Starting phenix.real_space_refine
on Sun Apr  5 20:03:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zc4_14619/04_2026/7zc4_14619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zc4_14619/04_2026/7zc4_14619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zc4_14619/04_2026/7zc4_14619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zc4_14619/04_2026/7zc4_14619.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zc4_14619/04_2026/7zc4_14619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zc4_14619/04_2026/7zc4_14619.map"
  }
  resolution = 3.24
  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=   0.001 sd=   0.015
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 7224 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      48      5.16       5
     C    4630      2.51       5
     N    1303      2.21       5
     O    1291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7272
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7272
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 926, 7254
          Classifications: {'peptide': 926}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 62, 'TRANS': 863}
          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: 926, 7254
          Classifications: {'peptide': 926}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 62, 'TRANS': 863}
          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: 7404
  Time building chain proxies: 2.92, per 1000 atoms: 0.40
  Number of scatterers: 7272
  At special positions: 0
  Unit cell: (79.79, 93.93, 107.06, 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      48     16.00
     O    1291      8.00
     N    1303      7.00
     C    4630      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: 0.36
  Conformation dependent library (CDL) restraints added in 388.4 milliseconds
  

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1772

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      69.0% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 221 through 236
    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 323
      removed outlier: 3.565A  pdb=" N   ILE A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 336
    Processing helix  chain 'A' and resid 340 through 354
    Processing helix  chain 'A' and resid 371 through 379
      removed outlier: 4.533A  pdb=" N   ASP A 376 " --> pdb=" O   LYS A 372 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   VAL A 377 " --> pdb=" O   LEU A 373 " (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 473
    Processing helix  chain 'A' and resid 475 through 490
    Processing helix  chain 'A' and resid 496 through 520
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 3.862A  pdb=" N   CYS A 535 " --> pdb=" O   ARG A 531 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 537 " --> pdb=" O   TYR A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 557
    Processing helix  chain 'A' and resid 561 through 565
    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: 3.806A  pdb=" N   LEU A 692 " --> pdb=" O   PRO A 688 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   GLY A 694 " --> pdb=" O   THR A 690 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ALA A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   CYS A 705 " --> pdb=" O   GLN A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 723
      removed outlier: 3.524A  pdb=" N   ALA A 723 " --> pdb=" O   GLN A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 789
    Processing helix  chain 'A' and resid 814 through 817
    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
      removed outlier: 4.122A  pdb=" N   GLY A 887 " --> pdb=" O   LYS A 883 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA A 888 " --> pdb=" O   TRP A 884 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 883 through 888'
    Processing helix  chain 'A' and resid 890 through 907
    Processing helix  chain 'A' and resid 925 through 935
    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 981
    Processing helix  chain 'A' and resid 986 through 1000
    Processing helix  chain 'A' and resid 1008 through 1017
      removed outlier: 3.783A  pdb=" N   LEU A1017 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1023
      No H-bonds generated for 'chain 'A' and resid 1021 through 1023'
    Processing helix  chain 'A' and resid 1024 through 1044
    Processing helix  chain 'A' and resid 1044 through 1063
    Processing helix  chain 'A' and resid 1111 through 1143
      Proline residue:  A1120  - end of helix
    Processing helix  chain 'A' and resid 1159 through 1177
    Processing helix  chain 'A' and resid 1178 through 1191
    Processing helix  chain 'A' and resid 1197 through 1210
      removed outlier: 4.093A  pdb=" N   GLN A1203 " --> pdb=" O   LEU A1199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1223
      removed outlier: 3.639A  pdb=" N   GLN A1221 " --> pdb=" O   ASP A1218 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 415
    Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 607
    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
      removed outlier: 3.952A  pdb=" N   TYR A1153 " --> pdb=" O   GLN A 921 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1069 through 1071

    465 hydrogen bonds defined for protein.
