Starting phenix.real_space_refine
on Fri Feb  6 04:41:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lcq_62990/02_2026/9lcq_62990.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lcq_62990/02_2026/9lcq_62990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lcq_62990/02_2026/9lcq_62990.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lcq_62990/02_2026/9lcq_62990.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lcq_62990/02_2026/9lcq_62990.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lcq_62990/02_2026/9lcq_62990.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    6994      2.51       5
     N    1974      2.21       5
     O    2035      1.98       5
     H   10821      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 119 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21858
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 20859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1332, 20859
          Classifications: {'peptide': 1332}
          Link IDs: {'PTRANS': 85, 'TRANS': 1246}
    Chain: "B"
      Number of atoms: 999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 999
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 3, 'TRANS': 57}
  Time building chain proxies: 3.39, per 1000 atoms: 0.16
  Number of scatterers: 21858
  At special positions: 0
  Unit cell: (79.928, 118.656, 178.808, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     O    2035      8.00
     N    1974      7.00
     C    6994      6.00
     H   10821      1.00
    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: 1.80
  Conformation dependent library (CDL) restraints added in 644.2 milliseconds
  

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2574

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 12 sheets defined
      44.0% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2793 through 2802
    Processing helix  chain 'A' and resid 2823 through 2838
      removed outlier: 4.056A  pdb=" N   LYS A2829 " --> pdb=" O   GLY A2825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2839 through 2843
      removed outlier: 3.526A  pdb=" N   ARG A2842 " --> pdb=" O   ASP A2839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2876 through 2886
    Processing helix  chain 'A' and resid 2916 through 2918
      No H-bonds generated for 'chain 'A' and resid 2916 through 2918'
    Processing helix  chain 'A' and resid 2919 through 2939
    Processing helix  chain 'A' and resid 2951 through 2964
      removed outlier: 4.180A  pdb=" N   GLY A2964 " --> pdb=" O   GLN A2960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2965 through 2979
      removed outlier: 4.168A  pdb=" N   GLU A2971 " --> pdb=" O   SER A2967 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU A2972 " --> pdb=" O   LEU A2968 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY A2973 " --> pdb=" O   ARG A2969 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TRP A2974 " --> pdb=" O   GLU A2970 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA A2977 " --> pdb=" O   GLY A2973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2996 through 2998
      No H-bonds generated for 'chain 'A' and resid 2996 through 2998'
    Processing helix  chain 'A' and resid 3008 through 3018
    Processing helix  chain 'A' and resid 3019 through 3025
      removed outlier: 4.836A  pdb=" N   TYR A3023 " --> pdb=" O   PRO A3020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3026 through 3043
      removed outlier: 3.508A  pdb=" N   LEU A3030 " --> pdb=" O   GLN A3026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3086 through 3101
      removed outlier: 3.829A  pdb=" N   VAL A3101 " --> pdb=" O   GLN A3097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3102 through 3104
      No H-bonds generated for 'chain 'A' and resid 3102 through 3104'
    Processing helix  chain 'A' and resid 3105 through 3114
      removed outlier: 4.130A  pdb=" N   GLY A3109 " --> pdb=" O   GLY A3105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3116 through 3125
      removed outlier: 3.708A  pdb=" N   ALA A3125 " --> pdb=" O   GLN A3121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3140 through 3143
    Processing helix  chain 'A' and resid 3192 through 3216
    Processing helix  chain 'A' and resid 3223 through 3227
    Processing helix  chain 'A' and resid 3233 through 3238
    Processing helix  chain 'A' and resid 3254 through 3267
      removed outlier: 3.806A  pdb=" N   GLY A3259 " --> pdb=" O   PRO A3255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3286 through 3301
    Processing helix  chain 'A' and resid 3302 through 3304
      No H-bonds generated for 'chain 'A' and resid 3302 through 3304'
    Processing helix  chain 'A' and resid 3337 through 3339
      No H-bonds generated for 'chain 'A' and resid 3337 through 3339'
    Processing helix  chain 'A' and resid 3340 through 3356
    Processing helix  chain 'A' and resid 3389 through 3410
      removed outlier: 3.878A  pdb=" N   ALA A3393 " --> pdb=" O   ASP A3389 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   GLY A3394 " --> pdb=" O   ALA A3390 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU A3395 " --> pdb=" O   TRP A3391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3420 through 3429
      removed outlier: 4.237A  pdb=" N   TYR A3424 " --> pdb=" O   ARG A3420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3432 through 3445
    Processing helix  chain 'A' and resid 3462 through 3466
    Processing helix  chain 'A' and resid 3480 through 3493
      removed outlier: 4.310A  pdb=" N   ALA A3491 " --> pdb=" O   LEU A3487 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLN A3492 " --> pdb=" O   ARG A3488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3497 through 3515
      removed outlier: 3.579A  pdb=" N   PHE A3501 " --> pdb=" O   THR A3497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3532 through 3538
      removed outlier: 3.619A  pdb=" N   GLN A3536 " --> pdb=" O   PRO A3533 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A3537 " --> pdb=" O   GLU A3534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3560 through 3576
    Processing helix  chain 'A' and resid 3582 through 3589
    Processing helix  chain 'A' and resid 3614 through 3619
    Processing helix  chain 'A' and resid 3658 through 3679
      removed outlier: 3.504A  pdb=" N   VAL A3662 " --> pdb=" O   GLU A3658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3683 through 3687
    Processing helix  chain 'A' and resid 3691 through 3700
    Processing helix  chain 'A' and resid 3710 through 3712
