# Date 2008-01-16 Time 05:21:22 PST -0800 (1200489682.52 s)
#phil __OFF__

Command line arguments: "../699.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19380
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 699

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.6339, 86.822, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00057
Completeness in resolution range: 0.967358
Completeness with d_max=infinity: 0.96431

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   2.0006

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00057
Completeness in resolution range: 0.967358
Completeness with d_max=infinity: 0.96431

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2799 [2125/2152]  1912   213  10.0%
  bin  2:  4.2799 -  3.4102 [2036/2052]  1833   203  10.0%
  bin  3:  3.4102 -  2.9830 [2028/2047]  1826   202  10.0%
  bin  4:  2.9830 -  2.7120 [1992/2022]  1794   198   9.9%
  bin  5:  2.7120 -  2.5186 [1987/2006]  1788   199  10.0%
  bin  6:  2.5186 -  2.3707 [1968/2004]  1771   197  10.0%
  bin  7:  2.3707 -  2.2524 [1965/1998]  1767   198  10.1%
  bin  8:  2.2524 -  2.1546 [1949/1983]  1754   195  10.0%
  bin  9:  2.1546 -  2.0719 [1941/1969]  1745   196  10.1%
  bin 10:  2.0719 -  2.0006 [1598/2017]  1440   158   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_699/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: 0.11 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: 14
        2.42 -     3.04: 2161
        3.04 -     3.66: 4639
        3.66 -     4.28: 8907
        4.28 -     4.90: 12314
  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 207 " - " O   HOH Z 341 "  2.005 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.248 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.259 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28030 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_699/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_699/model_refine_001.geo

CPU time processing inputs: 8.01


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.63395 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3353   r_free= 0.3251   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.092415                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7732 0.99   1381  153 0.2887 0.3011       6.359      6.3363|
|  2:  4.7732 -  3.8090 0.99   1323  149 0.2662 0.2616      6.5038      6.4973|
|  3:  3.8090 -  3.3335 0.99   1309  146 0.2910 0.2817      6.4049      6.3874|
|  4:  3.3335 -  3.0315 0.99   1292  136 0.3190 0.2879      6.3066      6.1701|
|  5:  3.0315 -  2.8157 0.99   1284  145 0.3430 0.2849      6.1674      6.0872|
|  6:  2.8157 -  2.6507 0.99   1278  146 0.3496 0.3528      6.0923      6.0156|
|  7:  2.6507 -  2.5186 0.99   1286  140 0.3537 0.3424      6.0453      5.9536|
|  8:  2.5186 -  2.4094 0.98   1263  142 0.3627 0.3657      6.0222      6.0386|
|  9:  2.4094 -  2.3170 0.98   1274  143 0.3713 0.3650      5.9618      5.9364|
| 10:  2.3170 -  2.2373 0.98   1248  135 0.3907 0.3559      5.9981      5.8904|
| 11:  2.2373 -  2.1676 1.00   1260  146 0.3730 0.3479      5.8972       5.889|
| 12:  2.1676 -  2.1058 0.97   1262  134 0.3899 0.3827       5.851      5.9315|
| 13:  2.1058 -  2.0505 0.98   1260  141 0.4032 0.3851      5.7952       5.765|
| 14:  2.0505 -  2.0006 0.72    910  103 0.3672 0.4426      5.7231      5.7222|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.7732  1381   153  0.77  27.67   0.86     0.79      47154.66|
|  2:  4.7732 -  3.8090  1323   149  0.83  23.03   0.96     0.89      49766.49|
|  3:  3.8090 -  3.3335  1309   146  0.81  25.84   0.97     0.93      46307.08|
|  4:  3.3335 -  3.0315  1292   136  0.79  27.92   0.96     0.91      38509.80|
|  5:  3.0315 -  2.8157  1284   145  0.72  33.36   0.97     0.88      33047.03|
|  6:  2.8157 -  2.6507  1278   146  0.70  35.30   0.98     0.86      30667.89|
|  7:  2.6507 -  2.5186  1286   140  0.68  36.96   0.99     0.85      29157.15|
|  8:  2.5186 -  2.4094  1263   142  0.68  37.28   0.99     0.87      27947.58|
|  9:  2.4094 -  2.3170  1274   143  0.67  38.25   0.99     0.88      25663.44|
| 10:  2.3170 -  2.2373  1248   135  0.68  37.95   1.01     0.88      23727.54|
| 11:  2.2373 -  2.1676  1260   146  0.67  38.56   1.01     0.91      22843.68|
| 12:  2.1676 -  2.1058  1262   134  0.64  41.36   1.01     0.88      22806.47|
| 13:  2.1058 -  2.0505  1260   141  0.59  45.14   0.98     0.81      23011.97|
| 14:  2.0505 -  2.0006   910   103  0.51  51.31   1.03     0.69      22907.91|
|alpha:            min =        0.69 max =            0.93 mean =         0.86|
|beta:             min =    22806.47 max =        49766.49 mean =     32074.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.97 mean =        35.26|
|phase err.(test): min =        0.00 max =           89.75 mean =        35.58|
|-----------------------------------------------------------------------------|

