Starting phenix.real_space_refine
on Fri Feb  6 04:48:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lcp_62989/02_2026/9lcp_62989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lcp_62989/02_2026/9lcp_62989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lcp_62989/02_2026/9lcp_62989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lcp_62989/02_2026/9lcp_62989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lcp_62989/02_2026/9lcp_62989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lcp_62989/02_2026/9lcp_62989.cif"
  }
  resolution = 3.76
  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    6997      2.51       5
     N    1977      2.21       5
     O    2035      1.98       5
     H   10829      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 116 residue(s): 0.02s

  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: 21872
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 20873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1332, 20873
          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: 4.07, per 1000 atoms: 0.19
  Number of scatterers: 21872
  At special positions: 0
  Unit cell: (84.048, 118.656, 173.864, 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    1977      7.00
     C    6997      6.00
     H   10829      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: 2.25
  Conformation dependent library (CDL) restraints added in 662.0 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:
      57 helices and 13 sheets defined
      44.1% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2793 through 2802
    Processing helix  chain 'A' and resid 2823 through 2838
      removed outlier: 4.089A  pdb=" N   LYS A2829 " --> pdb=" O   GLY A2825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2839 through 2841
      No H-bonds generated for 'chain 'A' and resid 2839 through 2841'
    Processing helix  chain 'A' and resid 2872 through 2875
    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 2963
      removed outlier: 3.530A  pdb=" N   TRP A2955 " --> pdb=" O   ALA A2951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2965 through 2980
      removed outlier: 3.873A  pdb=" N   GLU A2971 " --> pdb=" O   SER A2967 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLY A2973 " --> pdb=" O   ARG A2969 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP A2974 " --> pdb=" O   GLU A2970 " (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 3022
    Processing helix  chain 'A' and resid 3026 through 3042
      removed outlier: 3.689A  pdb=" N   LEU A3030 " --> pdb=" O   GLN A3026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3086 through 3101
      removed outlier: 3.800A  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: 4.324A  pdb=" N   GLY A3109 " --> pdb=" O   GLY A3105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3116 through 3125
      removed outlier: 3.670A  pdb=" N   GLN A3121 " --> pdb=" O   PRO A3117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3192 through 3215
    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: 3.626A  pdb=" N   GLY A3259 " --> pdb=" O   PRO A3255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3286 through 3302
      removed outlier: 3.837A  pdb=" N   GLU A3302 " --> pdb=" O   VAL A3298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3339 through 3356
      removed outlier: 4.714A  pdb=" N   GLU A3343 " --> pdb=" O   ASP A3339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3391 through 3409
      removed outlier: 4.068A  pdb=" N   LEU A3395 " --> pdb=" O   TRP A3391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3420 through 3431
      removed outlier: 4.053A  pdb=" N   TYR A3424 " --> pdb=" O   ARG A3420 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A3430 " --> pdb=" O   ALA A3426 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN A3431 " --> pdb=" O   TRP A3427 " (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: 4.322A  pdb=" N   ALA A3491 " --> pdb=" O   LEU A3487 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLN A3492 " --> pdb=" O   ARG A3488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3497 through 3515
    Processing helix  chain 'A' and resid 3532 through 3538
      removed outlier: 3.928A  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 3577 through 3579
      No H-bonds generated for 'chain 'A' and resid 3577 through 3579'
    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
    Processing helix  chain 'A' and resid 3683 through 3687
    Processing helix  chain 'A' and resid 3691 through 3700
    Processing helix  chain 'A' and resid 3701 through 3704
      removed outlier: 3.975A  pdb=" N   ARG A3704 " --> pdb=" O   GLY A3701 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3701 through 3704'
    Processing helix  chain 'A' and resid 3710 through 3713
    Processing helix  chain 'A' and resid 3714 through 3726
      removed outlier: 3.922A  pdb=" N   GLU A3720 " --> pdb=" O   VAL A3716 " (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 3810
    Processing helix  chain 'A' and resid 3817 through 3831
      removed outlier: 4.495A  pdb=" N   GLU A3822 " --> pdb=" O   GLN A3818 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   GLN A3823 " --> pdb=" O   ALA A3819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3842 through 3846
    Processing helix  chain 'A' and resid 3884 through 3898
      removed outlier: 3.640A  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: 4.014A  pdb=" N   TRP A3919 " --> pdb=" O   ASP A3915 " (cutoff:3.500A)
      removed outlier: 4.965A  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