      No H-bonds generated for 'chain 'A' and resid 3710 through 3712'
    Processing helix  chain 'A' and resid 3713 through 3726
      removed outlier: 4.230A  pdb=" N   ARG A3717 " --> pdb=" O   GLN A3713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3740 through 3758
    Processing helix  chain 'A' and resid 3773 through 3786
    Processing helix  chain 'A' and resid 3798 through 3809
    Processing helix  chain 'A' and resid 3817 through 3831
      removed outlier: 4.598A  pdb=" N   GLU A3822 " --> pdb=" O   GLN A3818 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   GLN A3823 " --> pdb=" O   ALA A3819 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A3831 " --> pdb=" O   LEU A3827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3842 through 3846
    Processing helix  chain 'A' and resid 3884 through 3898
      removed outlier: 3.831A  pdb=" N   VAL A3895 " --> pdb=" O   GLN A3891 " (cutoff:3.500A)
      Proline residue:  A3896  - end of helix
    Processing helix  chain 'A' and resid 3915 through 3927
      removed outlier: 4.165A  pdb=" N   TRP A3919 " --> pdb=" O   ASP A3915 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ALA A3924 " --> pdb=" O   GLN A3920 " (cutoff:3.500A)
      Proline residue:  A3925  - end of helix
    Processing helix  chain 'A' and resid 3935 through 3940
    Processing helix  chain 'A' and resid 3941 through 3952
    Processing helix  chain 'A' and resid 3960 through 3968
      removed outlier: 3.684A  pdb=" N   GLY A3966 " --> pdb=" O   SER A3962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3989 through 4000
      removed outlier: 3.934A  pdb=" N   ARG A3999 " --> pdb=" O   GLN A3995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4011 through 4015
    Processing helix  chain 'A' and resid 4025 through 4030
    Processing helix  chain 'A' and resid 4080 through 4087
    Processing helix  chain 'B' and resid 44 through 55
      removed outlier: 3.618A  pdb=" N   GLU B  53 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 67
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2865 through 2869
      removed outlier: 7.386A  pdb=" N   GLN A2907 " --> pdb=" O   PRO A2818 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   LEU A2815 " --> pdb=" O   LEU A3151 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2844 through 2847
    Processing sheet with id=AA3, first strand: chain 'A' and resid 3000 through 3007
      removed outlier: 3.586A  pdb=" N   LEU A3180 " --> pdb=" O   LEU A3007 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   VAL A3175 " --> pdb=" O   LEU A3136 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLN A3138 " --> pdb=" O   VAL A3175 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ILE A3131 " --> pdb=" O   LEU A3049 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLU A3053 " --> pdb=" O   PHE A3133 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TYR A3135 " --> pdb=" O   GLU A3053 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 3247 through 3252
      removed outlier: 3.596A  pdb=" N   ASP A3249 " --> pdb=" O   ILE A3320 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 3327 through 3332
      removed outlier: 6.457A  pdb=" N   ARG A3327 " --> pdb=" O   LEU A3367 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   LEU A3369 " --> pdb=" O   ARG A3327 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLU A3329 " --> pdb=" O   LEU A3369 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   ARG A3371 " --> pdb=" O   GLU A3329 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   LEU A3331 " --> pdb=" O   ARG A3371 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   GLY A3373 " --> pdb=" O   LEU A3331 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ARG A3376 " --> pdb=" O   LEU A3372 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TYR A3377 " --> pdb=" O   ILE A3281 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 3472 through 3478
      removed outlier: 6.303A  pdb=" N   LEU A3602 " --> pdb=" O   VAL A3638 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   CYS A3640 " --> pdb=" O   LEU A3602 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   VAL A3604 " --> pdb=" O   CYS A3640 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   SER A3601 " --> pdb=" O   LEU A3520 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   PHE A3605 " --> pdb=" O   THR A3524 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 3789 through 3793
      removed outlier: 8.413A  pdb=" N   VAL A3815 " --> pdb=" O   PRO A3765 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ALA A3767 " --> pdb=" O   VAL A3815 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3864 through 3870
      removed outlier: 4.258A  pdb=" N   GLY A4076 " --> pdb=" O   MET A3881 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3905 through 3908
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3956 through 3959
      removed outlier: 3.661A  pdb=" N   VAL A4006 " --> pdb=" O   MET A3981 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   ALA A4008 " --> pdb=" O   PRO A3983 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ARG A4022 " --> pdb=" O   ILE A4035 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   ILE A4035 " --> pdb=" O   ARG A4022 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TYR A4117 " --> pdb=" O   PRO A4034 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ARG A4099 " --> pdb=" O   GLY A4070 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLY A4070 " --> pdb=" O   ARG A4099 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   LEU A4066 " --> pdb=" O   THR A4103 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ASP A4105 " --> pdb=" O   GLY A4064 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   GLY A4064 " --> pdb=" O   ASP A4105 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3956 through 3959
      removed outlier: 3.661A  pdb=" N   VAL A4006 " --> pdb=" O   MET A3981 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   ALA A4008 " --> pdb=" O   PRO A3983 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ARG A4022 " --> pdb=" O   ILE A4035 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   ILE A4035 " --> pdb=" O   ARG A4022 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TYR A4117 " --> pdb=" O   PRO A4034 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 26
      removed outlier: 5.242A  pdb=" N   LYS B  40 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   VAL B  16 " --> pdb=" O   ALA B  38 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA B  38 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)

