Starting phenix.real_space_refine
on Wed Mar  4 11:35:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pzr_13736/03_2026/7pzr_13736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pzr_13736/03_2026/7pzr_13736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pzr_13736/03_2026/7pzr_13736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pzr_13736/03_2026/7pzr_13736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pzr_13736/03_2026/7pzr_13736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pzr_13736/03_2026/7pzr_13736.cif"
  }
  resolution = 3.0
  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=  -0.007 sd=   0.123
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7365 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4712      2.51       5
     N    1336      2.21       5
     O    1307      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7404
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7404
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 935, 7362
          Classifications: {'peptide': 935}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 61, 'TRANS': 873}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 45
      Conformer: "B"
        Number of residues, atoms: 935, 7362
          Classifications: {'peptide': 935}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 61, 'TRANS': 873}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 45
          bond proxies already assigned to first conformer: 7485
  Time building chain proxies: 3.08, per 1000 atoms: 0.42
  Number of scatterers: 7404
  At special positions: 0
  Unit cell: (81.81, 93.93, 103.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1307      8.00
     N    1336      7.00
     C    4712      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: 0.61
  Conformation dependent library (CDL) restraints added in 565.2 milliseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1792

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      68.8% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 220 through 237
    Processing helix  chain 'A' and resid 238 through 252
    Processing helix  chain 'A' and resid 252 through 259
    Processing helix  chain 'A' and resid 260 through 275
    Processing helix  chain 'A' and resid 276 through 291
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 312 through 326
    Processing helix  chain 'A' and resid 329 through 337
    Processing helix  chain 'A' and resid 340 through 354
    Processing helix  chain 'A' and resid 371 through 376
      removed outlier: 4.116A  pdb=" N   ASP A 376 " --> pdb=" O   LYS A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 410
    Processing helix  chain 'A' and resid 424 through 463
    Processing helix  chain 'A' and resid 467 through 474
      removed outlier: 4.030A  pdb=" N   LEU A 474 " --> pdb=" O   PHE A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 490
    Processing helix  chain 'A' and resid 497 through 521
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 3.810A  pdb=" N   LEU A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 557
    Processing helix  chain 'A' and resid 568 through 587
    Processing helix  chain 'A' and resid 624 through 635
    Processing helix  chain 'A' and resid 676 through 687
    Processing helix  chain 'A' and resid 688 through 705
      removed outlier: 3.918A  pdb=" N   ALA A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 723
    Processing helix  chain 'A' and resid 771 through 789
    Processing helix  chain 'A' and resid 818 through 824
    Processing helix  chain 'A' and resid 836 through 850
    Processing helix  chain 'A' and resid 856 through 867
    Processing helix  chain 'A' and resid 867 through 877
    Processing helix  chain 'A' and resid 883 through 888
    Processing helix  chain 'A' and resid 890 through 907
    Processing helix  chain 'A' and resid 925 through 936
    Processing helix  chain 'A' and resid 937 through 944
    Processing helix  chain 'A' and resid 954 through 973
    Processing helix  chain 'A' and resid 976 through 982
    Processing helix  chain 'A' and resid 986 through 999
    Processing helix  chain 'A' and resid 1003 through 1017
      removed outlier: 4.424A  pdb=" N   ARG A1007 " --> pdb=" O   ARG A1003 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU A1017 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1044
    Processing helix  chain 'A' and resid 1044 through 1065
    Processing helix  chain 'A' and resid 1111 through 1143
      Proline residue:  A1120  - end of helix
    Processing helix  chain 'A' and resid 1156 through 1177
      removed outlier: 4.318A  pdb=" N   SER A1161 " --> pdb=" O   ALA A1157 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   VAL A1162 " --> pdb=" O   ALA A1158 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A1172 " --> pdb=" O   ARG A1168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1192
    Processing helix  chain 'A' and resid 1201 through 1210
    Processing helix  chain 'A' and resid 1220 through 1225
      removed outlier: 3.664A  pdb=" N   ARG A1224 " --> pdb=" O   GLU A1220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1229
      removed outlier: 4.093A  pdb=" N   PHE A1229 " --> pdb=" O   THR A1226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1226 through 1229'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415
    Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496
    Processing sheet with id=AA3, first strand: chain 'A' and resid 794 through 795
    Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 800
    Processing sheet with id=AA5, first strand: chain 'A' and resid 919 through 921
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1069 through 1071

    484 hydrogen bonds defined for protein.