============================== 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 = 6.962405              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.228   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.709439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.948   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      183 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1978 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2798 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4571 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4336 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5611 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6703 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.146 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3353   r_free= 0.3251   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.092415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3197   r_free= 0.3090   ksol= 0.31   Bsol= 50.00   scale= 0.970   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.39,3.56,-1.03,0.00,-0.00,-0.00); trace/3= -0.29                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.067102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.488062              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.183   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.395728              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.784   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3197      final r-factor (work) = 0.1847          |
| start r-factor (free) = 0.3090      final r-factor (free) = 0.2046          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8644 = 6.49 * 0.50 * 6.0736 + 1.00 * 0.1615                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8204 = 6.49 * 0.50 * 5.7691 + 1.00 * 0.1051                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1847      final r-factor (work) = 0.1668          |
| start r-factor (free) = 0.2046      final r-factor (free) = 0.2065          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2894 = 0.40 * 1.00 * 5.7691 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1766 = 0.40 * 1.00 * 5.4708 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.82   17.11    None  None   None       |
|    all(noH): 2823   0      0.00    77.82   17.11    None  None   None       |
|    Sol.    : 438    0      6.12    77.82   39.67    None  None   None       |
|    Mac.    : 2385   0      0.00    73.31   12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.782:  558   |   5:    38.910 -  46.692:  113        |
|      1:     7.782 -  15.564: 1300   |   6:    46.692 -  54.474:   80        |
|      2:    15.564 -  23.346:  422   |   7:    54.474 -  62.256:   63        |
|      3:    23.346 -  31.128:  145   |   8:    62.256 -  70.038:   26        |
|      4:    31.128 -  38.910:  107   |   9:    70.038 -  77.820:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1668 r_free = 0.2065             target_work(ml) = 5.477         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1665 r_free = 0.2064             target_work(ml) = 5.476         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1665   r_free= 0.2064   ksol= 0.31   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.39,3.56,-1.03,0.00,-0.00,-0.00); trace/3= -0.29                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.475601                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1629   r_free= 0.2019   ksol= 0.33   Bsol= 66.35   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-0.29,-1.18,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459252                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.965604              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.591   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216324              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.620   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1629      final r-factor (work) = 0.1284          |
| start r-factor (free) = 0.2019      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2170 = 2.97 * 0.50 * 5.4707 + 1.00 * 0.1051                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0047 = 2.97 * 0.50 * 5.3551 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1231          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1698 = 0.22 * 1.00 * 5.3551 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1404 = 0.22 * 1.00 * 5.2186 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.99   16.74    None  None   None       |
|    all(noH): 2823   0      0.00    80.99   16.74    None  None   None       |
|    Sol.    : 438    0      5.68    78.07   38.88    None  None   None       |
|    Mac.    : 2385   0      0.00    80.99   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.099:  606   |   5:    40.494 -  48.593:  113        |
|      1:     8.099 -  16.198: 1368   |   6:    48.593 -  56.692:   82        |
|      2:    16.198 -  24.296:  341   |   7:    56.692 -  64.790:   45        |
|      3:    24.296 -  32.395:  129   |   8:    64.790 -  72.889:   13        |