    526 hydrogen bonds defined for protein.
    1488 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: 5.04

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 10806
        1.12 -     1.29: 1902
        1.29 -     1.47: 4163
        1.47 -     1.64: 5205
        1.64 -     1.82: 53
  Bond restraints: 22129
  Sorted by residual:
  bond pdb=" CD2 PHE A3330 "
       pdb=" HD2 PHE A3330 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" CH2 TRP A3439 "
       pdb=" HH2 TRP A3439 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   VAL A3604 "
       pdb=" H   VAL A3604 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" NE1 TRP A2923 "
       pdb=" HE1 TRP A2923 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   TYR A3869 "
       pdb=" H   TYR A3869 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 22124 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 34859
        2.85 -     5.69: 4087
        5.69 -     8.54: 992
        8.54 -    11.39: 3
       11.39 -    14.24: 15
  Bond angle restraints: 39956
  Sorted by residual:
  angle pdb=" OE1 GLN A3318 "
        pdb=" CD  GLN A3318 "
        pdb=" NE2 GLN A3318 "
      ideal   model   delta    sigma   weight residual
     122.60  116.69    5.91 1.00e+00 1.00e+00 3.49e+01
  angle pdb=" N   ASP A4040 "
        pdb=" CA  ASP A4040 "
        pdb=" C   ASP A4040 "
      ideal   model   delta    sigma   weight residual
     111.75  118.66   -6.91 1.28e+00 6.10e-01 2.91e+01
  angle pdb=" N   TYR A3251 "
        pdb=" CA  TYR A3251 "
        pdb=" C   TYR A3251 "
      ideal   model   delta    sigma   weight residual
     108.22  113.04   -4.82 9.00e-01 1.23e+00 2.87e+01
  angle pdb=" CB  HIS A3578 "
        pdb=" CG  HIS A3578 "
        pdb=" CD2 HIS A3578 "
      ideal   model   delta    sigma   weight residual
     131.20  124.49    6.71 1.30e+00 5.92e-01 2.66e+01
  angle pdb=" CB  HIS A3055 "
        pdb=" CG  HIS A3055 "
        pdb=" CD2 HIS A3055 "
      ideal   model   delta    sigma   weight residual
     131.20  124.61    6.59 1.30e+00 5.92e-01 2.57e+01
  ... (remaining 39951 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 9556
       17.95 -    35.90: 556
       35.90 -    53.85: 210
       53.85 -    71.80: 71
       71.80 -    89.75: 15
  Dihedral angle restraints: 10408
    sinusoidal: 5706
      harmonic: 4702
  Sorted by residual:
  dihedral pdb=" CA  ASN A3311 "
           pdb=" C   ASN A3311 "
           pdb=" N   ALA A3312 "
           pdb=" CA  ALA A3312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.28   28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  SER A3625 "
           pdb=" C   SER A3625 "
           pdb=" N   ASP A3626 "
           pdb=" CA  ASP A3626 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.94   28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  GLY A4061 "
           pdb=" C   GLY A4061 "
           pdb=" N   ALA A4062 "
           pdb=" CA  ALA A4062 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.11   27.89     0      5.00e+00 4.00e-02 3.11e+01
  ... (remaining 10405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1046
       0.083 -    0.167: 516
       0.167 -    0.250: 81
       0.250 -    0.334: 11
       0.334 -    0.417: 2
  Chirality restraints: 1656
  Sorted by residual:
  chirality pdb=" CA  ARG A3972 "
            pdb=" N   ARG A3972 "
            pdb=" C   ARG A3972 "
            pdb=" CB  ARG A3972 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.35e+00
  chirality pdb=" CA  PHE A4055 "
            pdb=" N   PHE A4055 "
            pdb=" C   PHE A4055 "
            pdb=" CB  PHE A4055 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.04e+00
  chirality pdb=" CA  ASN A3311 "
            pdb=" N   ASN A3311 "
            pdb=" C   ASN A3311 "
            pdb=" CB  ASN A3311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  ... (remaining 1653 not shown)