    1434 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1599
        1.33 -     1.45: 1602
        1.45 -     1.57: 4309
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 7585
  Sorted by residual:
  bond pdb=" CB  ILE A1124 "
       pdb=" CG1 ILE A1124 "
    ideal  model  delta    sigma   weight residual
    1.530  1.498  0.032 2.00e-02 2.50e+03 2.59e+00
  bond pdb=" CG1 ILE A1124 "
       pdb=" CD1 ILE A1124 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.21e+00
  bond pdb=" CB  ASN A 799 "
       pdb=" CG  ASN A 799 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.18e+00
  bond pdb=" CG  LEU A 490 "
       pdb=" CD2 LEU A 490 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.48e+00
  bond pdb=" CB  VAL A1149 "
       pdb=" CG2 VAL A1149 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.27e+00
  ... (remaining 7580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 9972
        1.77 -     3.53: 290
        3.53 -     5.30: 34
        5.30 -     7.06: 8
        7.06 -     8.83: 2
  Bond angle restraints: 10306
  Sorted by residual:
  angle pdb=" N   PHE A1229 "
        pdb=" CA  PHE A1229 "
        pdb=" CB  PHE A1229 "
      ideal   model   delta    sigma   weight residual
     110.68  119.51   -8.83 1.68e+00 3.54e-01 2.76e+01
  angle pdb=" N   ARG A 273 "
        pdb=" CA  ARG A 273 "
        pdb=" C   ARG A 273 "
      ideal   model   delta    sigma   weight residual
     113.97  109.29    4.68 1.28e+00 6.10e-01 1.34e+01
  angle pdb=" C   ARG A 273 "
        pdb=" N   GLN A 274 "
        pdb=" CA  GLN A 274 "
      ideal   model   delta    sigma   weight residual
     121.52  127.19   -5.67 1.84e+00 2.95e-01 9.51e+00
  angle pdb=" C   GLY A 923 "
        pdb=" N   SER A 924 "
        pdb=" CA  SER A 924 "
      ideal   model   delta    sigma   weight residual
     121.54  127.35   -5.81 1.91e+00 2.74e-01 9.25e+00
  angle pdb=" N   GLY A 521 "
        pdb=" CA  GLY A 521 "
        pdb=" C   GLY A 521 "
      ideal   model   delta    sigma   weight residual
     115.64  111.30    4.34 1.46e+00 4.69e-01 8.83e+00
  ... (remaining 10301 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4251
       17.83 -    35.66: 315
       35.66 -    53.48: 52
       53.48 -    71.31: 12
       71.31 -    89.14: 3
  Dihedral angle restraints: 4633
    sinusoidal: 1873
      harmonic: 2760
  Sorted by residual:
  dihedral pdb=" N   PHE A1229 "
           pdb=" C   PHE A1229 "
           pdb=" CA  PHE A1229 "
           pdb=" CB  PHE A1229 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.61   -7.81     0      2.50e+00 1.60e-01 9.75e+00
  dihedral pdb=" CB AMET A 671 "
           pdb=" CG AMET A 671 "
           pdb=" SD AMET A 671 "
           pdb=" CE AMET A 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.68  -59.68     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  ARG A 967 "
           pdb=" CB  ARG A 967 "
           pdb=" CG  ARG A 967 "
           pdb=" CD  ARG A 967 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -130.70  -49.30     3      1.50e+01 4.44e-03 8.76e+00
  ... (remaining 4630 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 881
       0.043 -    0.086: 187
       0.086 -    0.129: 64
       0.129 -    0.172: 11
       0.172 -    0.216: 5
  Chirality restraints: 1148
  Sorted by residual:
  chirality pdb=" CB  VAL A1149 "
            pdb=" CA  VAL A1149 "
            pdb=" CG1 VAL A1149 "
            pdb=" CG2 VAL A1149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CG  LEU A 473 "
            pdb=" CB  LEU A 473 "
            pdb=" CD1 LEU A 473 "
            pdb=" CD2 LEU A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.94e-01
  chirality pdb=" CB  VAL A 867 "
            pdb=" CA  VAL A 867 "
            pdb=" CG1 VAL A 867 "
            pdb=" CG2 VAL A 867 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.67e-01
  ... (remaining 1145 not shown)

  Planarity restraints: 1337
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1229 "    0.049 2.00e-02 2.50e+03   4.54e-02 3.61e+01
        pdb=" CG  PHE A1229 "   -0.105 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1229 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1229 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1229 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1229 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1229 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 512 "   -0.030 2.00e-02 2.50e+03   2.78e-02 1.16e+01
