# Date 2008-01-16 Time 05:17:51 PST -0800 (1200489471.88 s)
#phil __OFF__

Command line arguments: "../673.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13389
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 673

-------------------------------------------------------------------------------
  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, 47.1647, 85.0941, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97123
Completeness in resolution range: 0.955002
Completeness with d_max=infinity: 0.952031

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9712

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, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97123
Completeness in resolution range: 0.955002
Completeness with d_max=infinity: 0.952031

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.2180 [2151/2179]  1939   212   9.9%
  bin  2:  4.2180 -  3.3605 [2065/2084]  1855   210  10.2%
  bin  3:  3.3605 -  2.9394 [2047/2067]  1843   204  10.0%
  bin  4:  2.9394 -  2.6723 [2034/2059]  1836   198   9.7%
  bin  5:  2.6723 -  2.4817 [2012/2031]  1807   205  10.2%
  bin  6:  2.4817 -  2.3360 [1999/2045]  1799   200  10.0%
  bin  7:  2.3360 -  2.2194 [1976/2009]  1776   200  10.1%
  bin  8:  2.2194 -  2.1230 [1988/2024]  1789   199  10.0%
  bin  9:  2.1230 -  2.0415 [1992/2021]  1797   195   9.8%
  bin 10:  2.0415 -  1.9712 [1325/1993]  1189   136  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_673/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2202
        3.04 -     3.66: 4712
        3.66 -     4.28: 9031
        4.28 -     4.90: 12459
  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 100 " - " O   HOH Z 352 "  1.917 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.981 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  2.119 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.148 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28425 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_673/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_673/model_refine_001.geo

CPU time processing inputs: 9.55


============================ 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 47.16465 85.09415 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: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2985   r_free= 0.2949   ksol= 0.00   Bsol= 0.00   scale= 0.985    |
|                                                                             |
| 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:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.979428                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7045 0.99   1393  154 0.2730 0.2745      6.3254      6.2885|
|  2:  4.7045 -  3.7536 0.99   1360  148 0.2303 0.2171      6.3468      6.3264|
|  3:  3.7536 -  3.2849 0.99   1309  153 0.2520 0.2486      6.2376      6.3543|
|  4:  3.2849 -  2.9872 0.99   1326  143 0.2659 0.2729      6.1266      6.1088|
|  5:  2.9872 -  2.7745 0.99   1303  145 0.2891 0.2490      6.0079      5.9647|
|  6:  2.7745 -  2.6119 0.98   1284  143 0.3142 0.3073       5.966      5.9081|
|  7:  2.6119 -  2.4817 0.99   1305  143 0.3117 0.2691      5.9605       5.841|
|  8:  2.4817 -  2.3741 0.98   1272  146 0.3235 0.3407      5.8997      5.9558|
|  9:  2.3741 -  2.2830 0.98   1299  143 0.3331 0.3300      5.8806      5.8836|
| 10:  2.2830 -  2.2045 0.98   1272  136 0.3417 0.3878      5.8534      5.9717|
| 11:  2.2045 -  2.1358 0.99   1271  146 0.3438 0.3663      5.8041      5.9277|
| 12:  2.1358 -  2.0749 0.98   1271  138 0.3461 0.3545      5.7497      5.7975|
| 13:  2.0749 -  2.0204 0.97   1267  141 0.3487 0.3355      5.6615       5.614|
| 14:  2.0204 -  1.9712 0.55    698   80 0.3986 0.3744      5.6901      5.6094|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7045  1393   154  0.80  25.50   0.87     0.80      40943.62|
|  2:  4.7045 -  3.7536  1360   148  0.85  21.04   0.99     0.92      40508.44|
|  3:  3.7536 -  3.2849  1309   153  0.83  23.62   1.00     0.98      37157.16|
|  4:  3.2849 -  2.9872  1326   143  0.81  25.51   1.02     0.98      31408.30|
|  5:  2.9872 -  2.7745  1303   145  0.77  29.02   1.00     0.96      25875.02|
|  6:  2.7745 -  2.6119  1284   143  0.76  30.11   1.01     0.96      22735.47|
|  7:  2.6119 -  2.4817  1305   143  0.77  29.33   1.01     0.96      21079.47|
|  8:  2.4817 -  2.3741  1272   146  0.74  32.52   1.02     0.95      21241.16|
|  9:  2.3741 -  2.2830  1299   143  0.72  34.02   1.05     0.92      20618.21|
| 10:  2.2830 -  2.2045  1272   136  0.68  37.11   1.06     0.91      21796.40|
| 11:  2.2045 -  2.1358  1271   146  0.68  37.23   1.07     0.92      20374.45|
| 12:  2.1358 -  2.0749  1271   138  0.68  37.35   1.07     0.96      19615.85|
| 13:  2.0749 -  2.0204  1267   141  0.67  38.51   1.06     0.93      16686.15|
| 14:  2.0204 -  1.9712   698    80  0.66  39.42   1.03     0.86      14959.91|
|alpha:            min =        0.80 max =            0.98 mean =         0.93|
|beta:             min =    14959.91 max =        40943.62 mean =     25908.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           90.00 mean =        31.05|
|phase err.(test): min =        0.00 max =           89.69 mean =        30.83|
|-----------------------------------------------------------------------------|