  Planarity restraints: 3355
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A3439 "    0.227 2.00e-02 2.50e+03   1.12e-01 5.03e+02
        pdb=" CG  TRP A3439 "    0.071 2.00e-02 2.50e+03
        pdb=" CD1 TRP A3439 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A3439 "   -0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A3439 "   -0.085 2.00e-02 2.50e+03
        pdb=" CE2 TRP A3439 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE3 TRP A3439 "   -0.092 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A3439 "    0.054 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A3439 "   -0.039 2.00e-02 2.50e+03
        pdb=" CH2 TRP A3439 "    0.062 2.00e-02 2.50e+03
        pdb=" HD1 TRP A3439 "    0.042 2.00e-02 2.50e+03
        pdb=" HE1 TRP A3439 "   -0.236 2.00e-02 2.50e+03
        pdb=" HE3 TRP A3439 "   -0.161 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A3439 "    0.118 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A3439 "   -0.062 2.00e-02 2.50e+03
        pdb=" HH2 TRP A3439 "    0.135 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A3772 "    0.289 9.50e-02 1.11e+02   1.45e-01 2.72e+02
        pdb=" NE  ARG A3772 "    0.053 2.00e-02 2.50e+03
        pdb=" CZ  ARG A3772 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A3772 "    0.046 2.00e-02 2.50e+03
        pdb=" NH2 ARG A3772 "   -0.057 2.00e-02 2.50e+03
        pdb="HH11 ARG A3772 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG A3772 "   -0.150 2.00e-02 2.50e+03
        pdb="HH21 ARG A3772 "   -0.145 2.00e-02 2.50e+03
        pdb="HH22 ARG A3772 "    0.231 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A3739 "   -0.201 2.00e-02 2.50e+03   7.81e-02 2.44e+02
        pdb=" CG  TRP A3739 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 TRP A3739 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP A3739 "    0.033 2.00e-02 2.50e+03
        pdb=" NE1 TRP A3739 "    0.061 2.00e-02 2.50e+03
        pdb=" CE2 TRP A3739 "    0.027 2.00e-02 2.50e+03
        pdb=" CE3 TRP A3739 "    0.080 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A3739 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A3739 "    0.046 2.00e-02 2.50e+03
        pdb=" CH2 TRP A3739 "   -0.037 2.00e-02 2.50e+03
        pdb=" HD1 TRP A3739 "    0.021 2.00e-02 2.50e+03
        pdb=" HE1 TRP A3739 "    0.080 2.00e-02 2.50e+03
        pdb=" HE3 TRP A3739 "    0.090 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A3739 "   -0.070 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A3739 "    0.043 2.00e-02 2.50e+03
        pdb=" HH2 TRP A3739 "   -0.120 2.00e-02 2.50e+03
  ... (remaining 3352 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1546
        2.19 -     2.79: 39291
        2.79 -     3.39: 61832
        3.39 -     4.00: 83068
        4.00 -     4.60: 120399
  Nonbonded interactions: 306136
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A4024 "
            pdb=" HG  SER A4027 "
     model   vdw
     1.587 2.450
  nonbonded pdb=" OE2 GLU A3096 "
            pdb=" HG1 THR A3223 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" OE2 GLU A3096 "
            pdb=" HG  SER A3225 "
     model   vdw
     1.599 2.450
  nonbonded pdb=" OD1 ASP A3332 "
            pdb=" HG  SER A3334 "
     model   vdw
     1.604 2.450
  nonbonded pdb=" HH  TYR A4009 "
            pdb=" OD2 ASP A4105 "
     model   vdw
     1.624 2.450
  ... (remaining 306131 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.710
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5778
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      :  0.012   0.043  11308  Z= 0.741
  Angle     :  1.771   7.159  15389  Z= 1.205
  Chirality :  0.092   0.417   1656
  Planarity :  0.017   0.168   2052
  Dihedral  : 13.566  89.750   4194
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 0.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.74 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.97 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.21), residues: 1389
  helix: -0.97 (0.19), residues: 535
  sheet:  0.20 (0.30), residues: 255
  loop : -0.35 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A3655 
 TYR   0.127   0.021   TYR A4032 
 PHE   0.052   0.012   PHE A2800 
 TRP   0.136   0.026   TRP A2798 
 HIS   0.014   0.004   HIS A3649 

