# Date 2008-01-16 Time 05:53:33 PST -0800 (1200491613.42 s)
#phil __OFF__

Command line arguments: "../923.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3697
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 923

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.1647, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.01212
Completeness in resolution range: 0.964643
Completeness with d_max=infinity: 0.961659

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0121

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.01212
Completeness in resolution range: 0.964643
Completeness with d_max=infinity: 0.961659

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.3052 [2140/2164]  1922   218  10.2%
  bin  2:  4.3052 -  3.4301 [2041/2061]  1841   200   9.8%
  bin  3:  3.4301 -  3.0003 [2021/2040]  1818   203  10.0%
  bin  4:  3.0003 -  2.7277 [1994/2024]  1793   201  10.1%
  bin  5:  2.7277 -  2.5332 [2002/2021]  1803   199   9.9%
  bin  6:  2.5332 -  2.3844 [1986/2011]  1784   202  10.2%
  bin  7:  2.3844 -  2.2654 [1960/1988]  1767   193   9.8%
  bin  8:  2.2654 -  2.1671 [1964/2000]  1769   195   9.9%
  bin  9:  2.1671 -  2.0839 [1945/1987]  1753   192   9.9%
  bin 10:  2.0839 -  2.0121 [1536/2011]  1380   156  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.73 -     2.36: 11
        2.36 -     3.00: 1866
        3.00 -     3.63: 4483
        3.63 -     4.27: 8927
        4.27 -     4.90: 12473
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.729 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.827 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.827 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.989 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27755 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_001.geo

CPU time processing inputs: 9.08


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.16465 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3939   r_free= 0.3858   ksol= 0.00   Bsol= 0.00   scale= 0.918    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.188753                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8017 0.99   1389  152 0.3204 0.3055      6.4501      6.3448|
|  2:  4.8017 -  3.8314 0.99   1331  152 0.3173 0.3160      6.6579      6.7052|
|  3:  3.8314 -  3.3530 0.99   1298  143 0.3572 0.3085      6.5585      6.4873|
|  4:  3.3530 -  3.0491 0.99   1306  144 0.3682 0.3820      6.4083      6.3857|
|  5:  3.0491 -  2.8321 0.99   1283  146 0.4087 0.3644      6.2764      6.2664|
|  6:  2.8321 -  2.6660 0.99   1289  141 0.4089 0.4544      6.1815      6.1233|
|  7:  2.6660 -  2.5332 0.99   1281  143 0.4262 0.4169        6.15      6.1299|
|  8:  2.5332 -  2.4233 0.98   1276  137 0.4457 0.4108      6.1256      6.1156|
|  9:  2.4233 -  2.3304 0.98   1261  144 0.4284 0.4323      6.0393      6.0723|
| 10:  2.3304 -  2.2502 1.00   1279  143 0.4623 0.4340      6.0638      6.0189|
| 11:  2.2502 -  2.1801 0.97   1248  137 0.4660 0.4651      5.9881      6.0416|
| 12:  2.1801 -  2.1179 0.98   1256  142 0.4512 0.4509      5.9262      5.9921|
| 13:  2.1179 -  2.0623 0.99   1273  133 0.4598 0.4539      5.8347      5.7856|
| 14:  2.0623 -  2.0121 0.67    860  102 0.4297 0.4513      5.7844      5.7284|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8017  1389   152  0.78  27.30   0.84     0.80      47034.62|
|  2:  4.8017 -  3.8314  1331   152  0.80  25.82   0.93     0.87      64502.45|
|  3:  3.8314 -  3.3530  1298   143  0.74  32.07   0.93     0.86      65999.62|
|  4:  3.3530 -  3.0491  1306   144  0.68  37.28   0.93     0.80      60787.39|
|  5:  3.0491 -  2.8321  1283   146  0.60  43.84   0.94     0.74      50807.98|
|  6:  2.8321 -  2.6660  1289   141  0.56  47.27   0.92     0.70      49263.81|
|  7:  2.6660 -  2.5332  1281   143  0.54  48.68   0.94     0.70      45465.14|
|  8:  2.5332 -  2.4233  1276   137  0.55  48.38   0.93     0.72      41032.70|
|  9:  2.4233 -  2.3304  1261   144  0.56  47.62   0.95     0.74      37354.63|
| 10:  2.3304 -  2.2502  1279   143  0.54  49.20   0.98     0.72      34157.10|
| 11:  2.2502 -  2.1801  1248   137  0.51  51.04   0.94     0.71      34810.99|
| 12:  2.1801 -  2.1179  1256   142  0.51  51.44   0.96     0.71      31768.03|
| 13:  2.1179 -  2.0623  1273   133  0.50  52.23   0.94     0.72      27641.36|
| 14:  2.0623 -  2.0121   860   102  0.56  47.58   0.98     0.73      21210.65|
|alpha:            min =        0.70 max =            0.87 mean =         0.75|
|beta:             min =    21210.65 max =        65999.62 mean =     44418.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.99 mean =        43.25|
|phase err.(test): min =        0.00 max =           89.81 mean =        43.02|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.289834              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.123   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.200192              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.398   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.729 -  2.046:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.046 -  2.363:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.363 -  2.680:       79 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.680 -  2.997:     1787 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.997 -  3.315:     1847 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.315 -  3.632:     2636 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.632 -  3.949:     4638 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.949 -  4.266:     4289 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.266 -  4.583:     5667 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.583 -  4.900:     6806 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.729 |       0.184 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3939   r_free= 0.3858   ksol= 0.00   Bsol= 0.00   scale= 0.918    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.188753                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3805   r_free= 0.3746   ksol= 0.31   Bsol= 65.47   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.50,5.62,-0.00,0.00,0.00); trace/3= 0.26                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.169810                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.144616              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.826   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.657368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.055   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3805      final r-factor (work) = 0.2337          |
| start r-factor (free) = 0.3746      final r-factor (free) = 0.2618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2858 = 8.14 * 0.50 * 6.1686 + 1.00 * 0.1653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2856 = 8.14 * 0.50 * 5.9366 + 1.00 * 0.1101                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2337      final r-factor (work) = 0.2112          |
| start r-factor (free) = 0.2618      final r-factor (free) = 0.2658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9088 = 0.66 * 1.00 * 5.9366 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7478 = 0.66 * 1.00 * 5.6816 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.66   18.01    None  None   None       |
|    all(noH): 2823   0      0.00    93.66   18.01    None  None   None       |
|    Sol.    : 438    0      2.77    93.66   42.78    None  None   None       |
|    Mac.    : 2385   0      0.00    85.27   13.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.366:  858   |   5:    46.828 -  56.193:  109        |
|      1:     9.366 -  18.731: 1152   |   6:    56.193 -  65.559:   61        |
|      2:    18.731 -  28.097:  329   |   7:    65.559 -  74.924:   38        |
|      3:    28.097 -  37.462:  147   |   8:    74.924 -  84.290:   12        |