      removed outlier: 3.699A  pdb=" N   GLY A3950 " --> pdb=" O   LEU A3946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3960 through 3968
      removed outlier: 3.769A  pdb=" N   GLY A3966 " --> pdb=" O   SER A3962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3989 through 4000
    Processing helix  chain 'A' and resid 4011 through 4015
    Processing helix  chain 'A' and resid 4025 through 4030
      removed outlier: 4.015A  pdb=" N   GLU A4029 " --> pdb=" O   ALA A4026 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER A4030 " --> pdb=" O   SER A4027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4050 through 4054
    Processing helix  chain 'A' and resid 4080 through 4087
      removed outlier: 3.617A  pdb=" N   GLN A4086 " --> pdb=" O   LEU A4082 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 55
    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: 6.389A  pdb=" N   GLN A2907 " --> pdb=" O   PRO A2818 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2843 through 2847
    Processing sheet with id=AA3, first strand: chain 'A' and resid 3000 through 3006
      removed outlier: 6.343A  pdb=" N   THR A3132 " --> pdb=" O   VAL A3171 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLY A3173 " --> pdb=" O   THR A3132 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ASN A3134 " --> pdb=" O   GLY A3173 " (cutoff:3.500A)
      removed outlier: 8.598A  pdb=" N   VAL A3175 " --> pdb=" O   ASN A3134 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   LEU A3136 " --> pdb=" O   VAL A3175 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ILE A3131 " --> pdb=" O   LEU A3049 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   GLU A3053 " --> pdb=" O   PHE A3133 " (cutoff:3.500A)
      removed outlier: 6.524A  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: 3.509A  pdb=" N   ASP A3249 " --> pdb=" O   ILE A3320 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE A3308 " --> pdb=" O   VAL A3319 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   HIS A3321 " --> pdb=" O   ALA A3306 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ALA A3306 " --> pdb=" O   HIS A3321 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 3327 through 3332
      removed outlier: 6.535A  pdb=" N   ARG A3327 " --> pdb=" O   LEU A3367 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   LEU A3369 " --> pdb=" O   ARG A3327 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   GLU A3329 " --> pdb=" O   LEU A3369 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   ARG A3371 " --> pdb=" O   GLU A3329 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   LEU A3331 " --> pdb=" O   ARG A3371 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 3472 through 3478
      removed outlier: 6.579A  pdb=" N   LEU A3602 " --> pdb=" O   VAL A3638 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   CYS A3640 " --> pdb=" O   LEU A3602 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL A3604 " --> pdb=" O   CYS A3640 " (cutoff:3.500A)
      removed outlier: 12.179A  pdb=" N   SER A3601 " --> pdb=" O   ASP A3518 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   LEU A3520 " --> pdb=" O   SER A3601 " (cutoff:3.500A)
      removed outlier: 8.973A  pdb=" N   PHE A3603 " --> pdb=" O   LEU A3520 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   GLY A3522 " --> pdb=" O   PHE A3603 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   PHE A3605 " --> pdb=" O   GLY A3522 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   THR A3524 " --> pdb=" O   PHE A3605 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 3789 through 3792
      removed outlier: 5.746A  pdb=" N   VAL A3813 " --> pdb=" O   PRO A3765 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A3767 " --> pdb=" O   VAL A3813 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS A3816 " --> pdb=" O   LEU A3840 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3864 through 3870
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3905 through 3908
      removed outlier: 6.592A  pdb=" N   ILE A3906 " --> pdb=" O   ALA A3932 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3956 through 3959
      removed outlier: 7.050A  pdb=" N   LEU A3957 " --> pdb=" O   LEU A3982 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 4042 through 4047
      removed outlier: 6.491A  pdb=" N   GLY A4064 " --> pdb=" O   ASP A4105 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ASP A4105 " --> pdb=" O   GLY A4064 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LEU A4066 " --> pdb=" O   THR A4103 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   GLY A4070 " --> pdb=" O   ARG A4099 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   ARG A4099 " --> pdb=" O   GLY A4070 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 4042 through 4047
      removed outlier: 6.491A  pdb=" N   GLY A4064 " --> pdb=" O   ASP A4105 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ASP A4105 " --> pdb=" O   GLY A4064 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LEU A4066 " --> pdb=" O   THR A4103 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   GLY A4070 " --> pdb=" O   ARG A4099 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   ARG A4099 " --> pdb=" O   GLY A4070 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU A4106 " --> pdb=" O   VAL A4118 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 22 through 26
      removed outlier: 4.708A  pdb=" N   LYS B  40 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   VAL B  16 " --> pdb=" O   ALA B  38 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ALA B  38 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)

    505 hydrogen bonds defined for protein.
    1437 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: 5.68