============================== 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 = 4.243419              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.459   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.624117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.969   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      196 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2006 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1876 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2836 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4657 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4374 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5718 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6741 |
|-----------------------------------------------------------------------------|
|-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 |   4.112    4.900  1.806 |       0.204 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    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: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2985   r_free= 0.2949   ksol= 0.00   Bsol= 0.00   scale= 0.985    |
|                                                                             |
| 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:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.979428                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2824   r_free= 0.2762   ksol= 0.32   Bsol= 37.16   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,-1.73,1.22,-0.00,0.00,0.00); trace/3= -1.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.954585                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.642387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.899   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2824      final r-factor (work) = 0.1614          |
| start r-factor (free) = 0.2762      final r-factor (free) = 0.1824          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0301 = 3.64 * 0.50 * 5.9667 + 1.00 * 0.1636                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3560 = 3.64 * 0.50 * 5.6522 + 1.00 * 0.0623                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1614      final r-factor (work) = 0.1471          |
| start r-factor (free) = 0.1824      final r-factor (free) = 0.1880          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7646 = 0.31 * 1.00 * 5.6522 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6724 = 0.31 * 1.00 * 5.3497 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    72.85   16.98    None  None   None       |
|    all(noH): 2823   0      1.36    72.85   16.98    None  None   None       |
|    Sol.    : 438    0      7.68    68.06   38.33    None  None   None       |
|    Mac.    : 2385   0      1.36    72.85   13.06    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:     1.357 -   8.507:  602   |   5:    37.104 -  44.254:  119        |
|      1:     8.507 -  15.656: 1281   |   6:    44.254 -  51.403:  105        |
|      2:    15.656 -  22.806:  384   |   7:    51.403 -  58.552:   60        |
|      3:    22.806 -  29.955:  132   |   8:    58.552 -  65.702:   23        |
|      4:    29.955 -  37.104:  113   |   9:    65.702 -  72.851:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1471 r_free = 0.1880             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1468 r_free = 0.1884             target_work(ml) = 5.360         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1884   ksol= 0.32   Bsol= 37.16   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,-1.73,1.22,-0.00,0.00,0.00); trace/3= -1.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.359892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1449   r_free= 0.1856   ksol= 0.31   Bsol= 42.67   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.35,-1.21,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.349042                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.354029              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.277  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161231              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.192  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1449      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1856      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3676 = 2.35 * 0.50 * 5.3570 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2457 = 2.35 * 0.50 * 5.2588 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8559 = 0.16 * 1.00 * 5.2588 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8390 = 0.16 * 1.00 * 5.1610 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.33    74.08   16.69    None  None   None       |
|    all(noH): 2823   0      2.33    74.08   16.69    None  None   None       |
|    Sol.    : 438    0      5.49    66.35   37.30    None  None   None       |
|    Mac.    : 2385   0      2.33    74.08   12.90    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:     2.329 -   9.504:  846   |   5:    38.205 -  45.381:  115        |
|      1:     9.504 -  16.680: 1154   |   6:    45.381 -  52.556:   88        |
|      2:    16.680 -  23.855:  313   |   7:    52.556 -  59.731:   48        |
|      3:    23.855 -  31.030:  122   |   8:    59.731 -  66.907:   16        |
|      4:    31.030 -  38.205:  117   |   9:    66.907 -  74.082:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1544             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1541             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1541   ksol= 0.31   Bsol= 42.67   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.35,-1.21,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148444                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1535   ksol= 0.32   Bsol= 42.67   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.25,-1.58,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147929                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.875135              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.765  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382362              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.931  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1519          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8944 = 1.88 * 0.50 * 5.1606 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8654 = 1.88 * 0.50 * 5.1294 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1519      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9682 = 0.38 * 1.00 * 5.1294 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9643 = 0.38 * 1.00 * 5.1166 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    79.70   16.79    None  None   None       |
|    all(noH): 2823   0      1.43    79.70   16.79    None  None   None       |
|    Sol.    : 438    0      5.67    67.52   38.20    None  None   None       |
|    Mac.    : 2385   0      1.43    79.70   12.86    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:     1.434 -   9.261:  817   |   5:    40.565 -  48.391:  126        |
|      1:     9.261 -  17.087: 1214   |   6:    48.391 -  56.217:   83        |
|      2:    17.087 -  24.913:  294   |   7:    56.217 -  64.044:   38        |
|      3:    24.913 -  32.739:  134   |   8:    64.044 -  71.870:   11        |
|      4:    32.739 -  40.565:  101   |   9:    71.870 -  79.696:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1528             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1529             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1529   ksol= 0.32   Bsol= 42.67   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.25,-1.58,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121598                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1528   ksol= 0.32   Bsol= 43.59   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.12,-1.59,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121301                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.792132              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.587  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.510  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6411 = 1.79 * 0.50 * 5.1167 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6408 = 1.79 * 0.50 * 5.1183 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6027 = 0.51 * 1.00 * 5.1183 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6031 = 0.51 * 1.00 * 5.1183 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    80.45   16.69    None  None   None       |
|    all(noH): 2823   0      0.96    80.45   16.69    None  None   None       |
|    Sol.    : 438    0      5.90    67.83   38.26    None  None   None       |
|    Mac.    : 2385   0      0.96    80.45   12.73    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:     0.964 -   8.913:  773   |   5:    40.706 -  48.655:  122        |
|      1:     8.913 -  16.861: 1248   |   6:    48.655 -  56.603:   82        |
|      2:    16.861 -  24.809:  308   |   7:    56.603 -  64.551:   38        |