|      4:    37.462 -  46.828:  114   |   9:    84.290 -  93.655:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2112 r_free = 0.2658             target_work(ml) = 5.688         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2107 r_free = 0.2653             target_work(ml) = 5.688         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2107   r_free= 0.2653   ksol= 0.31   Bsol= 65.47   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.50,5.62,-0.00,0.00,0.00); trace/3= 0.26                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.687693                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2069   r_free= 0.2628   ksol= 0.34   Bsol= 85.04   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.28,1.27,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.678314                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.688971              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.530   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.327836              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.326  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2069      final r-factor (work) = 0.1615          |
| start r-factor (free) = 0.2628      final r-factor (free) = 0.2074          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7496 = 2.69 * 0.50 * 5.6821 + 1.00 * 0.1101                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5528 = 2.69 * 0.50 * 5.5728 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1615      final r-factor (work) = 0.1527          |
| start r-factor (free) = 0.2074      final r-factor (free) = 0.1966          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8399 = 0.33 * 1.00 * 5.5728 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7893 = 0.33 * 1.00 * 5.4256 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.44    94.19   17.71    None  None   None       |
|    all(noH): 2823   0      0.44    94.19   17.71    None  None   None       |
|    Sol.    : 438    0      4.96    94.19   42.49    None  None   None       |
|    Mac.    : 2385   0      0.44    82.70   13.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.435 -   9.811:  968   |   5:    47.312 -  56.687:  117        |
|      1:     9.811 -  19.186: 1127   |   6:    56.687 -  66.063:   59        |
|      2:    19.186 -  28.561:  270   |   7:    66.063 -  75.438:   33        |
|      3:    28.561 -  37.937:  128   |   8:    75.438 -  84.814:   10        |
|      4:    37.937 -  47.312:  108   |   9:    84.814 -  94.189:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1527 r_free = 0.1966             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1525 r_free = 0.1965             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1525   r_free= 0.1965   ksol= 0.34   Bsol= 85.04   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.28,1.27,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.401290                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1523   r_free= 0.1960   ksol= 0.34   Bsol= 82.04   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.21,0.15,-0.00,0.00,0.00); trace/3= -1.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.399163                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.091899              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.753  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.103875              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.891  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1523      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1960      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4475 = 3.09 * 0.50 * 5.4253 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3001 = 3.09 * 0.50 * 5.3212 + 1.00 * 0.0738                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8844 = 1.10 * 1.00 * 5.3212 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7873 = 1.10 * 1.00 * 5.2319 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.10  17.78    None  None   None       |
|    all(noH): 2823   0      0.00    103.10  17.78    None  None   None       |
|    Sol.    : 438    0      5.40    103.10  43.89    None  None   None       |
|    Mac.    : 2385   0      0.00    87.24   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.310: 1110   |   5:    51.552 -  61.862:  100        |
|      1:    10.310 -  20.621: 1076   |   6:    61.862 -  72.173:   57        |
|      2:    20.621 -  30.931:  213   |   7:    72.173 -  82.483:   26        |
|      3:    30.931 -  41.242:  131   |   8:    82.483 -  92.793:   12        |
|      4:    41.242 -  51.552:   96   |   9:    92.793 - 103.104:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1229 r_free = 0.1702             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1701             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1701   ksol= 0.34   Bsol= 82.04   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.21,0.15,-0.00,0.00,0.00); trace/3= -1.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.221977                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1697   ksol= 0.34   Bsol= 80.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.93,0.08,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220835                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.706758              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.418  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.323876              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.856  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5390 = 1.71 * 0.50 * 5.2323 + 1.00 * 0.0738                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5122 = 1.71 * 0.50 * 5.2190 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1675      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7020 = 0.32 * 1.00 * 5.2190 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6996 = 0.32 * 1.00 * 5.2142 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    102.87  17.43    None  None   None       |
|    all(noH): 2823   0      0.46    102.87  17.43    None  None   None       |
|    Sol.    : 438    0      1.92    102.87  42.91    None  None   None       |
|    Mac.    : 2385   0      0.46    87.22   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.459 -  10.700: 1252   |   5:    51.663 -  61.904:   94        |
|      1:    10.700 -  20.941:  960   |   6:    61.904 -  72.145:   51        |
|      2:    20.941 -  31.182:  208   |   7:    72.145 -  82.386:   27        |
|      3:    31.182 -  41.422:  127   |   8:    82.386 -  92.626:    9        |
|      4:    41.422 -  51.663:   93   |   9:    92.626 - 102.867:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1660             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1215 r_free = 0.1660             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1660   ksol= 0.34   Bsol= 80.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.93,0.08,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.209836                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1660   ksol= 0.33   Bsol= 72.80   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.80,0.05,-0.00,0.00,0.00); trace/3= -1.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209731                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.699755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.832  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.569930              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.093  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4898 = 1.70 * 0.50 * 5.2141 + 1.00 * 0.0585                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4804 = 1.70 * 0.50 * 5.1986 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3707 = 2.57 * 1.00 * 5.1986 + 1.00 * 0.0107                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3545 = 2.57 * 1.00 * 5.1917 + 1.00 * 0.0121                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.75  17.34    None  None   None       |
|    all(noH): 2823   0      0.00    112.75  17.34    None  None   None       |
|    Sol.    : 438    0      2.89    112.75  42.83    None  None   None       |
|    Mac.    : 2385   0      0.00    97.55   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.275: 1395   |   5:    56.375 -  67.650:   74        |
|      1:    11.275 -  22.550:  863   |   6:    67.650 -  78.925:   35        |
|      2:    22.550 -  33.825:  193   |   7:    78.925 -  90.200:   18        |
|      3:    33.825 -  45.100:  130   |   8:    90.200 - 101.475:    8        |
