# Date 2008-01-16 Time 05:22:07 PST -0800 (1200489727.35 s)
#phil __OFF__

Command line arguments: "../701.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18292
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 701

-------------------------------------------------------------------------------
  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: (70.25, 47.6339, 87.6859, 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: 3.25, per 1000 atoms: 1.15


================================== 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: (70.25, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00066
Completeness in resolution range: 0.959023
Completeness with d_max=infinity: 0.956027

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   2.0007

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: (70.25, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00066
Completeness in resolution range: 0.959023
Completeness with d_max=infinity: 0.956027

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2804 [2156/2183]  1939   217  10.1%
  bin  2:  4.2804 -  3.4104 [2048/2064]  1845   203   9.9%
  bin  3:  3.4104 -  2.9832 [2044/2063]  1840   204  10.0%
  bin  4:  2.9832 -  2.7121 [2010/2040]  1810   200  10.0%
  bin  5:  2.7121 -  2.5187 [1998/2017]  1793   205  10.3%
  bin  6:  2.5187 -  2.3708 [2002/2038]  1806   196   9.8%
  bin  7:  2.3708 -  2.2525 [1982/2015]  1784   198  10.0%
  bin  8:  2.2525 -  2.1547 [1977/2011]  1776   201  10.2%
  bin  9:  2.1547 -  2.0720 [1955/1983]  1757   198  10.1%
  bin 10:  2.0720 -  2.0007 [1417/2012]  1280   137   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_701/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: 0.13 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:
        1.81 -     2.42: 16
        2.42 -     3.04: 2152
        3.04 -     3.66: 4609
        3.66 -     4.28: 8867
        4.28 -     4.90: 12255
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.835 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.082 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.104 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.104 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27894 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_701/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_701/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 = 70.25 47.63395 87.68585 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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3906   r_free= 0.3794   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.180599                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1395  154 0.3085 0.3125      6.4115      6.3779|
|  2:  4.7738 -  3.8093 0.99   1339  151 0.3129 0.3252      6.6256      6.6662|
|  3:  3.8093 -  3.3338 0.99   1320  148 0.3527 0.3329      6.5316      6.4773|
|  4:  3.3338 -  3.0317 0.99   1299  135 0.3779 0.3794      6.4024      6.3529|
|  5:  3.0317 -  2.8159 0.99   1301  149 0.4036 0.3392      6.2556      6.1897|
|  6:  2.8159 -  2.6508 0.99   1298  147 0.4135 0.4342      6.1748        6.13|
|  7:  2.6508 -  2.5187 0.99   1275  145 0.4100 0.3958      6.1338      6.0595|
|  8:  2.5187 -  2.4095 0.98   1303  138 0.4345 0.4103      6.1138      6.1026|
|  9:  2.4095 -  2.3171 0.98   1271  146 0.4411 0.3957      6.0344      6.0074|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.4662 0.3983      6.0794      5.9871|
| 11:  2.2374 -  2.1677 1.00   1280  147 0.4458 0.4374      5.9731      5.9997|
| 12:  2.1677 -  2.1059 0.97   1278  137 0.4473 0.4688      5.9115      6.0112|
| 13:  2.1059 -  2.0506 0.98   1255  141 0.4747 0.4470      5.8595      5.7988|
| 14:  2.0506 -  2.0007 0.60    761   86 0.4295 0.4910      5.8033      5.7523|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1395   154  0.76  28.43   0.85     0.78      50553.25|
|  2:  4.7738 -  3.8093  1339   151  0.79  26.76   0.94     0.86      66237.32|
|  3:  3.8093 -  3.3338  1320   148  0.74  32.19   0.94     0.87      66487.28|
|  4:  3.3338 -  3.0317  1299   135  0.69  35.94   0.93     0.83      57993.47|
|  5:  3.0317 -  2.8159  1301   149  0.63  41.12   0.95     0.79      46204.38|
|  6:  2.8159 -  2.6508  1298   147  0.60  43.76   0.93     0.76      42847.36|
|  7:  2.6508 -  2.5187  1275   145  0.60  44.32   0.97     0.75      39236.05|
|  8:  2.5187 -  2.4095  1303   138  0.59  44.52   0.94     0.77      36915.58|
|  9:  2.4095 -  2.3171  1271   146  0.59  44.83   0.95     0.80      32839.88|
| 10:  2.3171 -  2.2374  1255   135  0.59  45.03   0.96     0.80      30744.52|
| 11:  2.2374 -  2.1677  1280   147  0.56  47.52   0.96     0.78      30763.54|
| 12:  2.1677 -  2.1059  1278   137  0.50  52.04   0.96     0.72      32227.41|
| 13:  2.1059 -  2.0506  1255   141  0.43  57.68   0.93     0.62      31651.92|
| 14:  2.0506 -  2.0007   761    86  0.37  62.57   1.00     0.49      28985.28|
|alpha:            min =        0.49 max =            0.87 mean =         0.77|
|beta:             min =    28985.28 max =        66487.28 mean =     43042.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.96 mean =        42.56|
|phase err.(test): min =        0.00 max =           89.76 mean =        42.75|
|-----------------------------------------------------------------------------|