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 10814
        1.12 -     1.30: 1921
        1.30 -     1.47: 4357
        1.47 -     1.65: 4998
        1.65 -     1.82: 53
  Bond restraints: 22143
  Sorted by residual:
  bond pdb=" N   GLU A2970 "
       pdb=" H   GLU A2970 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" CE2 TYR A3191 "
       pdb=" HE2 TYR A3191 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CZ  PHE A3061 "
       pdb=" HZ  PHE A3061 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   LEU A2959 "
       pdb=" H   LEU A2959 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" CE1 TYR A3274 "
       pdb=" HE1 TYR A3274 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 22138 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.86: 34898
        2.86 -     5.72: 4112
        5.72 -     8.57: 949
        8.57 -    11.43: 12
       11.43 -    14.29: 9
  Bond angle restraints: 39980
  Sorted by residual:
  angle pdb=" C   ASP A3358 "
        pdb=" N   LEU A3359 "
        pdb=" CA  LEU A3359 "
      ideal   model   delta    sigma   weight residual
     120.28  128.77   -8.49 1.44e+00 4.82e-01 3.48e+01
  angle pdb=" CB  HIS A3341 "
        pdb=" CG  HIS A3341 "
        pdb=" CD2 HIS A3341 "
      ideal   model   delta    sigma   weight residual
     131.20  124.21    6.99 1.30e+00 5.92e-01 2.89e+01
  angle pdb=" CA  PHE A3308 "
        pdb=" CB  PHE A3308 "
        pdb=" CG  PHE A3308 "
      ideal   model   delta    sigma   weight residual
     113.80  119.00   -5.20 1.00e+00 1.00e+00 2.70e+01
  angle pdb=" N   ALA A3732 "
        pdb=" CA  ALA A3732 "
        pdb=" C   ALA A3732 "
      ideal   model   delta    sigma   weight residual
     108.79  116.67   -7.88 1.53e+00 4.27e-01 2.65e+01
  angle pdb=" N   LEU A3359 "
        pdb=" CA  LEU A3359 "
        pdb=" CB  LEU A3359 "
      ideal   model   delta    sigma   weight residual
     110.22  102.36    7.86 1.54e+00 4.22e-01 2.60e+01
  ... (remaining 39975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 9548
       17.87 -    35.74: 555
       35.74 -    53.60: 215
       53.60 -    71.47: 77
       71.47 -    89.34: 18
  Dihedral angle restraints: 10413
    sinusoidal: 5711
      harmonic: 4702
  Sorted by residual:
  dihedral pdb=" CA  ALA A3306 "
           pdb=" C   ALA A3306 "
           pdb=" N   SER A3307 "
           pdb=" CA  SER A3307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.79  -29.21     0      5.00e+00 4.00e-02 3.41e+01
  dihedral pdb=" CA  ASP A3140 "
           pdb=" C   ASP A3140 "
           pdb=" N   GLN A3141 "
           pdb=" CA  GLN A3141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.05  -28.95     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  GLN A2820 "
           pdb=" C   GLN A2820 "
           pdb=" N   ALA A2821 "
           pdb=" CA  ALA A2821 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.62   28.38     0      5.00e+00 4.00e-02 3.22e+01
  ... (remaining 10410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1265
       0.110 -    0.221: 358
       0.221 -    0.331: 30
       0.331 -    0.442: 2
       0.442 -    0.552: 1
  Chirality restraints: 1656
  Sorted by residual:
  chirality pdb=" CA  ASP A4040 "
            pdb=" N   ASP A4040 "
            pdb=" C   ASP A4040 "
            pdb=" CB  ASP A4040 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.62e+00
  chirality pdb=" CA  ARG A3558 "
            pdb=" N   ARG A3558 "
            pdb=" C   ARG A3558 "
            pdb=" CB  ARG A3558 "
    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  GLU A3302 "
            pdb=" N   GLU A3302 "
            pdb=" C   GLU A3302 "
            pdb=" CB  GLU A3302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.08e+00
  ... (remaining 1653 not shown)