        pdb=" CG  HIS A 512 "    0.059 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 512 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 512 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 512 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 512 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A1167 "   -0.016 2.00e-02 2.50e+03   3.13e-02 9.81e+00
        pdb=" C   CYS A1167 "    0.054 2.00e-02 2.50e+03
        pdb=" O   CYS A1167 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A1168 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1334 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 25
        2.63 -     3.20: 6794
        3.20 -     3.76: 12635
        3.76 -     4.33: 17269
        4.33 -     4.90: 27323
  Nonbonded interactions: 64046
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 900 "
            pdb=" OH  TYR A 913 "
     model   vdw
     2.062 3.040
  nonbonded pdb=" O   VAL A 963 "
            pdb=" NE2 GLN A1035 "
     model   vdw
     2.156 3.120
  nonbonded pdb=" OD1 ASN A 528 "
            pdb=" NH2 ARG A 531 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" ND2 ASN A 369 "
            pdb=" O   THR A 690 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   LEU A 235 "
            pdb=" NH2 ARG A 516 "
     model   vdw
     2.295 3.120
  ... (remaining 64041 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:8.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
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      :  0.004   0.058   7585  Z= 0.177
  Angle     :  0.706   8.828  10306  Z= 0.417
  Chirality :  0.043   0.216   1148
  Planarity :  0.005   0.075   1337
  Dihedral  : 12.708  89.141   2841
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  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:  3.84 (0.27), residues: 930
  helix:  3.32 (0.20), residues: 626
  sheet:  0.96 (1.13), residues: 23
  loop :  0.89 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 516 
 TYR   0.043   0.002   TYR A 610 
 PHE   0.105   0.003   PHE A1229 
 TRP   0.015   0.002   TRP A 892 
 HIS   0.025   0.003   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7585)
  covalent geometry    : angle       0.70621 (10306)
  hydrogen bonds       : bond        0.12859 (  484)
  hydrogen bonds       : angle       5.12755 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.281 
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  395 THR cc_start: 0.8442 (m) cc_final: 0.8148 (p)
REVERT: A  482 MET cc_start: 0.8007 (ttp) cc_final: 0.7771 (ttm)
REVERT: A  495 GLU cc_start: 0.8442 (tp30) cc_final: 0.8220 (tm-30)
REVERT: A  988 LYS cc_start: 0.7535 (mtpt) cc_final: 0.6980 (mptt)
REVERT: A  992 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7230 (tm-30)
REVERT: A 1038 LYS cc_start: 0.7461 (mtmt) cc_final: 0.7234 (mmpt)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.6348
  time to fit residues: 157.7445
Evaluate side-chains
  124 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0050
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0970
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 390 HIS
A 704 ASN
A 788 HIS
** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.148879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.116899 restraints weight = 35714.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 6.02
r_work: 0.3745 rms_B_bonded: 5.90 restraints_weight: 2.0000
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3754 r_free = 0.3754    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3754 r_free = 0.3754    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7585  Z= 0.163
  Angle     :  0.746  12.049  10306  Z= 0.368
  Chirality :  0.039   0.150   1148
  Planarity :  0.006   0.067   1337
  Dihedral  :  4.246  46.472   1035
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.60 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.26), residues: 930
  helix:  2.40 (0.19), residues: 637
  sheet:  0.33 (0.87), residues: 33
  loop :  0.57 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 936 
 TYR   0.016   0.002   TYR A1031 
 PHE   0.046   0.003   PHE A 802 
 TRP   0.044   0.002   TRP A1154 
 HIS   0.009   0.002   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7585)
  covalent geometry    : angle       0.74610 (10306)
  hydrogen bonds       : bond        0.05221 (  484)