Details of bonding type rmsd
  covalent geometry    : bond        0.01202 (11308)
  covalent geometry    : angle       1.77142 (15389)
  hydrogen bonds       : bond        0.16097 (  512)
  hydrogen bonds       : angle       6.85972 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 133
  time to evaluate  : 0.458 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 137
  average time/residue: 0.2465
  time to fit residues: 46.4597
Evaluate side-chains
  82 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3428 LEU
Chi-restraints excluded: chain A residue 3984 THR
Chi-restraints excluded: chain A residue 4016 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A2812 GLN
A3159 HIS
A3321 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.102803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.066889 restraints weight = 123958.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.070671 restraints weight = 50439.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.073145 restraints weight = 30763.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.074659 restraints weight = 22731.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.075462 restraints weight = 18735.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11308  Z= 0.218
  Angle     :  0.664   5.940  15389  Z= 0.356
  Chirality :  0.041   0.154   1656
  Planarity :  0.006   0.046   2052
  Dihedral  :  6.269  43.159   1554
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  6.81 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.22), residues: 1389
  helix:  0.33 (0.21), residues: 538
  sheet:  0.17 (0.29), residues: 286
  loop :  0.07 (0.28), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A2958 
 TYR   0.012   0.002   TYR B  28 
 PHE   0.016   0.002   PHE A3669 
 TRP   0.015   0.002   TRP A3042 
 HIS   0.006   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (11308)
  covalent geometry    : angle       0.66449 (15389)
  hydrogen bonds       : bond        0.04800 (  512)
  hydrogen bonds       : angle       5.42313 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.452 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3516 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8013 (mp0)
REVERT: A 3532 MET cc_start: 0.7868 (mpp) cc_final: 0.7496 (mpp)
REVERT: A 3741 TYR cc_start: 0.7928 (m-80) cc_final: 0.7117 (m-80)
REVERT: A 4065 GLU cc_start: 0.6810 (tt0) cc_final: 0.6449 (tm-30)
  outliers start: 9
  outliers final: 3
  residues processed: 77
  average time/residue: 0.2539
  time to fit residues: 27.0430
Evaluate side-chains
  63 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3069 SER
Chi-restraints excluded: chain A residue 3428 LEU
Chi-restraints excluded: chain A residue 3897 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 138 optimal weight:    4.9990
   chunk 13 optimal weight:    0.2980
   chunk 42 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 34 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 107 optimal weight:   20.0000
   chunk 108 optimal weight:    5.9990
   chunk 132 optimal weight:    8.9990
   chunk 97 optimal weight:   20.0000
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A2838 HIS
** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3429 GLN
** A3503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.102650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.067048 restraints weight = 124034.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.070783 restraints weight = 49892.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 73)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.073228 restraints weight = 30309.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.074665 restraints weight = 22432.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.075593 restraints weight = 18595.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11308  Z= 0.149
  Angle     :  0.550   5.471  15389  Z= 0.290
  Chirality :  0.039   0.144   1656
  Planarity :  0.004   0.045   2052
  Dihedral  :  5.331  36.368   1551
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  7.77 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.23), residues: 1389
  helix:  1.09 (0.22), residues: 545
  sheet:  0.08 (0.29), residues: 290
  loop :  0.23 (0.29), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A4083 
 TYR   0.011   0.002   TYR A3176 
 PHE   0.011   0.002   PHE A4093 
 TRP   0.019   0.001   TRP A2974 
 HIS   0.004   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11308)
  covalent geometry    : angle       0.55020 (15389)
  hydrogen bonds       : bond        0.03763 (  512)
  hydrogen bonds       : angle       4.85135 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.546 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3619 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7171 (tp-100)
REVERT: A 4065 GLU cc_start: 0.7025 (tt0) cc_final: 0.6793 (tm-30)
REVERT: A 4067 CYS cc_start: 0.7171 (m) cc_final: 0.5626 (m)
REVERT: B   11 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8959 (tt0)
REVERT: B   33 GLN cc_start: 0.9022 (pt0) cc_final: 0.8796 (pt0)
  outliers start: 6
  outliers final: 4
  residues processed: 70
  average time/residue: 0.2151
  time to fit residues: 21.8318
Evaluate side-chains
  67 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3069 SER
Chi-restraints excluded: chain A residue 3627 SER