============================== 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 = 8.045473              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.580   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.031643              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.087   (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 |  1.806 -  2.115:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      180 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1972 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1827 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2782 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4561 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4306 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5573 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6682 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| 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  1.806 |       0.169 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3906   r_free= 0.3794   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.180599                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3783   r_free= 0.3680   ksol= 0.30   Bsol= 51.05   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.64,2.71,1.88,0.00,0.00,0.00); trace/3= 0.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.163754                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.174640              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.292   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.580219              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.911   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3783      final r-factor (work) = 0.2290          |
| start r-factor (free) = 0.3680      final r-factor (free) = 0.2516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2814 = 7.17 * 0.50 * 6.1655 + 1.00 * 0.1637                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3275 = 7.17 * 0.50 * 5.9193 + 1.00 * 0.0932                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2290      final r-factor (work) = 0.2084          |
| start r-factor (free) = 0.2516      final r-factor (free) = 0.2580          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4406 = 0.58 * 1.00 * 5.9193 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3020 = 0.58 * 1.00 * 5.6704 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.30   17.33    None  None   None       |
|    all(noH): 2823   0      0.00    86.30   17.33    None  None   None       |
|    Sol.    : 438    0      5.41    86.30   40.46    None  None   None       |
|    Mac.    : 2385   0      0.00    78.10   13.08    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 -   8.630:  794   |   5:    43.148 -  51.777:  108        |
|      1:     8.630 -  17.259: 1142   |   6:    51.777 -  60.407:   65        |
|      2:    17.259 -  25.889:  362   |   7:    60.407 -  69.036:   46        |
|      3:    25.889 -  34.518:  161   |   8:    69.036 -  77.666:   13        |
|      4:    34.518 -  43.148:  124   |   9:    77.666 -  86.295:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2084 r_free = 0.2580             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2082 r_free = 0.2587             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2082   r_free= 0.2587   ksol= 0.30   Bsol= 51.05   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.64,2.71,1.88,0.00,0.00,0.00); trace/3= 0.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.678061                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2055   r_free= 0.2558   ksol= 0.33   Bsol= 78.51   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,0.00,0.06,0.00,0.00,0.00); trace/3= -0.91                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.669685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.242726              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.725  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.269805              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.215  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2055      final r-factor (work) = 0.1520          |
| start r-factor (free) = 0.2558      final r-factor (free) = 0.1900          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2892 = 3.24 * 0.50 * 5.6718 + 1.00 * 0.0932                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0599 = 3.24 * 0.50 * 5.5500 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1520      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.1900      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5093 = 0.27 * 1.00 * 5.5500 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4553 = 0.27 * 1.00 * 5.3586 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.20   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    85.20   16.96    None  None   None       |
|    Sol.    : 438    0      5.55    85.20   40.30    None  None   None       |
|    Mac.    : 2385   0      0.00    80.47   12.67    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 -   8.520:  794   |   5:    42.602 -  51.122:   96        |
|      1:     8.520 -  17.041: 1225   |   6:    51.122 -  59.642:   84        |
|      2:    17.041 -  25.561:  308   |   7:    59.642 -  68.163:   41        |
|      3:    25.561 -  34.081:  136   |   8:    68.163 -  76.683:   19        |
|      4:    34.081 -  42.602:  115   |   9:    76.683 -  85.203:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1426 r_free = 0.1804             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1803             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1803   ksol= 0.33   Bsol= 78.51   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,0.00,0.06,0.00,0.00,0.00); trace/3= -0.91                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.333832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1424   r_free= 0.1799   ksol= 0.33   Bsol= 73.38   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.90,-0.19,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.332132                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.495894              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.323110              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.426  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1424      final r-factor (work) = 0.1231          |
| start r-factor (free) = 0.1799      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7480 = 2.50 * 0.50 * 5.3581 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6368 = 2.50 * 0.50 * 5.2669 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7112 = 0.32 * 1.00 * 5.2669 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6924 = 0.32 * 1.00 * 5.2084 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.40    84.11   16.68    None  None   None       |
|    all(noH): 2823   0      0.40    84.11   16.68    None  None   None       |
|    Sol.    : 438    0      1.77    84.11   40.07    None  None   None       |
|    Mac.    : 2385   0      0.40    83.15   12.39    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:     0.399 -   8.770:  888   |   5:    42.254 -  50.625:   99        |
|      1:     8.770 -  17.141: 1175   |   6:    50.625 -  58.996:   78        |
|      2:    17.141 -  25.512:  276   |   7:    58.996 -  67.367:   40        |
|      3:    25.512 -  33.883:  127   |   8:    67.367 -  75.738:   20        |
|      4:    33.883 -  42.254:  113   |   9:    75.738 -  84.110:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1204 r_free = 0.1631             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1204 r_free = 0.1630             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1630   ksol= 0.33   Bsol= 73.38   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.90,-0.19,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.200908                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1203   r_free= 0.1630   ksol= 0.33   Bsol= 66.46   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.16,-0.22,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.200390                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.155440              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.086  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.966884              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.867  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6767 = 2.16 * 0.50 * 5.2080 + 1.00 * 0.0640                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6516 = 2.16 * 0.50 * 5.1852 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2080 = 1.97 * 1.00 * 5.1852 + 1.00 * 0.0093                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1800 = 1.97 * 1.00 * 5.1700 + 1.00 * 0.0112                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.86   16.77    None  None   None       |
|    all(noH): 2823   0      0.00    93.86   16.77    None  None   None       |
|    Sol.    : 438    0      0.71    84.56   41.09    None  None   None       |