  hydrogen bonds       : angle       4.43800 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8380 (mm-40)
REVERT: A  425 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8475 (pptt)
REVERT: A  450 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8237 (mtp85)
REVERT: A  495 GLU cc_start: 0.8874 (tp30) cc_final: 0.8350 (tm-30)
REVERT: A  822 ARG cc_start: 0.7593 (mtt90) cc_final: 0.7320 (mtt-85)
REVERT: A  972 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7873 (mp10)
REVERT: A  975 MET cc_start: 0.8006 (mmm) cc_final: 0.7198 (ttt)
REVERT: A  992 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7432 (tm-30)
REVERT: A 1038 LYS cc_start: 0.7109 (mtmt) cc_final: 0.6782 (mmpt)
REVERT: A 1042 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8311 (mp0)
REVERT: A 1062 SER cc_start: 0.9078 (m) cc_final: 0.8647 (p)
  outliers start: 30
  outliers final: 5
  residues processed: 151
  average time/residue: 0.4999
  time to fit residues: 80.1834
Evaluate side-chains
  111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  972 GLN
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1042 GLU
Chi-restraints excluded: chain A residue 1230 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 75 optimal weight:    0.0060
   chunk 60 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 78 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.5374

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 815 HIS
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 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 = 0.4372 r_free = 0.4372 target = 0.147386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.113605 restraints weight = 41058.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 5.90
r_work: 0.3711 rms_B_bonded: 5.89 restraints_weight: 2.0000
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7585  Z= 0.145
  Angle     :  0.734  13.712  10306  Z= 0.351
  Chirality :  0.038   0.140   1148
  Planarity :  0.005   0.044   1337
  Dihedral  :  4.179  47.390   1035
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.26 %
    Favored  : 77.57 %
  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:  2.50 (0.27), residues: 930
  helix:  2.21 (0.20), residues: 627
  sheet:  0.36 (0.85), residues: 33
  loop :  0.62 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 936 
 TYR   0.018   0.002   TYR A 468 
 PHE   0.032   0.003   PHE A 277 
 TRP   0.037   0.002   TRP A 567 
 HIS   0.007   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7585)
  covalent geometry    : angle       0.73446 (10306)
  hydrogen bonds       : bond        0.04587 (  484)
  hydrogen bonds       : angle       4.40412 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8354 (mm-40)
REVERT: A  263 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7887 (ptm)
REVERT: A  268 MET cc_start: 0.8398 (mpt) cc_final: 0.8157 (mmm)
REVERT: A  321 GLU cc_start: 0.7931 (pt0) cc_final: 0.7633 (pp20)
REVERT: A  372 LYS cc_start: 0.7619 (pmtt) cc_final: 0.7201 (tptp)
REVERT: A  471 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8883 (mm)
REVERT: A  495 GLU cc_start: 0.8900 (tp30) cc_final: 0.8377 (tm-30)
REVERT: A  822 ARG cc_start: 0.7732 (mtt90) cc_final: 0.7483 (mpt-90)
REVERT: A  868 MET cc_start: 0.7536 (tmm) cc_final: 0.6459 (tpp)
REVERT: A  975 MET cc_start: 0.7944 (mmm) cc_final: 0.7155 (ttm)
REVERT: A 1062 SER cc_start: 0.9015 (m) cc_final: 0.8539 (p)
REVERT: A 1208 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7546 (mp)
  outliers start: 25
  outliers final: 9
  residues processed: 124
  average time/residue: 0.4822
  time to fit residues: 63.5441
Evaluate side-chains
  100 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  510 SER
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1208 LEU
Chi-restraints excluded: chain A residue 1230 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 38 optimal weight:    0.0570
   chunk 62 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0670
   chunk 81 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.2040

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

Flipped N/Q/H residues before XYZ refinement:
A 252 GLN
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 680 HIS
A 788 HIS
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.142698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.108336 restraints weight = 38680.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 5.79