|      3:    24.809 -  32.758:  128   |   8:    64.551 -  72.500:   10        |
|      4:    32.758 -  40.706:  109   |   9:    72.500 -  80.448:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1077 r_free = 0.1542             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1076 r_free = 0.1542             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1542   ksol= 0.32   Bsol= 43.59   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.12,-1.59,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122267                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1543   ksol= 0.32   Bsol= 43.59   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.94,-1.44,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122332                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.464850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.603  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.953634              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.016  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1076      final r-factor (work) = 0.1038          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9229 = 3.46 * 0.50 * 5.1191 + 1.00 * 0.0545                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9196 = 3.46 * 0.50 * 5.1064 + 1.00 * 0.0731                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1038      final r-factor (work) = 0.1034          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9844 = 1.95 * 1.00 * 5.1064 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9771 = 1.95 * 1.00 * 5.1021 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    91.77   16.81    None  None   None       |
|    all(noH): 2823   0      0.37    91.77   16.81    None  None   None       |
|    Sol.    : 438    0      5.96    78.23   39.37    None  None   None       |
|    Mac.    : 2385   0      0.37    91.77   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:     0.371 -   9.511:  980   |   5:    46.069 -  55.209:  103        |
|      1:     9.511 -  18.650: 1153   |   6:    55.209 -  64.349:   64        |
|      2:    18.650 -  27.790:  240   |   7:    64.349 -  73.489:   19        |
|      3:    27.790 -  36.930:  138   |   8:    73.489 -  82.628:    4        |
|      4:    36.930 -  46.069:  117   |   9:    82.628 -  91.768:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1034 r_free = 0.1560             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1034 r_free = 0.1561             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1034   r_free= 0.1561   ksol= 0.32   Bsol= 43.59   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.94,-1.44,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106204                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7045 0.99   1393  154 0.0941 0.1253      5.3483      5.5103|
|  2:  4.7045 -  3.7536 0.99   1360  148 0.0784 0.1091      5.3782      5.5916|
|  3:  3.7536 -  3.2849 0.99   1309  153 0.0984 0.1491      5.4211      5.8435|
|  4:  3.2849 -  2.9872 0.99   1326  143 0.1132 0.1564      5.4175      5.5851|
|  5:  2.9872 -  2.7745 0.99   1303  145 0.1191 0.1713       5.274      5.5106|
|  6:  2.7745 -  2.6119 0.98   1284  143 0.1146 0.1815      5.1757      5.4185|
|  7:  2.6119 -  2.4817 0.99   1305  143 0.1124 0.1641      5.1073      5.3527|
|  8:  2.4817 -  2.3741 0.98   1272  146 0.1056 0.1712      5.0225       5.304|
|  9:  2.3741 -  2.2830 0.98   1299  143 0.1091 0.1761      4.9914      5.3072|
| 10:  2.2830 -  2.2045 0.98   1272  136 0.1028 0.1810      4.9298      5.2238|
| 11:  2.2045 -  2.1358 0.99   1271  146 0.1055 0.1721      4.9082      5.2571|
| 12:  2.1358 -  2.0749 0.98   1271  138 0.1010 0.1619       4.836      5.1058|
| 13:  2.0749 -  2.0204 0.97   1267  141 0.1048 0.1765      4.7591      5.0694|
| 14:  2.0204 -  1.9712 0.55    698   80 0.0987 0.1651      4.6385      4.8947|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7045  1393   154  0.94   8.90   0.98     0.95       6790.53|
|  2:  4.7045 -  3.7536  1360   148  0.95   7.62   1.02     1.00       8435.02|
|  3:  3.7536 -  3.2849  1309   153  0.94  10.93   1.03     1.03       9736.83|
|  4:  3.2849 -  2.9872  1326   143  0.92  13.60   1.01     0.99      10170.19|
|  5:  2.9872 -  2.7745  1303   145  0.90  15.64   0.99     0.97       7942.75|
|  6:  2.7745 -  2.6119  1284   143  0.90  15.79   0.98     0.96       6897.38|
|  7:  2.6119 -  2.4817  1305   143  0.91  14.57   0.99     0.95       5724.38|
|  8:  2.4817 -  2.3741  1272   146  0.91  15.06   0.99     0.97       5214.66|
|  9:  2.3741 -  2.2830  1299   143  0.91  14.88   1.00     0.96       4725.42|
| 10:  2.2830 -  2.2045  1272   136  0.90  15.52   0.99     0.96       4369.31|
| 11:  2.2045 -  2.1358  1271   146  0.90  16.33   1.00     0.97       4334.75|
| 12:  2.1358 -  2.0749  1271   138  0.92  14.59   0.99     0.97       3790.59|
| 13:  2.0749 -  2.0204  1267   141  0.90  15.93   1.00     0.99       3316.86|
| 14:  2.0204 -  1.9712   698    80  0.91  14.89   0.98     0.94       2508.53|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2508.53 max =        10170.19 mean =      6151.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1032   r_free= 0.1560   ksol= 0.32   Bsol= 46.26   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.70,-1.22,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106039                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1032   r_free= 0.1560   ksol= 0.32   Bsol= 46.26   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.70,-1.22,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106039                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7045 0.99   1393  154 0.0943 0.1257      5.3498      5.5125|
|  2:  4.7045 -  3.7536 0.99   1360  148 0.0787 0.1092      5.3804      5.5928|
|  3:  3.7536 -  3.2849 0.99   1309  153 0.0985 0.1491       5.422      5.8435|
|  4:  3.2849 -  2.9872 0.99   1326  143 0.1131 0.1563      5.4168      5.5845|
|  5:  2.9872 -  2.7745 0.99   1303  145 0.1189 0.1711      5.2726      5.5091|
|  6:  2.7745 -  2.6119 0.98   1284  143 0.1144 0.1814      5.1746      5.4176|
|  7:  2.6119 -  2.4817 0.99   1305  143 0.1124 0.1638      5.1066      5.3519|
|  8:  2.4817 -  2.3741 0.98   1272  146 0.1056 0.1709      5.0219      5.3026|
|  9:  2.3741 -  2.2830 0.98   1299  143 0.1091 0.1764      4.9911      5.3081|
| 10:  2.2830 -  2.2045 0.98   1272  136 0.1027 0.1809      4.9295      5.2224|
| 11:  2.2045 -  2.1358 0.99   1271  146 0.1054 0.1720      4.9078      5.2568|
| 12:  2.1358 -  2.0749 0.98   1271  138 0.1010 0.1617      4.8354      5.1051|
| 13:  2.0749 -  2.0204 0.97   1267  141 0.1048 0.1764      4.7584      5.0684|
| 14:  2.0204 -  1.9712 0.55    698   80 0.0987 0.1649       4.638      4.8945|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7045  1393   154  0.94   8.93   0.98     0.95       6815.00|
|  2:  4.7045 -  3.7536  1360   148  0.95   7.64   1.02     1.01       8459.67|
|  3:  3.7536 -  3.2849  1309   153  0.94  10.95   1.03     1.03       9751.21|
|  4:  3.2849 -  2.9872  1326   143  0.92  13.59   1.01     0.99      10155.28|
|  5:  2.9872 -  2.7745  1303   145  0.90  15.62   1.00     0.97       7927.51|
|  6:  2.7745 -  2.6119  1284   143  0.90  15.78   0.99     0.96       6880.12|
|  7:  2.6119 -  2.4817  1305   143  0.91  14.56   1.00     0.96       5712.01|
|  8:  2.4817 -  2.3741  1272   146  0.91  15.05   1.00     0.98       5205.82|
|  9:  2.3741 -  2.2830  1299   143  0.91  14.88   1.01     0.97       4721.07|
| 10:  2.2830 -  2.2045  1272   136  0.90  15.52   1.00     0.97       4366.14|
| 11:  2.2045 -  2.1358  1271   146  0.90  16.32   1.01     0.98       4328.83|
| 12:  2.1358 -  2.0749  1271   138  0.92  14.58   1.01     0.98       3783.97|
| 13:  2.0749 -  2.0204  1267   141  0.90  15.92   1.01     1.01       3311.20|
| 14:  2.0204 -  1.9712   698    80  0.91  14.88   0.99     0.95       2505.50|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2505.50 max =        10155.28 mean =      6149.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.77|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    91.76   16.80    None  None   None       |
|    all(noH): 2823   0      0.36    91.76   16.80    None  None   None       |
|    Sol.    : 438    0      5.95    78.22   39.36    None  None   None       |
|    Mac.    : 2385   0      0.36    91.76   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.360 -   9.500:  980   |   5:    46.058 -  55.198:  103        |
|      1:     9.500 -  18.639: 1153   |   6:    55.198 -  64.338:   64        |
|      2:    18.639 -  27.779:  240   |   7:    64.338 -  73.478:   19        |
|      3:    27.779 -  36.919:  138   |   8:    73.478 -  82.617:    4        |
|      4:    36.919 -  46.058:  117   |   9:    82.617 -  91.757:    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)= 272         
Filter by distance & map next to the model:
   mapped sites are within: 0.492 - 4.577
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 272
   mapped sites are within: 0.753 - 4.577