|    Mac.    : 2385   0      0.00    93.86   12.31    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 -   9.386: 1063   |   5:    46.928 -  56.314:   84        |
|      1:     9.386 -  18.771: 1092   |   6:    56.314 -  65.700:   70        |
|      2:    18.771 -  28.157:  216   |   7:    65.700 -  75.085:   35        |
|      3:    28.157 -  37.543:  132   |   8:    75.085 -  84.471:   11        |
|      4:    37.543 -  46.928:  115   |   9:    84.471 -  93.857:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1627             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1628             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1628   ksol= 0.33   Bsol= 66.46   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.16,-0.22,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.175548                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1619   ksol= 0.32   Bsol= 66.15   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-1.05,-0.02,-0.00,-0.00,-0.00); trace/3= -1.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.173368                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.267543              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.773  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.506399              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.541  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9253 = 2.27 * 0.50 * 5.1702 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9225 = 2.27 * 0.50 * 5.1665 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7938 = 1.51 * 1.00 * 5.1665 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7934 = 1.51 * 1.00 * 5.1660 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.36   16.50    None  None   None       |
|    all(noH): 2823   0      0.00    95.36   16.50    None  None   None       |
|    Sol.    : 438    0      2.67    86.23   40.80    None  None   None       |
|    Mac.    : 2385   0      0.00    95.36   12.04    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 -   9.536: 1171   |   5:    47.679 -  57.215:   82        |
|      1:     9.536 -  19.072: 1000   |   6:    57.215 -  66.751:   68        |
|      2:    19.072 -  28.608:  213   |   7:    66.751 -  76.287:   27        |
|      3:    28.608 -  38.143:  129   |   8:    76.287 -  85.822:   11        |
|      4:    38.143 -  47.679:  117   |   9:    85.822 -  95.358:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1128 r_free = 0.1623             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1624             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1624   ksol= 0.32   Bsol= 66.15   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-1.05,-0.02,-0.00,-0.00,-0.00); trace/3= -1.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166067                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1395  154 0.0962 0.1268      5.3772      5.5238|
|  2:  4.7738 -  3.8093 0.99   1339  151 0.0831 0.1073      5.4182      5.6203|
|  3:  3.8093 -  3.3338 0.99   1320  148 0.1036 0.1500      5.4608      5.8475|
|  4:  3.3338 -  3.0317 0.99   1299  135 0.1205 0.1587      5.4557      5.6208|
|  5:  3.0317 -  2.8159 0.99   1301  149 0.1362 0.1774      5.3578      5.5498|
|  6:  2.8159 -  2.6508 0.99   1298  147 0.1267 0.2135      5.2518      5.5439|
|  7:  2.6508 -  2.5187 0.99   1275  145 0.1267 0.1682       5.186      5.3505|
|  8:  2.5187 -  2.4095 0.98   1303  138 0.1162 0.1656      5.0989      5.3518|
|  9:  2.4095 -  2.3171 0.98   1271  146 0.1190 0.1957      5.0496      5.3435|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.1182 0.1738      5.0217      5.2432|
| 11:  2.2374 -  2.1677 1.00   1280  147 0.1184 0.1925      4.9674      5.2943|
| 12:  2.1677 -  2.1059 0.97   1278  137 0.1166 0.1744      4.9135      5.2323|
| 13:  2.1059 -  2.0506 0.98   1255  141 0.1128 0.1823      4.8144      5.0591|
| 14:  2.0506 -  2.0007 0.60    761   86 0.1071 0.1851      4.7083      5.0172|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1395   154  0.94   9.39   0.96     0.93       7390.17|
|  2:  4.7738 -  3.8093  1339   151  0.95   7.81   1.00     0.98       8784.38|
|  3:  3.8093 -  3.3338  1320   148  0.94  11.06   1.01     1.01      10211.06|
|  4:  3.3338 -  3.0317  1299   135  0.92  13.63   1.00     0.98      10448.10|
|  5:  3.0317 -  2.8159  1301   149  0.90  16.46   0.99     0.96       8917.19|
|  6:  2.8159 -  2.6508  1298   147  0.89  17.11   0.97     0.95       7756.87|
|  7:  2.6508 -  2.5187  1275   145  0.90  15.90   0.98     0.95       6532.76|
|  8:  2.5187 -  2.4095  1303   138  0.90  15.68   0.98     0.95       5774.54|
|  9:  2.4095 -  2.3171  1271   146  0.90  16.30   0.98     0.94       5324.86|
| 10:  2.3171 -  2.2374  1255   135  0.89  16.99   0.97     0.92       5003.57|
| 11:  2.2374 -  2.1677  1280   147  0.90  16.73   0.97     0.93       4644.20|
| 12:  2.1677 -  2.1059  1278   137  0.90  16.13   0.98     0.97       4278.25|
| 13:  2.1059 -  2.0506  1255   141  0.90  16.56   0.97     0.95       3585.38|
| 14:  2.0506 -  2.0007   761    86  0.91  15.32   0.94     0.89       2795.25|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     2795.25 max =        10448.10 mean =      6677.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.56|
|phase err.(test): min =        0.00 max =           88.46 mean =        14.05|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1622   ksol= 0.32   Bsol= 63.85   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-0.81,0.25,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166175                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1622   ksol= 0.32   Bsol= 63.85   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-0.81,0.25,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1395  154 0.0961 0.1270      5.3768      5.5245|
|  2:  4.7738 -  3.8093 0.99   1339  151 0.0831 0.1071      5.4179      5.6192|
|  3:  3.8093 -  3.3338 0.99   1320  148 0.1036 0.1501      5.4605      5.8485|
|  4:  3.3338 -  3.0317 0.99   1299  135 0.1205 0.1588      5.4563      5.6214|
|  5:  3.0317 -  2.8159 0.99   1301  149 0.1363 0.1775      5.3584      5.5501|
|  6:  2.8159 -  2.6508 0.99   1298  147 0.1267 0.2137      5.2521      5.5443|
|  7:  2.6508 -  2.5187 0.99   1275  145 0.1267 0.1683      5.1864      5.3508|
|  8:  2.5187 -  2.4095 0.98   1303  138 0.1162 0.1657      5.0992      5.3517|
|  9:  2.4095 -  2.3171 0.98   1271  146 0.1190 0.1956      5.0498      5.3433|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.1181 0.1739      5.0219      5.2439|
| 11:  2.2374 -  2.1677 1.00   1280  147 0.1184 0.1924      4.9674       5.294|
| 12:  2.1677 -  2.1059 0.97   1278  137 0.1166 0.1742      4.9133      5.2321|
| 13:  2.1059 -  2.0506 0.98   1255  141 0.1128 0.1823      4.8143      5.0589|
| 14:  2.0506 -  2.0007 0.60    761   86 0.1071 0.1849      4.7086      5.0169|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1395   154  0.94   9.39   0.96     0.94       7386.37|
|  2:  4.7738 -  3.8093  1339   151  0.95   7.81   1.00     0.98       8778.19|
|  3:  3.8093 -  3.3338  1320   148  0.94  11.05   1.02     1.01      10206.47|
|  4:  3.3338 -  3.0317  1299   135  0.92  13.65   1.00     0.98      10457.53|
|  5:  3.0317 -  2.8159  1301   149  0.90  16.47   1.00     0.97       8925.51|
|  6:  2.8159 -  2.6508  1298   147  0.89  17.11   0.98     0.95       7760.47|
|  7:  2.6508 -  2.5187  1275   145  0.90  15.90   0.99     0.96       6536.67|
|  8:  2.5187 -  2.4095  1303   138  0.90  15.69   0.99     0.96       5776.15|
|  9:  2.4095 -  2.3171  1271   146  0.90  16.31   0.99     0.95       5328.54|
| 10:  2.3171 -  2.2374  1255   135  0.89  16.99   0.99     0.94       5002.87|
| 11:  2.2374 -  2.1677  1280   147  0.90  16.73   0.98     0.94       4642.64|
| 12:  2.1677 -  2.1059  1278   137  0.90  16.13   1.00     0.99       4277.37|
| 13:  2.1059 -  2.0506  1255   141  0.90  16.56   0.98     0.96       3584.04|
| 14:  2.0506 -  2.0007   761    86  0.91  15.32   0.95     0.91       2793.75|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2793.75 max =        10457.53 mean =      6678.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.56|
|phase err.(test): min =        0.00 max =           88.60 mean =        14.05|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.217)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.36   16.51    None  None   None       |
|    all(noH): 2823   0      0.00    95.36   16.51    None  None   None       |
|    Sol.    : 438    0      2.68    86.23   40.80    None  None   None       |
|    Mac.    : 2385   0      0.00    95.36   12.05    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 -   9.539: 1171   |   5:    47.682 -  57.218:   82        |
|      1:     9.539 -  19.075: 1000   |   6:    57.218 -  66.754:   68        |
|      2:    19.075 -  28.610:  213   |   7:    66.754 -  76.290:   27        |
|      3:    28.610 -  38.146:  129   |   8:    76.290 -  85.825:   11        |
|      4:    38.146 -  47.682:  117   |   9:    85.825 -  95.361:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.438 - 4.893
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 319
   mapped sites are within: 0.710 - 4.893