    1359 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: 1.27

  Time building geometry restraints manager: 0.53 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: 1472
        1.33 -     1.45: 1667
        1.45 -     1.57: 4236
        1.57 -     1.69: 0
        1.69 -     1.81: 73
  Bond restraints: 7448
  Sorted by residual:
  bond pdb=" CG  PHE A 802 "
       pdb=" CD1 PHE A 802 "
    ideal  model  delta    sigma   weight residual
    1.384  1.349  0.035 2.10e-02 2.27e+03 2.73e+00
  bond pdb=" CE2 PHE A 802 "
       pdb=" CZ  PHE A 802 "
    ideal  model  delta    sigma   weight residual
    1.382  1.333  0.049 3.00e-02 1.11e+03 2.68e+00
  bond pdb=" CA  VAL A 603 "
       pdb=" C   VAL A 603 "
    ideal  model  delta    sigma   weight residual
    1.525  1.551 -0.026 2.10e-02 2.27e+03 1.53e+00
  bond pdb=" CA  MET A 800 "
       pdb=" C   MET A 800 "
    ideal  model  delta    sigma   weight residual
    1.528  1.545 -0.017 1.39e-02 5.18e+03 1.46e+00
  bond pdb=" CG  ASN A 799 "
       pdb=" OD1 ASN A 799 "
    ideal  model  delta    sigma   weight residual
    1.231  1.208  0.023 1.90e-02 2.77e+03 1.44e+00
  ... (remaining 7443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 9732
        1.52 -     3.04: 324
        3.04 -     4.57: 54
        4.57 -     6.09: 15
        6.09 -     7.61: 4
  Bond angle restraints: 10129
  Sorted by residual:
  angle pdb=" N   PHE A 802 "
        pdb=" CA  PHE A 802 "
        pdb=" CB  PHE A 802 "
      ideal   model   delta    sigma   weight residual
     110.12  116.45   -6.33 1.47e+00 4.63e-01 1.85e+01
  angle pdb=" CA  PHE A 802 "
        pdb=" CB  PHE A 802 "
        pdb=" CG  PHE A 802 "
      ideal   model   delta    sigma   weight residual
     113.80  117.36   -3.56 1.00e+00 1.00e+00 1.27e+01
  angle pdb=" C   THR A 357 "
        pdb=" N   PHE A 358 "
        pdb=" CA  PHE A 358 "
      ideal   model   delta    sigma   weight residual
     121.54  126.65   -5.11 1.91e+00 2.74e-01 7.17e+00
  angle pdb=" CA  TYR A 999 "
        pdb=" CB  TYR A 999 "
        pdb=" CG  TYR A 999 "
      ideal   model   delta    sigma   weight residual
     113.90  118.66   -4.76 1.80e+00 3.09e-01 6.98e+00
  angle pdb=" C   MET A 323 "
        pdb=" N   SER A 324 "
        pdb=" CA  SER A 324 "
      ideal   model   delta    sigma   weight residual
     121.54  126.26   -4.72 1.91e+00 2.74e-01 6.11e+00
  ... (remaining 10124 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 3963
       16.72 -    33.45: 443
       33.45 -    50.17: 90
       50.17 -    66.90: 23
       66.90 -    83.62: 13
  Dihedral angle restraints: 4532
    sinusoidal: 1811
      harmonic: 2721
  Sorted by residual:
  dihedral pdb=" CA  ASP A 873 "
           pdb=" CB  ASP A 873 "
           pdb=" CG  ASP A 873 "
           pdb=" OD1 ASP A 873 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.31   58.31     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  ASP A 310 "
           pdb=" CB  ASP A 310 "
           pdb=" CG  ASP A 310 "
           pdb=" OD1 ASP A 310 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.27   58.27     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CG  ARG A 431 "
           pdb=" CD  ARG A 431 "
           pdb=" NE  ARG A 431 "
           pdb=" CZ  ARG A 431 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.03  -44.97     2      1.50e+01 4.44e-03 1.07e+01
  ... (remaining 4529 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 914
       0.048 -    0.097: 173
       0.097 -    0.145: 43
       0.145 -    0.194: 4
       0.194 -    0.242: 2
  Chirality restraints: 1136
  Sorted by residual:
  chirality pdb=" CA  HIS A1150 "
            pdb=" N   HIS A1150 "
            pdb=" C   HIS A1150 "
            pdb=" CB  HIS A1150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  VAL A1149 "
            pdb=" N   VAL A1149 "
            pdb=" C   VAL A1149 "
            pdb=" CB  VAL A1149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.69e-01
  chirality pdb=" CA  PHE A 802 "
            pdb=" N   PHE A 802 "
            pdb=" C   PHE A 802 "
            pdb=" CB  PHE A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.69e-01
  ... (remaining 1133 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 553 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   TRP A 553 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TRP A 553 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A 554 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 900 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.96e+00
        pdb=" C   GLU A 900 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLU A 900 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 901 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 802 "   -0.030 2.00e-02 2.50e+03   2.10e-02 7.70e+00