peak=    5.961 closest distance to " NH2 ARG A  56 " =    2.256
peak=    5.291 closest distance to " O   HOH Z 126 " =    1.818
peak=    5.277 closest distance to " CB  SER A  63 " =    1.156
peak=    5.196 closest distance to " CB  GLN A 223 " =    1.495
peak=    5.142 closest distance to " CG  PRO A  54 " =    1.132
peak=    5.038 closest distance to " O   HOH Z 232 " =    2.301
peak=    5.024 closest distance to " O   HOH Z 142 " =    1.655
peak=    4.980 closest distance to " NE2 GLN A  11 " =    1.060
peak=    4.897 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.810 closest distance to " CB  GLN A 183 " =    1.277
peak=    4.707 closest distance to " C   PRO A 198 " =    1.480
peak=    4.650 closest distance to " O   HOH Z 298 " =    1.884
peak=    4.552 closest distance to " OD1 ASN A  69 " =    2.584
peak=    4.546 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.510 closest distance to " O   HOH Z 236 " =    1.993
peak=    4.509 closest distance to " O   HOH Z 193 " =    1.807
peak=    4.505 closest distance to " CA  TYR A  30 " =    0.922
peak=    4.479 closest distance to " CB  GLU A 152 " =    1.182
peak=    4.428 closest distance to " O   HOH Z 427 " =    2.888
peak=    4.345 closest distance to " O   HOH Z 144 " =    2.202
peak=    4.324 closest distance to " CB  TYR A 169 " =    0.828
peak=    4.314 closest distance to " O   HOH Z 234 " =    3.713
peak=    4.303 closest distance to " O   HOH Z 203 " =    1.822
peak=    4.256 closest distance to " CB  PRO A  54 " =    0.844
peak=    4.222 closest distance to " CG  PRO A 213 " =    1.156
peak=    4.211 closest distance to " O   HOH Z 272 " =    1.808
peak=    4.204 closest distance to " O   HOH Z 316 " =    3.010
peak=    4.191 closest distance to " CB  ASN A 148 " =    1.479
peak=    4.191 closest distance to " CB  ARG A  79 " =    1.464
peak=    4.184 closest distance to " O   HOH Z 403 " =    1.693
peak=    4.165 closest distance to " O   HOH Z  40 " =    1.758
peak=    4.161 closest distance to " CB  GLU A 128 " =    1.116
peak=    4.160 closest distance to " O   HOH Z  15 " =    2.134
peak=    4.143 closest distance to " O   HOH Z 368 " =    2.029
peak=    4.099 closest distance to " CA  ALA A  21 " =    1.206
peak=    4.091 closest distance to " OD2 ASP A 286 " =    2.810
peak=    4.090 closest distance to " O   HOH Z 303 " =    2.017
peak=    4.069 closest distance to " NZ  LYS A 117 " =    3.263
peak=    4.064 closest distance to " CB  LEU A 228 " =    1.099
peak=    4.057 closest distance to " O   HOH Z  54 " =    1.723
peak=    4.036 closest distance to " CB  SER A   3 " =    1.293
peak=    4.035 closest distance to " ND2 ASN A 187 " =    1.396
peak=    4.026 closest distance to " O   HOH Z 369 " =    2.064
peak=    4.025 closest distance to " O   HOH Z 346 " =    1.702
peak=    4.012 closest distance to " O   HOH Z  44 " =    1.863
peak=    3.986 closest distance to " O   MET A 105 " =    1.849
peak=    3.976 closest distance to " O   HOH Z 389 " =    1.886
peak=    3.957 closest distance to " O   HOH Z 132 " =    2.538
peak=    3.947 closest distance to " CB  GLU A 277 " =    3.540
peak=    3.942 closest distance to " OG BSER A 164 " =    2.321
peak=    3.935 closest distance to " O   HOH Z 197 " =    2.900
peak=    3.926 closest distance to " CA  ASN A 215 " =    1.230
peak=    3.919 closest distance to " O   HOH Z  43 " =    1.947
peak=    3.918 closest distance to " CG1 ILE A  33 " =    1.209
peak=    3.916 closest distance to " CB  ARG A 190 " =    1.673
peak=    3.912 closest distance to " O   HOH Z 158 " =    3.031
peak=    3.894 closest distance to " CG  ARG A  66 " =    2.451
peak=    3.893 closest distance to " O   HOH Z  61 " =    1.645
peak=    3.892 closest distance to " O   HOH Z 344 " =    3.138
peak=    3.882 closest distance to " O   SER A  87 " =    2.325
peak=    3.879 closest distance to " CB  TRP A 179 " =    1.300
peak=    3.877 closest distance to " O   HOH Z  97 " =    2.647
peak=    3.857 closest distance to " O   HOH Z 128 " =    2.018
peak=    3.848 closest distance to " O   HOH Z 108 " =    2.404
peak=    3.837 closest distance to " CB  VAL A 265 " =    1.357
peak=    3.831 closest distance to " O   HOH Z 279 " =    2.122
peak=    3.830 closest distance to " O   HOH Z 280 " =    3.005
peak=    3.826 closest distance to " O   HOH Z  97 " =    1.945
peak=    3.822 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.814 closest distance to " CA  THR A 221 " =    0.990
peak=    3.805 closest distance to " O   HOH Z 250 " =    1.353
peak=    3.767 closest distance to " O   HOH Z 423 " =    1.969
peak=    3.759 closest distance to " O   HOH Z 371 " =    3.416
peak=    3.754 closest distance to " O   HOH Z  10 " =    1.852
peak=    3.754 closest distance to " CD2 TRP A 179 " =    1.389
peak=    3.750 closest distance to " O   HOH Z 214 " =    2.046
peak=    3.747 closest distance to " NH2BARG A 145 " =    2.008
peak=    3.729 closest distance to " O   HOH Z  66 " =    1.992
peak=    3.714 closest distance to " O   HOH Z 425 " =    1.999
peak=    3.712 closest distance to " CA  ASN A 176 " =    1.223
peak=    3.712 closest distance to " O   HOH Z   6 " =    2.231
peak=    3.705 closest distance to " O   HOH Z 133 " =    2.581
peak=    3.691 closest distance to " CB  VAL A 202 " =    1.558
peak=    3.690 closest distance to " O   HOH Z 407 " =    2.667
peak=    3.689 closest distance to " O   HOH Z 426 " =    1.567
peak=    3.687 closest distance to " O   HOH Z 245 " =    1.329
peak=    3.684 closest distance to " O   HOH Z 327 " =    1.614
peak=    3.676 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.675 closest distance to " CD2 LEU A 297 " =    0.853
peak=    3.675 closest distance to " O   HOH Z  59 " =    2.110
peak=    3.673 closest distance to " CD BLYS A 290 " =    1.213
peak=    3.668 closest distance to " CA  THR A 264 " =    0.879
peak=    3.659 closest distance to " ND1 HIS A  81 " =    1.587
peak=    3.659 closest distance to " CB  ASP A 140 " =    0.944
peak=    3.659 closest distance to " O   HOH Z  19 " =    2.365
peak=    3.644 closest distance to " CA  MET A  40 " =    1.115
peak=    3.639 closest distance to " O   HOH Z 147 " =    1.739
peak=    3.639 closest distance to " O   HOH Z 411 " =    3.879
peak=    3.626 closest distance to " O   HOH Z  61 " =    1.525
peak=    3.619 closest distance to " CA  ALA A 291 " =    0.900
peak=    3.617 closest distance to " CB  TYR A 169 " =    0.919
peak=    3.614 closest distance to " O   HOH Z 193 " =    2.129
peak=    3.612 closest distance to " O   HOH Z 172 " =    3.759
peak=    3.604 closest distance to " O   HOH Z   1 " =    1.957
peak=    3.601 closest distance to " CG2 ILE A 120 " =    1.057
peak=    3.600 closest distance to " CE1 TYR A 186 " =    1.248
peak=    3.596 closest distance to " NH2 ARG A 156 " =    1.161
peak=    3.595 closest distance to " ND2 ASN A 110 " =    1.719
peak=    3.592 closest distance to " O   HOH Z 180 " =    2.208
peak=    3.591 closest distance to " CG  PRO A 243 " =    1.234
peak=    3.590 closest distance to " NH1AARG A 145 " =    1.107
peak=    3.579 closest distance to " CZ2 TRP A 179 " =    1.617
peak=    3.578 closest distance to " CB  ARG A 139 " =    0.969
peak=    3.575 closest distance to " O   HOH Z 291 " =    1.552
peak=    3.566 closest distance to " CG2 ILE A  20 " =    1.323
peak=    3.559 closest distance to " CA  ASP A 140 " =    1.098
peak=    3.558 closest distance to " CA  ARG A  36 " =    1.085
peak=    3.554 closest distance to " O   HOH Z 299 " =    4.401
peak=    3.550 closest distance to " CG2 THR A 221 " =    1.158
peak=    3.546 closest distance to " O   HOH Z  63 " =    2.047
peak=    3.544 closest distance to " CG1BVAL A  72 " =    1.557
peak=    3.543 closest distance to " O   HOH Z 337 " =    3.752
peak=    3.536 closest distance to " O   HOH Z 365 " =    3.008
peak=    3.532 closest distance to " O   HOH Z 406 " =    1.627
peak=    3.530 closest distance to " CA  ARG A 195 " =    1.282
peak=    3.524 closest distance to " O   HOH Z 368 " =    3.654
peak=    3.523 closest distance to " CD  ARG A 159 " =    0.753
peak=    3.522 closest distance to " CG  GLN A  58 " =    2.581
peak=    3.519 closest distance to " O   HOH Z 402 " =    1.443
peak=    3.517 closest distance to " CD1 ILE A 106 " =    0.874
peak=    3.504 closest distance to " O   HOH Z 209 " =    2.430
peak=    3.502 closest distance to " CG  PRO A  90 " =    1.049
peak=    3.499 closest distance to " O   HOH Z 126 " =    1.597
peak=    3.498 closest distance to " O   HOH Z 135 " =    1.617
peak=    3.494 closest distance to " O   HOH Z 173 " =    1.895