peak=    5.754 closest distance to " O   HOH Z 113 " =    2.213
peak=    5.230 closest distance to " CB  GLN A 223 " =    1.408
peak=    5.139 closest distance to " CG  PRO A  54 " =    1.339
peak=    4.991 closest distance to " CB  ARG A 190 " =    1.693
peak=    4.893 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.830 closest distance to " CB  SER A  63 " =    1.158
peak=    4.799 closest distance to " CG  PRO A 213 " =    1.208
peak=    4.791 closest distance to " CG  PRO A 280 " =    0.858
peak=    4.715 closest distance to " C   PRO A 198 " =    1.530
peak=    4.697 closest distance to " CB  ARG A 275 " =    0.966
peak=    4.633 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.594 closest distance to " O   HOH Z 232 " =    2.299
peak=    4.567 closest distance to " CG  PRO A  90 " =    1.227
peak=    4.540 closest distance to " CZ  PHE A 218 " =    1.095
peak=    4.536 closest distance to " O   HOH Z 298 " =    1.882
peak=    4.466 closest distance to " CG  PRO A 198 " =    1.244
peak=    4.409 closest distance to " CB  ARG A  79 " =    1.349
peak=    4.321 closest distance to " CB  GLU A 152 " =    1.153
peak=    4.305 closest distance to " O   HOH Z 369 " =    2.304
peak=    4.239 closest distance to " NE2 GLN A  11 " =    1.076
peak=    4.211 closest distance to " O   HOH Z 234 " =    3.807
peak=    4.174 closest distance to " CD  ARG A 269 " =    0.990
peak=    4.171 closest distance to " O   SER A  87 " =    2.211
peak=    4.170 closest distance to " CB  PRO A  54 " =    0.945
peak=    4.166 closest distance to " CE  LYS A  76 " =    0.828
peak=    4.157 closest distance to " O   HOH Z  15 " =    2.193
peak=    4.146 closest distance to " O   HOH Z 189 " =    2.702
peak=    4.131 closest distance to " CB  LEU A 228 " =    1.112
peak=    4.118 closest distance to " O   HOH Z 142 " =    1.578
peak=    4.100 closest distance to " O   HOH Z 126 " =    1.969
peak=    4.097 closest distance to " O   HOH Z 158 " =    3.156
peak=    4.054 closest distance to " CB  GLU A 128 " =    1.135
peak=    4.043 closest distance to " CA  ARG A  36 " =    1.098
peak=    4.032 closest distance to " CA  ARG A 195 " =    1.308
peak=    4.026 closest distance to " CB  TYR A 169 " =    0.764
peak=    4.022 closest distance to " CB  ASN A 148 " =    1.409
peak=    4.014 closest distance to " CB  TRP A 266 " =    1.030
peak=    4.007 closest distance to " CA  ALA A  51 " =    0.940
peak=    3.990 closest distance to " CD2 TRP A 179 " =    1.332
peak=    3.990 closest distance to " O   HOH Z 403 " =    1.664
peak=    3.986 closest distance to " O   HOH Z 303 " =    2.234
peak=    3.974 closest distance to " O   HOH Z 265 " =    2.084
peak=    3.966 closest distance to " OD1 ASN A  69 " =    2.544
peak=    3.952 closest distance to " O   HOH Z  43 " =    1.931
peak=    3.949 closest distance to " O   HOH Z  40 " =    1.972
peak=    3.946 closest distance to " N   HIS A 108 " =    1.903
peak=    3.946 closest distance to " CB  GLU A 277 " =    3.736
peak=    3.941 closest distance to " CD2 LEU A 297 " =    0.913
peak=    3.936 closest distance to " CG  PRO A 243 " =    1.065
peak=    3.931 closest distance to " NZ  LYS A 117 " =    3.197
peak=    3.925 closest distance to " O   HOH Z 280 " =    2.955
peak=    3.923 closest distance to " O   HOH Z 427 " =    3.062
peak=    3.922 closest distance to " O   HOH Z 368 " =    2.137
peak=    3.910 closest distance to " O   HOH Z 353 " =    2.696
peak=    3.905 closest distance to " CB  VAL A 202 " =    1.560
peak=    3.885 closest distance to " O   HOH Z 346 " =    1.663
peak=    3.884 closest distance to " CG  ARG A  66 " =    2.491
peak=    3.877 closest distance to " O   HOH Z 412 " =    3.747
peak=    3.876 closest distance to " CB  ASP A 140 " =    1.021
peak=    3.875 closest distance to " O   HOH Z 368 " =    3.688
peak=    3.870 closest distance to " CD1 LEU A 300 " =    1.172
peak=    3.858 closest distance to " O   HOH Z 203 " =    1.803
peak=    3.844 closest distance to " O   HOH Z 406 " =    1.599
peak=    3.837 closest distance to " CZ3 TRP A 266 " =    1.103
peak=    3.833 closest distance to " ND2 ASN A 187 " =    1.472
peak=    3.808 closest distance to " O   HOH Z 402 " =    1.440
peak=    3.802 closest distance to " CD1 LEU A  96 " =    0.787
peak=    3.793 closest distance to " O   HOH Z 214 " =    2.292
peak=    3.791 closest distance to " O   HOH Z 287 " =    1.926
peak=    3.778 closest distance to " O   HOH Z 133 " =    2.614
peak=    3.769 closest distance to " CD  LYS A 166 " =    1.304
peak=    3.764 closest distance to " NH1AARG A 145 " =    1.311
peak=    3.763 closest distance to " O   HOH Z  78 " =    1.613
peak=    3.751 closest distance to " NH2 ARG A 156 " =    1.185
peak=    3.740 closest distance to " CG  MET A 185 " =    1.166
peak=    3.740 closest distance to " O   HOH Z 316 " =    3.127
peak=    3.736 closest distance to " O   HOH Z  44 " =    2.265
peak=    3.735 closest distance to " O   HOH Z  21 " =    1.853
peak=    3.726 closest distance to " CA  ALA A 160 " =    0.937
peak=    3.725 closest distance to " OG BSER A 164 " =    2.337
peak=    3.720 closest distance to " O   HOH Z 128 " =    2.085
peak=    3.720 closest distance to " O   HOH Z  59 " =    2.312
peak=    3.715 closest distance to " CA  ASN A 176 " =    1.287
peak=    3.704 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.704 closest distance to " CD  ARG A 159 " =    0.818
peak=    3.704 closest distance to " CB  VAL A 265 " =    1.216
peak=    3.699 closest distance to " CA  MET A 105 " =    1.039
peak=    3.696 closest distance to " O   ASN A  74 " =    1.530
peak=    3.695 closest distance to " ND2 ASN A 249 " =    1.934
peak=    3.693 closest distance to " O   HOH Z  19 " =    1.793
peak=    3.683 closest distance to " O   HOH Z 180 " =    2.184
peak=    3.683 closest distance to " CB  ASN A  39 " =    0.860
peak=    3.674 closest distance to " O   ALA A 165 " =    1.453
peak=    3.666 closest distance to " OG BSER A 134 " =    2.829
peak=    3.662 closest distance to " O   HOH Z 423 " =    1.958
peak=    3.656 closest distance to " O   HOH Z  97 " =    2.004
peak=    3.652 closest distance to " ND2 ASN A 249 " =    0.887
peak=    3.649 closest distance to " O   HOH Z  80 " =    1.783
peak=    3.645 closest distance to " NE2 GLN A  77 " =    3.360
peak=    3.644 closest distance to " CZ  PHE A  38 " =    1.252
peak=    3.636 closest distance to " O   HOH Z 359 " =    1.565
peak=    3.636 closest distance to " CA  PRO A  54 " =    1.373
peak=    3.630 closest distance to " O   HOH Z 250 " =    1.426
peak=    3.624 closest distance to " CB  GLU A  46 " =    0.953
peak=    3.623 closest distance to " CG2 ILE A 120 " =    1.051
peak=    3.612 closest distance to " CA  ASN A 215 " =    1.042
peak=    3.608 closest distance to " O  BHOH Z 338 " =    2.217
peak=    3.599 closest distance to " O   HOH Z 403 " =    1.464
peak=    3.590 closest distance to " O   HOH Z 193 " =    1.826
peak=    3.589 closest distance to " CA  THR A 221 " =    0.950
peak=    3.586 closest distance to " CB  TYR A 116 " =    0.810
peak=    3.584 closest distance to " CG1 ILE A  33 " =    1.221
peak=    3.580 closest distance to " CA  VAL A 125 " =    1.169
peak=    3.580 closest distance to " O   HOH Z  63 " =    1.957
peak=    3.579 closest distance to " O   HOH Z 325 " =    2.347
peak=    3.572 closest distance to " O   HOH Z 371 " =    3.191
peak=    3.571 closest distance to " O   HOH Z 272 " =    1.882
peak=    3.566 closest distance to " O   HOH Z 279 " =    2.202
peak=    3.564 closest distance to " O   HOH Z 383 " =    2.184
peak=    3.561 closest distance to " O   HOH Z 261 " =    1.815
peak=    3.557 closest distance to " CB  GLN A  89 " =    1.284
peak=    3.554 closest distance to " CA  ALA A 295 " =    1.070
peak=    3.546 closest distance to " CG2 VAL A 257 " =    0.818
peak=    3.539 closest distance to " O   HOH Z  44 " =    1.766
peak=    3.536 closest distance to " O   HOH Z 299 " =    4.383
peak=    3.534 closest distance to " NH2BARG A 145 " =    2.182
peak=    3.527 closest distance to " CG2AVAL A  72 " =    1.849
peak=    3.524 closest distance to " CB  LEU A  83 " =    0.833
peak=    3.520 closest distance to " O   HOH Z 426 " =    1.601
peak=    3.519 closest distance to " NZ  LYS A  48 " =    1.253
peak=    3.513 closest distance to " O   HOH Z 185 " =    1.828
peak=    3.506 closest distance to " CG  GLU A  37 " =    0.906
peak=    3.505 closest distance to " O   HOH Z 421 " =    1.707
peak=    3.496 closest distance to " O   HOH Z 285 " =    1.722
peak=    3.491 closest distance to " O   THR A 251 " =    1.132
peak=    3.488 closest distance to " O   HOH Z 258 " =    2.086
peak=    3.487 closest distance to " CG2 VAL A 197 " =    1.135
peak=    3.486 closest distance to " OD2 ASP A 298 " =    4.037
peak=    3.486 closest distance to " O   HOH Z 126 " =    1.601
peak=    3.484 closest distance to " O   ASN A  74 " =    2.058
peak=    3.480 closest distance to " CA  SER A  87 " =    1.078
peak=    3.480 closest distance to " O   HOH Z 134 " =    1.215
peak=    3.474 closest distance to " CB  ASN A 142 " =    1.143
peak=    3.473 closest distance to " CA  ALA A  21 " =    1.225
peak=    3.471 closest distance to " CG  GLN A  11 " =    1.513
peak=    3.467 closest distance to " CD1 ILE A 199 " =    1.068
peak=    3.453 closest distance to " O   HOH Z 365 " =    2.816
peak=    3.447 closest distance to " O   HOH Z 285 " =    2.548
peak=    3.445 closest distance to " CB  ALA A 291 " =    1.293
peak=    3.442 closest distance to " O   HOH Z 391 " =    2.921
peak=    3.442 closest distance to " O   HOH Z 147 " =    1.835
peak=    3.437 closest distance to " O   HOH Z 128 " =    2.250
peak=    3.437 closest distance to " CB  TRP A 179 " =    1.386
peak=    3.435 closest distance to " O   HOH Z 271 " =    2.650
peak=    3.433 closest distance to " CB  GLN A  88 " =    1.188
peak=    3.431 closest distance to " N   ASN A  39 " =    1.309
peak=    3.430 closest distance to " O   THR A 220 " =    1.172
