirality :  0.040   0.136    656
  Planarity :  0.005   0.038    604
  Dihedral  : 27.581 178.130    907
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  :  8.86 %
    Favored  : 88.57 %
  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 (0.47), residues: 383
  helix:  1.12 (0.42), residues: 172
  sheet: -3.25 (0.81), residues: 22
  loop : -1.49 (0.50), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1369 
 TYR   0.011   0.001   TYR A1001 
 PHE   0.017   0.001   PHE A 569 
 TRP   0.017   0.001   TRP A 562 
 HIS   0.002   0.001   HIS A 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4256)
  covalent geometry    : angle       0.66923 ( 5947)
  hydrogen bonds       : bond        0.05317 (  167)
  hydrogen bonds       : angle       5.53889 (  433)
  metal coordination   : bond        0.01431 (    4)
  metal coordination   : angle      20.79288 (   12)
  Misc. bond           : bond        0.00110 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  929 LEU cc_start: 0.9162 (mt) cc_final: 0.8879 (mp)
REVERT: A 1378 LEU cc_start: 0.7206 (mt) cc_final: 0.6803 (mp)
  outliers start: 9
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0576
  time to fit residues: 4.5502
Evaluate side-chains
  51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain A residue 1038 CYS
Chi-restraints excluded: chain A residue 1039 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0670
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
A 567 ASN
** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1297 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.131620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.107232 restraints weight = 11814.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.109828 restraints weight = 7107.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.111550 restraints weight = 5049.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.112561 restraints weight = 4043.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.113406 restraints weight = 3513.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4263  Z= 0.135
  Angle     :  0.969  37.256   5959  Z= 0.330
  Chirality :  0.040   0.161    656
  Planarity :  0.005   0.034    604
  Dihedral  : 27.203 176.648    903
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.86 %
    Favored  : 84.00 %
  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: -0.65 (0.46), residues: 383
  helix:  1.23 (0.42), residues: 172
  sheet: -3.59 (0.77), residues: 22
  loop : -1.67 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1221 
 TYR   0.010   0.001   TYR A1001 
 PHE   0.011   0.001   PHE A1033 
 TRP   0.010   0.001   TRP A 562 
 HIS   0.001   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4256)
  covalent geometry    : angle       0.60957 ( 5947)
  hydrogen bonds       : bond        0.04311 (  167)
  hydrogen bonds       : angle       5.19413 (  433)
  metal coordination   : bond        0.01224 (    4)
  metal coordination   : angle      16.80259 (   12)
  Misc. bond           : bond        0.00062 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  562 TRP cc_start: 0.6519 (t-100) cc_final: 0.5959 (t60)
REVERT: A  929 LEU cc_start: 0.9167 (mt) cc_final: 0.8857 (mp)
REVERT: A 1003 MET cc_start: 0.6517 (tpp) cc_final: 0.6165 (tpp)
REVERT: A 1378 LEU cc_start: 0.7194 (mt) cc_final: 0.6732 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0687
  time to fit residues: 5.1321
Evaluate side-chains
  48 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue 1038 CYS
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0050
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1029 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.129086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.105009 restraints weight = 11980.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.107402 restraints weight = 7208.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.109152 restraints weight = 5123.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.110100 restraints weight = 4128.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.110511 restraints weight = 3608.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4263  Z= 0.153
  Angle     :  0.950  36.506   5959  Z= 0.340
  Chirality :  0.040   0.194    656
  Planarity :  0.005   0.033    604
  Dihedral  : 26.940 175.232    903
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.43 %
    Favored  : 81.43 %
  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: -0.68 (0.46), residues: 383
  helix:  1.29 (0.42), residues: 172
  sheet: -3.54 (0.81), residues: 22
  loop : -1.78 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1221 
 TYR   0.011   0.001   TYR A1028 
 PHE   0.010   0.001   PHE A1033 
 TRP   0.009   0.001   TRP A 561 
 HIS   0.002   0.001   HIS A1203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4256)
  covalent geometry    : angle       0.63071 ( 5947)