  Planarity restraints: 3356
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A2806 "   -0.427 9.50e-02 1.11e+02   1.76e-01 2.58e+02
        pdb=" NE  ARG A2806 "   -0.071 2.00e-02 2.50e+03
        pdb=" CZ  ARG A2806 "   -0.066 2.00e-02 2.50e+03
        pdb=" NH1 ARG A2806 "   -0.099 2.00e-02 2.50e+03
        pdb=" NH2 ARG A2806 "   -0.008 2.00e-02 2.50e+03
        pdb="HH11 ARG A2806 "    0.230 2.00e-02 2.50e+03
        pdb="HH12 ARG A2806 "   -0.094 2.00e-02 2.50e+03
        pdb="HH21 ARG A2806 "    0.118 2.00e-02 2.50e+03
        pdb="HH22 ARG A2806 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A3439 "    0.196 2.00e-02 2.50e+03   8.02e-02 2.57e+02
        pdb=" CG  TRP A3439 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP A3439 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A3439 "   -0.068 2.00e-02 2.50e+03
        pdb=" NE1 TRP A3439 "   -0.083 2.00e-02 2.50e+03
        pdb=" CE2 TRP A3439 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE3 TRP A3439 "   -0.083 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A3439 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A3439 "   -0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP A3439 "    0.047 2.00e-02 2.50e+03
        pdb=" HD1 TRP A3439 "    0.067 2.00e-02 2.50e+03
        pdb=" HE1 TRP A3439 "   -0.073 2.00e-02 2.50e+03
        pdb=" HE3 TRP A3439 "   -0.114 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A3439 "    0.049 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A3439 "    0.010 2.00e-02 2.50e+03
        pdb=" HH2 TRP A3439 "    0.124 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A3617 "   -0.381 9.50e-02 1.11e+02   1.58e-01 2.17e+02
        pdb=" NE  ARG A3617 "   -0.070 2.00e-02 2.50e+03
        pdb=" CZ  ARG A3617 "   -0.055 2.00e-02 2.50e+03
        pdb=" NH1 ARG A3617 "   -0.083 2.00e-02 2.50e+03
        pdb=" NH2 ARG A3617 "    0.008 2.00e-02 2.50e+03
        pdb="HH11 ARG A3617 "    0.216 2.00e-02 2.50e+03
        pdb="HH12 ARG A3617 "   -0.102 2.00e-02 2.50e+03
        pdb="HH21 ARG A3617 "    0.092 2.00e-02 2.50e+03
        pdb="HH22 ARG A3617 "    0.012 2.00e-02 2.50e+03
  ... (remaining 3353 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 1534
        2.18 -     2.79: 39151
        2.79 -     3.39: 63174
        3.39 -     4.00: 84234
        4.00 -     4.60: 122581
  Nonbonded interactions: 310674
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A3096 "
            pdb=" HG  SER A3225 "
     model   vdw
     1.578 2.450
  nonbonded pdb=" OD1 ASP A3332 "
            pdb=" HG  SER A3334 "
     model   vdw
     1.591 2.450
  nonbonded pdb=" OD1 ASP A4024 "
            pdb=" HG  SER A4027 "
     model   vdw
     1.595 2.450
  nonbonded pdb=" OE2 GLU A4013 "
            pdb=" HH  TYR A4077 "
     model   vdw
     1.604 2.450
  nonbonded pdb=" OD1 ASP A3065 "
            pdb=" HG1 THR A3067 "
     model   vdw
     1.614 2.450
  ... (remaining 310669 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:             2.780
  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:             0.170
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     23.070
  Find NCS groups from input model:        0.080
  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:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6054
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   0.052  11314  Z= 0.748
  Angle     :  1.798   8.490  15396  Z= 1.219
  Chirality :  0.094   0.552   1656
  Planarity :  0.017   0.204   2053
  Dihedral  : 14.088  89.340   4199
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 0.27
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.61 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  2.88 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.16 %
  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: -1.23 (0.21), residues: 1389
  helix: -1.07 (0.19), residues: 542
  sheet: -0.28 (0.31), residues: 232
  loop : -0.59 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A2857 
 TYR   0.142   0.022   TYR A3191 
 PHE   0.080   0.015   PHE A3061 
 TRP   0.130   0.022   TRP A3439 
 HIS   0.017   0.004   HIS A4091 

Details of bonding type rmsd
  covalent geometry    : bond        0.01201 (11314)
  covalent geometry    : angle       1.79761 (15396)
  hydrogen bonds       : bond        0.15126 (  496)
  hydrogen bonds       : angle       7.11472 ( 1437)

*********************** 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
  127 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.630 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3277 ASP cc_start: 0.8008 (t0) cc_final: 0.7596 (t0)
REVERT: A 3532 MET cc_start: 0.7716 (mtm) cc_final: 0.7489 (mtm)
REVERT: B   16 VAL cc_start: 0.5885 (OUTLIER) cc_final: 0.5601 (t)
  outliers start: 9
  outliers final: 3
  residues processed: 126
  average time/residue: 0.3314
  time to fit residues: 55.4447
Evaluate side-chains
  80 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3428 LEU
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3683 GLU
Chi-restraints excluded: chain B residue   16 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    3.1786

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.103458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.063541 restraints weight = 111913.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.066500 restraints weight = 51350.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.068747 restraints weight = 32643.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.070082 restraints weight = 24438.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.071019 restraints weight = 20411.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  11314  Z= 0.302
  Angle     :  0.733   5.909  15396  Z= 0.390
  Chirality :  0.042   0.134   1656
  Planarity :  0.006   0.083   2053
  Dihedral  :  7.159  98.297   1558
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.59 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.80 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.21), residues: 1389
  helix: -0.14 (0.21), residues: 542
  sheet: -1.09 (0.29), residues: 267
  loop : -0.47 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A3558 
 TYR   0.017   0.002   TYR A2962 
 PHE   0.019   0.002   PHE A3921 
 TRP   0.017   0.002   TRP A2923 
 HIS   0.011   0.002   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00689 (11314)
  covalent geometry    : angle       0.73319 (15396)
  hydrogen bonds       : bond        0.05439 (  496)
  hydrogen bonds       : angle       5.77649 ( 1437)