peak=    3.488 closest distance to " CA  ALA A  84 " =    1.378
peak=    3.484 closest distance to " O   HOH Z 263 " =    2.269
peak=    3.482 closest distance to " O   HOH Z 345 " =    3.200
peak=    3.478 closest distance to " CB  GLN A  88 " =    1.221
peak=    3.470 closest distance to " O   HOH Z 128 " =    2.207
peak=    3.468 closest distance to " O   HOH Z  35 " =    2.583
peak=    3.466 closest distance to " O   HOH Z  88 " =    3.314
peak=    3.462 closest distance to " O   HOH Z 134 " =    1.273
peak=    3.454 closest distance to " CD  LYS A 119 " =    1.291
peak=    3.448 closest distance to " O   HOH Z 189 " =    1.929
peak=    3.446 closest distance to " CD1 LEU A 300 " =    1.234
peak=    3.443 closest distance to " CA  ALA A 248 " =    1.240
peak=    3.442 closest distance to " O   HOH Z 427 " =    3.081
peak=    3.442 closest distance to " CZ  PHE A 218 " =    1.088
peak=    3.440 closest distance to " O   HOH Z 374 " =    2.591
peak=    3.438 closest distance to " O   HOH Z 273 " =    2.693
peak=    3.434 closest distance to " O   HOH Z 305 " =    3.613
peak=    3.428 closest distance to " CB  SER A 212 " =    1.040
peak=    3.423 closest distance to " CB  SER A  26 " =    1.566
peak=    3.422 closest distance to " CD  LYS A 166 " =    1.285
peak=    3.412 closest distance to " CB  GLN A  89 " =    1.319
peak=    3.407 closest distance to " O   HOH Z  21 " =    1.703
peak=    3.406 closest distance to " OE1 GLU A 277 " =    1.999
peak=    3.404 closest distance to " CD  ARG A 269 " =    0.951
peak=    3.403 closest distance to " O   HOH Z 326 " =    1.487
peak=    3.403 closest distance to " CA  LYS A 117 " =    1.199
peak=    3.400 closest distance to " CB  ALA A   9 " =    1.572
peak=    3.400 closest distance to " O   HOH Z 423 " =    3.194
peak=    3.397 closest distance to " CG  LYS A  76 " =    1.013
peak=    3.393 closest distance to " CG  GLN A  77 " =    2.060
peak=    3.363 closest distance to " OD1 ASP A 231 " =    1.904
peak=    3.362 closest distance to " O   HOH Z 193 " =    1.632
peak=    3.362 closest distance to " CG2BVAL A  41 " =    0.825
peak=    3.361 closest distance to " CA  ALA A  43 " =    1.288
peak=    3.359 closest distance to " O   HOH Z 185 " =    1.694
peak=    3.349 closest distance to " CA  ILE A  33 " =    1.501
peak=    3.345 closest distance to " O   HOH Z 250 " =    1.867
peak=    3.343 closest distance to " CG2 VAL A 257 " =    0.855
peak=    3.342 closest distance to " CB  ALA A  71 " =    1.319
peak=    3.341 closest distance to " N   ARG A 156 " =    1.307
peak=    3.340 closest distance to " O   HOH Z 183 " =    1.419
peak=    3.336 closest distance to " O   HOH Z 267 " =    2.065
peak=    3.333 closest distance to " OG  SER A  22 " =    2.767
peak=    3.330 closest distance to " O   HOH Z 199 " =    1.512
peak=    3.328 closest distance to " CB  SER A 141 " =    1.007
peak=    3.326 closest distance to " O   TRP A 274 " =    1.932
peak=    3.326 closest distance to " O   HOH Z 281 " =    4.577
peak=    3.326 closest distance to " O   HOH Z 368 " =    2.651
peak=    3.325 closest distance to " O   HOH Z 292 " =    1.591
peak=    3.323 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.320 closest distance to " O   HOH Z 411 " =    1.760
peak=    3.316 closest distance to " O   HOH Z 329 " =    3.747
peak=    3.316 closest distance to " O   HOH Z 334 " =    1.428
peak=    3.315 closest distance to " O   ALA A 165 " =    1.442
peak=    3.315 closest distance to " O   HOH Z 175 " =    2.148
peak=    3.314 closest distance to " O   HOH Z 422 " =    2.709
peak=    3.309 closest distance to " O   HOH Z 133 " =    1.488
peak=    3.308 closest distance to " CD2 LEU A 255 " =    1.424
peak=    3.305 closest distance to " O   HOH Z  71 " =    2.264
peak=    3.300 closest distance to " CA  ASP A 162 " =    1.141
peak=    3.298 closest distance to " CB  ASN A  39 " =    0.867
peak=    3.298 closest distance to " O   HOH Z 295 " =    1.467
peak=    3.294 closest distance to " CG  MET A 185 " =    1.086
peak=    3.293 closest distance to " O   HOH Z 341 " =    1.812
peak=    3.292 closest distance to " O   HOH Z 359 " =    1.400
peak=    3.287 closest distance to " CB  THR A  31 " =    1.827
peak=    3.285 closest distance to " O   HOH Z 219 " =    1.824
peak=    3.283 closest distance to " CG  MET A 185 " =    1.130
peak=    3.277 closest distance to " N   ASN A  39 " =    1.285
peak=    3.277 closest distance to " ND1 HIS A  86 " =    1.752
peak=    3.274 closest distance to " O   HOH Z 163 " =    1.867
peak=    3.273 closest distance to " O   HOH Z 227 " =    2.187
peak=    3.272 closest distance to " O   HOH Z 391 " =    2.953
peak=    3.272 closest distance to " CB  LEU A 255 " =    0.761
peak=    3.270 closest distance to " O   HOH Z 148 " =    3.187
peak=    3.268 closest distance to " O   HOH Z 403 " =    1.319
peak=    3.264 closest distance to " O   HOH Z  85 " =    2.296
peak=    3.259 closest distance to " CB  ALA A 291 " =    1.408
peak=    3.259 closest distance to " CB  SER A 216 " =    0.851
peak=    3.255 closest distance to " O   HOH Z 417 " =    3.003
peak=    3.247 closest distance to " O   HOH Z 171 " =    1.918
peak=    3.239 closest distance to " O   HOH Z 209 " =    2.296
peak=    3.239 closest distance to " CD  ARG A  66 " =    2.583
peak=    3.238 closest distance to " O   HOH Z  68 " =    1.515
peak=    3.233 closest distance to " CB  ASN A 215 " =    1.124
peak=    3.232 closest distance to " OG1 THR A 294 " =    2.423
peak=    3.227 closest distance to " O   HOH Z 421 " =    1.707
peak=    3.226 closest distance to " C   TYR A 214 " =    1.396
peak=    3.217 closest distance to " O   HOH Z 163 " =    1.655
peak=    3.214 closest distance to " O   HOH Z 248 " =    1.704
peak=    3.206 closest distance to " O   HOH Z  66 " =    1.936
peak=    3.204 closest distance to " CG  GLU A 277 " =    2.087
peak=    3.202 closest distance to " NE2 GLN A  77 " =    3.189
peak=    3.196 closest distance to " CG  MET A 113 " =    1.279
peak=    3.191 closest distance to " CB  ILE A 120 " =    1.349
peak=    3.190 closest distance to " O   ALA A 158 " =    1.240
peak=    3.186 closest distance to " O   HOH Z 409 " =    3.172
peak=    3.183 closest distance to " O   HOH Z 353 " =    2.723
peak=    3.181 closest distance to " CA  ALA A 158 " =    1.155
peak=    3.179 closest distance to " NH2 ARG A 219 " =    1.838
peak=    3.176 closest distance to " O   HOH Z  49 " =    2.842
peak=    3.175 closest distance to " O   GLY A  57 " =    2.607
peak=    3.162 closest distance to " OG BSER A 258 " =    3.568
peak=    3.161 closest distance to " OG  SER A  62 " =    2.917
peak=    3.140 closest distance to " O   HOH Z 250 " =    1.530
peak=    3.139 closest distance to " O   HOH Z 336 " =    1.749
peak=    3.139 closest distance to " O   HOH Z 189 " =    2.804
peak=    3.138 closest distance to " N   VAL A 126 " =    1.326
peak=    3.137 closest distance to " O   HOH Z 371 " =    3.486
peak=    3.137 closest distance to " O   HOH Z 211 " =    2.802
peak=    3.136 closest distance to " CB  ASN A 285 " =    0.904
peak=    3.134 closest distance to " O   HOH Z 392 " =    2.007
peak=    3.130 closest distance to " CG2 VAL A 202 " =    1.170
peak=    3.128 closest distance to " CB  ASN A 110 " =    1.145
peak=    3.126 closest distance to " O   HOH Z 112 " =    2.702
peak=    3.125 closest distance to " CA  GLY A  80 " =    1.075
peak=    3.119 closest distance to " O   HOH Z 261 " =    1.406
peak=    3.116 closest distance to " O   HOH Z 256 " =    2.398
peak=    3.113 closest distance to " N   ASN A 127 " =    1.252
peak=    3.112 closest distance to " CA  MET A 105 " =    0.981
peak=    3.106 closest distance to " NZ  LYS A 166 " =    2.982
peak=    3.104 closest distance to " O   HOH Z 383 " =    2.090
peak=    3.101 closest distance to " O   HOH Z 417 " =    2.104
peak=    3.099 closest distance to " O   HOH Z  88 " =    2.778
peak=    3.093 closest distance to " O   HOH Z 213 " =    1.481
peak=    3.089 closest distance to " O   HOH Z 393 " =    3.341
peak=    3.081 closest distance to " CB  ASN A 224 " =    1.017
peak=    3.073 closest distance to " CB  TYR A 116 " =    0.844
peak=    3.065 closest distance to " N   ALA A 154 " =    1.019
peak=    3.053 closest distance to " O   HOH Z 425 " =    1.156
peak=    3.045 closest distance to " O   HOH Z  49 " =    2.202
peak=    3.045 closest distance to " N   SER A 135 " =    1.327
peak=    3.044 closest distance to " CB  ARG A 138 " =    0.938
peak=    3.040 closest distance to " O   HOH Z 124 " =    1.276