        pdb=" CG  PHE A 802 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 802 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 802 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 802 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 802 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 802 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 104
        2.70 -     3.25: 7490
        3.25 -     3.80: 12475
        3.80 -     4.35: 15963
        4.35 -     4.90: 25657
  Nonbonded interactions: 61689
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 485 "
            pdb=" OG1 THR A 640 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" NH2 ARG A 782 "
            pdb=" OG  SER A 818 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" NH2 ARG A 411 "
            pdb=" OE1 GLU A 642 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   GLN A 585 "
            pdb=" NE2 GLN A 588 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" OD1 ASN A 265 "
            pdb=" OG  SER A 298 "
     model   vdw
     2.343 3.040
  ... (remaining 61684 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=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.310
  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:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5578
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7448  Z= 0.159
  Angle     :  0.662   7.612  10129  Z= 0.362
  Chirality :  0.043   0.242   1136
  Planarity :  0.005   0.036   1316
  Dihedral  : 15.191  83.623   2760
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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:  2.81 (0.28), residues: 917
  helix:  2.66 (0.21), residues: 606
  sheet: -0.84 (0.98), residues: 32
  loop :  0.45 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 477 
 TYR   0.025   0.002   TYR A 461 
 PHE   0.045   0.002   PHE A 802 
 TRP   0.018   0.002   TRP A 553 
 HIS   0.011   0.001   HIS A1150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7448)
  covalent geometry    : angle       0.66183 (10129)
  hydrogen bonds       : bond        0.10666 (  465)
  hydrogen bonds       : angle       5.00520 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  269 LEU cc_start: 0.7496 (mm) cc_final: 0.7278 (mm)
REVERT: A  533 TYR cc_start: 0.5654 (t80) cc_final: 0.5216 (t80)
REVERT: A  778 GLU cc_start: 0.6536 (tm-30) cc_final: 0.6195 (tp30)
REVERT: A  987 ARG cc_start: 0.6277 (tmt170) cc_final: 0.5949 (tmt170)
REVERT: A 1154 TRP cc_start: 0.6101 (m-10) cc_final: 0.5035 (m-10)
REVERT: A 1177 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6457 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1039
  time to fit residues: 15.7978
Evaluate side-chains
  101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
A 588 GLN
A 893 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
A1170 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.204753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.176100 restraints weight = 24002.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.4232 rms_B_bonded: 4.09
r_work: 0.4033 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4034 r_free = 0.4034    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4034 r_free = 0.4034    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6196
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7448  Z= 0.206
  Angle     :  0.673  12.909  10129  Z= 0.339
  Chirality :  0.043   0.179   1136
  Planarity :  0.005   0.050   1316
  Dihedral  :  3.950  17.094   1010
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.40 %
    Favored  : 91.56 %
  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:  2.19 (0.27), residues: 917
  helix:  2.07 (0.20), residues: 603
  sheet: -0.54 (0.83), residues: 42
  loop :  0.49 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 450 
 TYR   0.020   0.002   TYR A 299 
 PHE   0.027   0.003   PHE A 794 
 TRP   0.025   0.002   TRP A1154 
 HIS   0.009   0.002   HIS A 920 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 7448)
  covalent geometry    : angle       0.67328 (10129)
  hydrogen bonds       : bond        0.05058 (  465)
  hydrogen bonds       : angle       4.50867 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6539 (tp40) cc_final: 0.5363 (tp40)
REVERT: A  503 GLU cc_start: 0.6682 (tp30) cc_final: 0.6241 (tp30)
REVERT: A  533 TYR cc_start: 0.6551 (t80) cc_final: 0.6277 (t80)
REVERT: A  648 MET cc_start: 0.7489 (mtm) cc_final: 0.7041 (mtp)
REVERT: A  852 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7247 (mmmm)