*********************** 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
  80 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.454 
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 2899 LEU cc_start: 0.8384 (tp) cc_final: 0.8141 (tp)
REVERT: A 3277 ASP cc_start: 0.7795 (t0) cc_final: 0.7501 (t0)
REVERT: B   20 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8601 (mt-10)
REVERT: B   50 TYR cc_start: 0.9571 (t80) cc_final: 0.9349 (t80)
REVERT: B   58 MET cc_start: 0.7844 (mtp) cc_final: 0.7498 (mtp)
  outliers start: 11
  outliers final: 5
  residues processed: 79
  average time/residue: 0.2943
  time to fit residues: 31.9764
Evaluate side-chains
  69 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3308 PHE
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain A residue 3689 LEU
Chi-restraints excluded: chain A residue 3946 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 132 optimal weight:    9.9990
   chunk 97 optimal weight:   50.0000
   chunk 40 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 126 optimal weight:    6.9990
   chunk 57 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 95 optimal weight:   30.0000
   chunk 121 optimal weight:   30.0000
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.105178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.064395 restraints weight = 114420.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.067792 restraints weight = 48730.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.070206 restraints weight = 30076.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 68)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.071644 restraints weight = 22107.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.072473 restraints weight = 18177.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11314  Z= 0.135
  Angle     :  0.585   6.169  15396  Z= 0.307
  Chirality :  0.040   0.239   1656
  Planarity :  0.005   0.063   2053
  Dihedral  :  5.757  55.049   1552
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.59 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  7.41 %
    Favored  : 91.89 %
  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: -0.34 (0.22), residues: 1389
  helix:  0.48 (0.22), residues: 533
  sheet: -0.99 (0.30), residues: 257
  loop : -0.34 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A3558 
 TYR   0.015   0.002   TYR A2962 
 PHE   0.012   0.001   PHE A3921 
 TRP   0.013   0.001   TRP A3310 
 HIS   0.010   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11314)
  covalent geometry    : angle       0.58509 (15396)
  hydrogen bonds       : bond        0.04339 (  496)
  hydrogen bonds       : angle       5.16997 ( 1437)

*********************** 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
  73 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.593 
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 2899 LEU cc_start: 0.8415 (tp) cc_final: 0.8174 (tp)
REVERT: A 3275 MET cc_start: 0.7874 (mtt) cc_final: 0.7577 (mtm)
REVERT: A 3277 ASP cc_start: 0.7641 (t0) cc_final: 0.7280 (t0)
REVERT: B   16 VAL cc_start: 0.9605 (OUTLIER) cc_final: 0.9162 (p)
REVERT: B   36 ARG cc_start: 0.8966 (ptt-90) cc_final: 0.8727 (ptt-90)
REVERT: B   58 MET cc_start: 0.7840 (mtp) cc_final: 0.7461 (mtp)
  outliers start: 8
  outliers final: 5
  residues processed: 72
  average time/residue: 0.3107
  time to fit residues: 30.4273
Evaluate side-chains
  69 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain A residue 3604 VAL
Chi-restraints excluded: chain A residue 3665 LEU
Chi-restraints excluded: chain A residue 3689 LEU
Chi-restraints excluded: chain B residue   16 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 134 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 138 optimal weight:    8.9990
   chunk 121 optimal weight:   20.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A3383 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.104592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.063400 restraints weight = 113836.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.066861 restraints weight = 49783.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.069124 restraints weight = 30988.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.070528 restraints weight = 22961.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.071360 restraints weight = 19048.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11314  Z= 0.168
  Angle     :  0.563   5.679  15396  Z= 0.294
  Chirality :  0.039   0.136   1656
  Planarity :  0.004   0.047   2053
  Dihedral  :  5.374  54.844   1552
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.88 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.02 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.22), residues: 1389
  helix:  0.78 (0.22), residues: 541
  sheet: -1.07 (0.30), residues: 257
  loop : -0.30 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A4075 
 TYR   0.018   0.002   TYR B  50 
 PHE   0.010   0.001   PHE A3921 
 TRP   0.016   0.001   TRP A2923 
 HIS   0.010   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (11314)
  covalent geometry    : angle       0.56290 (15396)
  hydrogen bonds       : bond        0.03894 (  496)
  hydrogen bonds       : angle       4.96094 ( 1437)