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.804 - 5.229
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.804 - 5.229

peak=   -4.922 closest distance to " O   HOH Z 266 " =    4.512
peak=   -4.514 closest distance to " O   VAL A  67 " =    2.732
peak=   -4.497 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.468 closest distance to " CB  PRO A 243 " =    2.588
peak=   -4.396 closest distance to " SG  CYS A 254 " =    3.268
peak=   -4.394 closest distance to " CB  ALA A 161 " =    2.552
peak=   -4.314 closest distance to " CB  PRO A 280 " =    2.182
peak=   -4.301 closest distance to " C   HIS A 108 " =    1.093
peak=   -4.281 closest distance to " O   HOH Z 372 " =    2.403
peak=   -4.270 closest distance to " CG  GLN A 223 " =    2.011
peak=   -4.229 closest distance to " O   HOH Z 198 " =    2.180
peak=   -4.171 closest distance to " O   HOH Z 126 " =    1.898
peak=   -4.160 closest distance to " OG BSER A 134 " =    1.206
peak=   -4.064 closest distance to " CD1 PHE A  59 " =    1.823
peak=   -4.039 closest distance to " OXT GLY A 302 " =    2.801
peak=   -4.020 closest distance to " OG  SER A  97 " =    2.127
peak=   -3.956 closest distance to " N   ALA A  43 " =    2.628
peak=   -3.931 closest distance to " CG1 VAL A 112 " =    2.755
peak=   -3.922 closest distance to " O   HOH Z  13 " =    1.618
peak=   -3.917 closest distance to " CD2 LEU A 300 " =    2.885
peak=   -3.897 closest distance to " O   VAL A  67 " =    2.696
peak=   -3.880 closest distance to " O   PRO A 163 " =    2.131
peak=   -3.871 closest distance to " O   HOH Z 353 " =    2.198
peak=   -3.852 closest distance to " O   HOH Z 196 " =    2.046
peak=   -3.848 closest distance to " CD  ARG A 139 " =    1.585
peak=   -3.846 closest distance to " O   HOH Z  10 " =    1.532
peak=   -3.844 closest distance to " O   HOH Z 114 " =    3.229
peak=   -3.828 closest distance to " N   GLN A  58 " =    1.632
peak=   -3.804 closest distance to " CZ  PHE A  59 " =    1.656
peak=   -3.803 closest distance to " O   HOH Z 185 " =    2.236
peak=   -3.802 closest distance to " CD1 LEU A 228 " =    2.197
peak=   -3.794 closest distance to " O   HOH Z  52 " =    1.383
peak=   -3.787 closest distance to " CE2 TYR A  30 " =    2.752
peak=   -3.772 closest distance to " O   HOH Z 231 " =    2.242
peak=   -3.744 closest distance to " ND2 ASN A  45 " =    1.620
peak=   -3.718 closest distance to " NH1 ARG A 195 " =    2.620
peak=   -3.711 closest distance to " CZ  TYR A 169 " =    1.741
peak=   -3.701 closest distance to " CA  ASP A 298 " =    1.026
peak=   -3.696 closest distance to " O   HOH Z 292 " =    4.509
peak=   -3.694 closest distance to " CB  TYR A  15 " =    2.218
peak=   -3.671 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.660 closest distance to " O   SER A 210 " =    1.933
peak=   -3.660 closest distance to " OG  SER A  62 " =    1.616
peak=   -3.653 closest distance to " CG  ASP A 231 " =    0.804
peak=   -3.650 closest distance to " O   HOH Z 198 " =    1.428
peak=   -3.645 closest distance to " CG1 VAL A 112 " =    2.870
peak=   -3.644 closest distance to " CB  ASP A 132 " =    2.323
peak=   -3.643 closest distance to " O   HOH Z  43 " =    1.588
peak=   -3.635 closest distance to " O   HOH Z 290 " =    1.191
peak=   -3.632 closest distance to " O   HOH Z 389 " =    1.780
peak=   -3.630 closest distance to " CG  PHE A 283 " =    2.698
peak=   -3.619 closest distance to " CZ3 TRP A 179 " =    1.204
peak=   -3.617 closest distance to " CB  ASN A  39 " =    2.252
peak=   -3.617 closest distance to " N   ALA A 248 " =    1.595
peak=   -3.616 closest distance to " ND2 ASN A  45 " =    1.054
peak=   -3.612 closest distance to " NH2AARG A 275 " =    5.229
peak=   -3.599 closest distance to " CB  ALA A 291 " =    2.456
peak=   -3.596 closest distance to " SG ACYS A 201 " =    1.867
peak=   -3.587 closest distance to " OG BSER A 134 " =    1.716
peak=   -3.586 closest distance to " CB  ALA A 291 " =    2.236
peak=   -3.584 closest distance to " CG2 ILE A 263 " =    2.247
peak=   -3.579 closest distance to " CD  GLN A  58 " =    1.182
peak=   -3.575 closest distance to " CG  GLU A   2 " =    1.877
peak=   -3.575 closest distance to " CA  GLY A 203 " =    2.247
peak=   -3.574 closest distance to " NE2 GLN A  88 " =    1.858
peak=   -3.560 closest distance to " O   HOH Z 407 " =    2.986
peak=   -3.558 closest distance to " CD1 LEU A 101 " =    2.394
peak=   -3.552 closest distance to " OG BSER A 210 " =    2.065
peak=   -3.549 closest distance to " C   LEU A 143 " =    1.078
peak=   -3.539 closest distance to " O   HOH Z 311 " =    3.638
peak=   -3.538 closest distance to " C   ALA A 158 " =    1.248
peak=   -3.532 closest distance to " O   HOH Z 435 " =    2.717
peak=   -3.524 closest distance to " C   ILE A 234 " =    1.358
peak=   -3.520 closest distance to " OD1 ASN A 187 " =    1.616
peak=   -3.517 closest distance to " O   MET A  40 " =    2.778
peak=   -3.513 closest distance to " CB  PHE A 192 " =    2.035
peak=   -3.513 closest distance to " NH2 ARG A  79 " =    1.941
peak=   -3.505 closest distance to " CE  MET A 105 " =    2.188
peak=   -3.491 closest distance to " O   HOH Z  90 " =    2.793
peak=   -3.489 closest distance to " OD1 ASP A 171 " =    1.606
peak=   -3.484 closest distance to " CG1 VAL A 250 " =    2.619
peak=   -3.482 closest distance to " O   PHE A 218 " =    1.612
peak=   -3.481 closest distance to " CG  ARG A 269 " =    2.321
peak=   -3.473 closest distance to " OD1 ASN A 148 " =    1.606
peak=   -3.472 closest distance to " O   LYS A 117 " =    1.589
peak=   -3.454 closest distance to " O   HOH Z 166 " =    1.846
peak=   -3.450 closest distance to " O   HOH Z 385 " =    1.945
peak=   -3.450 closest distance to " O   VAL A 174 " =    2.053
peak=   -3.449 closest distance to " O   HOH Z 348 " =    2.230
peak=   -3.446 closest distance to " CB  CYS A 201 " =    2.564
peak=   -3.438 closest distance to " O   SER A 135 " =    1.525
peak=   -3.437 closest distance to " O   HOH Z 252 " =    3.751
peak=   -3.432 closest distance to " O   HOH Z  47 " =    1.590
peak=   -3.427 closest distance to " CG  ARG A  66 " =    2.412
peak=   -3.418 closest distance to " O   HOH Z 313 " =    1.995
peak=   -3.416 closest distance to " O   HOH Z 211 " =    1.702
peak=   -3.411 closest distance to " O   HOH Z 166 " =    1.452
peak=   -3.410 closest distance to " O   HOH Z 283 " =    2.248
peak=   -3.401 closest distance to " O   HOH Z 111 " =    2.282
peak=   -3.390 closest distance to " NH2 ARG A 159 " =    2.403
peak=   -3.389 closest distance to " O   HOH Z  38 " =    1.604
peak=   -3.378 closest distance to " ND2 ASN A 249 " =    2.306
peak=   -3.378 closest distance to " CD2 TYR A 247 " =    2.416
peak=   -3.371 closest distance to " CB  ASP A 286 " =    1.997
peak=   -3.369 closest distance to " CB  ALA A 248 " =    2.267