peak=    3.428 closest distance to " O   THR A 182 " =    1.419
peak=    3.423 closest distance to " CB  SER A  62 " =    0.798
peak=    3.420 closest distance to " N   GLY A  98 " =    1.198
peak=    3.420 closest distance to " O   ASP A 124 " =    1.283
peak=    3.415 closest distance to " O   HOH Z 361 " =    2.637
peak=    3.412 closest distance to " NH2AARG A 275 " =    3.567
peak=    3.410 closest distance to " CG2 ILE A  20 " =    1.266
peak=    3.408 closest distance to " O   HOH Z 291 " =    1.474
peak=    3.399 closest distance to " CA  GLU A 152 " =    0.880
peak=    3.396 closest distance to " O   HOH Z 327 " =    1.592
peak=    3.395 closest distance to " CB  MET A  47 " =    0.951
peak=    3.393 closest distance to " O   HOH Z 294 " =    1.503
peak=    3.392 closest distance to " O   TYR A 116 " =    1.416
peak=    3.390 closest distance to " O   HOH Z  20 " =    1.434
peak=    3.387 closest distance to " CB  PRO A  90 " =    1.095
peak=    3.381 closest distance to " CG1 VAL A 153 " =    1.003
peak=    3.377 closest distance to " OG  SER A  22 " =    2.751
peak=    3.377 closest distance to " O   HOH Z 148 " =    3.394
peak=    3.375 closest distance to " O  BHOH Z  74 " =    1.343
peak=    3.374 closest distance to " CB  ASN A 215 " =    1.194
peak=    3.373 closest distance to " O   HOH Z 393 " =    3.198
peak=    3.371 closest distance to " O   HOH Z  68 " =    1.882
peak=    3.369 closest distance to " CA  ASP A 191 " =    0.871
peak=    3.361 closest distance to " O   HOH Z   1 " =    2.405
peak=    3.345 closest distance to " CA  ASP A 124 " =    0.715
peak=    3.339 closest distance to " O   HOH Z 197 " =    2.761
peak=    3.336 closest distance to " CB  SER A 141 " =    1.030
peak=    3.335 closest distance to " O   HOH Z 313 " =    1.927
peak=    3.329 closest distance to " CA  ALA A 291 " =    0.755
peak=    3.329 closest distance to " O   HOH Z 193 " =    2.203
peak=    3.328 closest distance to " CA  ASN A 217 " =    1.235
peak=    3.323 closest distance to " O   HOH Z 261 " =    1.710
peak=    3.322 closest distance to " CB  THR A  31 " =    1.670
peak=    3.321 closest distance to " CG2 THR A 221 " =    1.118
peak=    3.321 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.320 closest distance to " N   CYS A 260 " =    0.802
peak=    3.319 closest distance to " CB  ARG A 139 " =    1.140
peak=    3.318 closest distance to " O   HOH Z 171 " =    1.833
peak=    3.316 closest distance to " O   HOH Z 250 " =    1.493
peak=    3.313 closest distance to " CA  ASP A 191 " =    1.145
peak=    3.310 closest distance to " CB  SER A 212 " =    1.063
peak=    3.308 closest distance to " CA  ALA A 233 " =    1.558
peak=    3.307 closest distance to " O   HOH Z 411 " =    1.727
peak=    3.299 closest distance to " OE1 GLU A 236 " =    1.034
peak=    3.297 closest distance to " O   HOH Z  49 " =    0.790
peak=    3.296 closest distance to " O   HOH Z 305 " =    3.768
peak=    3.296 closest distance to " O   HOH Z 245 " =    1.312
peak=    3.296 closest distance to " CG  LEU A 167 " =    1.168
peak=    3.295 closest distance to " CB  ASP A 298 " =    1.211
peak=    3.293 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.289 closest distance to " NE2 HIS A 207 " =    1.161
peak=    3.287 closest distance to " ND2 ASN A 110 " =    1.564
peak=    3.287 closest distance to " O   HOH Z 345 " =    1.644
peak=    3.281 closest distance to " O   HOH Z  66 " =    2.211
peak=    3.280 closest distance to " CA  ALA A 100 " =    0.973
peak=    3.278 closest distance to " CG  GLN A  58 " =    2.809
peak=    3.273 closest distance to " CA  ALA A 248 " =    1.167
peak=    3.270 closest distance to " CB  TYR A 247 " =    0.948
peak=    3.269 closest distance to " CA  MET A 188 " =    0.955
peak=    3.269 closest distance to " CA  ALA A  84 " =    1.220
peak=    3.269 closest distance to " CB  PHE A 204 " =    0.746
peak=    3.267 closest distance to " CB  ALA A 248 " =    1.300
peak=    3.266 closest distance to " CG  ARG A 219 " =    1.145
peak=    3.262 closest distance to " CA  ASN A 127 " =    1.222
peak=    3.260 closest distance to " CB  THR A  52 " =    0.771
peak=    3.260 closest distance to " OE1 GLN A  11 " =    2.032
peak=    3.260 closest distance to " CA  GLY A 241 " =    0.860
peak=    3.258 closest distance to " CA  TYR A 116 " =    1.370
peak=    3.257 closest distance to " N   VAL A 265 " =    1.163
peak=    3.254 closest distance to " CA  LEU A  83 " =    1.278
peak=    3.253 closest distance to " CG2 ILE A 234 " =    0.876
peak=    3.252 closest distance to " O   HOH Z 422 " =    2.641
peak=    3.251 closest distance to " CA  THR A 264 " =    0.877
peak=    3.248 closest distance to " CG2 THR A  29 " =    1.313
peak=    3.245 closest distance to " NH2BARG A 190 " =    1.768
peak=    3.241 closest distance to " OH  TYR A 116 " =    1.102
peak=    3.239 closest distance to " CB  SER A   3 " =    1.411
peak=    3.238 closest distance to " O   HOH Z 247 " =    1.429
peak=    3.235 closest distance to " ND1 HIS A  81 " =    1.658
peak=    3.235 closest distance to " O   HOH Z 227 " =    2.046
peak=    3.235 closest distance to " O   HOH Z 183 " =    1.519
peak=    3.232 closest distance to " O   HOH Z 380 " =    1.925
peak=    3.232 closest distance to " CD  ARG A  66 " =    2.391
peak=    3.231 closest distance to " O   HOH Z 251 " =    1.552
peak=    3.229 closest distance to " N   ARG A 156 " =    1.435
peak=    3.224 closest distance to " N   ASN A 127 " =    1.296
peak=    3.218 closest distance to " CB  ILE A 120 " =    1.297
peak=    3.217 closest distance to " O   HOH Z  44 " =    2.352
peak=    3.216 closest distance to " O   HOH Z 248 " =    1.673
peak=    3.215 closest distance to " CG  PHE A 204 " =    0.893
peak=    3.215 closest distance to " O   HOH Z  48 " =    1.694
peak=    3.213 closest distance to " CA  GLU A  46 " =    0.849
peak=    3.210 closest distance to " O   HOH Z 295 " =    1.514
peak=    3.210 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.209 closest distance to " O   HOH Z 374 " =    2.723
peak=    3.207 closest distance to " OG  SER A 245 " =    1.655
peak=    3.205 closest distance to " O   HOH Z  97 " =    2.325
peak=    3.204 closest distance to " CB  TYR A 169 " =    0.774
peak=    3.203 closest distance to " CD BLYS A 290 " =    0.952
peak=    3.203 closest distance to " O   HOH Z 171 " =    3.964
peak=    3.198 closest distance to " CB  ASN A 285 " =    0.971
peak=    3.195 closest distance to " O   HOH Z 357 " =    2.093
peak=    3.192 closest distance to " CB  PHE A 204 " =    0.887
peak=    3.192 closest distance to " O   HOH Z 163 " =    1.505
peak=    3.191 closest distance to " O   HOH Z 132 " =    2.713
peak=    3.189 closest distance to " O   HOH Z 116 " =    1.784
peak=    3.186 closest distance to " O   HOH Z  62 " =    2.310
peak=    3.184 closest distance to " O   HOH Z  88 " =    3.370
peak=    3.183 closest distance to " CA  ASP A 162 " =    1.135
peak=    3.181 closest distance to " C   TYR A 214 " =    1.546
peak=    3.180 closest distance to " O   HOH Z 106 " =    4.095
peak=    3.177 closest distance to " CB  ALA A   1 " =    4.893
peak=    3.176 closest distance to " CB  MET A 105 " =    0.852
peak=    3.169 closest distance to " CA  ILE A 106 " =    0.814
peak=    3.166 closest distance to " O   HOH Z 109 " =    2.720
peak=    3.166 closest distance to " CG  ARG A 138 " =    1.178
peak=    3.163 closest distance to " CA  ALA A 158 " =    1.235
peak=    3.162 closest distance to " OG1 THR A 294 " =    2.445
peak=    3.153 closest distance to " NE  ARG A  79 " =    0.980
peak=    3.152 closest distance to " CA  ARG A 102 " =    1.123
peak=    3.150 closest distance to " O   HOH Z 234 " =    1.899
peak=    3.148 closest distance to " O   HOH Z 173 " =    2.117
peak=    3.146 closest distance to " O   HOH Z 199 " =    1.613
peak=    3.146 closest distance to " ND2 ASN A 301 " =    1.726
peak=    3.145 closest distance to " O   HOH Z 174 " =    2.447
peak=    3.137 closest distance to " CB  PRO A 243 " =    1.548
peak=    3.137 closest distance to " CB  GLN A 103 " =    0.870
peak=    3.137 closest distance to " O   HOH Z 213 " =    1.745
peak=    3.137 closest distance to " CE1 HIS A 108 " =    1.076
peak=    3.135 closest distance to " O   HOH Z 193 " =    1.705
peak=    3.133 closest distance to " O   HOH Z 240 " =    2.533
peak=    3.129 closest distance to " NE2 HIS A 115 " =    0.950
peak=    3.127 closest distance to " CE3 TRP A 150 " =    1.084
peak=    3.123 closest distance to " CB  GLN A 205 " =    1.049
peak=    3.123 closest distance to " CG1 ILE A  49 " =    1.595
peak=    3.122 closest distance to " NH1AARG A 145 " =    0.986
peak=    3.115 closest distance to " NZ ALYS A 290 " =    1.006
peak=    3.113 closest distance to " OG  SER A  62 " =    2.874
peak=    3.112 closest distance to " CG BARG A 102 " =    1.846
peak=    3.108 closest distance to " CB  ALA A  43 " =    0.810
peak=    3.103 closest distance to " O   HOH Z 156 " =    2.618
peak=    3.096 closest distance to " CB  ALA A 114 " =    0.710
peak=    3.086 closest distance to " OG1 THR A 279 " =    1.856
peak=    3.082 closest distance to " CB  ARG A 138 " =    0.977
peak=    3.082 closest distance to " CG2BVAL A  41 " =    0.808
peak=    3.080 closest distance to " CE  LYS A  48 " =    1.068
peak=    3.073 closest distance to " N   PHE A 130 " =    1.285
peak=    3.068 closest distance to " ND2 ASN A 249 " =    0.725
peak=    3.061 closest distance to " CB  ALA A 104 " =    0.731
peak=    3.055 closest distance to " N   ASP A 162 " =    1.179
peak=    3.047 closest distance to " O   TRP A 274 " =    1.887
peak=    3.044 closest distance to " CB  LEU A 300 " =    0.911
peak=    3.042 closest distance to " O   HOH Z  85 " =    2.109
peak=    3.038 closest distance to " O   ALA A 100 " =    1.713
peak=    3.036 closest distance to " O   HOH Z 425 " =    1.255
peak=    3.007 closest distance to " NE1 TRP A 266 " =    1.500
peak=    3.004 closest distance to " CE1 PHE A 218 " =    1.210