r_work: 0.3623 rms_B_bonded: 5.79 restraints_weight: 2.0000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.4552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7585  Z= 0.159
  Angle     :  0.738  13.098  10306  Z= 0.349
  Chirality :  0.040   0.155   1148
  Planarity :  0.005   0.036   1337
  Dihedral  :  4.175  40.669   1035
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.15 %
    Favored  : 76.30 %
  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:  2.28 (0.27), residues: 930
  helix:  2.03 (0.20), residues: 621
  sheet:  0.12 (0.88), residues: 35
  loop :  0.66 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 447 
 TYR   0.012   0.001   TYR A 530 
 PHE   0.026   0.003   PHE A 802 
 TRP   0.028   0.002   TRP A1154 
 HIS   0.006   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7585)
  covalent geometry    : angle       0.73796 (10306)
  hydrogen bonds       : bond        0.04471 (  484)
  hydrogen bonds       : angle       4.35774 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7617 (ptm)
REVERT: A  268 MET cc_start: 0.8352 (mpt) cc_final: 0.7995 (mmm)
REVERT: A  277 PHE cc_start: 0.8407 (t80) cc_final: 0.8103 (t80)
REVERT: A  286 MET cc_start: 0.7673 (mmp) cc_final: 0.7470 (tpp)
REVERT: A  321 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7649 (pp20)
REVERT: A  372 LYS cc_start: 0.7773 (pmtt) cc_final: 0.7315 (tptp)
REVERT: A  495 GLU cc_start: 0.8976 (tp30) cc_final: 0.8464 (tm-30)
REVERT: A  533 TYR cc_start: 0.7853 (t80) cc_final: 0.7424 (t80)
REVERT: A  566 PRO cc_start: 0.8155 (Cg_endo) cc_final: 0.7909 (Cg_exo)
REVERT: A  772 MET cc_start: 0.7547 (tmm) cc_final: 0.7042 (tmm)
REVERT: A  868 MET cc_start: 0.7632 (tmm) cc_final: 0.6633 (tpp)
REVERT: A  975 MET cc_start: 0.7982 (mmm) cc_final: 0.7198 (ttm)
REVERT: A 1062 SER cc_start: 0.9090 (m) cc_final: 0.8599 (p)
  outliers start: 28
  outliers final: 12
  residues processed: 120
  average time/residue: 0.4370
  time to fit residues: 56.3661
Evaluate side-chains
  101 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  632 GLU
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 921 GLN
A 953 GLN
A1170 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.135479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.100255 restraints weight = 46363.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 6.00
r_work: 0.3499 rms_B_bonded: 5.79 restraints_weight: 2.0000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.5300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7585  Z= 0.233
  Angle     :  0.809  15.500  10306  Z= 0.386
  Chirality :  0.043   0.225   1148
  Planarity :  0.005   0.048   1337
  Dihedral  :  4.332  26.268   1035
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 21.17 %
    Favored  : 74.90 %
  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:  1.55 (0.27), residues: 930
  helix:  1.48 (0.20), residues: 627
  sheet:  0.00 (0.89), residues: 35
  loop :  0.30 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 502 
 TYR   0.021   0.002   TYR A 530 
 PHE   0.025   0.003   PHE A1186 
 TRP   0.032   0.002   TRP A1154 
 HIS   0.008   0.002   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 7585)
  covalent geometry    : angle       0.80920 (10306)
  hydrogen bonds       : bond        0.05049 (  484)
  hydrogen bonds       : angle       4.65967 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7723 (ptm)
REVERT: A  268 MET cc_start: 0.8406 (mpt) cc_final: 0.7985 (mmm)
REVERT: A  277 PHE cc_start: 0.8428 (t80) cc_final: 0.8105 (t80)
REVERT: A  321 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7672 (pp20)
REVERT: A  441 TRP cc_start: 0.8037 (m-10) cc_final: 0.7501 (m-90)
REVERT: A  451 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8971 (mm-30)
REVERT: A  495 GLU cc_start: 0.9042 (tp30) cc_final: 0.8513 (tm-30)
REVERT: A  533 TYR cc_start: 0.8078 (t80) cc_final: 0.7481 (t80)
REVERT: A  772 MET cc_start: 0.7651 (tmm) cc_final: 0.7135 (tmm)
REVERT: A  868 MET cc_start: 0.7649 (tmm) cc_final: 0.6619 (tpp)
  outliers start: 31
  outliers final: 14
  residues processed: 115
  average time/residue: 0.4351
  time to fit residues: 53.7597
Evaluate side-chains
  100 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1010 ILE
Chi-restraints excluded: chain A residue 1019 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 83 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.138869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.104437 restraints weight = 36677.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 5.49