peak=   -3.365 closest distance to " CB  ALA A 131 " =    2.089
peak=   -3.365 closest distance to " C   MET A 188 " =    1.538
peak=   -3.364 closest distance to " O   HOH Z 103 " =    1.828
peak=   -3.363 closest distance to " O   HOH Z  11 " =    2.084
peak=   -3.357 closest distance to " CB  PRO A 163 " =    2.515
peak=   -3.356 closest distance to " CG1 VAL A 125 " =    2.378
peak=   -3.355 closest distance to " O   HOH Z 351 " =    1.518
peak=   -3.354 closest distance to " O   HOH Z  11 " =    1.807
peak=   -3.353 closest distance to " O   HOH Z 395 " =    5.193
peak=   -3.348 closest distance to " O   HOH Z 234 " =    4.160
peak=   -3.343 closest distance to " O   HOH Z 361 " =    3.431
peak=   -3.342 closest distance to " O   HOH Z 165 " =    1.972
peak=   -3.340 closest distance to " CD  LYS A 289 " =    2.436
peak=   -3.337 closest distance to " N   ASP A 286 " =    2.396
peak=   -3.333 closest distance to " O   VAL A 189 " =    2.535
peak=   -3.321 closest distance to " CD2 LEU A 237 " =    2.513
peak=   -3.316 closest distance to " CG1 VAL A 230 " =    1.972
peak=   -3.315 closest distance to " CG2 VAL A 189 " =    2.118
peak=   -3.309 closest distance to " O   SER A  95 " =    1.537
peak=   -3.298 closest distance to " O   HOH Z 436 " =    1.427
peak=   -3.297 closest distance to " CG  GLU A  53 " =    1.480
peak=   -3.297 closest distance to " N   ALA A 226 " =    2.053
peak=   -3.296 closest distance to " O   HOH Z  60 " =    2.492
peak=   -3.293 closest distance to " O   PRO A 198 " =    1.329
peak=   -3.291 closest distance to " OD2 ASP A 171 " =    1.691
peak=   -3.291 closest distance to " O   HOH Z 298 " =    1.354
peak=   -3.287 closest distance to " OH  TYR A 214 " =    1.274
peak=   -3.287 closest distance to " OD2 ASP A 270 " =    1.476
peak=   -3.285 closest distance to " ND2 ASN A  60 " =    1.461
peak=   -3.282 closest distance to " O   HOH Z 317 " =    2.402
peak=   -3.279 closest distance to " CB  TRP A  85 " =    2.565
peak=   -3.275 closest distance to " N   THR A 157 " =    1.555
peak=   -3.275 closest distance to " O   HOH Z   6 " =    1.572
peak=   -3.271 closest distance to " O   ALA A 161 " =    1.710
peak=   -3.269 closest distance to " N   GLN A 122 " =    1.419
peak=   -3.268 closest distance to " OG ASER A 134 " =    1.113
peak=   -3.265 closest distance to " OG  SER A  26 " =    1.247
peak=   -3.262 closest distance to " CB  ALA A 248 " =    1.994
peak=   -3.261 closest distance to " O   HOH Z 394 " =    1.518
peak=   -3.259 closest distance to " NZ  LYS A 119 " =    3.587
peak=   -3.257 closest distance to " O   ASN A 187 " =    1.471
peak=   -3.256 closest distance to " OG1 THR A 178 " =    1.267
peak=   -3.248 closest distance to " N   ALA A 248 " =    1.877
peak=   -3.248 closest distance to " O   HOH Z  97 " =    1.672
peak=   -3.246 closest distance to " OD1 ASN A 176 " =    1.227
peak=   -3.234 closest distance to " OD1 ASP A 191 " =    1.495
peak=   -3.230 closest distance to " CG  PRO A 163 " =    2.604
peak=   -3.228 closest distance to " CE  MET A  93 " =    1.280
peak=   -3.226 closest distance to " NH2 ARG A  66 " =    1.975
peak=   -3.226 closest distance to " O   HOH Z 281 " =    2.690
peak=   -3.225 closest distance to " CD1 LEU A 297 " =    2.436
peak=   -3.225 closest distance to " CD2 PHE A 225 " =    1.259
peak=   -3.221 closest distance to " O   HOH Z 263 " =    2.931
peak=   -3.219 closest distance to " O   TRP A  70 " =    1.561
peak=   -3.210 closest distance to " CA  GLY A 241 " =    3.105
peak=   -3.210 closest distance to " CB  ASP A 132 " =    2.349
peak=   -3.206 closest distance to " O   GLY A 196 " =    1.035
peak=   -3.198 closest distance to " ND2 ASN A 187 " =    1.548
peak=   -3.198 closest distance to " O   GLY A 211 " =    1.629
peak=   -3.197 closest distance to " O   HOH Z  93 " =    1.809
peak=   -3.197 closest distance to " OXT GLY A 302 " =    3.201
peak=   -3.193 closest distance to " O   HOH Z  76 " =    1.896
peak=   -3.190 closest distance to " CZ  PHE A  38 " =    2.284
peak=   -3.184 closest distance to " O   HOH Z  89 " =    2.990
peak=   -3.179 closest distance to " N   SER A 276 " =    1.304
peak=   -3.178 closest distance to " O   HOH Z 414 " =    1.596
peak=   -3.178 closest distance to " OD2 ASP A  50 " =    1.550
peak=   -3.177 closest distance to " CG  TRP A 266 " =    1.800
peak=   -3.177 closest distance to " CG1 VAL A  78 " =    3.149
peak=   -3.174 closest distance to " O   HOH Z 393 " =    1.396
peak=   -3.172 closest distance to " O   GLY A 111 " =    1.208
peak=   -3.172 closest distance to " CD2 PHE A  61 " =    2.525
peak=   -3.170 closest distance to " CG  GLU A 152 " =    2.136
peak=   -3.164 closest distance to " O   HOH Z  63 " =    1.391
peak=   -3.162 closest distance to " CB  ALA A   1 " =    2.729
peak=   -3.161 closest distance to " CA  GLY A 133 " =    2.001
peak=   -3.157 closest distance to " CE3 TRP A 150 " =    2.062
peak=   -3.154 closest distance to " CG  GLU A 152 " =    1.391
peak=   -3.152 closest distance to " O   HOH Z 427 " =    1.443
peak=   -3.147 closest distance to " NE  ARG A  36 " =    1.881
peak=   -3.145 closest distance to " NH2 ARG A  66 " =    5.161
peak=   -3.143 closest distance to " N   ALA A 248 " =    2.487
peak=   -3.141 closest distance to " NH2BARG A 275 " =    2.190
peak=   -3.133 closest distance to " CE3 TRP A 274 " =    2.435
peak=   -3.129 closest distance to " O   ALA A   1 " =    1.851
peak=   -3.127 closest distance to " O   HOH Z 200 " =    3.674
peak=   -3.126 closest distance to " OD2 ASP A  50 " =    2.292
peak=   -3.124 closest distance to " O   HOH Z 407 " =    3.339
peak=   -3.121 closest distance to " O   ALA A  10 " =    1.747
peak=   -3.120 closest distance to " CB  ALA A  51 " =    1.877
peak=   -3.120 closest distance to " O   ASN A 301 " =    1.449
peak=   -3.105 closest distance to " CE2 PHE A 218 " =    2.373
peak=   -3.105 closest distance to " NE2 GLN A  58 " =    1.245
peak=   -3.096 closest distance to " CG1 VAL A 197 " =    2.195
peak=   -3.095 closest distance to " O   HOH Z 275 " =    1.549
peak=   -3.091 closest distance to " CD2 TYR A 293 " =    2.022
peak=   -3.090 closest distance to " O   ASP A 231 " =    2.384
peak=   -3.090 closest distance to " CB  ASP A 149 " =    2.015
peak=   -3.081 closest distance to " O   HOH Z 134 " =    2.832
peak=   -3.079 closest distance to " CG  ASN A 301 " =    1.997
peak=   -3.077 closest distance to " O   ALA A  51 " =    1.330
peak=   -3.076 closest distance to " CG2 THR A 221 " =    2.273
peak=   -3.076 closest distance to " O   HOH Z 422 " =    1.593
peak=   -3.072 closest distance to " O   HOH Z 168 " =    1.716
peak=   -3.062 closest distance to " O   HOH Z 388 " =    1.962
peak=   -3.044 closest distance to " CB  ASP A 132 " =    2.391
peak=   -3.031 closest distance to " O   HOH Z 193 " =    1.654