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Chi-restraints excluded: chain B residue   11 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 108 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 123 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3383 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.101537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.065729 restraints weight = 123447.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.069322 restraints weight = 51513.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.071662 restraints weight = 32075.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.073168 restraints weight = 24069.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.073955 restraints weight = 19836.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11308  Z= 0.140
  Angle     :  0.514   5.524  15389  Z= 0.267
  Chirality :  0.037   0.143   1656
  Planarity :  0.004   0.040   2052
  Dihedral  :  4.821  21.906   1549
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.73 %
    Favored  : 90.66 %
  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:  1.07 (0.23), residues: 1389
  helix:  1.54 (0.22), residues: 550
  sheet: -0.04 (0.29), residues: 296
  loop :  0.47 (0.30), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  36 
 TYR   0.009   0.001   TYR A2934 
 PHE   0.010   0.001   PHE A3719 
 TRP   0.010   0.001   TRP A2974 
 HIS   0.006   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (11308)
  covalent geometry    : angle       0.51419 (15389)
  hydrogen bonds       : bond        0.03286 (  512)
  hydrogen bonds       : angle       4.61808 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.552 
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: symmetry clash
   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 3383 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8389 (p0)
REVERT: A 3619 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7193 (tp40)
REVERT: A 4065 GLU cc_start: 0.7222 (tt0) cc_final: 0.6688 (tm-30)
REVERT: B   33 GLN cc_start: 0.9066 (pt0) cc_final: 0.8832 (pt0)
REVERT: B   58 MET cc_start: 0.4820 (mmt) cc_final: 0.4331 (mmt)
  outliers start: 7
  outliers final: 3
  residues processed: 67
  average time/residue: 0.2284
  time to fit residues: 22.0420
Evaluate side-chains
  64 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3069 SER
Chi-restraints excluded: chain A residue 3383 ASN
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 136 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 19 optimal weight:    0.4980
   chunk 119 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 121 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.101103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.064978 restraints weight = 122271.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.068675 restraints weight = 52051.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.071108 restraints weight = 32091.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.072484 restraints weight = 23913.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 69)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.073415 restraints weight = 19942.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11308  Z= 0.140
  Angle     :  0.501   5.436  15389  Z= 0.260
  Chirality :  0.037   0.142   1656
  Planarity :  0.004   0.041   2052
  Dihedral  :  4.657  20.552   1549
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.34 %
    Favored  : 89.97 %
  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:  1.15 (0.24), residues: 1389
  helix:  1.71 (0.22), residues: 552
  sheet: -0.07 (0.29), residues: 296
  loop :  0.43 (0.30), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A4083 
 TYR   0.010   0.001   TYR A4000 
 PHE   0.008   0.001   PHE A3513 
 TRP   0.011   0.001   TRP A2974 
 HIS   0.005   0.001   HIS A3384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (11308)
  covalent geometry    : angle       0.50094 (15389)
  hydrogen bonds       : bond        0.03205 (  512)
  hydrogen bonds       : angle       4.51526 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.534 
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: symmetry clash
   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 3470 MET cc_start: 0.8012 (tpp) cc_final: 0.7615 (tpp)
REVERT: A 3619 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7175 (tp40)
REVERT: A 3741 TYR cc_start: 0.7774 (m-80) cc_final: 0.7050 (m-80)
REVERT: A 4065 GLU cc_start: 0.7278 (tt0) cc_final: 0.6863 (tm-30)
REVERT: A 4067 CYS cc_start: 0.7119 (m) cc_final: 0.5309 (m)
REVERT: B   33 GLN cc_start: 0.9121 (pt0) cc_final: 0.8893 (pt0)
REVERT: B   58 MET cc_start: 0.4706 (mmt) cc_final: 0.4295 (mmt)
  outliers start: 8
  outliers final: 7
  residues processed: 67
  average time/residue: 0.2286
  time to fit residues: 22.2406
Evaluate side-chains
  67 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3069 SER
Chi-restraints excluded: chain A residue 3627 SER
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Chi-restraints excluded: chain A residue 4039 THR
Chi-restraints excluded: chain A residue 4089 VAL
Chi-restraints excluded: chain B residue   11 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 82 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 127 optimal weight:    6.9990
   chunk 119 optimal weight:   40.0000
   chunk 54 optimal weight:    0.0020
   chunk 57 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.9794