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7585  Z= 0.148
  Angle     :  0.791  13.429  10306  Z= 0.362
  Chirality :  0.042   0.335   1148
  Planarity :  0.005   0.070   1337
  Dihedral  :  4.220  32.949   1035
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.94 %
    Favored  : 74.02 %
  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:  1.74 (0.27), residues: 930
  helix:  1.62 (0.21), residues: 629
  sheet:  0.09 (0.90), residues: 35
  loop :  0.35 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 976 
 TYR   0.014   0.002   TYR A 468 
 PHE   0.024   0.002   PHE A 497 
 TRP   0.025   0.002   TRP A1154 
 HIS   0.006   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7585)
  covalent geometry    : angle       0.79127 (10306)
  hydrogen bonds       : bond        0.04405 (  484)
  hydrogen bonds       : angle       4.51062 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8171 (p)
REVERT: A  268 MET cc_start: 0.8327 (mpt) cc_final: 0.8025 (mmm)
REVERT: A  321 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7722 (pp20)
REVERT: A  451 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8727 (mm-30)
REVERT: A  495 GLU cc_start: 0.9000 (tp30) cc_final: 0.8347 (tm-30)
REVERT: A  566 PRO cc_start: 0.7982 (Cg_endo) cc_final: 0.7779 (Cg_exo)
REVERT: A  772 MET cc_start: 0.7694 (tmm) cc_final: 0.7260 (tmm)
REVERT: A  868 MET cc_start: 0.7123 (tmm) cc_final: 0.6418 (tpp)
REVERT: A  975 MET cc_start: 0.7841 (mmm) cc_final: 0.7113 (ttt)
REVERT: A  977 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.8957 (p)
REVERT: A 1062 SER cc_start: 0.8908 (m) cc_final: 0.8491 (p)
  outliers start: 24
  outliers final: 10
  residues processed: 113
  average time/residue: 0.4599
  time to fit residues: 55.7186
Evaluate side-chains
  103 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 92 optimal weight:    0.1980
   chunk 82 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 512 HIS
A 893 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.139314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.104571 restraints weight = 41137.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 5.84
r_work: 0.3579 rms_B_bonded: 5.73 restraints_weight: 2.0000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.5596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7585  Z= 0.147
  Angle     :  0.797  13.638  10306  Z= 0.369
  Chirality :  0.041   0.332   1148
  Planarity :  0.005   0.042   1337
  Dihedral  :  4.165  35.501   1035
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.70 %
    Favored  : 73.51 %
  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:  1.76 (0.27), residues: 930
  helix:  1.65 (0.21), residues: 629
  sheet:  0.07 (0.89), residues: 35
  loop :  0.34 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 976 
 TYR   0.012   0.002   TYR A 468 
 PHE   0.034   0.002   PHE A 277 
 TRP   0.021   0.002   TRP A1154 
 HIS   0.006   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7585)
  covalent geometry    : angle       0.79664 (10306)
  hydrogen bonds       : bond        0.04300 (  484)
  hydrogen bonds       : angle       4.49141 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7764 (ptm)
REVERT: A  268 MET cc_start: 0.8362 (mpt) cc_final: 0.7994 (mmm)
REVERT: A  286 MET cc_start: 0.7374 (tpp) cc_final: 0.7092 (mpp)
REVERT: A  321 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7662 (pp20)
REVERT: A  451 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8934 (mm-30)
REVERT: A  495 GLU cc_start: 0.9048 (tp30) cc_final: 0.8560 (tm-30)
REVERT: A  533 TYR cc_start: 0.7821 (t80) cc_final: 0.7610 (t80)
REVERT: A  772 MET cc_start: 0.7715 (tmm) cc_final: 0.7277 (tmm)
REVERT: A  868 MET cc_start: 0.7594 (tmm) cc_final: 0.6670 (tpp)
REVERT: A  975 MET cc_start: 0.7964 (mmm) cc_final: 0.7222 (ttt)
REVERT: A  977 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8847 (p)
REVERT: A 1042 GLU cc_start: 0.8585 (tp30) cc_final: 0.8330 (tm-30)
REVERT: A 1062 SER cc_start: 0.9120 (m) cc_final: 0.8710 (p)
  outliers start: 22
  outliers final: 10
  residues processed: 111
  average time/residue: 0.4144
  time to fit residues: 49.8890
Evaluate side-chains
  102 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 13 optimal weight:   30.0000
   chunk 61 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.139156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.103610 restraints weight = 42734.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 5.98