REVERT: A  993 THR cc_start: 0.6359 (t) cc_final: 0.6093 (t)
  outliers start: 8
  outliers final: 4
  residues processed: 105
  average time/residue: 0.0887
  time to fit residues: 12.2966
Evaluate side-chains
  101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0770
   chunk 45 optimal weight:    0.3980
   chunk 46 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0670
   chunk 85 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 58 optimal weight:    0.1980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.2676

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.205629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.177359 restraints weight = 29615.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.4285 rms_B_bonded: 4.83
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4279 r_free = 0.4279    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4279 r_free = 0.4279    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5963
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7448  Z= 0.132
  Angle     :  0.577  11.941  10129  Z= 0.284
  Chirality :  0.038   0.143   1136
  Planarity :  0.005   0.046   1316
  Dihedral  :  3.706  13.690   1010
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.70 %
    Favored  : 89.87 %
  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:  2.35 (0.27), residues: 917
  helix:  2.18 (0.20), residues: 605
  sheet: -0.32 (0.82), residues: 42
  loop :  0.56 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 516 
 TYR   0.020   0.001   TYR A 530 
 PHE   0.023   0.002   PHE A1186 
 TRP   0.015   0.001   TRP A1154 
 HIS   0.008   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7448)
  covalent geometry    : angle       0.57677 (10129)
  hydrogen bonds       : bond        0.04324 (  465)
  hydrogen bonds       : angle       4.22992 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6095 (tp40) cc_final: 0.5001 (tp40)
REVERT: A  406 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.6115 (mmt)
REVERT: A  503 GLU cc_start: 0.6209 (tp30) cc_final: 0.5844 (tp30)
REVERT: A  522 GLN cc_start: 0.6685 (tp40) cc_final: 0.6368 (tp40)
REVERT: A  533 TYR cc_start: 0.6081 (t80) cc_final: 0.5851 (t80)
REVERT: A  690 THR cc_start: 0.5595 (OUTLIER) cc_final: 0.5323 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 101
  average time/residue: 0.0948
  time to fit residues: 12.6794
Evaluate side-chains
  99 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0770
   chunk 85 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 79 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0870
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.204372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.176390 restraints weight = 30672.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.4263 rms_B_bonded: 4.93
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4264 r_free = 0.4264    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4264 r_free = 0.4264    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5996
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7448  Z= 0.135
  Angle     :  0.572  11.806  10129  Z= 0.279
  Chirality :  0.038   0.170   1136
  Planarity :  0.005   0.055   1316
  Dihedral  :  3.701  13.873   1010
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 10.13 %
    Favored  : 88.96 %
  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:  2.37 (0.27), residues: 917
  helix:  2.19 (0.20), residues: 606
  sheet: -0.23 (0.80), residues: 42
  loop :  0.55 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 987 
 TYR   0.015   0.001   TYR A 999 
 PHE   0.033   0.002   PHE A 465 
 TRP   0.013   0.001   TRP A1154 
 HIS   0.006   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7448)
  covalent geometry    : angle       0.57187 (10129)
  hydrogen bonds       : bond        0.04176 (  465)
  hydrogen bonds       : angle       4.14971 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6174 (tp40) cc_final: 0.4947 (tp40)
REVERT: A  522 GLN cc_start: 0.6709 (tp40) cc_final: 0.6365 (tp40)
REVERT: A  782 ARG cc_start: 0.5932 (ttp-110) cc_final: 0.5728 (ttp-110)
  outliers start: 7
  outliers final: 4
  residues processed: 93
  average time/residue: 0.0927
  time to fit residues: 11.3730
Evaluate side-chains
  93 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0980
   chunk 29 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0980
   chunk 51 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
A1131 HIS
** A1165 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 = 0.4529 r_free = 0.4529 target = 0.203264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.173656 restraints weight = 28128.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 4.78
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4205 r_free = 0.4205    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4205 r_free = 0.4205    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6047