|      4:    45.100 -  56.375:  106   |   9:   101.475 - 112.750:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1178 r_free = 0.1662             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1662             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1662   ksol= 0.33   Bsol= 72.80   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.80,0.05,-0.00,0.00,0.00); trace/3= -1.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.195451                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8017 0.99   1389  152 0.0988 0.1320      5.3904      5.5233|
|  2:  4.8017 -  3.8314 0.99   1331  152 0.0846 0.1121      5.4367      5.6574|
|  3:  3.8314 -  3.3530 0.99   1298  143 0.1088 0.1502      5.5043      5.8462|
|  4:  3.3530 -  3.0491 0.99   1306  144 0.1256 0.1782      5.4918      5.6749|
|  5:  3.0491 -  2.8321 0.99   1283  146 0.1449 0.1692       5.401      5.5748|
|  6:  2.8321 -  2.6660 0.99   1289  141 0.1315 0.2324      5.2851       5.614|
|  7:  2.6660 -  2.5332 0.99   1281  143 0.1382 0.1652       5.243      5.3698|
|  8:  2.5332 -  2.4233 0.98   1276  137 0.1255 0.1727       5.145      5.4132|
|  9:  2.4233 -  2.3304 0.98   1261  144 0.1257 0.1923      5.0956      5.3547|
| 10:  2.3304 -  2.2502 1.00   1279  143 0.1205 0.1795      5.0113      5.2458|
| 11:  2.2502 -  2.1801 0.97   1248  137 0.1239 0.1768      5.0009      5.2566|
| 12:  2.1801 -  2.1179 0.98   1256  142 0.1196 0.1952      4.9485      5.3267|
| 13:  2.1179 -  2.0623 0.99   1273  133 0.1207 0.1809      4.8597       5.088|
| 14:  2.0623 -  2.0121 0.67    860  102 0.1050 0.1806      4.7144      4.9834|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8017  1389   152  0.94   9.28   0.96     0.93       7433.70|
|  2:  4.8017 -  3.8314  1331   152  0.95   7.99   1.00     0.98       9178.00|
|  3:  3.8314 -  3.3530  1298   143  0.93  11.39   1.02     1.01      10793.16|
|  4:  3.3530 -  3.0491  1306   144  0.91  14.34   1.00     0.98      11130.37|
|  5:  3.0491 -  2.8321  1283   146  0.89  16.80   1.00     0.98       9473.84|
|  6:  2.8321 -  2.6660  1289   141  0.89  17.62   0.98     0.95       8272.22|
|  7:  2.6660 -  2.5332  1281   143  0.89  17.09   0.98     0.95       7236.89|
|  8:  2.5332 -  2.4233  1276   137  0.90  16.50   0.98     0.95       6164.16|
|  9:  2.4233 -  2.3304  1261   144  0.90  16.13   1.00     0.95       5665.82|
| 10:  2.3304 -  2.2502  1279   143  0.89  16.57   0.98     0.94       4799.97|
| 11:  2.2502 -  2.1801  1248   137  0.89  16.97   0.97     0.93       4824.74|
| 12:  2.1801 -  2.1179  1256   142  0.90  16.92   0.99     0.98       4606.25|
| 13:  2.1179 -  2.0623  1273   133  0.89  17.49   0.97     0.94       3905.08|
| 14:  2.0623 -  2.0121   860   102  0.92  14.80   0.94     0.91       2825.94|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2825.94 max =        11130.37 mean =      7006.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.93|
|phase err.(test): min =        0.00 max =           89.96 mean =        14.34|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1661   ksol= 0.33   Bsol= 72.80   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.68,0.07,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.195495                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1661   ksol= 0.33   Bsol= 72.80   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.68,0.07,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.195495                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8017 0.99   1389  152 0.0988 0.1320      5.3906      5.5238|
|  2:  4.8017 -  3.8314 0.99   1331  152 0.0846 0.1121       5.437      5.6575|
|  3:  3.8314 -  3.3530 0.99   1298  143 0.1089 0.1502      5.5044      5.8467|
|  4:  3.3530 -  3.0491 0.99   1306  144 0.1256 0.1782       5.492       5.675|
|  5:  3.0491 -  2.8321 0.99   1283  146 0.1449 0.1690      5.4009      5.5746|
|  6:  2.8321 -  2.6660 0.99   1289  141 0.1315 0.2327      5.2852      5.6147|
|  7:  2.6660 -  2.5332 0.99   1281  143 0.1381 0.1652      5.2431      5.3697|
|  8:  2.5332 -  2.4233 0.98   1276  137 0.1256 0.1726      5.1452      5.4133|
|  9:  2.4233 -  2.3304 0.98   1261  144 0.1257 0.1924      5.0954      5.3551|
| 10:  2.3304 -  2.2502 1.00   1279  143 0.1206 0.1793       5.011      5.2449|
| 11:  2.2502 -  2.1801 0.97   1248  137 0.1239 0.1766      5.0005      5.2555|
| 12:  2.1801 -  2.1179 0.98   1256  142 0.1195 0.1948      4.9482      5.3257|
| 13:  2.1179 -  2.0623 0.99   1273  133 0.1206 0.1814      4.8598      5.0896|
| 14:  2.0623 -  2.0121 0.67    860  102 0.1050 0.1808      4.7151      4.9832|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8017  1389   152  0.94   9.29   0.96     0.93       7440.39|
|  2:  4.8017 -  3.8314  1331   152  0.95   7.99   1.00     0.98       9184.13|
|  3:  3.8314 -  3.3530  1298   143  0.93  11.40   1.02     1.02      10797.08|
|  4:  3.3530 -  3.0491  1306   144  0.91  14.34   1.00     0.98      11130.83|
|  5:  3.0491 -  2.8321  1283   146  0.89  16.81   1.00     0.98       9477.99|
|  6:  2.8321 -  2.6660  1289   141  0.89  17.63   0.98     0.95       8272.86|
|  7:  2.6660 -  2.5332  1281   143  0.89  17.10   0.99     0.95       7240.69|
|  8:  2.5332 -  2.4233  1276   137  0.90  16.50   0.99     0.96       6167.18|
|  9:  2.4233 -  2.3304  1261   144  0.90  16.14   1.00     0.96       5668.02|
| 10:  2.3304 -  2.2502  1279   143  0.89  16.56   0.99     0.94       4794.90|
| 11:  2.2502 -  2.1801  1248   137  0.89  16.95   0.98     0.94       4815.78|
| 12:  2.1801 -  2.1179  1256   142  0.90  16.90   0.99     0.98       4600.98|
| 13:  2.1179 -  2.0623  1273   133  0.89  17.49   0.98     0.95       3906.03|
| 14:  2.0623 -  2.0121   860   102  0.92  14.82   0.95     0.91       2830.74|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2830.74 max =        11130.83 mean =      7008.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.93|
|phase err.(test): min =        0.00 max =           89.96 mean =        14.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.75  17.34    None  None   None       |
|    all(noH): 2823   0      0.00    112.75  17.34    None  None   None       |
|    Sol.    : 438    0      2.89    112.75  42.83    None  None   None       |
|    Mac.    : 2385   0      0.00    97.56   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.278: 1395   |   5:    56.378 -  67.653:   74        |
|      1:    11.278 -  22.553:  863   |   6:    67.653 -  78.928:   35        |
|      2:    22.553 -  33.828:  193   |   7:    78.928 -  90.203:   18        |
|      3:    33.828 -  45.103:  130   |   8:    90.203 - 101.478:    8        |
|      4:    45.103 -  56.378:  106   |   9:   101.478 - 112.753:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.527 - 4.819
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 302
   mapped sites are within: 0.712 - 4.819

peak=    5.545 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.201 closest distance to " CZ  PHE A 218 " =    1.127
peak=    5.082 closest distance to " O   HOH Z 113 " =    2.149
peak=    4.957 closest distance to " CG  PRO A  54 " =    1.369
peak=    4.780 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.725 closest distance to " CB  ARG A 190 " =    1.562
peak=    4.644 closest distance to " O   HOH Z 369 " =    2.076
peak=    4.600 closest distance to " CB  PRO A  54 " =    1.015
peak=    4.585 closest distance to " CG  PRO A 213 " =    1.173
peak=    4.534 closest distance to " CB  GLN A 183 " =    1.280
peak=    4.522 closest distance to " NE2 GLN A  11 " =    1.055
peak=    4.492 closest distance to " O   HOH Z  53 " =    2.493
peak=    4.470 closest distance to " CZ3 TRP A 266 " =    1.159
peak=    4.459 closest distance to " O   HOH Z 232 " =    2.296
peak=    4.405 closest distance to " O   HOH Z 188 " =    2.914
peak=    4.390 closest distance to " CB  SER A  63 " =    1.185
peak=    4.381 closest distance to " O   HOH Z 142 " =    1.760
peak=    4.374 closest distance to " CE  LYS A  76 " =    0.865
peak=    4.355 closest distance to " O   HOH Z 298 " =    2.075
peak=    4.310 closest distance to " CB  ARG A  79 " =    1.417
peak=    4.307 closest distance to " CA  TYR A  30 " =    0.997
peak=    4.217 closest distance to " CD  ARG A 159 " =    0.775
peak=    4.213 closest distance to " CB  TYR A 169 " =    0.792
peak=    4.210 closest distance to " O   HOH Z 265 " =    2.068