r_work: 0.3563 rms_B_bonded: 5.78 restraints_weight: 2.0000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.5766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7585  Z= 0.152
  Angle     :  0.792  13.585  10306  Z= 0.367
  Chirality :  0.043   0.331   1148
  Planarity :  0.005   0.089   1337
  Dihedral  :  4.192  35.358   1035
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.95 %
    Favored  : 73.38 %
  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:  1.76 (0.27), residues: 930
  helix:  1.63 (0.21), residues: 629
  sheet:  0.22 (0.92), residues: 35
  loop :  0.34 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 447 
 TYR   0.011   0.002   TYR A 468 
 PHE   0.026   0.002   PHE A 497 
 TRP   0.020   0.002   TRP A1154 
 HIS   0.006   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7585)
  covalent geometry    : angle       0.79230 (10306)
  hydrogen bonds       : bond        0.04308 (  484)
  hydrogen bonds       : angle       4.51254 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7736 (ptm)
REVERT: A  268 MET cc_start: 0.8363 (mpt) cc_final: 0.8009 (mmm)
REVERT: A  321 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7673 (pp20)
REVERT: A  441 TRP cc_start: 0.7879 (m-10) cc_final: 0.7377 (m-90)
REVERT: A  451 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8920 (mm-30)
REVERT: A  487 LEU cc_start: 0.8022 (tp) cc_final: 0.7782 (tt)
REVERT: A  495 GLU cc_start: 0.9081 (tp30) cc_final: 0.8598 (tm-30)
REVERT: A  533 TYR cc_start: 0.7894 (t80) cc_final: 0.7624 (t80)
REVERT: A  772 MET cc_start: 0.7760 (tmm) cc_final: 0.7336 (tmm)
REVERT: A  805 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7718 (mtp85)
REVERT: A  868 MET cc_start: 0.7579 (tmm) cc_final: 0.6669 (tpp)
REVERT: A  975 MET cc_start: 0.7933 (mmm) cc_final: 0.7043 (ttt)
REVERT: A 1042 GLU cc_start: 0.8562 (tp30) cc_final: 0.8334 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 105
  average time/residue: 0.4191
  time to fit residues: 47.3318
Evaluate side-chains
  103 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  502 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  805 ARG
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 30 optimal weight:    0.0470
   chunk 79 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** A1115 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 = 0.4289 r_free = 0.4289 target = 0.141031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.105450 restraints weight = 45794.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 6.18
r_work: 0.3588 rms_B_bonded: 5.96 restraints_weight: 2.0000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3598 r_free = 0.3598    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3598 r_free = 0.3598    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3598
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.5887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7585  Z= 0.139
  Angle     :  0.791  13.618  10306  Z= 0.365
  Chirality :  0.041   0.321   1148
  Planarity :  0.005   0.073   1337
  Dihedral  :  4.148  39.503   1035
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.59 %
    Favored  : 72.75 %
  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:  1.81 (0.27), residues: 930
  helix:  1.69 (0.21), residues: 630
  sheet:  0.13 (0.93), residues: 35
  loop :  0.33 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 447 
 TYR   0.013   0.001   TYR A 282 
 PHE   0.043   0.002   PHE A 465 
 TRP   0.020   0.001   TRP A 567 
 HIS   0.006   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7585)
  covalent geometry    : angle       0.79070 (10306)
  hydrogen bonds       : bond        0.04077 (  484)
  hydrogen bonds       : angle       4.42504 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 MET cc_start: 0.8344 (mpt) cc_final: 0.7969 (mmm)
REVERT: A  289 ASP cc_start: 0.8550 (t0) cc_final: 0.8309 (t0)
REVERT: A  321 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7653 (pp20)
REVERT: A  441 TRP cc_start: 0.7954 (m-10) cc_final: 0.7413 (m-90)
REVERT: A  451 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8957 (mm-30)
REVERT: A  495 GLU cc_start: 0.9061 (tp30) cc_final: 0.8573 (tm-30)
REVERT: A  533 TYR cc_start: 0.7856 (t80) cc_final: 0.7603 (OUTLIER)
REVERT: A  560 GLU cc_start: 0.8112 (pm20) cc_final: 0.6654 (tp30)