*********************** 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
  73 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.591 
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 2899 LEU cc_start: 0.8447 (tp) cc_final: 0.8210 (tp)
REVERT: A 3275 MET cc_start: 0.7910 (mtt) cc_final: 0.7656 (mtm)
REVERT: A 3277 ASP cc_start: 0.7531 (t0) cc_final: 0.7150 (t0)
REVERT: A 3532 MET cc_start: 0.7500 (mtm) cc_final: 0.7219 (mtm)
REVERT: B   22 TYR cc_start: 0.9536 (m-80) cc_final: 0.9306 (m-80)
REVERT: B   58 MET cc_start: 0.7803 (mtp) cc_final: 0.7366 (mtp)
  outliers start: 10
  outliers final: 7
  residues processed: 71
  average time/residue: 0.3354
  time to fit residues: 31.8638
Evaluate side-chains
  67 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2811 ASN
Chi-restraints excluded: chain A residue 2814 LEU
Chi-restraints excluded: chain A residue 3116 ASP
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain A residue 3665 LEU
Chi-restraints excluded: chain A residue 3689 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 96 optimal weight:   50.0000
   chunk 103 optimal weight:   30.0000
   chunk 10 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 118 optimal weight:   50.0000
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.104415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.063346 restraints weight = 112627.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.066751 restraints weight = 49381.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.068973 restraints weight = 30719.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 70)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.070382 restraints weight = 22847.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.071197 restraints weight = 18911.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11314  Z= 0.162
  Angle     :  0.538   5.796  15396  Z= 0.280
  Chirality :  0.038   0.137   1656
  Planarity :  0.004   0.043   2053
  Dihedral  :  5.140  53.331   1552
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.24 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.37 %
    Favored  : 90.85 %
  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:  0.07 (0.23), residues: 1389
  helix:  1.03 (0.22), residues: 542
  sheet: -1.09 (0.30), residues: 257
  loop : -0.21 (0.27), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A3300 
 TYR   0.014   0.002   TYR A3191 
 PHE   0.009   0.001   PHE A3921 
 TRP   0.014   0.001   TRP A2923 
 HIS   0.009   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (11314)
  covalent geometry    : angle       0.53775 (15396)
  hydrogen bonds       : bond        0.03642 (  496)
  hydrogen bonds       : angle       4.81897 ( 1437)

*********************** 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 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.441 
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 3275 MET cc_start: 0.7904 (mtt) cc_final: 0.7644 (mtm)
REVERT: A 3277 ASP cc_start: 0.7479 (t0) cc_final: 0.7119 (t0)
REVERT: A 3532 MET cc_start: 0.7563 (mtm) cc_final: 0.7305 (mtm)
REVERT: B   58 MET cc_start: 0.7698 (mtp) cc_final: 0.7308 (mtp)
  outliers start: 9
  outliers final: 9
  residues processed: 69
  average time/residue: 0.3153
  time to fit residues: 29.5754
Evaluate side-chains
  66 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2811 ASN
Chi-restraints excluded: chain A residue 2814 LEU
Chi-restraints excluded: chain A residue 3116 ASP
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain A residue 3665 LEU
Chi-restraints excluded: chain A residue 3689 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   41 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 102 optimal weight:   20.0000
   chunk 96 optimal weight:   30.0000
   chunk 97 optimal weight:    0.0020
   chunk 93 optimal weight:   30.0000
   chunk 18 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    1.9996

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.103996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.062940 restraints weight = 113602.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.066266 restraints weight = 49350.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.068472 restraints weight = 30643.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.069875 restraints weight = 22817.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.070640 restraints weight = 18875.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11314  Z= 0.180
  Angle     :  0.542   5.328  15396  Z= 0.280
  Chirality :  0.038   0.136   1656
  Planarity :  0.004   0.054   2053
  Dihedral  :  5.004  52.305   1552
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.46 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.63 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.05 (0.23), residues: 1389
  helix:  1.11 (0.22), residues: 544
  sheet: -1.33 (0.29), residues: 262
  loop : -0.18 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A3300 
 TYR   0.015   0.001   TYR A3191 
 PHE   0.009   0.001   PHE A2952 
 TRP   0.015   0.001   TRP A2923 
 HIS   0.009   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (11314)
  covalent geometry    : angle       0.54191 (15396)
  hydrogen bonds       : bond        0.03577 (  496)
  hydrogen bonds       : angle       4.75887 ( 1437)