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

Flipped N/Q/H residues before XYZ refinement:
** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3141 GLN
A3745 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.099503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.063057 restraints weight = 122604.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.066616 restraints weight = 51695.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.068946 restraints weight = 32305.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.070317 restraints weight = 24157.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.071309 restraints weight = 20106.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11308  Z= 0.175
  Angle     :  0.524   6.669  15389  Z= 0.272
  Chirality :  0.038   0.147   1656
  Planarity :  0.004   0.038   2052
  Dihedral  :  4.555  21.397   1549
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.90 %
    Favored  : 90.14 %
  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:  1.06 (0.24), residues: 1389
  helix:  1.75 (0.22), residues: 551
  sheet: -0.34 (0.29), residues: 296
  loop :  0.39 (0.30), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A3695 
 TYR   0.011   0.001   TYR A3377 
 PHE   0.011   0.001   PHE A3513 
 TRP   0.010   0.001   TRP A2974 
 HIS   0.007   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (11308)
  covalent geometry    : angle       0.52410 (15389)
  hydrogen bonds       : bond        0.03253 (  512)
  hydrogen bonds       : angle       4.51460 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.513 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3516 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8099 (mp0)
REVERT: A 3619 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7201 (tp-100)
REVERT: B   33 GLN cc_start: 0.9211 (pt0) cc_final: 0.9000 (pt0)
  outliers start: 11
  outliers final: 8
  residues processed: 70
  average time/residue: 0.2395
  time to fit residues: 23.8084
Evaluate side-chains
  65 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2841 LEU
Chi-restraints excluded: chain A residue 3069 SER
Chi-restraints excluded: chain A residue 3627 SER
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Chi-restraints excluded: chain A residue 4039 THR
Chi-restraints excluded: chain A residue 4089 VAL
Chi-restraints excluded: chain B residue   11 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 129 optimal weight:    9.9990
   chunk 93 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 121 optimal weight:   20.0000
   chunk 110 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A2915 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 = 0.4106 r_free = 0.4106 target = 0.099504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.063098 restraints weight = 121782.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.066636 restraints weight = 52250.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.068984 restraints weight = 32611.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.070413 restraints weight = 24304.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.071366 restraints weight = 20214.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11308  Z= 0.148
  Angle     :  0.493   5.760  15389  Z= 0.255
  Chirality :  0.037   0.145   1656
  Planarity :  0.004   0.040   2052
  Dihedral  :  4.434  20.972   1549
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  9.34 %
    Favored  : 89.88 %
  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:  1.11 (0.24), residues: 1389
  helix:  1.86 (0.22), residues: 550
  sheet: -0.35 (0.29), residues: 294
  loop :  0.36 (0.29), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A3112 
 TYR   0.010   0.001   TYR A3251 
 PHE   0.010   0.001   PHE A3513 
 TRP   0.011   0.001   TRP A2974 
 HIS   0.006   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11308)
  covalent geometry    : angle       0.49311 (15389)
  hydrogen bonds       : bond        0.03095 (  512)
  hydrogen bonds       : angle       4.39621 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.500 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3470 MET cc_start: 0.8290 (tpp) cc_final: 0.7923 (tpp)
REVERT: A 3516 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8188 (mp0)
REVERT: A 3551 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6316 (pp30)
REVERT: A 3552 MET cc_start: 0.8582 (mmt) cc_final: 0.8243 (mmt)
REVERT: A 3619 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7226 (tp40)
REVERT: B   33 GLN cc_start: 0.9199 (pt0) cc_final: 0.8986 (pt0)
  outliers start: 9
  outliers final: 7
  residues processed: 65
  average time/residue: 0.2573
  time to fit residues: 23.6509
Evaluate side-chains
  64 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3069 SER
Chi-restraints excluded: chain A residue 3551 GLN
Chi-restraints excluded: chain A residue 3627 SER
Chi-restraints excluded: chain A residue 3683 GLU
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Chi-restraints excluded: chain A residue 4039 THR
Chi-restraints excluded: chain A residue 4089 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 121 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0040
   overall best weight:    2.2000

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

Flipped N/Q/H residues before XYZ refinement:
A2817 GLN
** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3141 GLN
** A3745 ASN ** 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 = 0.4085 r_free = 0.4085 target = 0.098455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.061567 restraints weight = 121550.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.065035 restraints weight = 52750.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.067372 restraints weight = 33155.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.068795 restraints weight = 24855.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.069649 restraints weight = 20671.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11308  Z= 0.189
  Angle     :  0.517   5.991  15389  Z= 0.269
  Chirality :  0.038   0.149   1656
  Planarity :  0.004   0.037   2052
  Dihedral  :  4.451  21.443   1549
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.74 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.34 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.23), residues: 1389
  helix:  1.71 (0.22), residues: 552
  sheet: -0.46 (0.29), residues: 295
  loop :  0.31 (0.29), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2978 
 TYR   0.017   0.002   TYR A4000 
 PHE   0.012   0.001   PHE A3357 
 TRP   0.010   0.001   TRP A2974 
 HIS   0.007   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (11308)
  covalent geometry    : angle       0.51665 (15389)
  hydrogen bonds       : bond        0.03220 (  512)
  hydrogen bonds       : angle       4.48422 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.509 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
REVERT: A 3516 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8246 (mp0)
REVERT: A 3551 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6435 (pp30)
REVERT: A 3619 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7288 (tp40)
  outliers start: 12
  outliers final: 7
  residues processed: 67
  average time/residue: 0.2751
  time to fit residues: 25.2651
Evaluate side-chains
  62 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2841 LEU
Chi-restraints excluded: chain A residue 3069 SER
Chi-restraints excluded: chain A residue 3551 GLN
Chi-restraints excluded: chain A residue 3627 SER
Chi-restraints excluded: chain A residue 3683 GLU
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Chi-restraints excluded: chain A residue 4089 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 114 optimal weight:   50.0000
   chunk 71 optimal weight:    3.9990
   chunk 100 optimal weight:   20.0000
   chunk 121 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0070
   chunk 1 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.3204