================= 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    :  0.2985 0.2949   5.979428e+00   5.984873e+00
   1_bss:  0.2824 0.2762   5.954585e+00   5.941560e+00
   1_xyz:  0.1614 0.1824   5.415462e+00   5.523785e+00
   1_adp:  0.1471 0.1880   5.361098e+00   5.551935e+00
   1_occ:  0.1468 0.1884   5.359892e+00   5.551064e+00
   2_bss:  0.1449 0.1856   5.349042e+00   5.537595e+00
   2_xyz:  0.1183 0.1575   5.174188e+00   5.390450e+00
   2_adp:  0.1151 0.1544   5.149217e+00   5.366652e+00
   2_occ:  0.1149 0.1541   5.148444e+00   5.365981e+00
   3_bss:  0.1150 0.1535   5.147929e+00   5.364773e+00
   3_xyz:  0.1103 0.1519   5.123784e+00   5.355447e+00
   3_adp:  0.1088 0.1528   5.121574e+00   5.361766e+00
   3_occ:  0.1087 0.1529   5.121598e+00   5.362034e+00
   4_bss:  0.1087 0.1528   5.121301e+00   5.361785e+00
   4_xyz:  0.1079 0.1534   5.120371e+00   5.365347e+00
   4_adp:  0.1077 0.1542   5.122099e+00   5.370519e+00
   4_occ:  0.1076 0.1542   5.122267e+00   5.370950e+00
   5_bss:  0.1076 0.1543   5.122332e+00   5.370998e+00
   5_xyz:  0.1038 0.1551   5.105171e+00   5.370566e+00
   5_adp:  0.1034 0.1560   5.106175e+00   5.375208e+00
   5_occ:  0.1034 0.1561   5.106204e+00   5.375415e+00
   5_bss:  0.1032 0.1560   5.106039e+00   5.375118e+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:  0.320  37.157  -3.197  -1.725   1.216  -0.000   0.000   0.000
   1_xyz:  0.320  37.157  -3.197  -1.725   1.216  -0.000   0.000   0.000
   1_adp:  0.320  37.157  -3.197  -1.725   1.216  -0.000   0.000   0.000
   1_occ:  0.320  37.157  -3.197  -1.725   1.216  -0.000   0.000   0.000
   2_bss:  0.313  42.666  -3.123  -2.353  -1.211  -0.000  -0.000  -0.000
   2_xyz:  0.313  42.666  -3.123  -2.353  -1.211  -0.000  -0.000  -0.000
   2_adp:  0.313  42.666  -3.123  -2.353  -1.211  -0.000  -0.000  -0.000
   2_occ:  0.313  42.666  -3.123  -2.353  -1.211  -0.000  -0.000  -0.000
   3_bss:  0.320  42.666  -2.812  -2.250  -1.584  -0.000  -0.000  -0.000
   3_xyz:  0.320  42.666  -2.812  -2.250  -1.584  -0.000  -0.000  -0.000
   3_adp:  0.320  42.666  -2.812  -2.250  -1.584  -0.000  -0.000  -0.000
   3_occ:  0.320  42.666  -2.812  -2.250  -1.584  -0.000  -0.000  -0.000
   4_bss:  0.320  43.593  -2.617  -2.124  -1.589  -0.000  -0.000  -0.000
   4_xyz:  0.320  43.593  -2.617  -2.124  -1.589  -0.000  -0.000  -0.000
   4_adp:  0.320  43.593  -2.617  -2.124  -1.589  -0.000  -0.000  -0.000
   4_occ:  0.320  43.593  -2.617  -2.124  -1.589  -0.000  -0.000  -0.000
   5_bss:  0.320  43.593  -2.402  -1.936  -1.441  -0.000  -0.000  -0.000
   5_xyz:  0.320  43.593  -2.402  -1.936  -1.441  -0.000  -0.000  -0.000
   5_adp:  0.320  43.593  -2.402  -1.936  -1.441  -0.000  -0.000  -0.000
   5_occ:  0.320  43.593  -2.402  -1.936  -1.441  -0.000  -0.000  -0.000
   5_bss:  0.322  46.257  -2.138  -1.697  -1.223  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.032 0.7494  0.9317    25907.687
   1_bss:  29.298 0.7662  0.9123    22032.817
   1_xyz:  16.761 0.8927  1.0052     8452.814
   1_adp:  17.488 0.8857  1.0003     8870.338
   1_occ:  17.485 0.8856  1.0001     8853.057
   2_bss:  17.115 0.8890  0.9682     8595.846
   2_xyz:  14.191 0.9131  0.9803     6350.671
   2_adp:  13.679 0.9174  0.9793     6096.064
   2_occ:  13.665 0.9175  0.9792     6081.252
   3_bss:  13.631 0.9178  0.9797     6069.309
   3_xyz:  13.385 0.9199  0.9805     5925.234
   3_adp:  13.490 0.9192  0.9756     5988.877
   3_occ:  13.493 0.9192  0.9755     5991.387
   4_bss:  13.488 0.9192  0.9793     5990.744
   4_xyz:  13.555 0.9186  0.9785     6041.356
   4_adp:  13.645 0.9180  0.9725     6093.867
   4_occ:  13.651 0.9179  0.9724     6098.996
   5_bss:  13.653 0.9179  0.9789     6100.610
   5_xyz:  13.645 0.9179  0.9795     6113.904
   5_adp:  13.737 0.9172  0.9725     6147.999
   5_occ:  13.740 0.9172  0.9725     6151.323
   5_bss:  13.736 0.9172  0.9807     6149.189
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6362e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6362e-01
   1_xyz:   1.052  0.007  0.068 14.918  0.004  4.111   6.2269e-02
   1_adp:   1.052  0.007  0.068 14.918  0.004  4.111   6.2269e-02
   1_occ:   1.052  0.007  0.068 14.918  0.004  4.111   6.2269e-02
   2_bss:   1.052  0.007  0.068 14.918  0.004  4.111   6.2269e-02
   2_xyz:   0.976  0.006  0.073 14.588  0.004  4.116   5.6019e-02
   2_adp:   0.976  0.006  0.073 14.588  0.004  4.116   5.6019e-02
   2_occ:   0.976  0.006  0.073 14.588  0.004  4.116   5.6019e-02
   3_bss:   0.976  0.006  0.073 14.588  0.004  4.116   5.6019e-02
   3_xyz:   0.964  0.006  0.073 14.629  0.004  4.116   5.6212e-02
   3_adp:   0.964  0.006  0.073 14.629  0.004  4.116   5.6212e-02
   3_occ:   0.964  0.006  0.073 14.629  0.004  4.116   5.6212e-02
   4_bss:   0.964  0.006  0.073 14.629  0.004  4.116   5.6212e-02
   4_xyz:   0.951  0.006  0.072 14.536  0.004  4.116   5.4517e-02
   4_adp:   0.951  0.006  0.072 14.536  0.004  4.116   5.4517e-02
   4_occ:   0.951  0.006  0.072 14.536  0.004  4.116   5.4517e-02
   5_bss:   0.951  0.006  0.072 14.536  0.004  4.116   5.4517e-02
   5_xyz:   1.114  0.009  0.083 14.974  0.005  4.117   7.3062e-02
   5_adp:   1.114  0.009  0.083 14.974  0.005  4.117   7.3062e-02
   5_occ:   1.114  0.009  0.083 14.974  0.005  4.117   7.3062e-02
   5_bss:   1.114  0.009  0.083 14.974  0.005  4.117   7.3062e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_xyz:   7.276  0.056  0.272 83.531  0.036  2.357   5.4633e-02
   1_adp:   7.276  0.056  0.272 83.531  0.036  2.357   5.4633e-02
   1_occ:   7.276  0.056  0.272 83.531  0.036  2.357   5.4633e-02
   2_bss:   7.276  0.056  0.272 83.531  0.036  2.357   5.4633e-02
   2_xyz:   6.306  0.038  0.231 84.186  0.035  2.351   3.8531e-02
   2_adp:   6.306  0.038  0.231 84.186  0.035  2.351   3.8531e-02
   2_occ:   6.306  0.038  0.231 84.186  0.035  2.351   3.8531e-02
   3_bss:   6.306  0.038  0.231 84.186  0.035  2.351   3.8531e-02
   3_xyz:   6.692  0.039  0.235 82.898  0.036  2.341   4.5068e-02
   3_adp:   6.692  0.039  0.235 82.898  0.036  2.341   4.5068e-02
   3_occ:   6.692  0.039  0.235 82.898  0.036  2.341   4.5068e-02
   4_bss:   6.692  0.039  0.235 82.898  0.036  2.341   4.5068e-02
   4_xyz:   6.548  0.040  0.231 83.150  0.034  2.339   3.5907e-02
   4_adp:   6.548  0.040  0.231 83.150  0.034  2.339   3.5907e-02
   4_occ:   6.548  0.040  0.231 83.150  0.034  2.339   3.5907e-02
   5_bss:   6.548  0.040  0.231 83.150  0.034  2.339   3.5907e-02
   5_xyz:   7.252  0.049  0.270 82.686  0.038  2.246   6.0512e-02
   5_adp:   7.252  0.049  0.270 82.686  0.038  2.246   6.0512e-02
   5_occ:   7.252  0.049  0.270 82.686  0.038  2.246   6.0512e-02
   5_bss:   7.252  0.049  0.270 82.686  0.038  2.246   6.0512e-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:  72.85   1.36  16.98  72.85   1.36  13.06  68.06   7.68  38.33
   1_occ:  72.85   1.36  16.98  72.85   1.36  13.06  68.06   7.68  38.33
   2_bss:  72.85   1.36  16.98  72.85   1.36  13.06  68.06   7.68  38.33
   2_xyz:  72.85   1.36  16.98  72.85   1.36  13.06  68.06   7.68  38.33
   2_adp:  74.08   2.33  16.69  74.08   2.33  12.90  66.35   5.49  37.30
   2_occ:  74.08   2.33  16.69  74.08   2.33  12.90  66.35   5.49  37.30
   3_bss:  74.08   2.33  16.69  74.08   2.33  12.90  66.35   5.49  37.30
   3_xyz:  74.08   2.33  16.69  74.08   2.33  12.90  66.35   5.49  37.30
   3_adp:  79.70   1.43  16.79  79.70   1.43  12.86  67.52   5.67  38.20
   3_occ:  79.70   1.43  16.79  79.70   1.43  12.86  67.52   5.67  38.20
   4_bss:  79.70   1.43  16.79  79.70   1.43  12.86  67.52   5.67  38.20
   4_xyz:  79.70   1.43  16.79  79.70   1.43  12.86  67.52   5.67  38.20
   4_adp:  80.45   0.96  16.69  80.45   0.96  12.73  67.83   5.90  38.26
   4_occ:  80.45   0.96  16.69  80.45   0.96  12.73  67.83   5.90  38.26
   5_bss:  80.45   0.96  16.69  80.45   0.96  12.73  67.83   5.90  38.26
   5_xyz:  80.45   0.96  16.69  80.45   0.96  12.73  67.83   5.90  38.26
   5_adp:  91.77   0.37  16.81  91.77   0.37  12.67  78.23   5.96  39.37
   5_occ:  91.77   0.37  16.81  91.77   0.37  12.67  78.23   5.96  39.37
   5_bss:  91.76   0.36  16.80  91.76   0.36  12.66  78.22   5.95  39.36
------------------------------------------------------------------------
 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:    1.168    0.018    0.280
   1_adp:    1.168    0.018    0.280
   1_occ:    1.168    0.018    0.280
   2_bss:    1.168    0.018    0.280
   2_xyz:    0.855    0.037    0.326
   2_adp:    0.855    0.037    0.326
   2_occ:    0.855    0.037    0.326
   3_bss:    0.855    0.037    0.326
   3_xyz:    1.041    0.044    0.345
   3_adp:    1.041    0.044    0.345
   3_occ:    1.041    0.044    0.345
   4_bss:    1.041    0.044    0.345
   4_xyz:    1.072    0.018    0.353
   4_adp:    1.072    0.018    0.353
   4_occ:    1.072    0.018    0.353
   5_bss:    1.072    0.018    0.353
   5_xyz:    1.111    0.017    0.359
   5_adp:    1.111    0.017    0.359
   5_occ:    1.111    0.017    0.359
   5_bss:    1.111    0.017    0.359
------------------------------------------------------------------------

CPU time actual refinement: 327.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_673/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_673/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_673/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_673/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_673/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.42 
  Macro-tasks:
    bulk solvent and scale       = 37.82  
    individual site refinement   = 140.67 
    weights calculation          = 28.93  
    collect and process          = 6.62   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.16 
  Micro-tasks:
    mask                            = 1.19   
    f_calc                          = 103.66 
    alpha_beta                      = 8.52   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 114.39 
    fmodel                         = 6.35   
    r_factors                      = 0.19   
    phase_errors                   = 11.13  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 246.87 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.558 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    658 calls, 103.30 s
gradients_fft:          603 calls,  99.87 s

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

# Date 2008-01-16 Time 05:23:32 PST -0800 (1200489812.03 s)
Start R-work = 0.2985, R-free = 0.2949 (no bulk solvent and anisotropic scale)
Final R-work = 0.1272, R-free = 0.1742 (no bulk solvent and anisotropic scale)

Start R-work = 0.2824, R-free = 0.2762
Final R-work = 0.1032, R-free = 0.1560