  hydrogen bonds       : bond        0.04356 (  167)
  hydrogen bonds       : angle       5.11164 (  433)
  metal coordination   : bond        0.00959 (    4)
  metal coordination   : angle      15.84091 (   12)
  Misc. bond           : bond        0.00059 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 TRP cc_start: 0.7796 (p90) cc_final: 0.7367 (p90)
REVERT: A  929 LEU cc_start: 0.9215 (mt) cc_final: 0.8913 (mp)
REVERT: A  942 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8099 (tm-30)
REVERT: A 1003 MET cc_start: 0.6467 (tpp) cc_final: 0.6186 (tpp)
REVERT: A 1378 LEU cc_start: 0.7223 (mt) cc_final: 0.6807 (mp)
  outliers start: 11
  outliers final: 8
  residues processed: 50
  average time/residue: 0.0618
  time to fit residues: 4.0831
Evaluate side-chains
  51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue 1038 CYS
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 612 HIS
** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.125209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.101021 restraints weight = 12296.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.103367 restraints weight = 7540.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.104748 restraints weight = 5451.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.105995 restraints weight = 4456.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.106723 restraints weight = 3862.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4263  Z= 0.182
  Angle     :  0.991  37.961   5959  Z= 0.356
  Chirality :  0.041   0.170    656
  Planarity :  0.005   0.037    604
  Dihedral  : 26.905 174.667    899
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.14 %
    Favored  : 79.71 %
  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: -0.98 (0.45), residues: 383
  helix:  0.92 (0.41), residues: 178
  sheet: -3.90 (0.71), residues: 22
  loop : -1.87 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1330 
 TYR   0.016   0.002   TYR A1028 
 PHE   0.013   0.002   PHE A1334 
 TRP   0.035   0.002   TRP A 562 
 HIS   0.003   0.001   HIS A 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 4256)
  covalent geometry    : angle       0.66282 ( 5947)
  hydrogen bonds       : bond        0.04656 (  167)
  hydrogen bonds       : angle       5.19036 (  433)
  metal coordination   : bond        0.00955 (    4)
  metal coordination   : angle      16.43532 (   12)
  Misc. bond           : bond        0.00069 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 TRP cc_start: 0.7696 (p90) cc_final: 0.7093 (p90)
REVERT: A  942 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: A 1378 LEU cc_start: 0.7253 (mt) cc_final: 0.6837 (mp)
  outliers start: 11
  outliers final: 11
  residues processed: 56
  average time/residue: 0.0396
  time to fit residues: 3.2091
Evaluate side-chains
  54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1038 CYS
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Chi-restraints excluded: chain A residue 1338 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.0020
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A1029 GLN ** 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 = 0.4079 r_free = 0.4079 target = 0.125847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.102557 restraints weight = 12365.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.104741 restraints weight = 7663.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.106351 restraints weight = 5546.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.107436 restraints weight = 4476.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.107996 restraints weight = 3869.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4263  Z= 0.149
  Angle     :  0.946  34.735   5959  Z= 0.346
  Chirality :  0.040   0.146    656
  Planarity :  0.004   0.035    604
  Dihedral  : 26.860 174.106    899
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.00 %
    Favored  : 76.86 %
  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: -0.93 (0.45), residues: 383
  helix:  0.97 (0.41), residues: 178
  sheet: -3.93 (0.71), residues: 22
  loop : -1.85 (0.47), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 566 
 TYR   0.011   0.001   TYR A1028 
 PHE   0.028   0.002   PHE A 618 
 TRP   0.037   0.002   TRP A 562 
 HIS   0.003   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4256)
  covalent geometry    : angle       0.65105 ( 5947)
  hydrogen bonds       : bond        0.04132 (  167)
  hydrogen bonds       : angle       5.04382 (  433)
  metal coordination   : bond        0.00799 (    4)
  metal coordination   : angle      15.31422 (   12)
  Misc. bond           : bond        0.00066 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 TRP cc_start: 0.7603 (p90) cc_final: 0.7395 (p90)
REVERT: A 1378 LEU cc_start: 0.7177 (mt) cc_final: 0.6752 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 54
  average time/residue: 0.0434