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

Flipped N/Q/H residues before XYZ refinement:
** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3722 GLN
A3726 HIS
B  13 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.099055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062249 restraints weight = 121780.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.065785 restraints weight = 52433.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.068167 restraints weight = 32899.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.069589 restraints weight = 24520.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.070382 restraints weight = 20374.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11308  Z= 0.120
  Angle     :  0.485   7.183  15389  Z= 0.248
  Chirality :  0.037   0.146   1656
  Planarity :  0.004   0.037   2052
  Dihedral  :  4.300  20.328   1549
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.86 %
    Favored  : 89.53 %
  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:  1.14 (0.24), residues: 1389
  helix:  1.93 (0.23), residues: 551
  sheet: -0.46 (0.29), residues: 294
  loop :  0.41 (0.30), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4099 
 TYR   0.010   0.001   TYR A3251 
 PHE   0.007   0.001   PHE A3357 
 TRP   0.012   0.001   TRP A2974 
 HIS   0.005   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (11308)
  covalent geometry    : angle       0.48486 (15389)
  hydrogen bonds       : bond        0.02934 (  512)
  hydrogen bonds       : angle       4.28856 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.445 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3470 MET cc_start: 0.8314 (tpp) cc_final: 0.7589 (tpp)
REVERT: A 3516 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8247 (mp0)
REVERT: A 3551 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6415 (pp30)
REVERT: A 3552 MET cc_start: 0.8420 (mmt) cc_final: 0.8090 (mmt)
REVERT: A 3619 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7335 (tp40)
  outliers start: 7
  outliers final: 5
  residues processed: 63
  average time/residue: 0.2492
  time to fit residues: 21.8140
Evaluate side-chains
  62 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3551 GLN
Chi-restraints excluded: chain A residue 3627 SER
Chi-restraints excluded: chain A residue 3683 GLU
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Chi-restraints excluded: chain B residue   13 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 137 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 120 optimal weight:    8.9990
   chunk 108 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 70 optimal weight:    0.3980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.098744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.062068 restraints weight = 122110.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.065582 restraints weight = 53373.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.067889 restraints weight = 33540.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.069292 restraints weight = 25210.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.070251 restraints weight = 20995.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11308  Z= 0.143
  Angle     :  0.492   6.235  15389  Z= 0.252
  Chirality :  0.037   0.146   1656
  Planarity :  0.004   0.037   2052
  Dihedral  :  4.280  20.363   1549
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 10.21 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.24), residues: 1389
  helix:  1.92 (0.23), residues: 548
  sheet: -0.50 (0.29), residues: 294
  loop :  0.39 (0.29), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  36 
 TYR   0.010   0.001   TYR A3377 
 PHE   0.009   0.001   PHE A3357 
 TRP   0.012   0.001   TRP A2974 
 HIS   0.006   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11308)
  covalent geometry    : angle       0.49159 (15389)
  hydrogen bonds       : bond        0.02955 (  512)
  hydrogen bonds       : angle       4.30643 ( 1488)

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

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

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2778 Ramachandran restraints generated.
    1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.573 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
REVERT: A 3470 MET cc_start: 0.8355 (tpp) cc_final: 0.7620 (tpp)
REVERT: A 3551 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6453 (pp30)
REVERT: A 3552 MET cc_start: 0.8421 (mmt) cc_final: 0.8120 (mmt)
REVERT: A 3619 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7348 (tp40)
REVERT: B   22 TYR cc_start: 0.6960 (m-80) cc_final: 0.6750 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 60
  average time/residue: 0.2638
  time to fit residues: 21.7819
Evaluate side-chains
  59 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3551 GLN
Chi-restraints excluded: chain A residue 3627 SER
Chi-restraints excluded: chain A residue 3683 GLU
Chi-restraints excluded: chain A residue 3897 TYR
Chi-restraints excluded: chain A residue 3921 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 93 optimal weight:   30.0000
   chunk 89 optimal weight:    6.9990
   chunk 103 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 128 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 122 optimal weight:    4.9990
   chunk 98 optimal weight:   30.0000
   chunk 115 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4091 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 = 0.4064 r_free = 0.4064 target = 0.097419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.060555 restraints weight = 121798.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.063865 restraints weight = 53008.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.066115 restraints weight = 33398.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.067488 restraints weight = 25198.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.068429 restraints weight = 21120.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  11308  Z= 0.260
  Angle     :  0.569   6.567  15389  Z= 0.299
  Chirality :  0.039   0.154   1656
  Planarity :  0.004   0.040   2052
  Dihedral  :  4.485  21.667   1549
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.74 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.21 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.23), residues: 1389
  helix:  1.53 (0.22), residues: 547
  sheet: -0.56 (0.30), residues: 282
  loop :  0.15 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A2978 
 TYR   0.017   0.002   TYR A3377 
 PHE   0.013   0.002   PHE A3357 
 TRP   0.010   0.001   TRP A2974 
 HIS   0.008   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (11308)
  covalent geometry    : angle       0.56889 (15389)
  hydrogen bonds       : bond        0.03391 (  512)
  hydrogen bonds       : angle       4.59949 ( 1488)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4339.26 seconds
wall clock time: 74 minutes 10.10 seconds (4450.10 seconds total)