peak=    4.198 closest distance to " CA  ARG A 195 " =    1.250
peak=    4.194 closest distance to " CB  ARG A 275 " =    0.953
peak=    4.159 closest distance to " O   HOH Z 427 " =    3.119
peak=    4.154 closest distance to " CB  ASN A 148 " =    1.492
peak=    4.154 closest distance to " O   HOH Z 214 " =    2.344
peak=    4.150 closest distance to " ND2 ASN A 187 " =    1.466
peak=    4.142 closest distance to " CG  PRO A 243 " =    1.080
peak=    4.127 closest distance to " CB  GLU A 277 " =    3.803
peak=    4.108 closest distance to " CZ  PHE A  38 " =    1.264
peak=    4.077 closest distance to " CB  ASN A  39 " =    0.939
peak=    4.058 closest distance to " O   HOH Z   9 " =    2.102
peak=    4.056 closest distance to " CB  GLU A 128 " =    0.945
peak=    4.051 closest distance to " C   PRO A 198 " =    1.548
peak=    4.048 closest distance to " CB  ASP A 124 " =    0.790
peak=    4.038 closest distance to " O   HOH Z 368 " =    2.169
peak=    4.035 closest distance to " O   HOH Z 412 " =    4.002
peak=    4.034 closest distance to " CG2 VAL A 257 " =    0.815
peak=    4.032 closest distance to " O   HOH Z 126 " =    2.037
peak=    4.021 closest distance to " CB  VAL A 202 " =    1.568
peak=    4.016 closest distance to " CB  VAL A 265 " =    1.249
peak=    4.013 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.990 closest distance to " CD  ARG A 269 " =    0.977
peak=    3.984 closest distance to " O   HOH Z 406 " =    1.726
peak=    3.979 closest distance to " ND2 ASN A 249 " =    0.821
peak=    3.964 closest distance to " CD2 TRP A 179 " =    1.324
peak=    3.949 closest distance to " CB  LEU A 228 " =    1.108
peak=    3.948 closest distance to " O   HOH Z  78 " =    1.635
peak=    3.941 closest distance to " NH1AARG A 145 " =    1.357
peak=    3.922 closest distance to " CB  TRP A 266 " =    1.056
peak=    3.914 closest distance to " O  BHOH Z 338 " =    2.289
peak=    3.911 closest distance to " CD1 LEU A 300 " =    1.152
peak=    3.899 closest distance to " CB  PRO A  90 " =    1.109
peak=    3.898 closest distance to " CA  ALA A 160 " =    0.993
peak=    3.894 closest distance to " CA  PRO A  54 " =    1.399
peak=    3.891 closest distance to " CB  ASP A 140 " =    1.065
peak=    3.886 closest distance to " CD1 LEU A  96 " =    0.757
peak=    3.877 closest distance to " CA  MET A 105 " =    1.038
peak=    3.874 closest distance to " O   HOH Z 158 " =    3.055
peak=    3.870 closest distance to " O   HOH Z 290 " =    1.029
peak=    3.861 closest distance to " O   SER A  87 " =    2.279
peak=    3.852 closest distance to " CA  ARG A  36 " =    1.111
peak=    3.849 closest distance to " OE1 GLN A  55 " =    1.533
peak=    3.847 closest distance to " O   HOH Z 287 " =    1.987
peak=    3.841 closest distance to " CB  ASN A 142 " =    1.008
peak=    3.838 closest distance to " O   HOH Z 133 " =    2.822
peak=    3.828 closest distance to " O   THR A 220 " =    1.188
peak=    3.814 closest distance to " CA  VAL A 125 " =    1.250
peak=    3.812 closest distance to " CD  LYS A 166 " =    1.318
peak=    3.803 closest distance to " O   ASN A  74 " =    1.472
peak=    3.794 closest distance to " O   HOH Z 234 " =    3.819
peak=    3.792 closest distance to " CD  ARG A  66 " =    2.529
peak=    3.790 closest distance to " O   THR A 182 " =    1.421
peak=    3.785 closest distance to " O   HOH Z 353 " =    2.576
peak=    3.759 closest distance to " CB  ALA A 104 " =    0.771
peak=    3.745 closest distance to " O   HOH Z  63 " =    1.591
peak=    3.742 closest distance to " O   HOH Z 303 " =    2.174
peak=    3.731 closest distance to " NZ  LYS A 117 " =    3.128
peak=    3.723 closest distance to " O   HOH Z 316 " =    3.196
peak=    3.718 closest distance to " CB  LEU A  83 " =    0.802
peak=    3.680 closest distance to " CG  MET A 185 " =    1.233
peak=    3.652 closest distance to " O   HOH Z 180 " =    2.194
peak=    3.641 closest distance to " CB  GLU A  46 " =    0.948
peak=    3.638 closest distance to " CA  ALA A 154 " =    1.060
peak=    3.638 closest distance to " O   HOH Z  21 " =    1.804
peak=    3.624 closest distance to " CG  LEU A 167 " =    1.239
peak=    3.618 closest distance to " N   ASN A  39 " =    1.335
peak=    3.611 closest distance to " CG2AVAL A 121 " =    2.291
peak=    3.609 closest distance to " O   HOH Z  43 " =    2.052
peak=    3.607 closest distance to " O   THR A 251 " =    1.145
peak=    3.604 closest distance to " O   HOH Z 392 " =    2.712
peak=    3.603 closest distance to " O   HOH Z 285 " =    2.239
peak=    3.598 closest distance to " O   HOH Z 313 " =    1.892
peak=    3.598 closest distance to " O   HOH Z 294 " =    1.591
peak=    3.596 closest distance to " CA  ASP A 162 " =    1.068
peak=    3.590 closest distance to " CG2 THR A 221 " =    1.007
peak=    3.586 closest distance to " CG2 ILE A 120 " =    1.146
peak=    3.580 closest distance to " N   HIS A 108 " =    1.915
peak=    3.580 closest distance to " O   HOH Z 172 " =    3.802
peak=    3.573 closest distance to " O   TYR A 116 " =    1.301
peak=    3.568 closest distance to " ND2 ASN A 249 " =    1.906
peak=    3.566 closest distance to " CG  ARG A 138 " =    1.306
peak=    3.565 closest distance to " CG  GLU A  37 " =    0.940
peak=    3.548 closest distance to " NE2 HIS A 207 " =    1.117
peak=    3.547 closest distance to " O   HOH Z 148 " =    3.510
peak=    3.547 closest distance to " CA  ASN A 215 " =    1.168
peak=    3.546 closest distance to " O   HOH Z   1 " =    2.248
peak=    3.546 closest distance to " O   HOH Z 346 " =    1.630
peak=    3.545 closest distance to " CD BLYS A 290 " =    0.945
peak=    3.542 closest distance to " O   HOH Z 193 " =    1.868
peak=    3.537 closest distance to " O   HOH Z 272 " =    1.844
peak=    3.536 closest distance to " CB  GLU A 152 " =    1.198
peak=    3.529 closest distance to " OG BSER A 134 " =    2.821
peak=    3.527 closest distance to " CH2 TRP A  70 " =    0.913
peak=    3.526 closest distance to " O   HOH Z 394 " =    3.899
peak=    3.522 closest distance to " O   HOH Z 248 " =    1.633
peak=    3.512 closest distance to " O   HOH Z  90 " =    2.264
peak=    3.510 closest distance to " CA  ALA A 100 " =    1.033
peak=    3.506 closest distance to " O   HOH Z 368 " =    3.661
peak=    3.502 closest distance to " O   HOH Z  10 " =    1.804
peak=    3.494 closest distance to " CA  SER A  87 " =    1.024
peak=    3.493 closest distance to " OD1 ASN A  69 " =    2.587
peak=    3.491 closest distance to " O   HOH Z  88 " =    3.951
peak=    3.482 closest distance to " CB  LYS A 117 " =    1.198
peak=    3.480 closest distance to " CB  GLN A  89 " =    1.287
peak=    3.474 closest distance to " CB  SER A 210 " =    0.840
peak=    3.474 closest distance to " O   HOH Z  40 " =    1.980
peak=    3.472 closest distance to " N   ARG A 156 " =    1.428
peak=    3.468 closest distance to " CA  ILE A 234 " =    1.046
peak=    3.467 closest distance to " CA  THR A 264 " =    0.947
peak=    3.466 closest distance to " O   HOH Z 271 " =    2.556
peak=    3.466 closest distance to " CB  SER A  62 " =    0.712
peak=    3.465 closest distance to " O   HOH Z 425 " =    1.293
peak=    3.464 closest distance to " O   HOH Z 203 " =    1.792
peak=    3.461 closest distance to " O   HOH Z 359 " =    1.606
peak=    3.455 closest distance to " CB  MET A  47 " =    0.929
peak=    3.455 closest distance to " CA  GLU A 152 " =    0.882
peak=    3.447 closest distance to " CA  ASN A 127 " =    1.197
peak=    3.446 closest distance to " O   HOH Z  59 " =    2.152
peak=    3.443 closest distance to " CB  THR A  31 " =    1.615
peak=    3.439 closest distance to " O   HOH Z 261 " =    1.833
peak=    3.437 closest distance to " CB  ASN A 187 " =    1.208
peak=    3.436 closest distance to " O   SER A 164 " =    1.537
peak=    3.433 closest distance to " O   HOH Z 213 " =    2.127
peak=    3.429 closest distance to " O   HOH Z 166 " =    3.967
peak=    3.428 closest distance to " CA  THR A 221 " =    1.111
peak=    3.413 closest distance to " CB  SER A   3 " =    1.478
peak=    3.412 closest distance to " O   PHE A  61 " =    1.340
peak=    3.410 closest distance to " O   HOH Z 280 " =    2.920
peak=    3.408 closest distance to " CB  ALA A 114 " =    0.762
peak=    3.408 closest distance to " CB  MET A  40 " =    0.813