REVERT: A  800 MET cc_start: 0.8778 (ptm) cc_final: 0.8515 (ppp)
REVERT: A  805 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7769 (mtp85)
REVERT: A  868 MET cc_start: 0.7594 (tmm) cc_final: 0.6750 (tpp)
  outliers start: 21
  outliers final: 12
  residues processed: 116
  average time/residue: 0.4490
  time to fit residues: 55.8039
Evaluate side-chains
  106 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  502 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  648 MET
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  805 ARG
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 14 optimal weight:    0.1980
   chunk 55 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0670
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.139674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.104606 restraints weight = 44247.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 6.06
r_work: 0.3583 rms_B_bonded: 5.80 restraints_weight: 2.0000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.6013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7585  Z= 0.151
  Angle     :  0.820  13.202  10306  Z= 0.378
  Chirality :  0.044   0.444   1148
  Planarity :  0.005   0.064   1337
  Dihedral  :  4.188  38.589   1035
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 25.22 %
    Favored  : 72.24 %
  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:  1.69 (0.27), residues: 930
  helix:  1.64 (0.21), residues: 629
  sheet:  0.16 (0.96), residues: 35
  loop :  0.16 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 481 
 TYR   0.009   0.001   TYR A1004 
 PHE   0.027   0.002   PHE A 497 
 TRP   0.022   0.002   TRP A1154 
 HIS   0.007   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7585)
  covalent geometry    : angle       0.81998 (10306)
  hydrogen bonds       : bond        0.04208 (  484)
  hydrogen bonds       : angle       4.50005 ( 1434)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8033 (p)
REVERT: A  268 MET cc_start: 0.8346 (mpt) cc_final: 0.7968 (mmm)
REVERT: A  289 ASP cc_start: 0.8572 (t0) cc_final: 0.8314 (t0)
REVERT: A  321 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7625 (pp20)
REVERT: A  441 TRP cc_start: 0.7933 (m-10) cc_final: 0.7421 (m-90)
REVERT: A  451 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8950 (mm-30)
REVERT: A  495 GLU cc_start: 0.9112 (tp30) cc_final: 0.8579 (tm-30)
REVERT: A  772 MET cc_start: 0.7764 (tmm) cc_final: 0.7313 (pmt)
REVERT: A  805 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7786 (mtp85)
REVERT: A  868 MET cc_start: 0.7620 (tmm) cc_final: 0.6698 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 107
  average time/residue: 0.4464
  time to fit residues: 51.3836
Evaluate side-chains
  109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  502 ARG
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  648 MET
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  805 ARG
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  972 GLN
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 61 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 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 = 0.4289 r_free = 0.4289 target = 0.140308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.106063 restraints weight = 36408.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 6.22
r_work: 0.3593 rms_B_bonded: 5.79 restraints_weight: 2.0000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.6057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7585  Z= 0.148
  Angle     :  0.825  13.192  10306  Z= 0.380
  Chirality :  0.042   0.321   1148
  Planarity :  0.005   0.063   1337
  Dihedral  :  4.174  39.027   1035
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 25.60 %
    Favored  : 72.24 %
  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:  1.73 (0.27), residues: 930
  helix:  1.64 (0.21), residues: 627
  sheet:  0.13 (0.96), residues: 35
  loop :  0.27 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 481 
 TYR   0.010   0.001   TYR A 468 
 PHE   0.044   0.002   PHE A 465 
 TRP   0.021   0.002   TRP A1154 
 HIS   0.006   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7585)
  covalent geometry    : angle       0.82489 (10306)
  hydrogen bonds       : bond        0.04200 (  484)
  hydrogen bonds       : angle       4.48743 ( 1434)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3231.80 seconds
wall clock time: 55 minutes 32.09 seconds (3332.09 seconds total)