*********************** 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
  67 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.634 
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 3275 MET cc_start: 0.7951 (mtt) cc_final: 0.7683 (mtm)
REVERT: A 3277 ASP cc_start: 0.7448 (t0) cc_final: 0.7108 (t0)
REVERT: B   22 TYR cc_start: 0.9478 (m-80) cc_final: 0.9201 (m-80)
REVERT: B   58 MET cc_start: 0.7697 (mtp) cc_final: 0.7271 (mtp)
  outliers start: 8
  outliers final: 8
  residues processed: 67
  average time/residue: 0.2963
  time to fit residues: 26.9305
Evaluate side-chains
  66 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2811 ASN
Chi-restraints excluded: chain A residue 2814 LEU
Chi-restraints excluded: chain A residue 3116 ASP
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain A residue 3665 LEU
Chi-restraints excluded: chain A residue 3689 LEU
Chi-restraints excluded: chain B residue   16 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 111 optimal weight:   20.0000
   chunk 0 optimal weight:    2.9990
   chunk 97 optimal weight:   50.0000
   chunk 106 optimal weight:   50.0000
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 128 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
A2797 HIS
A2867 HIS
A3463 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.103424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.063356 restraints weight = 109578.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.066594 restraints weight = 47350.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.068706 restraints weight = 29266.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.069960 restraints weight = 21666.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 69)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.070963 restraints weight = 18048.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11314  Z= 0.201
  Angle     :  0.553   5.376  15396  Z= 0.286
  Chirality :  0.038   0.137   1656
  Planarity :  0.004   0.041   2053
  Dihedral  :  4.935  51.067   1552
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.03 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.98 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.01 (0.23), residues: 1389
  helix:  1.15 (0.22), residues: 543
  sheet: -1.55 (0.29), residues: 262
  loop : -0.21 (0.27), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A3368 
 TYR   0.016   0.002   TYR A3191 
 PHE   0.010   0.001   PHE A2952 
 TRP   0.016   0.001   TRP A3310 
 HIS   0.009   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (11314)
  covalent geometry    : angle       0.55263 (15396)
  hydrogen bonds       : bond        0.03584 (  496)
  hydrogen bonds       : angle       4.76419 ( 1437)

*********************** 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
  68 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.658 
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: A 3275 MET cc_start: 0.7883 (mtt) cc_final: 0.7598 (mtm)
REVERT: A 3277 ASP cc_start: 0.7513 (t0) cc_final: 0.7186 (t0)
REVERT: A 4083 ARG cc_start: 0.9472 (mmp80) cc_final: 0.9265 (mmm-85)
REVERT: B   58 MET cc_start: 0.7650 (mtp) cc_final: 0.7336 (mtp)
  outliers start: 9
  outliers final: 7
  residues processed: 67
  average time/residue: 0.3441
  time to fit residues: 30.7765
Evaluate side-chains
  65 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2811 ASN
Chi-restraints excluded: chain A residue 3116 ASP
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain A residue 3689 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 57 optimal weight:    0.1980
   chunk 26 optimal weight:    0.5980
   chunk 136 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 96 optimal weight:   50.0000
   chunk 87 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   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 = 0.4121 r_free = 0.4121 target = 0.103884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.064450 restraints weight = 108668.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.067674 restraints weight = 46175.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.069812 restraints weight = 28194.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.071093 restraints weight = 20691.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.072068 restraints weight = 17148.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11314  Z= 0.147
  Angle     :  0.523   5.161  15396  Z= 0.269
  Chirality :  0.038   0.136   1656
  Planarity :  0.004   0.043   2053
  Dihedral  :  4.810  50.015   1552
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.60 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.72 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.14 (0.23), residues: 1389
  helix:  1.29 (0.22), residues: 546
  sheet: -1.53 (0.29), residues: 254
  loop : -0.13 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A3300 
 TYR   0.032   0.002   TYR B  50 
 PHE   0.008   0.001   PHE A2952 
 TRP   0.011   0.001   TRP A2923 
 HIS   0.008   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11314)
  covalent geometry    : angle       0.52331 (15396)
  hydrogen bonds       : bond        0.03395 (  496)
  hydrogen bonds       : angle       4.63299 ( 1437)

*********************** 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
  67 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.567 
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 3275 MET cc_start: 0.7821 (mtt) cc_final: 0.7538 (mtm)
REVERT: A 3277 ASP cc_start: 0.7462 (t0) cc_final: 0.7084 (t0)
REVERT: B   22 TYR cc_start: 0.9475 (m-80) cc_final: 0.9204 (m-80)
REVERT: B   58 MET cc_start: 0.7617 (mtp) cc_final: 0.7257 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.3110
  time to fit residues: 27.7915
Evaluate side-chains
  65 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2814 LEU
Chi-restraints excluded: chain A residue 3116 ASP
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain A residue 3665 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 93 optimal weight:   30.0000
   chunk 134 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 99 optimal weight:   50.0000
   chunk 70 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 135 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 100 optimal weight:   30.0000
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.4106 r_free = 0.4106 target = 0.103306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.063183 restraints weight = 108957.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.066393 restraints weight = 46612.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.068478 restraints weight = 28630.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.069765 restraints weight = 21244.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.070723 restraints weight = 17649.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11314  Z= 0.194
  Angle     :  0.548   5.389  15396  Z= 0.284
  Chirality :  0.039   0.138   1656
  Planarity :  0.004   0.042   2053
  Dihedral  :  4.792  49.346   1552
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.32 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.24 %
    Favored  : 90.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.01 (0.23), residues: 1389
  helix:  1.19 (0.22), residues: 548
  sheet: -1.71 (0.29), residues: 252
  loop : -0.17 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A3368 
 TYR   0.034   0.002   TYR B  50 
 PHE   0.009   0.001   PHE A2952 
 TRP   0.018   0.001   TRP A2923 
 HIS   0.009   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (11314)
  covalent geometry    : angle       0.54775 (15396)
  hydrogen bonds       : bond        0.03520 (  496)
  hydrogen bonds       : angle       4.72463 ( 1437)