peak=    3.405 closest distance to " CB  ARG A 138 " =    0.980
peak=    3.402 closest distance to " CB  ILE A 120 " =    1.239
peak=    3.397 closest distance to " O   HOH Z 325 " =    2.407
peak=    3.395 closest distance to " CB  ALA A  43 " =    0.799
peak=    3.390 closest distance to " CA  GLN A  94 " =    0.787
peak=    3.388 closest distance to " O   ALA A 165 " =    1.511
peak=    3.385 closest distance to " O   HOH Z  88 " =    2.029
peak=    3.381 closest distance to " CD1 ILE A 199 " =    0.865
peak=    3.378 closest distance to " CG  PHE A 204 " =    0.839
peak=    3.366 closest distance to " CA  ARG A 102 " =    1.156
peak=    3.363 closest distance to " NE  ARG A  79 " =    1.049
peak=    3.357 closest distance to " NH2AARG A 275 " =    3.644
peak=    3.355 closest distance to " O   HOH Z 251 " =    1.667
peak=    3.354 closest distance to " CB  PRO A 198 " =    1.052
peak=    3.354 closest distance to " O   HOH Z 423 " =    1.854
peak=    3.352 closest distance to " NH2 ARG A 156 " =    1.158
peak=    3.349 closest distance to " O   ASP A 191 " =    1.471
peak=    3.345 closest distance to " CB  ASN A 215 " =    1.163
peak=    3.345 closest distance to " CA  TYR A 116 " =    1.407
peak=    3.341 closest distance to " O   HOH Z 419 " =    2.049
peak=    3.335 closest distance to " CG1 VAL A 153 " =    0.982
peak=    3.334 closest distance to " NE2 GLN A  77 " =    3.490
peak=    3.330 closest distance to " N   ASN A 127 " =    1.290
peak=    3.330 closest distance to " CB  ALA A 291 " =    1.168
peak=    3.329 closest distance to " N   ALA A 256 " =    1.268
peak=    3.329 closest distance to " O   HOH Z 305 " =    3.684
peak=    3.328 closest distance to " CB  ASP A 298 " =    1.184
peak=    3.328 closest distance to " CA  ALA A 295 " =    1.128
peak=    3.325 closest distance to " O   HOH Z 106 " =    4.174
peak=    3.322 closest distance to " CB  SER A 212 " =    1.245
peak=    3.321 closest distance to " CG  GLN A  11 " =    1.665
peak=    3.320 closest distance to " CB  ALA A 299 " =    0.810
peak=    3.320 closest distance to " O   HOH Z 261 " =    1.572
peak=    3.319 closest distance to " O   HOH Z 383 " =    2.200
peak=    3.314 closest distance to " O   HOH Z  80 " =    1.711
peak=    3.304 closest distance to " CD2 LEU A 255 " =    1.792
peak=    3.303 closest distance to " CB  GLU A  37 " =    0.940
peak=    3.301 closest distance to " O   HOH Z 126 " =    1.530
peak=    3.298 closest distance to " CG2 ILE A 234 " =    0.929
peak=    3.298 closest distance to " C   PHE A  59 " =    1.015
peak=    3.298 closest distance to " O   HOH Z 402 " =    1.370
peak=    3.292 closest distance to " CD2 LEU A 297 " =    0.951
peak=    3.292 closest distance to " O   HOH Z 128 " =    2.405
peak=    3.287 closest distance to " OE2 GLU A  53 " =    1.875
peak=    3.282 closest distance to " OG  SER A  62 " =    2.948
peak=    3.281 closest distance to " OG  SER A 245 " =    1.783
peak=    3.279 closest distance to " CD  ARG A 219 " =    1.104
peak=    3.274 closest distance to " O   HOH Z  88 " =    2.728
peak=    3.273 closest distance to " CB  TYR A 116 " =    0.792
peak=    3.270 closest distance to " O   HOH Z 116 " =    1.821
peak=    3.270 closest distance to " O   HOH Z 365 " =    2.858
peak=    3.268 closest distance to " O   HOH Z  61 " =    1.645
peak=    3.267 closest distance to " CA  ARG A 139 " =    1.092
peak=    3.266 closest distance to " CE  LYS A  48 " =    1.088
peak=    3.266 closest distance to " O   HOH Z 391 " =    2.971
peak=    3.266 closest distance to " CG2AVAL A  72 " =    1.857
peak=    3.262 closest distance to " O   HOH Z 422 " =    2.678
peak=    3.258 closest distance to " CG2 ILE A 239 " =    0.728
peak=    3.256 closest distance to " OH  TYR A 116 " =    1.124
peak=    3.253 closest distance to " CA  ALA A 233 " =    1.613
peak=    3.253 closest distance to " CB  TRP A 179 " =    1.464
peak=    3.252 closest distance to " O   HOH Z 371 " =    2.966
peak=    3.251 closest distance to " CA  ASP A 140 " =    1.676
peak=    3.249 closest distance to " CB  ALA A 248 " =    1.285
peak=    3.249 closest distance to " CA  ARG A 156 " =    1.141
peak=    3.246 closest distance to " CA  ALA A 291 " =    0.778
peak=    3.245 closest distance to " OG  SER A  22 " =    2.797
peak=    3.245 closest distance to " O   PHE A 192 " =    1.430
peak=    3.243 closest distance to " O   ALA A 158 " =    1.224
peak=    3.239 closest distance to " NH1 ARG A 138 " =    1.042
peak=    3.239 closest distance to " O   HOH Z 417 " =    3.279
peak=    3.238 closest distance to " CB  SER A 141 " =    1.068
peak=    3.237 closest distance to " CB  SER A 216 " =    0.965
peak=    3.232 closest distance to " O   HOH Z 426 " =    1.695
peak=    3.230 closest distance to " O   HOH Z 116 " =    3.335
peak=    3.226 closest distance to " CG2 VAL A 197 " =    1.112
peak=    3.226 closest distance to " CB  LEU A  96 " =    1.401
peak=    3.225 closest distance to " CB  ASN A 110 " =    1.187
peak=    3.223 closest distance to " CG2 THR A  29 " =    1.368
peak=    3.221 closest distance to " O   HOH Z 192 " =    1.884
peak=    3.221 closest distance to " CE1 TYR A 186 " =    1.395
peak=    3.217 closest distance to " CA  ALA A 158 " =    1.251
peak=    3.216 closest distance to " CD  GLU A 152 " =    0.764
peak=    3.215 closest distance to " CB  PRO A 243 " =    1.465
peak=    3.214 closest distance to " O   HOH Z  49 " =    0.912
peak=    3.214 closest distance to " CB  PHE A 204 " =    0.792
peak=    3.212 closest distance to " CA  GLU A  46 " =    0.860
peak=    3.207 closest distance to " OG1 THR A 279 " =    1.539
peak=    3.205 closest distance to " CG2 ILE A  20 " =    1.374
peak=    3.204 closest distance to " O   HOH Z  28 " =    1.907
peak=    3.203 closest distance to " OG1 THR A  82 " =    0.867
peak=    3.203 closest distance to " O   HOH Z  48 " =    1.616
peak=    3.201 closest distance to " CE1 HIS A 115 " =    0.969
peak=    3.200 closest distance to " CA  LEU A  83 " =    1.272
peak=    3.198 closest distance to " CZ  PHE A 192 " =    1.013
peak=    3.197 closest distance to " O   HOH Z 250 " =    1.354
peak=    3.197 closest distance to " O   HOH Z 211 " =    0.941
peak=    3.194 closest distance to " O   HOH Z 183 " =    1.409
peak=    3.189 closest distance to " CB  GLN A 205 " =    1.056
peak=    3.187 closest distance to " N   TYR A  15 " =    0.771
peak=    3.187 closest distance to " CG2 ILE A 151 " =    0.986
peak=    3.182 closest distance to " O   HOH Z  88 " =    3.672
peak=    3.176 closest distance to " CE3 TRP A  85 " =    0.981
peak=    3.176 closest distance to " OD1 ASN A 217 " =    1.536
peak=    3.176 closest distance to " CG1 ILE A  33 " =    1.268
peak=    3.171 closest distance to " OG  SER A  28 " =    1.613
peak=    3.160 closest distance to " CA  SER A 146 " =    1.794
peak=    3.157 closest distance to " O   HOH Z 248 " =    1.777
peak=    3.157 closest distance to " CB  ALA A   9 " =    1.632
peak=    3.156 closest distance to " O   HOH Z 285 " =    2.108
peak=    3.153 closest distance to " CA  ASN A 217 " =    1.263
peak=    3.143 closest distance to " CB  ASN A 285 " =    0.956
peak=    3.143 closest distance to " O   HOH Z  62 " =    2.198
peak=    3.141 closest distance to " N   PHE A 130 " =    1.254
peak=    3.135 closest distance to " O   HOH Z  94 " =    2.526
peak=    3.134 closest distance to " O   HOH Z 147 " =    1.828
peak=    3.134 closest distance to " CG1 ILE A  49 " =    1.592
peak=    3.133 closest distance to " OG BSER A 164 " =    2.326
peak=    3.130 closest distance to " ND1 HIS A  81 " =    1.711
peak=    3.127 closest distance to " O  BHOH Z  74 " =    1.271
peak=    3.127 closest distance to " OD1 ASP A 171 " =    1.177
peak=    3.123 closest distance to " O   HOH Z 299 " =    4.524
peak=    3.123 closest distance to " O   HOH Z 163 " =    1.881
peak=    3.122 closest distance to " CA  ALA A 248 " =    1.169
peak=    3.116 closest distance to " O   HOH Z 167 " =    1.684
peak=    3.106 closest distance to " CE2 PHE A  16 " =    0.892
peak=    3.103 closest distance to " O   HOH Z 409 " =    3.036
peak=    3.102 closest distance to " CE3 TRP A 150 " =    1.126
peak=    3.102 closest distance to " O   HOH Z 430 " =    1.560
peak=    3.101 closest distance to " CB  ASN A 173 " =    1.162
peak=    3.100 closest distance to " CD  ARG A 195 " =    3.414