|      4:    32.395 -  40.494:  120   |   9:    72.889 -  80.988:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1231 r_free = 0.1602             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1229 r_free = 0.1602             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1602   ksol= 0.33   Bsol= 66.35   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-0.29,-1.18,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204073                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1598   ksol= 0.33   Bsol= 62.19   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-1.17,-0.97,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201755                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.215824              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.703  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.233838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.115   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4529 = 3.22 * 0.50 * 5.2172 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3736 = 3.22 * 0.50 * 5.1601 + 1.00 * 0.0766                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2156 = 0.23 * 1.00 * 5.1601 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2099 = 0.23 * 1.00 * 5.1393 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    81.69   16.48    None  None   None       |
|    all(noH): 2823   0      1.09    81.69   16.48    None  None   None       |
|    Sol.    : 438    0      5.44    77.65   38.43    None  None   None       |
|    Mac.    : 2385   0      1.09    81.69   12.45    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:     1.089 -   9.149:  892   |   5:    41.389 -  49.449:  106        |
|      1:     9.149 -  17.209: 1175   |   6:    49.449 -  57.508:   77        |
|      2:    17.209 -  25.269:  278   |   7:    57.508 -  65.568:   39        |
|      3:    25.269 -  33.329:  125   |   8:    65.568 -  73.628:   11        |
|      4:    33.329 -  41.389:  114   |   9:    73.628 -  81.688:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1557             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1557             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1557   ksol= 0.33   Bsol= 62.19   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-1.17,-0.97,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.137206                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1557   ksol= 0.32   Bsol= 58.10   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.32,-0.76,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.136743                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.747380              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.972  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.683811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.664  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1365 = 2.75 * 0.50 * 5.1394 + 1.00 * 0.0766                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1241 = 2.75 * 0.50 * 5.1353 + 1.00 * 0.0697                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5196 = 0.68 * 1.00 * 5.1353 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5187 = 0.68 * 1.00 * 5.1321 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.15   16.42    None  None   None       |
|    all(noH): 2823   0      0.00    85.15   16.42    None  None   None       |
|    Sol.    : 438    0      5.53    77.31   38.91    None  None   None       |
|    Mac.    : 2385   0      0.00    85.15   12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.515:  821   |   5:    42.577 -  51.093:  109        |
|      1:     8.515 -  17.031: 1241   |   6:    51.093 -  59.608:   81        |
|      2:    17.031 -  25.546:  285   |   7:    59.608 -  68.123:   33        |
|      3:    25.546 -  34.062:  129   |   8:    68.123 -  76.639:    8        |
|      4:    34.062 -  42.577:  112   |   9:    76.639 -  85.154:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1577             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1578             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1578   ksol= 0.32   Bsol= 58.10   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.32,-0.76,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.138379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1577   ksol= 0.32   Bsol= 58.10   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.19,-0.51,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.138415                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.969721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.239  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.557733              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.545  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6917 = 2.97 * 0.50 * 5.1331 + 1.00 * 0.0697                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6967 = 2.97 * 0.50 * 5.1339 + 1.00 * 0.0735                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 43.9439 = 8.56 * 1.00 * 5.1339 + 1.00 * 0.0092                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 43.9276 = 8.56 * 1.00 * 5.1318 + 1.00 * 0.0111                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.23   16.59    None  None   None       |
|    all(noH): 2823   0      0.00    99.23   16.59    None  None   None       |
|    Sol.    : 438    0      5.19    86.60   40.31    None  None   None       |
|    Mac.    : 2385   0      0.00    99.23   12.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.923: 1215   |   5:    49.616 -  59.539:   92        |
|      1:     9.923 -  19.846:  977   |   6:    59.539 -  69.463:   54        |
|      2:    19.846 -  29.770:  215   |   7:    69.463 -  79.386:   16        |
|      3:    29.770 -  39.693:  130   |   8:    79.386 -  89.309:    6        |