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7448  Z= 0.160
  Angle     :  0.593  11.359  10129  Z= 0.291
  Chirality :  0.039   0.186   1136
  Planarity :  0.005   0.042   1316
  Dihedral  :  3.801  14.866   1010
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.91 %
    Favored  : 87.79 %
  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:  2.32 (0.27), residues: 917
  helix:  2.10 (0.20), residues: 605
  sheet: -0.15 (0.96), residues: 32
  loop :  0.62 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 516 
 TYR   0.012   0.001   TYR A 931 
 PHE   0.024   0.002   PHE A 465 
 TRP   0.011   0.001   TRP A1154 
 HIS   0.005   0.001   HIS A1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7448)
  covalent geometry    : angle       0.59301 (10129)
  hydrogen bonds       : bond        0.04312 (  465)
  hydrogen bonds       : angle       4.24092 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  236 THR cc_start: 0.7056 (p) cc_final: 0.6572 (p)
REVERT: A  522 GLN cc_start: 0.7006 (tp40) cc_final: 0.6732 (tp40)
REVERT: A  533 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.6582 (t80)
REVERT: A  831 ARG cc_start: 0.5914 (tpt170) cc_final: 0.5606 (tpt170)
REVERT: A  899 MET cc_start: 0.4184 (mtt) cc_final: 0.3820 (mtt)
  outliers start: 10
  outliers final: 7
  residues processed: 96
  average time/residue: 0.0991
  time to fit residues: 12.4691
Evaluate side-chains
  98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 65 optimal weight:    0.0870
   chunk 46 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0040
   chunk 25 optimal weight:    0.5980
   chunk 1 optimal weight:    0.2980
   chunk 57 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   overall best weight:    0.1768

-------------------------------------------------------------------------------
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**
A 515 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.204831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.176813 restraints weight = 28510.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.4269 rms_B_bonded: 4.71
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4269 r_free = 0.4269    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4269 r_free = 0.4269    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5973
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7448  Z= 0.114
  Angle     :  0.557  11.554  10129  Z= 0.269
  Chirality :  0.037   0.264   1136
  Planarity :  0.005   0.042   1316
  Dihedral  :  3.664  14.740   1010
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.34 %
    Favored  : 86.75 %
  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:  2.56 (0.27), residues: 917
  helix:  2.31 (0.21), residues: 606
  sheet: -0.17 (0.95), residues: 32
  loop :  0.66 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 987 
 TYR   0.014   0.001   TYR A 999 
 PHE   0.032   0.002   PHE A 465 
 TRP   0.010   0.001   TRP A1154 
 HIS   0.005   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7448)
  covalent geometry    : angle       0.55664 (10129)
  hydrogen bonds       : bond        0.03842 (  465)
  hydrogen bonds       : angle       4.08612 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 TYR cc_start: 0.6488 (t80) cc_final: 0.6282 (t80)
REVERT: A  403 GLN cc_start: 0.6251 (tp40) cc_final: 0.5864 (tp40)
REVERT: A  515 GLN cc_start: 0.5819 (mm-40) cc_final: 0.5618 (mm110)
REVERT: A  522 GLN cc_start: 0.6834 (tp40) cc_final: 0.6598 (tp-100)
REVERT: A  533 TYR cc_start: 0.6474 (OUTLIER) cc_final: 0.6152 (t80)
REVERT: A  729 LEU cc_start: 0.6696 (mt) cc_final: 0.6327 (mt)
REVERT: A  899 MET cc_start: 0.4522 (mtt) cc_final: 0.4144 (mtt)
  outliers start: 7
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1015
  time to fit residues: 12.5800
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0870
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.201991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.174735 restraints weight = 20877.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 3.62
r_work: 0.4065 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4068 r_free = 0.4068    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4068 r_free = 0.4068    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6161
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7448  Z= 0.154
  Angle     :  0.595  11.885  10129  Z= 0.288
  Chirality :  0.039   0.224   1136
  Planarity :  0.005   0.042   1316