peak=    3.099 closest distance to " NE2 GLN A  58 " =    4.319
peak=    3.094 closest distance to " O   HOH Z 134 " =    2.929
peak=    3.093 closest distance to " CB  ALA A   1 " =    4.819
peak=    3.091 closest distance to " CD1 ILE A  33 " =    1.721
peak=    3.086 closest distance to " O   ASP A 124 " =    1.176
peak=    3.083 closest distance to " N   SER A 164 " =    1.001
peak=    3.078 closest distance to " CA  GLY A 211 " =    1.357
peak=    3.075 closest distance to " O   HOH Z   1 " =    2.394
peak=    3.064 closest distance to " O   HOH Z 128 " =    2.305
peak=    3.062 closest distance to " O   THR A 294 " =    1.176
peak=    3.044 closest distance to " CA  ILE A 106 " =    0.837
peak=    3.033 closest distance to " CD2 LEU A 261 " =    1.427
peak=    3.013 closest distance to " CG  GLU A  37 " =    0.857

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.798 - 5.797
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 214
   mapped sites are within: 0.798 - 5.797

peak=   -4.745 closest distance to " CD  ARG A  14 " =    3.442
peak=   -4.731 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -4.541 closest distance to " CD  GLN A  58 " =    0.903
peak=   -4.356 closest distance to " O   HOH Z 377 " =    1.983
peak=   -4.346 closest distance to " O   PRO A 198 " =    1.311
peak=   -4.278 closest distance to " CD  ARG A 156 " =    2.037
peak=   -4.227 closest distance to " CD2 TYR A 293 " =    1.957
peak=   -4.181 closest distance to " O   HOH Z 231 " =    2.341
peak=   -4.175 closest distance to " CG1 VAL A 250 " =    2.727
peak=   -4.163 closest distance to " N   ALA A  43 " =    2.595
peak=   -4.129 closest distance to " O   HOH Z 267 " =    5.675
peak=   -4.077 closest distance to " CE2 PHE A  61 " =    2.711
peak=   -4.060 closest distance to " CB  PRO A 243 " =    2.689
peak=   -4.026 closest distance to " O   HOH Z  73 " =    2.410
peak=   -4.023 closest distance to " OD1 ASN A 148 " =    1.380
peak=   -4.016 closest distance to " CZ3 TRP A 179 " =    1.187
peak=   -3.998 closest distance to " CG2 ILE A  49 " =    2.771
peak=   -3.996 closest distance to " O   HOH Z 196 " =    2.152
peak=   -3.967 closest distance to " O   HOH Z 394 " =    1.564
peak=   -3.962 closest distance to " OG BSER A 134 " =    1.336
peak=   -3.933 closest distance to " CG  ARG A 269 " =    2.396
peak=   -3.928 closest distance to " CG  GLN A  11 " =    1.698
peak=   -3.923 closest distance to " O   HOH Z  10 " =    1.537
peak=   -3.912 closest distance to " O   VAL A  67 " =    2.713
peak=   -3.912 closest distance to " O   HOH Z  69 " =    1.581
peak=   -3.892 closest distance to " C   HIS A 108 " =    1.123
peak=   -3.892 closest distance to " CE2 TYR A  30 " =    2.720
peak=   -3.876 closest distance to " CA  GLY A 241 " =    3.271
peak=   -3.871 closest distance to " O   HOH Z 211 " =    1.027
peak=   -3.859 closest distance to " CA  VAL A  67 " =    2.989
peak=   -3.827 closest distance to " OE1 GLN A 223 " =    2.144
peak=   -3.811 closest distance to " CB  HIS A  86 " =    1.129
peak=   -3.779 closest distance to " CE3 TRP A 150 " =    2.189
peak=   -3.757 closest distance to " CG1 VAL A 112 " =    2.906
peak=   -3.753 closest distance to " CG  MET A 105 " =    1.001
peak=   -3.742 closest distance to " O   ALA A  10 " =    1.702
peak=   -3.736 closest distance to " O   HOH Z  11 " =    2.349
peak=   -3.729 closest distance to " O   HOH Z 128 " =    2.609
peak=   -3.725 closest distance to " CA  GLY A 241 " =    2.377
peak=   -3.707 closest distance to " OG  SER A  97 " =    2.330
peak=   -3.702 closest distance to " CA  ASP A 298 " =    1.092
peak=   -3.700 closest distance to " CB  ALA A  43 " =    2.660
peak=   -3.694 closest distance to " O   HOH Z 193 " =    1.337
peak=   -3.683 closest distance to " O   HOH Z 166 " =    1.865
peak=   -3.673 closest distance to " CD2 LEU A 237 " =    2.933
peak=   -3.673 closest distance to " O   HOH Z 216 " =    1.013
peak=   -3.656 closest distance to " O   HOH Z 198 " =    1.964
peak=   -3.652 closest distance to " NH2AARG A 275 " =    5.466
peak=   -3.643 closest distance to " O   HOH Z 185 " =    2.306
peak=   -3.642 closest distance to " N   THR A  52 " =    1.621
peak=   -3.622 closest distance to " CE BMET A  47 " =    1.621
peak=   -3.619 closest distance to " O   HOH Z  38 " =    1.502
peak=   -3.609 closest distance to " O   HOH Z 102 " =    1.627
peak=   -3.605 closest distance to " O   PHE A 218 " =    1.429
peak=   -3.580 closest distance to " O   ILE A 109 " =    2.595
peak=   -3.572 closest distance to " O   HOH Z 290 " =    1.237
peak=   -3.570 closest distance to " CZ  PHE A 155 " =    1.279
peak=   -3.559 closest distance to " O   HOH Z 393 " =    1.240
peak=   -3.552 closest distance to " O   HOH Z 407 " =    3.243
peak=   -3.550 closest distance to " CD  ARG A  79 " =    1.196
peak=   -3.547 closest distance to " ND2 ASN A 249 " =    2.493
peak=   -3.539 closest distance to " OD1 ASP A 171 " =    1.614
peak=   -3.527 closest distance to " CE3 TRP A  70 " =    1.874
peak=   -3.523 closest distance to " O   HOH Z 232 " =    1.841
peak=   -3.520 closest distance to " O   HOH Z 133 " =    1.220
peak=   -3.506 closest distance to " O   HOH Z  37 " =    1.820
peak=   -3.505 closest distance to " O   HOH Z 278 " =    1.153
peak=   -3.497 closest distance to " NE2 GLN A 194 " =    1.961
peak=   -3.489 closest distance to " N   THR A 264 " =    1.365
peak=   -3.486 closest distance to " O   HOH Z  51 " =    1.694
peak=   -3.483 closest distance to " CD1 LEU A 101 " =    2.404
peak=   -3.478 closest distance to " CB  PHE A 192 " =    2.032
peak=   -3.476 closest distance to " O   HOH Z 111 " =    1.618
peak=   -3.471 closest distance to " O   HOH Z  64 " =    1.425
peak=   -3.471 closest distance to " O   HOH Z 351 " =    1.581
peak=   -3.459 closest distance to " CE  MET A 105 " =    2.308
peak=   -3.452 closest distance to " O   HOH Z 275 " =    1.530
peak=   -3.450 closest distance to " CD  GLN A 223 " =    1.524
peak=   -3.444 closest distance to " ND2 ASN A  60 " =    1.373
peak=   -3.441 closest distance to " CA  GLY A 203 " =    2.490
peak=   -3.437 closest distance to " CB  ASN A  39 " =    2.332
peak=   -3.434 closest distance to " CG  PRO A 198 " =    1.948
peak=   -3.430 closest distance to " O   VAL A 189 " =    1.671
peak=   -3.422 closest distance to " CA  GLY A 241 " =    2.899
peak=   -3.419 closest distance to " CB  ALA A 100 " =    2.123
peak=   -3.413 closest distance to " CG1 VAL A 125 " =    1.812
peak=   -3.413 closest distance to " OH  TYR A 247 " =    2.242
peak=   -3.412 closest distance to " O   HOH Z 174 " =    3.848
peak=   -3.410 closest distance to " CA  GLY A 133 " =    2.333
peak=   -3.409 closest distance to " CG  GLU A  53 " =    1.522
peak=   -3.405 closest distance to " CA  ASP A  27 " =    2.493
peak=   -3.401 closest distance to " O   HOH Z 421 " =    3.210
peak=   -3.400 closest distance to " O   HOH Z 357 " =    2.214
peak=   -3.400 closest distance to " O   ALA A 180 " =    1.429
peak=   -3.399 closest distance to " CB  ALA A 129 " =    2.453
peak=   -3.398 closest distance to " CD1 PHE A  59 " =    2.067
peak=   -3.396 closest distance to " CG  PRO A 243 " =    1.755
peak=   -3.395 closest distance to " C   ASN A 285 " =    2.452
peak=   -3.395 closest distance to " O   HOH Z 191 " =    5.797
peak=   -3.394 closest distance to " ND2 ASN A  45 " =    2.093
peak=   -3.394 closest distance to " CG  GLU A 277 " =    1.169
peak=   -3.394 closest distance to " O   HOH Z 345 " =    2.302
peak=   -3.392 closest distance to " O   HOH Z  60 " =    1.453
peak=   -3.391 closest distance to " OD2 ASP A 171 " =    1.833
peak=   -3.391 closest distance to " NH2 ARG A  79 " =    1.539
peak=   -3.388 closest distance to " C   LEU A 143 " =    1.154
peak=   -3.387 closest distance to " ND2BASN A 224 " =    1.842
peak=   -3.387 closest distance to " CG1AVAL A  41 " =    2.753
peak=   -3.378 closest distance to " O   VAL A 189 " =    2.634
peak=   -3.378 closest distance to " CB  ALA A   9 " =    2.518
peak=   -3.375 closest distance to " CD1 TRP A  70 " =    1.109
peak=   -3.370 closest distance to " O   PRO A 163 " =    2.058
peak=   -3.365 closest distance to " O   SER A 210 " =    1.936
peak=   -3.361 closest distance to " OXT GLY A 302 " =    3.137