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.808 - 5.932
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 220
   mapped sites are within: 0.808 - 5.932

peak=   -4.751 closest distance to " O   HOH Z 266 " =    5.319
peak=   -4.730 closest distance to " CD  GLN A  58 " =    1.007
peak=   -4.487 closest distance to " CD  ARG A  14 " =    3.376
peak=   -4.438 closest distance to " CB  PRO A 243 " =    2.720
peak=   -4.311 closest distance to " CD  ARG A 156 " =    2.127
peak=   -4.296 closest distance to " C   HIS A 108 " =    1.126
peak=   -4.240 closest distance to " CG1 VAL A 112 " =    2.603
peak=   -4.236 closest distance to " O   HOH Z  10 " =    1.585
peak=   -4.216 closest distance to " O   HOH Z 231 " =    2.341
peak=   -4.201 closest distance to " OXT GLY A 302 " =    2.962
peak=   -4.191 closest distance to " CG1 VAL A 250 " =    2.689
peak=   -4.148 closest distance to " CE2 PHE A  61 " =    2.622
peak=   -4.127 closest distance to " O   VAL A  67 " =    2.665
peak=   -4.034 closest distance to " OG  SER A  97 " =    2.265
peak=   -4.023 closest distance to " O   HOH Z 196 " =    2.146
peak=   -4.012 closest distance to " OG BSER A 134 " =    1.361
peak=   -3.999 closest distance to " O   HOH Z 283 " =    2.367
peak=   -3.991 closest distance to " CD1 LEU A 101 " =    2.474
peak=   -3.961 closest distance to " CA  ASP A 298 " =    1.043
peak=   -3.953 closest distance to " CG2 ILE A  49 " =    2.773
peak=   -3.950 closest distance to " O   HOH Z 377 " =    2.040
peak=   -3.925 closest distance to " CE2 TYR A  30 " =    2.673
peak=   -3.914 closest distance to " CB  ALA A 161 " =    2.657
peak=   -3.908 closest distance to " CZ3 TRP A 179 " =    1.205
peak=   -3.881 closest distance to " O   PRO A 198 " =    1.324
peak=   -3.875 closest distance to " CA  VAL A  67 " =    2.998
peak=   -3.871 closest distance to " OD1 ASN A 148 " =    1.446
peak=   -3.868 closest distance to " O   HOH Z 198 " =    2.167
peak=   -3.859 closest distance to " O   ALA A  34 " =    2.365
peak=   -3.853 closest distance to " CG  ASP A 132 " =    2.367
peak=   -3.850 closest distance to " O   HOH Z 210 " =    1.100
peak=   -3.824 closest distance to " O   SER A 210 " =    1.924
peak=   -3.820 closest distance to " CD1 PHE A  59 " =    1.967
peak=   -3.816 closest distance to " CB  PHE A 208 " =    2.306
peak=   -3.786 closest distance to " CB  PHE A 192 " =    2.061
peak=   -3.783 closest distance to " OE1 GLN A 223 " =    1.955
peak=   -3.782 closest distance to " O   HOH Z 394 " =    1.505
peak=   -3.750 closest distance to " O   PRO A 163 " =    2.122
peak=   -3.745 closest distance to " CD2 TYR A 293 " =    1.971
peak=   -3.724 closest distance to " O   HOH Z   6 " =    2.225
peak=   -3.720 closest distance to " N   ALA A  43 " =    2.668
peak=   -3.716 closest distance to " CE3 TRP A 150 " =    2.302
peak=   -3.698 closest distance to " CD  GLN A 223 " =    1.472
peak=   -3.696 closest distance to " O   HOH Z 292 " =    4.708
peak=   -3.694 closest distance to " CD1 ILE A 151 " =    2.420
peak=   -3.689 closest distance to " NE  ARG A 156 " =    1.970
peak=   -3.685 closest distance to " O   HOH Z  13 " =    1.780
peak=   -3.670 closest distance to " CG2 ILE A 263 " =    2.345
peak=   -3.669 closest distance to " O   HOH Z 372 " =    2.395
peak=   -3.662 closest distance to " CG1 VAL A 112 " =    2.790
peak=   -3.659 closest distance to " O   HOH Z 374 " =    1.980
peak=   -3.648 closest distance to " N   THR A  52 " =    1.702
peak=   -3.641 closest distance to " ND2 ASN A  45 " =    1.895
peak=   -3.639 closest distance to " O   HOH Z 166 " =    1.802
peak=   -3.638 closest distance to " O   HOH Z 290 " =    1.201
peak=   -3.633 closest distance to " ND2 ASN A 187 " =    1.608
peak=   -3.621 closest distance to " CG  ARG A 269 " =    2.402
peak=   -3.605 closest distance to " CG  ARG A  66 " =    2.504
peak=   -3.602 closest distance to " CB  ALA A 291 " =    2.456
peak=   -3.598 closest distance to " O   PHE A 218 " =    1.518
peak=   -3.594 closest distance to " CD  ARG A 195 " =    5.085
peak=   -3.594 closest distance to " NE2 GLN A  88 " =    1.912
peak=   -3.588 closest distance to " C   SER A 206 " =    1.528
peak=   -3.587 closest distance to " O   HOH Z 264 " =    1.842
peak=   -3.578 closest distance to " O   HOH Z 111 " =    1.619
peak=   -3.573 closest distance to " CG  GLU A  53 " =    1.528
peak=   -3.571 closest distance to " CD  ARG A 139 " =    1.592
peak=   -3.570 closest distance to " CB  ASN A  39 " =    2.411
peak=   -3.569 closest distance to " ND2 ASN A  45 " =    1.229
peak=   -3.567 closest distance to " O   VAL A 189 " =    2.626
peak=   -3.563 closest distance to " O   HOH Z 177 " =    1.763
peak=   -3.548 closest distance to " CG  PRO A 243 " =    1.781
peak=   -3.540 closest distance to " CG  GLU A 277 " =    1.153
peak=   -3.538 closest distance to " O   HOH Z 185 " =    2.450
peak=   -3.528 closest distance to " O   HOH Z  71 " =    2.092
peak=   -3.525 closest distance to " ND2 ASN A 249 " =    2.463
peak=   -3.517 closest distance to " CA  GLY A 133 " =    2.361
peak=   -3.515 closest distance to " O   HOH Z 353 " =    2.265
peak=   -3.508 closest distance to " CA  GLY A 241 " =    2.358
peak=   -3.504 closest distance to " O   HOH Z  52 " =    1.616
peak=   -3.497 closest distance to " CB  PHE A  16 " =    2.542
peak=   -3.493 closest distance to " CE  MET A 105 " =    2.450
peak=   -3.489 closest distance to " CE BMET A  47 " =    1.825
peak=   -3.480 closest distance to " CB  ALA A 248 " =    2.264
peak=   -3.472 closest distance to " CG2 VAL A 189 " =    2.228
peak=   -3.471 closest distance to " CG  ARG A 219 " =    2.714
peak=   -3.465 closest distance to " O   ALA A  10 " =    1.743
peak=   -3.460 closest distance to " OD1 ASP A 171 " =    1.528
peak=   -3.460 closest distance to " NE  ARG A  66 " =    4.251
peak=   -3.457 closest distance to " O   HOH Z   6 " =    1.510
peak=   -3.456 closest distance to " N   ALA A 226 " =    2.031
peak=   -3.456 closest distance to " CD  ARG A  79 " =    1.169
peak=   -3.455 closest distance to " O   HOH Z 351 " =    1.584
peak=   -3.451 closest distance to " O   HOH Z 106 " =    1.994
peak=   -3.448 closest distance to " O   HOH Z 171 " =    2.142
peak=   -3.441 closest distance to " NH2 ARG A  79 " =    1.543
peak=   -3.436 closest distance to " CA  GLY A 241 " =    3.247
peak=   -3.433 closest distance to " CD  LYS A 289 " =    2.419
peak=   -3.431 closest distance to " O   HOH Z 211 " =    1.611
peak=   -3.415 closest distance to " O   HOH Z 407 " =    3.237
peak=   -3.399 closest distance to " OD1 ASP A 191 " =    1.578
peak=   -3.397 closest distance to " OG BSER A 134 " =    2.011
peak=   -3.392 closest distance to " O   HOH Z 393 " =    1.373
peak=   -3.386 closest distance to " CZ  PHE A 155 " =    1.240
peak=   -3.382 closest distance to " CB  ALA A 248 " =    2.212
peak=   -3.378 closest distance to " CB  TRP A  85 " =    2.509
peak=   -3.377 closest distance to " O   HOH Z 421 " =    3.688
peak=   -3.372 closest distance to " O   HOH Z 114 " =    3.212
peak=   -3.368 closest distance to " O   SER A 276 " =    1.727