  Dihedral  :  3.804  15.816   1010
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.95 %
    Favored  : 87.01 %
  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:  2.35 (0.27), residues: 917
  helix:  2.14 (0.21), residues: 606
  sheet: -0.24 (0.95), residues: 32
  loop :  0.60 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 854 
 TYR   0.012   0.001   TYR A 931 
 PHE   0.018   0.002   PHE A 802 
 TRP   0.011   0.001   TRP A 271 
 HIS   0.005   0.001   HIS A1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 7448)
  covalent geometry    : angle       0.59525 (10129)
  hydrogen bonds       : bond        0.04173 (  465)
  hydrogen bonds       : angle       4.20009 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 TYR cc_start: 0.6797 (t80) cc_final: 0.6440 (t80)
REVERT: A  515 GLN cc_start: 0.6317 (mm-40) cc_final: 0.6004 (mp10)
REVERT: A  522 GLN cc_start: 0.7352 (tp40) cc_final: 0.7070 (tp40)
REVERT: A  859 LYS cc_start: 0.7424 (mmtp) cc_final: 0.7022 (mmtm)
REVERT: A  899 MET cc_start: 0.4462 (mtt) cc_final: 0.4150 (mtt)
  outliers start: 8
  outliers final: 8
  residues processed: 99
  average time/residue: 0.1042
  time to fit residues: 13.4624
Evaluate side-chains
  98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0980
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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**
** A 921 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 = 0.4507 r_free = 0.4507 target = 0.200307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.172427 restraints weight = 22730.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 3.99
r_work: 0.4015 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4027 r_free = 0.4027    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4027 r_free = 0.4027    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6209
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7448  Z= 0.184
  Angle     :  0.625  11.445  10129  Z= 0.305
  Chirality :  0.040   0.192   1136
  Planarity :  0.005   0.044   1316
  Dihedral  :  3.940  16.716   1010
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 12.73 %
    Favored  : 86.49 %
  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:  2.18 (0.27), residues: 917
  helix:  1.99 (0.21), residues: 605
  sheet: -0.20 (0.96), residues: 32
  loop :  0.59 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 516 
 TYR   0.014   0.002   TYR A1227 
 PHE   0.019   0.002   PHE A 802 
 TRP   0.013   0.002   TRP A 271 
 HIS   0.006   0.001   HIS A1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 7448)
  covalent geometry    : angle       0.62526 (10129)
  hydrogen bonds       : bond        0.04356 (  465)
  hydrogen bonds       : angle       4.30019 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  282 TYR cc_start: 0.6772 (t80) cc_final: 0.6376 (t80)
REVERT: A  450 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.7130 (tpp80)
REVERT: A  515 GLN cc_start: 0.6345 (mm-40) cc_final: 0.6049 (mm110)
REVERT: A  522 GLN cc_start: 0.7387 (tp40) cc_final: 0.7132 (tp40)
REVERT: A  859 LYS cc_start: 0.7493 (mmtp) cc_final: 0.7068 (mmtm)
REVERT: A  899 MET cc_start: 0.4431 (mtt) cc_final: 0.4114 (mtt)
REVERT: A 1165 GLN cc_start: 0.6180 (tm-30) cc_final: 0.5970 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 94
  average time/residue: 0.1019
  time to fit residues: 12.6090
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    0.0070
   chunk 77 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    0.1980
   chunk 67 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0470
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0870
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.1874

-------------------------------------------------------------------------------
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**
** A 921 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 = 0.4547 r_free = 0.4547 target = 0.204496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.176790 restraints weight = 29854.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.4276 rms_B_bonded: 5.09
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4274 r_free = 0.4274    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4274 r_free = 0.4274    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5966
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7448  Z= 0.117
  Angle     :  0.565  11.936  10129  Z= 0.272
  Chirality :  0.036   0.195   1136
  Planarity :  0.004   0.044   1316
  Dihedral  :  3.690  16.835   1010
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.99 %
    Favored  : 86.36 %
  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:  2.53 (0.28), residues: 917