peak=   -3.360 closest distance to " O   HOH Z 348 " =    2.128
peak=   -3.355 closest distance to " O   TYR A 186 " =    1.777
peak=   -3.353 closest distance to " CD1 LEU A   5 " =    2.599
peak=   -3.350 closest distance to " O   HOH Z 357 " =    2.237
peak=   -3.344 closest distance to " O   HOH Z 264 " =    1.732
peak=   -3.343 closest distance to " CB  ALA A 291 " =    2.369
peak=   -3.342 closest distance to " O   HOH Z 359 " =    3.058
peak=   -3.340 closest distance to " O   ALA A  34 " =    2.521
peak=   -3.324 closest distance to " O   HOH Z 281 " =    2.489
peak=   -3.323 closest distance to " O   HOH Z   6 " =    1.337
peak=   -3.321 closest distance to " CG2 ILE A 263 " =    2.408
peak=   -3.321 closest distance to " CG2 VAL A 189 " =    2.160
peak=   -3.316 closest distance to " O   GLY A  17 " =    1.245
peak=   -3.314 closest distance to " NE2 GLN A 240 " =    1.823
peak=   -3.311 closest distance to " O   HOH Z 252 " =    3.976
peak=   -3.310 closest distance to " N   ASN A  60 " =    1.309
peak=   -3.308 closest distance to " O   HOH Z  52 " =    1.539
peak=   -3.307 closest distance to " CB  TRP A  85 " =    2.555
peak=   -3.306 closest distance to " O   HOH Z 372 " =    2.422
peak=   -3.304 closest distance to " SG BCYS A 201 " =    1.165
peak=   -3.294 closest distance to " C   SER A 206 " =    1.377
peak=   -3.293 closest distance to " O   HOH Z 275 " =    1.887
peak=   -3.293 closest distance to " CB  ASP A 286 " =    2.070
peak=   -3.292 closest distance to " O   HOH Z 265 " =    2.609
peak=   -3.289 closest distance to " CD2 PHE A  61 " =    2.100
peak=   -3.282 closest distance to " O   HOH Z 326 " =    4.976
peak=   -3.281 closest distance to " O   SER A  62 " =    2.277
peak=   -3.276 closest distance to " NH2 ARG A 159 " =    2.339
peak=   -3.273 closest distance to " O   SER A 276 " =    1.798
peak=   -3.270 closest distance to " O   HOH Z 350 " =    2.106
peak=   -3.268 closest distance to " OG BSER A 210 " =    1.596
peak=   -3.266 closest distance to " O   GLU A 152 " =    1.447
peak=   -3.266 closest distance to " C   MET A 188 " =    1.418
peak=   -3.264 closest distance to " OE1 GLN A  88 " =    1.081
peak=   -3.260 closest distance to " O   HOH Z  53 " =    1.663
peak=   -3.257 closest distance to " CG  TRP A 266 " =    1.765
peak=   -3.254 closest distance to " CG  GLN A 103 " =    2.470
peak=   -3.252 closest distance to " OD1 ASN A 173 " =    1.266
peak=   -3.244 closest distance to " O   TRP A  70 " =    1.471
peak=   -3.235 closest distance to " O   HOH Z 114 " =    1.242
peak=   -3.227 closest distance to " ND2 ASN A  45 " =    1.160
peak=   -3.227 closest distance to " O   HOH Z 171 " =    2.062
peak=   -3.226 closest distance to " O   HOH Z  71 " =    2.669
peak=   -3.226 closest distance to " O   GLN A  94 " =    2.182
peak=   -3.223 closest distance to " C   ALA A 158 " =    1.486
peak=   -3.223 closest distance to " O   ILE A 106 " =    1.943
peak=   -3.221 closest distance to " O   HOH Z  60 " =    2.448
peak=   -3.218 closest distance to " O   HOH Z 114 " =    3.354
peak=   -3.216 closest distance to " O   HOH Z 176 " =    0.798
peak=   -3.215 closest distance to " O   SER A 271 " =    2.175
peak=   -3.210 closest distance to " OD2 ASP A 191 " =    1.516
peak=   -3.209 closest distance to " O   HOH Z   9 " =    1.881
peak=   -3.206 closest distance to " CD2 HIS A 207 " =    2.267
peak=   -3.202 closest distance to " CG2 THR A 178 " =    2.443
peak=   -3.201 closest distance to " CZ  PHE A  38 " =    2.071
peak=   -3.200 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.198 closest distance to " N   ALA A 248 " =    1.730
peak=   -3.197 closest distance to " O   GLN A 240 " =    2.681
peak=   -3.194 closest distance to " O   HOH Z 174 " =    2.653
peak=   -3.192 closest distance to " CG  LEU A  83 " =    2.076
peak=   -3.191 closest distance to " CD  GLU A 236 " =    1.156
peak=   -3.184 closest distance to " CB  ALA A  10 " =    2.248
peak=   -3.183 closest distance to " O   HOH Z 298 " =    2.519
peak=   -3.179 closest distance to " CB  PHE A  16 " =    2.449
peak=   -3.176 closest distance to " O   HOH Z 177 " =    1.746
peak=   -3.174 closest distance to " O   HOH Z   9 " =    2.500
peak=   -3.174 closest distance to " CB  PRO A  54 " =    2.631
peak=   -3.173 closest distance to " O   HOH Z 145 " =    1.039
peak=   -3.173 closest distance to " CG  ARG A  66 " =    2.291
peak=   -3.172 closest distance to " O   HOH Z 389 " =    2.154
peak=   -3.171 closest distance to " O   HOH Z 313 " =    1.901
peak=   -3.169 closest distance to " O   GLY A 203 " =    2.427
peak=   -3.156 closest distance to " OD1 ASP A 191 " =    1.624
peak=   -3.155 closest distance to " O   HOH Z 251 " =    4.989
peak=   -3.154 closest distance to " CB  ALA A 291 " =    2.169
peak=   -3.152 closest distance to " NE2 GLN A  88 " =    2.035
peak=   -3.152 closest distance to " O   GLY A 211 " =    1.313
peak=   -3.152 closest distance to " O   HOH Z  69 " =    2.002
peak=   -3.149 closest distance to " CA  SER A 135 " =    1.237
peak=   -3.149 closest distance to " C   GLY A 262 " =    2.187
peak=   -3.144 closest distance to " O   HOH Z 189 " =    2.036
peak=   -3.140 closest distance to " O   HOH Z 353 " =    2.235
peak=   -3.134 closest distance to " CG1BVAL A  41 " =    2.725
peak=   -3.129 closest distance to " NZ  LYS A 166 " =    1.259
peak=   -3.124 closest distance to " O   HOH Z 389 " =    1.593
peak=   -3.119 closest distance to " O   HOH Z  90 " =    1.773
peak=   -3.117 closest distance to " CG  PRO A 163 " =    2.126
peak=   -3.117 closest distance to " CD1 LEU A  83 " =    2.676
peak=   -3.113 closest distance to " O   HOH Z 198 " =    1.526
peak=   -3.112 closest distance to " CG  PHE A 283 " =    2.652
peak=   -3.111 closest distance to " N   GLN A 223 " =    0.940
peak=   -3.102 closest distance to " O   HOH Z 154 " =    1.725
peak=   -3.099 closest distance to " CA  HIS A  86 " =    2.310
peak=   -3.090 closest distance to " C   ASN A 187 " =    1.876
peak=   -3.078 closest distance to " NE2 GLN A 278 " =    1.542
peak=   -3.064 closest distance to " O   ASP A 270 " =    1.931
peak=   -3.050 closest distance to " OG BSER A 134 " =    1.987
peak=   -3.044 closest distance to " CD2 PHE A  59 " =    2.546
peak=   -3.027 closest distance to " CG1 VAL A 112 " =    2.870
peak=   -3.020 closest distance to " O   HOH Z 351 " =    1.389

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.3939 0.3858   6.188753e+00   6.172014e+00
   1_bss:  0.3805 0.3746   6.169810e+00   6.151872e+00
   1_xyz:  0.2337 0.2618   5.748286e+00   5.834311e+00
   1_adp:  0.2112 0.2658   5.687730e+00   5.848996e+00
   1_occ:  0.2107 0.2653   5.687693e+00   5.850256e+00
   2_bss:  0.2069 0.2628   5.678314e+00   5.844273e+00
   2_xyz:  0.1615 0.2074   5.450672e+00   5.644296e+00
   2_adp:  0.1527 0.1966   5.402083e+00   5.597800e+00
   2_occ:  0.1525 0.1965   5.401290e+00   5.597426e+00
   3_bss:  0.1523 0.1960   5.399163e+00   5.594910e+00
   3_xyz:  0.1277 0.1729   5.251215e+00   5.475857e+00
   3_adp:  0.1229 0.1702   5.222261e+00   5.455821e+00
   3_occ:  0.1228 0.1701   5.221977e+00   5.455736e+00
   4_bss:  0.1227 0.1697   5.220835e+00   5.453804e+00
   4_xyz:  0.1220 0.1675   5.215529e+00   5.445125e+00
   4_adp:  0.1216 0.1660   5.209701e+00   5.435721e+00
   4_occ:  0.1215 0.1660   5.209836e+00   5.436305e+00
   5_bss:  0.1215 0.1660   5.209731e+00   5.436399e+00
   5_xyz:  0.1184 0.1653   5.195774e+00   5.431629e+00
   5_adp:  0.1178 0.1662   5.195356e+00   5.436339e+00
   5_occ:  0.1178 0.1662   5.195451e+00   5.436669e+00
   5_bss:  0.1177 0.1661   5.195495e+00   5.436708e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.311  65.474  -2.329  -2.500   5.621  -0.000   0.000   0.000
   1_xyz:  0.311  65.474  -2.329  -2.500   5.621  -0.000   0.000   0.000
   1_adp:  0.311  65.474  -2.329  -2.500   5.621  -0.000   0.000   0.000
   1_occ:  0.311  65.474  -2.329  -2.500   5.621  -0.000   0.000   0.000
   2_bss:  0.341  85.037  -2.418  -2.278   1.273  -0.000   0.000   0.000
   2_xyz:  0.341  85.037  -2.418  -2.278   1.273  -0.000   0.000   0.000
   2_adp:  0.341  85.037  -2.418  -2.278   1.273  -0.000   0.000   0.000
   2_occ:  0.341  85.037  -2.418  -2.278   1.273  -0.000   0.000   0.000
   3_bss:  0.339  82.042  -2.515  -2.213   0.145  -0.000   0.000   0.000