peak=   -3.367 closest distance to " O   HOH Z  60 " =    2.240
peak=   -3.363 closest distance to " NE2 GLN A 103 " =    1.850
peak=   -3.362 closest distance to " CB  ALA A  43 " =    2.650
peak=   -3.356 closest distance to " CB  ALA A  10 " =    2.224
peak=   -3.345 closest distance to " N   ALA A 248 " =    1.726
peak=   -3.334 closest distance to " N   SER A 276 " =    1.482
peak=   -3.331 closest distance to " ND2BASN A 224 " =    1.811
peak=   -3.330 closest distance to " CG  GLN A  11 " =    1.777
peak=   -3.329 closest distance to " O   SER A  62 " =    2.193
peak=   -3.325 closest distance to " CA  GLY A 203 " =    2.392
peak=   -3.323 closest distance to " O   HOH Z 357 " =    2.087
peak=   -3.322 closest distance to " O   HOH Z 216 " =    1.720
peak=   -3.321 closest distance to " O   HOH Z 128 " =    2.603
peak=   -3.320 closest distance to " CZ3 TRP A 274 " =    2.456
peak=   -3.316 closest distance to " CZ  PHE A  59 " =    1.816
peak=   -3.311 closest distance to " O   HOH Z  37 " =    1.873
peak=   -3.309 closest distance to " CG1 VAL A 125 " =    2.006
peak=   -3.306 closest distance to " O   HOH Z 102 " =    1.529
peak=   -3.303 closest distance to " O   HOH Z 236 " =    1.535
peak=   -3.302 closest distance to " O   HOH Z 243 " =    2.142
peak=   -3.301 closest distance to " O   HOH Z 126 " =    1.959
peak=   -3.299 closest distance to " CG  LEU A  83 " =    2.055
peak=   -3.297 closest distance to " O   HOH Z 191 " =    5.932
peak=   -3.292 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.291 closest distance to " O   HOH Z 253 " =    4.183
peak=   -3.291 closest distance to " O   HOH Z 150 " =    1.272
peak=   -3.289 closest distance to " C   GLY A 262 " =    2.127
peak=   -3.287 closest distance to " O   HOH Z 123 " =    2.501
peak=   -3.287 closest distance to " CB  ASP A 286 " =    1.896
peak=   -3.282 closest distance to " CD  GLU A 236 " =    1.102
peak=   -3.282 closest distance to " CZ  TYR A 169 " =    1.818
peak=   -3.275 closest distance to " O   HOH Z 366 " =    1.776
peak=   -3.272 closest distance to " O   HOH Z 165 " =    1.916
peak=   -3.269 closest distance to " O   TYR A 186 " =    1.845
peak=   -3.268 closest distance to " O   HOH Z  43 " =    1.549
peak=   -3.267 closest distance to " OG1 THR A 157 " =    2.916
peak=   -3.262 closest distance to " CB  ASP A 171 " =    2.441
peak=   -3.261 closest distance to " O   HOH Z 357 " =    2.202
peak=   -3.260 closest distance to " O   HOH Z 252 " =    3.881
peak=   -3.257 closest distance to " ND2 ASN A  69 " =    1.779
peak=   -3.251 closest distance to " O   HOH Z 350 " =    2.107
peak=   -3.250 closest distance to " N   GLN A  58 " =    1.631
peak=   -3.250 closest distance to " O   HOH Z 200 " =    1.636
peak=   -3.249 closest distance to " O   GLY A  17 " =    1.179
peak=   -3.244 closest distance to " O   SER A 135 " =    1.505
peak=   -3.241 closest distance to " OG BSER A 210 " =    2.139
peak=   -3.239 closest distance to " C   LEU A 143 " =    1.140
peak=   -3.236 closest distance to " O   HOH Z 265 " =    2.399
peak=   -3.233 closest distance to " O   HOH Z  38 " =    1.522
peak=   -3.223 closest distance to " O   HOH Z 426 " =    1.654
peak=   -3.221 closest distance to " O   HOH Z 234 " =    4.334
peak=   -3.218 closest distance to " CG  MET A 105 " =    1.032
peak=   -3.218 closest distance to " CE3 TRP A  70 " =    1.837
peak=   -3.216 closest distance to " O   HOH Z 139 " =    3.018
peak=   -3.215 closest distance to " O   HOH Z 166 " =    1.716
peak=   -3.215 closest distance to " O   HOH Z 256 " =    2.421
peak=   -3.211 closest distance to " CG  ASP A 231 " =    0.808
peak=   -3.210 closest distance to " NH2AARG A 275 " =    5.336
peak=   -3.208 closest distance to " O   HOH Z 322 " =    1.496
peak=   -3.208 closest distance to " C   THR A 264 " =    1.397
peak=   -3.207 closest distance to " OE1 GLN A 183 " =    1.589
peak=   -3.207 closest distance to " OD1 ASN A  39 " =    2.237
peak=   -3.195 closest distance to " CG  HIS A  86 " =    1.123
peak=   -3.191 closest distance to " CB  ALA A 291 " =    2.239
peak=   -3.188 closest distance to " O   HOH Z  19 " =    0.882
peak=   -3.187 closest distance to " C   ALA A 158 " =    1.386
peak=   -3.185 closest distance to " O   HOH Z 298 " =    2.693
peak=   -3.184 closest distance to " O   HOH Z 285 " =    1.509
peak=   -3.182 closest distance to " CG  TRP A 266 " =    1.884
peak=   -3.181 closest distance to " O   HOH Z  19 " =    2.171
peak=   -3.177 closest distance to " O   HOH Z 389 " =    1.912
peak=   -3.174 closest distance to " SG ACYS A 201 " =    2.155
peak=   -3.174 closest distance to " O   HOH Z 396 " =    1.846
peak=   -3.172 closest distance to " OD2 ASP A 171 " =    1.832
peak=   -3.172 closest distance to " O   HOH Z 145 " =    2.770
peak=   -3.168 closest distance to " CZ  PHE A  38 " =    1.985
peak=   -3.168 closest distance to " O   GLY A 196 " =    1.094
peak=   -3.168 closest distance to " O   HOH Z 311 " =    3.770
peak=   -3.162 closest distance to " O   HOH Z 174 " =    3.832
peak=   -3.160 closest distance to " O   SER A  95 " =    1.730
peak=   -3.158 closest distance to " NH2 ARG A  66 " =    3.818
peak=   -3.154 closest distance to " CG  GLN A  58 " =    1.187
peak=   -3.150 closest distance to " O   HOH Z 323 " =    1.467
peak=   -3.149 closest distance to " O   HOH Z 193 " =    1.746
peak=   -3.148 closest distance to " O   HOH Z 275 " =    1.546
peak=   -3.146 closest distance to " O   GLU A 152 " =    1.406
peak=   -3.137 closest distance to " O   HOH Z 134 " =    2.836
peak=   -3.137 closest distance to " CD2 TYR A 247 " =    2.414
peak=   -3.133 closest distance to " CG1AVAL A  41 " =    2.684
peak=   -3.132 closest distance to " O   ALA A 292 " =    2.128
peak=   -3.127 closest distance to " CG2BVAL A  41 " =    1.970
peak=   -3.127 closest distance to " O   HOH Z 351 " =    1.524
peak=   -3.126 closest distance to " N   TYR A  68 " =    3.099
peak=   -3.123 closest distance to " CD  PRO A 243 " =    2.138
peak=   -3.122 closest distance to " CD2 LEU A 237 " =    2.795
peak=   -3.117 closest distance to " O   TRP A  92 " =    1.913
peak=   -3.116 closest distance to " CD  PRO A 213 " =    2.153
peak=   -3.107 closest distance to " O   LEU A 101 " =    2.000
peak=   -3.106 closest distance to " N   MET A 105 " =    2.531
peak=   -3.103 closest distance to " OD1 ASN A 301 " =    2.022
peak=   -3.102 closest distance to " O   GLY A  80 " =    2.627
peak=   -3.099 closest distance to " CG  PHE A 283 " =    2.600
peak=   -3.092 closest distance to " O   HOH Z  78 " =    1.885
peak=   -3.088 closest distance to " CA  GLY A 241 " =    2.877
peak=   -3.080 closest distance to " O   GLN A 240 " =    2.550
peak=   -3.069 closest distance to " O   HOH Z 251 " =    1.654
peak=   -3.063 closest distance to " CD2 PHE A  61 " =    2.173
peak=   -3.056 closest distance to " OG  SER A  63 " =    1.275
peak=   -3.044 closest distance to " O   GLY A  98 " =    2.226
peak=   -3.031 closest distance to " O   HOH Z 377 " =    1.595
peak=   -3.018 closest distance to " O   HOH Z 353 " =    2.197