  helix:  2.28 (0.21), residues: 605
  sheet: -0.12 (0.96), residues: 32
  loop :  0.67 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 987 
 TYR   0.012   0.001   TYR A 999 
 PHE   0.014   0.002   PHE A 802 
 TRP   0.008   0.001   TRP A1154 
 HIS   0.005   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7448)
  covalent geometry    : angle       0.56499 (10129)
  hydrogen bonds       : bond        0.03799 (  465)
  hydrogen bonds       : angle       4.10212 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 THR cc_start: 0.7169 (p) cc_final: 0.6673 (p)
REVERT: A  899 MET cc_start: 0.4603 (mtt) cc_final: 0.4270 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 89
  average time/residue: 0.0822
  time to fit residues: 10.0417
Evaluate side-chains
  88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:    0.0770
   chunk 63 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0870
   chunk 57 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0770
   overall best weight:    0.3474

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
A 522 GLN
** A 921 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 = 0.4528 r_free = 0.4528 target = 0.202649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.174586 restraints weight = 26757.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4249 rms_B_bonded: 4.47
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4258 r_free = 0.4258    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4258 r_free = 0.4258    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5987
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7448  Z= 0.140
  Angle     :  0.596  12.796  10129  Z= 0.288
  Chirality :  0.038   0.209   1136
  Planarity :  0.005   0.044   1316
  Dihedral  :  3.741  16.661   1010
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 13.25 %
    Favored  : 85.84 %
  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:  2.47 (0.27), residues: 917
  helix:  2.23 (0.21), residues: 606
  sheet: -0.09 (0.97), residues: 32
  loop :  0.62 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 987 
 TYR   0.013   0.001   TYR A1227 
 PHE   0.016   0.002   PHE A 802 
 TRP   0.011   0.001   TRP A1154 
 HIS   0.005   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7448)
  covalent geometry    : angle       0.59572 (10129)
  hydrogen bonds       : bond        0.03974 (  465)
  hydrogen bonds       : angle       4.13018 ( 1359)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 TYR cc_start: 0.6412 (t80) cc_final: 0.6040 (t80)
REVERT: A  899 MET cc_start: 0.4486 (mtt) cc_final: 0.4147 (mtt)
REVERT: A 1177 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6797 (mp0)
  outliers start: 7
  outliers final: 5
  residues processed: 96
  average time/residue: 0.0989
  time to fit residues: 12.5587
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0050
   chunk 49 optimal weight:    0.0370
   chunk 76 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    0.1980
   overall best weight:    0.3272

-------------------------------------------------------------------------------
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**
** A 921 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 = 0.4535 r_free = 0.4535 target = 0.203520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.177302 restraints weight = 23102.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.4271 rms_B_bonded: 3.93
r_work: 0.4051 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4045 r_free = 0.4045    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4045 r_free = 0.4045    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6197
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7448  Z= 0.135
  Angle     :  0.584  12.503  10129  Z= 0.282
  Chirality :  0.037   0.199   1136
  Planarity :  0.005   0.044   1316
  Dihedral  :  3.753  16.899   1010
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.38 %
    Favored  : 85.84 %
  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:  2.48 (0.27), residues: 917
  helix:  2.24 (0.21), residues: 606
  sheet: -0.12 (0.97), residues: 32
  loop :  0.66 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 987 
 TYR   0.016   0.001   TYR A 999 
 PHE   0.016   0.002   PHE A 802 
 TRP   0.013   0.001   TRP A1154 
 HIS   0.010   0.001   HIS A 920 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7448)
  covalent geometry    : angle       0.58371 (10129)
  hydrogen bonds       : bond        0.03937 (  465)
  hydrogen bonds       : angle       4.09935 ( 1359)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1642.41 seconds
wall clock time: 28 minutes 46.50 seconds (1726.50 seconds total)