   3_xyz:  0.339  82.042  -2.515  -2.213   0.145  -0.000   0.000   0.000
   3_adp:  0.339  82.042  -2.515  -2.213   0.145  -0.000   0.000   0.000
   3_occ:  0.339  82.042  -2.515  -2.213   0.145  -0.000   0.000   0.000
   4_bss:  0.335  80.000  -2.139  -1.929   0.077  -0.000   0.000   0.000
   4_xyz:  0.335  80.000  -2.139  -1.929   0.077  -0.000   0.000   0.000
   4_adp:  0.335  80.000  -2.139  -1.929   0.077  -0.000   0.000   0.000
   4_occ:  0.335  80.000  -2.139  -1.929   0.077  -0.000   0.000   0.000
   5_bss:  0.326  72.795  -1.988  -1.799   0.053  -0.000   0.000   0.000
   5_xyz:  0.326  72.795  -1.988  -1.799   0.053  -0.000   0.000   0.000
   5_adp:  0.326  72.795  -1.988  -1.799   0.053  -0.000   0.000   0.000
   5_occ:  0.326  72.795  -1.988  -1.799   0.053  -0.000   0.000   0.000
   5_bss:  0.326  72.798  -1.860  -1.675   0.071  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.230 0.6056  0.7543    44418.094
   1_bss:  42.168 0.6173  0.7797    41836.175
   1_xyz:  25.810 0.8040  0.9717    17554.518
   1_adp:  26.479 0.7960  0.9699    18184.926
   1_occ:  26.534 0.7954  0.9683    18237.532
   2_bss:  26.004 0.8015  0.9311    17934.492
   2_xyz:  20.075 0.8605  0.9662    10947.531
   2_adp:  18.645 0.8748  0.9650     9954.173
   2_occ:  18.627 0.8749  0.9650     9937.477
   3_bss:  18.538 0.8757  0.9525     9860.140
   3_xyz:  15.866 0.8992  0.9673     7626.649
   3_adp:  15.356 0.9039  0.9598     7330.405
   3_occ:  15.352 0.9039  0.9598     7326.837
   4_bss:  15.315 0.9042  0.9668     7288.592
   4_xyz:  15.063 0.9067  0.9679     7116.302
   4_adp:  14.848 0.9086  0.9618     7002.917
   4_occ:  14.859 0.9085  0.9617     7007.898
   5_bss:  14.863 0.9085  0.9646     7009.084
   5_xyz:  14.783 0.9091  0.9662     6961.902
   5_adp:  14.868 0.9085  0.9577     7005.828
   5_occ:  14.871 0.9084  0.9576     7006.885
   5_bss:  14.872 0.9084  0.9607     7008.129
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6532e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6532e-01
   1_xyz:   1.429  0.013  0.088 15.596  0.006  4.123   1.1007e-01
   1_adp:   1.429  0.013  0.088 15.596  0.006  4.123   1.1007e-01
   1_occ:   1.429  0.013  0.088 15.596  0.006  4.123   1.1007e-01
   2_bss:   1.429  0.013  0.088 15.596  0.006  4.123   1.1007e-01
   2_xyz:   1.011  0.007  0.075 14.950  0.004  4.114   6.0183e-02
   2_adp:   1.011  0.007  0.075 14.950  0.004  4.114   6.0183e-02
   2_occ:   1.011  0.007  0.075 14.950  0.004  4.114   6.0183e-02
   3_bss:   1.011  0.007  0.075 14.950  0.004  4.114   6.0183e-02
   3_xyz:   1.117  0.010  0.082 14.958  0.004  4.127   7.3836e-02
   3_adp:   1.117  0.010  0.082 14.958  0.004  4.127   7.3836e-02
   3_occ:   1.117  0.010  0.082 14.958  0.004  4.127   7.3836e-02
   4_bss:   1.117  0.010  0.082 14.958  0.004  4.127   7.3836e-02
   4_xyz:   0.979  0.008  0.074 14.662  0.003  4.118   5.8464e-02
   4_adp:   0.979  0.008  0.074 14.662  0.003  4.118   5.8464e-02
   4_occ:   0.979  0.008  0.074 14.662  0.003  4.118   5.8464e-02
   5_bss:   0.979  0.008  0.074 14.662  0.003  4.118   5.8464e-02
   5_xyz:   1.021  0.009  0.078 14.614  0.003  4.121   6.2271e-02
   5_adp:   1.021  0.009  0.078 14.614  0.003  4.121   6.2271e-02
   5_occ:   1.021  0.009  0.078 14.614  0.003  4.121   6.2271e-02
   5_bss:   1.021  0.009  0.078 14.614  0.003  4.121   6.2271e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.729   2.4468e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.729   2.4468e-01
   1_xyz:  10.370  0.114  0.263 81.171  0.043  2.159   1.0769e-01
   1_adp:  10.370  0.114  0.263 81.171  0.043  2.159   1.0769e-01
   1_occ:  10.370  0.114  0.263 81.171  0.043  2.159   1.0769e-01
   2_bss:  10.370  0.114  0.263 81.171  0.043  2.159   1.0769e-01
   2_xyz:   7.203  0.038  0.254 83.987  0.048  2.339   5.1659e-02
   2_adp:   7.203  0.038  0.254 83.987  0.048  2.339   5.1659e-02
   2_occ:   7.203  0.038  0.254 83.987  0.048  2.339   5.1659e-02
   3_bss:   7.203  0.038  0.254 83.987  0.048  2.339   5.1659e-02
   3_xyz:   7.551  0.059  0.258 85.597  0.038  2.393   6.2191e-02
   3_adp:   7.551  0.059  0.258 85.597  0.038  2.393   6.2191e-02
   3_occ:   7.551  0.059  0.258 85.597  0.038  2.393   6.2191e-02
   4_bss:   7.551  0.059  0.258 85.597  0.038  2.393   6.2191e-02
   4_xyz:   7.339  0.048  0.224 82.477  0.035  2.444   3.5721e-02
   4_adp:   7.339  0.048  0.224 82.477  0.035  2.444   3.5721e-02
   4_occ:   7.339  0.048  0.224 82.477  0.035  2.444   3.5721e-02
   5_bss:   7.339  0.048  0.224 82.477  0.035  2.444   3.5721e-02
   5_xyz:   7.307  0.046  0.241 81.809  0.032  2.430   4.6177e-02
   5_adp:   7.307  0.046  0.241 81.809  0.032  2.430   4.6177e-02
   5_occ:   7.307  0.046  0.241 81.809  0.032  2.430   4.6177e-02
   5_bss:   7.307  0.046  0.241 81.809  0.032  2.430   4.6177e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  93.66   0.00  18.01  85.27   0.00  13.47  93.66   2.77  42.78
   1_occ:  93.66   0.00  18.01  85.27   0.00  13.47  93.66   2.77  42.78
   2_bss:  93.66   0.00  18.01  85.27   0.00  13.47  93.66   2.77  42.78
   2_xyz:  93.66   0.00  18.01  85.27   0.00  13.47  93.66   2.77  42.78
   2_adp:  94.19   0.44  17.71  82.70   0.44  13.15  94.19   4.96  42.49
   2_occ:  94.19   0.44  17.71  82.70   0.44  13.15  94.19   4.96  42.49
   3_bss:  94.19   0.44  17.71  82.70   0.44  13.15  94.19   4.96  42.49
   3_xyz:  94.19   0.44  17.71  82.70   0.44  13.15  94.19   4.96  42.49
   3_adp: 103.10   0.00  17.78  87.24   0.00  12.99 103.10   5.40  43.89
   3_occ: 103.10   0.00  17.78  87.24   0.00  12.99 103.10   5.40  43.89
   4_bss: 103.10   0.00  17.78  87.24   0.00  12.99 103.10   5.40  43.89
   4_xyz: 103.10   0.00  17.78  87.24   0.00  12.99 103.10   5.40  43.89
   4_adp: 102.87   0.46  17.43  87.22   0.46  12.75 102.87   1.92  42.91
   4_occ: 102.87   0.46  17.43  87.22   0.46  12.75 102.87   1.92  42.91
   5_bss: 102.87   0.46  17.43  87.22   0.46  12.75 102.87   1.92  42.91
   5_xyz: 102.87   0.46  17.43  87.22   0.46  12.75 102.87   1.92  42.91
   5_adp: 112.75   0.00  17.34  97.55   0.00  12.66 112.75   2.89  42.83
   5_occ: 112.75   0.00  17.34  97.55   0.00  12.66 112.75   2.89  42.83
   5_bss: 112.75   0.00  17.34  97.56   0.00  12.66 112.75   2.89  42.83
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.233    0.013    0.427
   1_adp:    1.233    0.013    0.427
   1_occ:    1.233    0.013    0.427
   2_bss:    1.233    0.013    0.427
   2_xyz:    1.179    0.038    0.462
   2_adp:    1.179    0.038    0.462
   2_occ:    1.179    0.038    0.462
   3_bss:    1.179    0.038    0.462
   3_xyz:    1.149    0.033    0.529
   3_adp:    1.149    0.033    0.529
   3_occ:    1.149    0.033    0.529
   4_bss:    1.149    0.033    0.529
   4_xyz:    1.250    0.045    0.539
   4_adp:    1.250    0.045    0.539
   4_occ:    1.250    0.045    0.539
   5_bss:    1.250    0.045    0.539
   5_xyz:    1.539    0.042    0.553
   5_adp:    1.539    0.042    0.553
   5_occ:    1.539    0.042    0.553
   5_bss:    1.539    0.042    0.553
------------------------------------------------------------------------

CPU time actual refinement: 337.40


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_923/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 337.25 
  Macro-tasks:
    bulk solvent and scale       = 57.03  
    individual site refinement   = 128.03 
    weights calculation          = 28.73  
    collect and process          = 6.61   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 220.51 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 100.32 
    alpha_beta                      = 8.02   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 108.68 
    fmodel                         = 8.64   
    r_factors                      = 0.37   
    phase_errors                   = 11.23  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 240.49 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.787 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    631 calls, 100.00 s
gradients_fft:          576 calls,  95.59 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 05:59:24 PST -0800 (1200491964.67 s)
Start R-work = 0.3939, R-free = 0.3858 (no bulk solvent and anisotropic scale)
Final R-work = 0.1374, R-free = 0.1822 (no bulk solvent and anisotropic scale)

Start R-work = 0.3805, R-free = 0.3746
Final R-work = 0.1177, R-free = 0.1661