*********************** 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
  67 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.567 
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: A 3275 MET cc_start: 0.7890 (mtt) cc_final: 0.7592 (mtm)
REVERT: A 3277 ASP cc_start: 0.7536 (t0) cc_final: 0.7179 (t0)
REVERT: A 4083 ARG cc_start: 0.9477 (mmp80) cc_final: 0.9263 (mmm-85)
REVERT: B   22 TYR cc_start: 0.9508 (m-80) cc_final: 0.9255 (m-80)
REVERT: B   58 MET cc_start: 0.7699 (mtp) cc_final: 0.7322 (mtp)
  outliers start: 8
  outliers final: 5
  residues processed: 66
  average time/residue: 0.3122
  time to fit residues: 27.4610
Evaluate side-chains
  63 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2814 LEU
Chi-restraints excluded: chain A residue 3116 ASP
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 119 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A3429 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.104223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.064622 restraints weight = 107995.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.067617 restraints weight = 45414.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.069796 restraints weight = 27805.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.071133 restraints weight = 20386.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.071996 restraints weight = 16837.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11314  Z= 0.123
  Angle     :  0.515   5.224  15396  Z= 0.265
  Chirality :  0.038   0.136   1656
  Planarity :  0.004   0.043   2053
  Dihedral  :  4.672  48.271   1552
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.38 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  9.68 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.23), residues: 1389
  helix:  1.41 (0.23), residues: 548
  sheet: -1.67 (0.29), residues: 252
  loop : -0.13 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A3068 
 TYR   0.014   0.001   TYR A3869 
 PHE   0.010   0.001   PHE A3401 
 TRP   0.012   0.001   TRP A2974 
 HIS   0.007   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11314)
  covalent geometry    : angle       0.51529 (15396)
  hydrogen bonds       : bond        0.03266 (  496)
  hydrogen bonds       : angle       4.56812 ( 1437)

********************** 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
  65 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.575 
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: A 3275 MET cc_start: 0.7778 (mtt) cc_final: 0.7472 (mtm)
REVERT: A 3277 ASP cc_start: 0.7446 (t0) cc_final: 0.6996 (t0)
REVERT: A 3397 MET cc_start: 0.8289 (mmm) cc_final: 0.7704 (tpp)
REVERT: B   22 TYR cc_start: 0.9461 (m-80) cc_final: 0.9158 (m-80)
REVERT: B   58 MET cc_start: 0.7656 (mtp) cc_final: 0.7259 (mtp)
  outliers start: 5
  outliers final: 5
  residues processed: 64
  average time/residue: 0.2810
  time to fit residues: 24.8011
Evaluate side-chains
  61 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2814 LEU
Chi-restraints excluded: chain A residue 3116 ASP
Chi-restraints excluded: chain A residue 3568 LEU
Chi-restraints excluded: chain A residue 3602 LEU
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 136 optimal weight:   20.0000
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 99 optimal weight:   50.0000
   chunk 133 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0270
   overall best weight:    1.3042

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.104554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.063365 restraints weight = 113207.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.066482 restraints weight = 49056.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.068711 restraints weight = 30504.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.070024 restraints weight = 22685.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.070973 restraints weight = 18892.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11314  Z= 0.134
  Angle     :  0.520   6.076  15396  Z= 0.267
  Chirality :  0.038   0.136   1656
  Planarity :  0.004   0.043   2053
  Dihedral  :  4.622  47.853   1552
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.25 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 10.11 %
    Favored  : 89.45 %
  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 (0.23), residues: 1389
  helix:  1.45 (0.23), residues: 548
  sheet: -1.77 (0.28), residues: 266
  loop : -0.10 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  59 
 TYR   0.013   0.001   TYR B  50 
 PHE   0.007   0.001   PHE A3921 
 TRP   0.026   0.001   TRP A3310 
 HIS   0.007   0.001   HIS A3213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (11314)
  covalent geometry    : angle       0.52012 (15396)
  hydrogen bonds       : bond        0.03248 (  496)
  hydrogen bonds       : angle       4.53244 ( 1437)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 4502.89 seconds
wall clock time: 77 minutes 7.17 seconds (4627.17 seconds total)