  time to fit residues: 3.2762
Evaluate side-chains
  50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue 1038 CYS
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0670
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0670
   chunk 34 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
** A1029 GLN ** 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 = 0.4095 r_free = 0.4095 target = 0.126973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.103367 restraints weight = 12292.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.105760 restraints weight = 7350.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.107575 restraints weight = 5222.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.108637 restraints weight = 4155.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.109489 restraints weight = 3580.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4263  Z= 0.135
  Angle     :  0.906  32.375   5959  Z= 0.334
  Chirality :  0.040   0.186    656
  Planarity :  0.004   0.036    604
  Dihedral  : 26.742 173.786    898
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 22.86 %
    Favored  : 74.57 %
  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: -0.82 (0.45), residues: 383
  helix:  1.03 (0.40), residues: 179
  sheet: -3.83 (0.73), residues: 22
  loop : -1.77 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1287 
 TYR   0.010   0.001   TYR A1028 
 PHE   0.024   0.001   PHE A 618 
 TRP   0.038   0.002   TRP A 562 
 HIS   0.004   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4256)
  covalent geometry    : angle       0.63504 ( 5947)
  hydrogen bonds       : bond        0.03867 (  167)
  hydrogen bonds       : angle       4.92940 (  433)
  metal coordination   : bond        0.00594 (    4)
  metal coordination   : angle      14.40657 (   12)
  Misc. bond           : bond        0.00057 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  561 TRP cc_start: 0.7599 (p90) cc_final: 0.7264 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0434
  time to fit residues: 3.2612
Evaluate side-chains
  47 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A1029 GLN ** 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 = 0.4066 r_free = 0.4066 target = 0.124730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.101411 restraints weight = 12113.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.103854 restraints weight = 7310.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.105547 restraints weight = 5184.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.106654 restraints weight = 4140.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.106975 restraints weight = 3558.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4263  Z= 0.158
  Angle     :  0.934  32.136   5959  Z= 0.355
  Chirality :  0.042   0.197    656
  Planarity :  0.005   0.035    604
  Dihedral  : 26.717 173.137    897
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 24.57 %
    Favored  : 72.86 %
  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: -0.89 (0.45), residues: 383
  helix:  0.93 (0.40), residues: 179
  sheet: -3.71 (0.71), residues: 22
  loop : -1.78 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1221 
 TYR   0.011   0.002   TYR A1028 
 PHE   0.023   0.002   PHE A 618 
 TRP   0.035   0.002   TRP A 562 
 HIS   0.006   0.001   HIS A1203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4256)
  covalent geometry    : angle       0.67325 ( 5947)
  hydrogen bonds       : bond        0.04266 (  167)
  hydrogen bonds       : angle       5.01888 (  433)
  metal coordination   : bond        0.00922 (    4)
  metal coordination   : angle      14.44594 (   12)
  Misc. bond           : bond        0.00063 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  561 TRP cc_start: 0.7622 (p90) cc_final: 0.7250 (p90)
  outliers start: 9
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0369
  time to fit residues: 2.7088
Evaluate side-chains
  47 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue 1038 CYS
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.0010
   chunk 38 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A1029 GLN ** 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 = 0.4094 r_free = 0.4094 target = 0.127494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.103876 restraints weight = 12189.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.106387 restraints weight = 7359.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.107927 restraints weight = 5184.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.109238 restraints weight = 4143.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.109880 restraints weight = 3526.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4263  Z= 0.140
  Angle     :  0.892  30.674   5959  Z= 0.342
  Chirality :  0.040   0.155    656
  Planarity :  0.005   0.034    604
  Dihedral  : 26.676 172.894    897