================= 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    :  0.3906 0.3794   6.180599e+00   6.152318e+00
   1_bss:  0.3783 0.3680   6.163754e+00   6.131797e+00
   1_xyz:  0.2290 0.2516   5.732923e+00   5.818952e+00
   1_adp:  0.2084 0.2580   5.678101e+00   5.839663e+00
   1_occ:  0.2082 0.2587   5.678061e+00   5.840556e+00
   2_bss:  0.2055 0.2558   5.669685e+00   5.831959e+00
   2_xyz:  0.1520 0.1900   5.388125e+00   5.575808e+00
   2_adp:  0.1426 0.1804   5.334460e+00   5.525486e+00
   2_occ:  0.1425 0.1803   5.333832e+00   5.525211e+00
   3_bss:  0.1424 0.1799   5.332132e+00   5.522967e+00
   3_xyz:  0.1231 0.1652   5.219168e+00   5.435456e+00
   3_adp:  0.1204 0.1631   5.200965e+00   5.420945e+00
   3_occ:  0.1204 0.1630   5.200908e+00   5.421000e+00
   4_bss:  0.1203 0.1630   5.200390e+00   5.420832e+00
   4_xyz:  0.1162 0.1610   5.177574e+00   5.409367e+00
   4_adp:  0.1147 0.1627   5.175303e+00   5.416451e+00
   4_occ:  0.1147 0.1628   5.175548e+00   5.416983e+00
   5_bss:  0.1146 0.1619   5.173368e+00   5.413384e+00
   5_xyz:  0.1128 0.1629   5.168477e+00   5.417081e+00
   5_adp:  0.1128 0.1623   5.165893e+00   5.414460e+00
   5_occ:  0.1127 0.1624   5.166067e+00   5.414849e+00
   5_bss:  0.1126 0.1622   5.166175e+00   5.414970e+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:  0.299  51.054  -3.641   2.711   1.883   0.000   0.000   0.000
   1_xyz:  0.299  51.054  -3.641   2.711   1.883   0.000   0.000   0.000
   1_adp:  0.299  51.054  -3.641   2.711   1.883   0.000   0.000   0.000
   1_occ:  0.299  51.054  -3.641   2.711   1.883   0.000   0.000   0.000
   2_bss:  0.334  78.513  -2.800   0.002   0.055   0.000   0.000   0.000
   2_xyz:  0.334  78.513  -2.800   0.002   0.055   0.000   0.000   0.000
   2_adp:  0.334  78.513  -2.800   0.002   0.055   0.000   0.000   0.000
   2_occ:  0.334  78.513  -2.800   0.002   0.055   0.000   0.000   0.000
   3_bss:  0.334  73.378  -2.460  -0.898  -0.194  -0.000  -0.000  -0.000
   3_xyz:  0.334  73.378  -2.460  -0.898  -0.194  -0.000  -0.000  -0.000
   3_adp:  0.334  73.378  -2.460  -0.898  -0.194  -0.000  -0.000  -0.000
   3_occ:  0.334  73.378  -2.460  -0.898  -0.194  -0.000  -0.000  -0.000
   4_bss:  0.327  66.464  -2.219  -1.161  -0.219  -0.000  -0.000  -0.000
   4_xyz:  0.327  66.464  -2.219  -1.161  -0.219  -0.000  -0.000  -0.000
   4_adp:  0.327  66.464  -2.219  -1.161  -0.219  -0.000  -0.000  -0.000
   4_occ:  0.327  66.464  -2.219  -1.161  -0.219  -0.000  -0.000  -0.000
   5_bss:  0.323  66.146  -1.916  -1.053  -0.022  -0.000  -0.000  -0.000
   5_xyz:  0.323  66.146  -1.916  -1.053  -0.022  -0.000  -0.000  -0.000
   5_adp:  0.323  66.146  -1.916  -1.053  -0.022  -0.000  -0.000  -0.000
   5_occ:  0.323  66.146  -1.916  -1.053  -0.022  -0.000  -0.000  -0.000
   5_bss:  0.320  63.851  -1.594  -0.805   0.249  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.577 0.6133  0.7683    43039.197
   1_bss:  41.532 0.6241  0.7924    39962.911
   1_xyz:  25.708 0.8046  0.9689    16848.991
   1_adp:  26.440 0.7962  0.9523    17677.068
   1_occ:  26.487 0.7957  0.9514    17716.884
   2_bss:  25.947 0.8017  0.9207    17288.226
   2_xyz:  18.497 0.8753  0.9714     9431.126
   2_adp:  17.093 0.8888  0.9683     8466.817
   2_occ:  17.081 0.8889  0.9683     8459.748
   3_bss:  17.007 0.8896  0.9604     8411.943
   3_xyz:  15.160 0.9053  0.9690     7015.315
   3_adp:  14.782 0.9088  0.9625     6855.449
   3_occ:  14.785 0.9087  0.9623     6855.724
   4_bss:  14.777 0.9088  0.9623     6853.308
   4_xyz:  14.435 0.9118  0.9643     6651.179
   4_adp:  14.530 0.9112  0.9554     6730.340
   4_occ:  14.537 0.9111  0.9552     6735.303
   5_bss:  14.475 0.9116  0.9621     6654.038
   5_xyz:  14.553 0.9109  0.9617     6714.163
   5_adp:  14.503 0.9113  0.9525     6673.738
   5_occ:  14.509 0.9112  0.9524     6677.157
   5_bss:  14.512 0.9112  0.9619     6677.893
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6365e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6365e-01
   1_xyz:   1.348  0.011  0.081 15.386  0.005  4.115   9.3236e-02
   1_adp:   1.348  0.011  0.081 15.386  0.005  4.115   9.3236e-02
   1_occ:   1.348  0.011  0.081 15.386  0.005  4.115   9.3236e-02
   2_bss:   1.348  0.011  0.081 15.386  0.005  4.115   9.3236e-02
   2_xyz:   1.035  0.007  0.074 14.600  0.004  4.131   6.1448e-02
   2_adp:   1.035  0.007  0.074 14.600  0.004  4.131   6.1448e-02
   2_occ:   1.035  0.007  0.074 14.600  0.004  4.131   6.1448e-02
   3_bss:   1.035  0.007  0.074 14.600  0.004  4.131   6.1448e-02
   3_xyz:   1.043  0.009  0.079 14.472  0.004  4.115   6.3989e-02
   3_adp:   1.043  0.009  0.079 14.472  0.004  4.115   6.3989e-02
   3_occ:   1.043  0.009  0.079 14.472  0.004  4.115   6.3989e-02
   4_bss:   1.043  0.009  0.079 14.472  0.004  4.115   6.3989e-02
   4_xyz:   1.035  0.009  0.079 14.355  0.004  4.120   6.3425e-02
   4_adp:   1.035  0.009  0.079 14.355  0.004  4.120   6.3425e-02
   4_occ:   1.035  0.009  0.079 14.355  0.004  4.120   6.3425e-02
   5_bss:   1.035  0.009  0.079 14.355  0.004  4.120   6.3425e-02
   5_xyz:   1.049  0.009  0.080 14.353  0.004  4.122   6.4911e-02
   5_adp:   1.049  0.009  0.080 14.353  0.004  4.122   6.4911e-02
   5_occ:   1.049  0.009  0.080 14.353  0.004  4.122   6.4911e-02
   5_bss:   1.049  0.009  0.080 14.353  0.004  4.122   6.4911e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4363e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4363e-01
   1_xyz:   8.240  0.080  0.290 85.121  0.039  2.127   7.2692e-02
   1_adp:   8.240  0.080  0.290 85.121  0.039  2.127   7.2692e-02
   1_occ:   8.240  0.080  0.290 85.121  0.039  2.127   7.2692e-02
   2_bss:   8.240  0.080  0.290 85.121  0.039  2.127   7.2692e-02
   2_xyz:   7.354  0.045  0.228 81.587  0.051  2.321   5.6012e-02
   2_adp:   7.354  0.045  0.228 81.587  0.051  2.321   5.6012e-02
   2_occ:   7.354  0.045  0.228 81.587  0.051  2.321   5.6012e-02
   3_bss:   7.354  0.045  0.228 81.587  0.051  2.321   5.6012e-02
   3_xyz:   7.722  0.048  0.245 83.532  0.036  2.344   4.4188e-02
   3_adp:   7.722  0.048  0.245 83.532  0.036  2.344   4.4188e-02
   3_occ:   7.722  0.048  0.245 83.532  0.036  2.344   4.4188e-02
   4_bss:   7.722  0.048  0.245 83.532  0.036  2.344   4.4188e-02
   4_xyz:   7.931  0.043  0.267 81.397  0.031  2.380   4.3895e-02
   4_adp:   7.931  0.043  0.267 81.397  0.031  2.380   4.3895e-02
   4_occ:   7.931  0.043  0.267 81.397  0.031  2.380   4.3895e-02
   5_bss:   7.931  0.043  0.267 81.397  0.031  2.380   4.3895e-02
   5_xyz:   7.730  0.047  0.267 82.137  0.033  2.355   4.3886e-02
   5_adp:   7.730  0.047  0.267 82.137  0.033  2.355   4.3886e-02
   5_occ:   7.730  0.047  0.267 82.137  0.033  2.355   4.3886e-02
   5_bss:   7.730  0.047  0.267 82.137  0.033  2.355   4.3886e-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:  86.30   0.00  17.33  78.10   0.00  13.08  86.30   5.41  40.46
   1_occ:  86.30   0.00  17.33  78.10   0.00  13.08  86.30   5.41  40.46
   2_bss:  86.30   0.00  17.33  78.10   0.00  13.08  86.30   5.41  40.46
   2_xyz:  86.30   0.00  17.33  78.10   0.00  13.08  86.30   5.41  40.46
   2_adp:  85.20   0.00  16.96  80.47   0.00  12.67  85.20   5.55  40.30
   2_occ:  85.20   0.00  16.96  80.47   0.00  12.67  85.20   5.55  40.30
   3_bss:  85.20   0.00  16.96  80.47   0.00  12.67  85.20   5.55  40.30
   3_xyz:  85.20   0.00  16.96  80.47   0.00  12.67  85.20   5.55  40.30
   3_adp:  84.11   0.40  16.68  83.15   0.40  12.39  84.11   1.77  40.07
   3_occ:  84.11   0.40  16.68  83.15   0.40  12.39  84.11   1.77  40.07
   4_bss:  84.11   0.40  16.68  83.15   0.40  12.39  84.11   1.77  40.07
   4_xyz:  84.11   0.40  16.68  83.15   0.40  12.39  84.11   1.77  40.07
   4_adp:  93.86   0.00  16.77  93.86   0.00  12.31  84.56   0.71  41.09
   4_occ:  93.86   0.00  16.77  93.86   0.00  12.31  84.56   0.71  41.09
   5_bss:  93.86   0.00  16.77  93.86   0.00  12.31  84.56   0.71  41.09
   5_xyz:  93.86   0.00  16.77  93.86   0.00  12.31  84.56   0.71  41.09
   5_adp:  95.36   0.00  16.50  95.36   0.00  12.04  86.23   2.67  40.80
   5_occ:  95.36   0.00  16.50  95.36   0.00  12.04  86.23   2.67  40.80
   5_bss:  95.36   0.00  16.51  95.36   0.00  12.05  86.23   2.68  40.80
------------------------------------------------------------------------
 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:    1.266    0.027    0.408
   1_adp:    1.266    0.027    0.408
   1_occ:    1.266    0.027    0.408
   2_bss:    1.266    0.027    0.408
   2_xyz:    1.003    0.053    0.476
   2_adp:    1.003    0.053    0.476
   2_occ:    1.003    0.053    0.476
   3_bss:    1.003    0.053    0.476
   3_xyz:    1.043    0.041    0.536
   3_adp:    1.043    0.041    0.536
   3_occ:    1.043    0.041    0.536
   4_bss:    1.043    0.041    0.536
   4_xyz:    1.175    0.090    0.559
   4_adp:    1.175    0.090    0.559
   4_occ:    1.175    0.090    0.559
   5_bss:    1.175    0.090    0.559
   5_xyz:    1.200    0.058    0.571
   5_adp:    1.200    0.058    0.571
   5_occ:    1.200    0.058    0.571
   5_bss:    1.200    0.058    0.571
------------------------------------------------------------------------

CPU time actual refinement: 326.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_701/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_701/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_701/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_701/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_701/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.99 
  Macro-tasks:
    bulk solvent and scale       = 44.02  
    individual site refinement   = 132.62 
    weights calculation          = 29.06  
    collect and process          = 6.71   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 212.52 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 99.99  
    alpha_beta                      = 8.22   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 109.64 
    fmodel                         = 7.19   
    r_factors                      = 0.27   
    phase_errors                   = 11.21  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 239.74 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.614 micro seconds
Total CPU time: 5.66 minutes
from_scatterers_fft:    635 calls, 99.61 s
gradients_fft:          580 calls, 96.26 s

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

# Date 2008-01-16 Time 05:27:46 PST -0800 (1200490066.18 s)
Start R-work = 0.3906, R-free = 0.3794 (no bulk solvent and anisotropic scale)
Final R-work = 0.1311, R-free = 0.1771 (no bulk solvent and anisotropic scale)

Start R-work = 0.3783, R-free = 0.3680
Final R-work = 0.1126, R-free = 0.1622