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 23.14 %
    Favored  : 74.29 %
  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: -0.83 (0.45), residues: 383
  helix:  0.99 (0.41), residues: 179
  sheet: -3.68 (0.75), residues: 22
  loop : -1.76 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1204 
 TYR   0.018   0.002   TYR A1333 
 PHE   0.024   0.002   PHE A 618 
 TRP   0.038   0.002   TRP A 562 
 HIS   0.003   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4256)
  covalent geometry    : angle       0.64715 ( 5947)
  hydrogen bonds       : bond        0.03897 (  167)
  hydrogen bonds       : angle       4.92222 (  433)
  metal coordination   : bond        0.00718 (    4)
  metal coordination   : angle      13.70649 (   12)
  Misc. bond           : bond        0.00058 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 TRP cc_start: 0.7590 (p90) cc_final: 0.7194 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0592
  time to fit residues: 4.1143
Evaluate side-chains
  46 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0970
   chunk 12 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A1029 GLN ** 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 = 0.4088 r_free = 0.4088 target = 0.126919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.105033 restraints weight = 12190.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.107381 restraints weight = 7349.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.108654 restraints weight = 5227.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.110023 restraints weight = 4244.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.110539 restraints weight = 3598.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.3927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4263  Z= 0.139
  Angle     :  0.896  30.673   5959  Z= 0.344
  Chirality :  0.040   0.151    656
  Planarity :  0.005   0.036    604
  Dihedral  : 26.629 172.216    897
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 23.71 %
    Favored  : 74.57 %
  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: -0.82 (0.45), residues: 383
  helix:  0.98 (0.40), residues: 179
  sheet: -3.46 (0.79), residues: 22
  loop : -1.77 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1221 
 TYR   0.011   0.001   TYR A1028 
 PHE   0.025   0.002   PHE A 618 
 TRP   0.038   0.002   TRP A 562 
 HIS   0.003   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4256)
  covalent geometry    : angle       0.65592 ( 5947)
  hydrogen bonds       : bond        0.04000 (  167)
  hydrogen bonds       : angle       4.92198 (  433)
  metal coordination   : bond        0.00833 (    4)
  metal coordination   : angle      13.60938 (   12)
  Misc. bond           : bond        0.00057 (    3)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A  561 TRP cc_start: 0.7586 (p90) cc_final: 0.7202 (p90)
  outliers start: 6
  outliers final: 5
  residues processed: 47
  average time/residue: 0.0372
  time to fit residues: 2.6763
Evaluate side-chains
  47 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain A residue  620 SER
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1319 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A1029 GLN ** 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 = 0.4067 r_free = 0.4067 target = 0.125348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.103785 restraints weight = 12218.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.106079 restraints weight = 7267.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.107668 restraints weight = 5136.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.108833 restraints weight = 4060.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.109346 restraints weight = 3465.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4263  Z= 0.157
  Angle     :  0.932  33.096   5959  Z= 0.353
  Chirality :  0.041   0.152    656
  Planarity :  0.005   0.035    604
  Dihedral  : 26.687 171.269    897
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 23.14 %
    Favored  : 74.57 %
  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: -0.87 (0.45), residues: 383
  helix:  0.98 (0.40), residues: 179
  sheet: -3.39 (0.81), residues: 22
  loop : -1.85 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 579 
 TYR   0.016   0.002   TYR A1333 
 PHE   0.024   0.002   PHE A 618 
 TRP   0.036   0.002   TRP A 562 
 HIS   0.003   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 4256)
  covalent geometry    : angle       0.67133 ( 5947)
  hydrogen bonds       : bond        0.04295 (  167)
  hydrogen bonds       : angle       5.02876 (  433)
  metal coordination   : bond        0.01210 (    4)
  metal coordination   : angle      14.42965 (   12)
  Misc. bond           : bond        0.00068 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 868.39 seconds
wall clock time: 15 minutes 43.04 seconds (943.04 seconds total)