|      4:    39.693 -  49.616:  114   |   9:    89.309 -  99.232:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1596             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1597             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1597   ksol= 0.32   Bsol= 58.10   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.19,-0.51,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.136487                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7732 0.99   1381  153 0.0966 0.1326      5.3817      5.5277|
|  2:  4.7732 -  3.8090 0.99   1323  149 0.0813 0.1085      5.4115      5.6214|
|  3:  3.8090 -  3.3335 0.99   1309  146 0.1003 0.1459      5.4455      5.8434|
|  4:  3.3335 -  3.0315 0.99   1292  136 0.1160 0.1555      5.4334      5.5884|
|  5:  3.0315 -  2.8157 0.99   1284  145 0.1279 0.1751      5.3186      5.5573|
|  6:  2.8157 -  2.6507 0.99   1278  146 0.1215 0.1947      5.2286      5.4825|
|  7:  2.6507 -  2.5186 0.99   1286  140 0.1199 0.1663      5.1489      5.3481|
|  8:  2.5186 -  2.4094 0.98   1263  142 0.1124 0.1746      5.0789       5.379|
|  9:  2.4094 -  2.3170 0.98   1274  143 0.1128 0.1844      5.0131      5.2963|
| 10:  2.3170 -  2.2373 0.98   1248  135 0.1084 0.1791      4.9852      5.2351|
| 11:  2.2373 -  2.1676 1.00   1260  146 0.1108 0.1832      4.9364      5.2984|
| 12:  2.1676 -  2.1058 0.97   1262  134 0.1085 0.1619      4.8801      5.1692|
| 13:  2.1058 -  2.0505 0.98   1260  141 0.1081 0.1767       4.787      5.0683|
| 14:  2.0505 -  2.0006 0.72    910  103 0.0998 0.1877      4.6713      5.0013|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.7732  1381   153  0.94   9.43   0.97     0.94       7570.21|
|  2:  4.7732 -  3.8090  1323   149  0.95   7.85   1.00     0.99       8874.96|
|  3:  3.8090 -  3.3335  1309   146  0.94  10.91   1.02     1.02      10000.74|
|  4:  3.3335 -  3.0315  1292   136  0.92  13.16   1.00     0.99      10114.71|
|  5:  3.0315 -  2.8157  1284   145  0.90  15.98   0.99     0.96       8515.69|
|  6:  2.8157 -  2.6507  1278   146  0.90  16.46   0.97     0.94       7390.61|
|  7:  2.6507 -  2.5186  1286   140  0.90  15.67   0.98     0.96       6286.13|
|  8:  2.5186 -  2.4094  1263   142  0.91  15.35   0.98     0.95       5593.08|
|  9:  2.4094 -  2.3170  1274   143  0.90  15.82   0.98     0.94       5002.42|
| 10:  2.3170 -  2.2373  1248   135  0.90  16.07   0.98     0.94       4782.65|
| 11:  2.2373 -  2.1676  1260   146  0.90  16.14   0.98     0.94       4440.98|
| 12:  2.1676 -  2.1058  1262   134  0.91  15.63   0.99     0.97       4111.85|
| 13:  2.1058 -  2.0505  1260   141  0.90  15.81   0.97     0.95       3410.29|
| 14:  2.0505 -  2.0006   910   103  0.91  15.06   0.95     0.91       2686.58|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2686.58 max =        10114.71 mean =      6452.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.16|
|phase err.(test): min =        0.00 max =           87.95 mean =        13.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1595   ksol= 0.32   Bsol= 58.74   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-0.91,-0.22,-0.00,-0.00,-0.00); trace/3= -0.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.136520                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1595   ksol= 0.32   Bsol= 58.74   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-0.91,-0.22,-0.00,-0.00,-0.00); trace/3= -0.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.136520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7732 0.99   1381  153 0.0966 0.1328      5.3821       5.529|
|  2:  4.7732 -  3.8090 0.99   1323  149 0.0814 0.1086       5.413      5.6224|
|  3:  3.8090 -  3.3335 0.99   1309  146 0.1004 0.1460       5.446      5.8438|
|  4:  3.3335 -  3.0315 0.99   1292  136 0.1159 0.1555      5.4331      5.5884|
|  5:  3.0315 -  2.8157 0.99   1284  145 0.1278 0.1750       5.318      5.5566|
|  6:  2.8157 -  2.6507 0.99   1278  146 0.1214 0.1946      5.2282      5.4818|
|  7:  2.6507 -  2.5186 0.99   1286  140 0.1199 0.1663      5.1488      5.3483|
|  8:  2.5186 -  2.4094 0.98   1263  142 0.1124 0.1745       5.079      5.3788|
|  9:  2.4094 -  2.3170 0.98   1274  143 0.1128 0.1844      5.0132      5.2964|
| 10:  2.3170 -  2.2373 0.98   1248  135 0.1083 0.1791      4.9852      5.2352|
| 11:  2.2373 -  2.1676 1.00   1260  146 0.1108 0.1830      4.9362      5.2981|
| 12:  2.1676 -  2.1058 0.97   1262  134 0.1084 0.1617      4.8798      5.1687|
| 13:  2.1058 -  2.0505 0.98   1260  141 0.1081 0.1766      4.7868      5.0681|
| 14:  2.0505 -  2.0006 0.72    910  103 0.0998 0.1876      4.6712       5.001|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.7732  1381   153  0.94   9.44   0.97     0.94       7591.03|
|  2:  4.7732 -  3.8090  1323   149  0.95   7.87   1.01     0.99       8895.58|
|  3:  3.8090 -  3.3335  1309   146  0.94  10.92   1.03     1.02      10013.01|
|  4:  3.3335 -  3.0315  1292   136  0.92  13.16   1.01     0.99      10109.54|
|  5:  3.0315 -  2.8157  1284   145  0.90  15.97   1.00     0.97       8506.13|
|  6:  2.8157 -  2.6507  1278   146  0.90  16.45   0.98     0.95       7382.27|
|  7:  2.6507 -  2.5186  1286   140  0.90  15.67   0.99     0.97       6283.22|
|  8:  2.5186 -  2.4094  1263   142  0.91  15.35   0.99     0.96       5592.51|
|  9:  2.4094 -  2.3170  1274   143  0.90  15.83   1.00     0.95       5003.83|
| 10:  2.3170 -  2.2373  1248   135  0.90  16.07   1.00     0.95       4780.96|
| 11:  2.2373 -  2.1676  1260   146  0.90  16.13   0.99     0.96       4438.45|
| 12:  2.1676 -  2.1058  1262   134  0.91  15.63   1.00     0.99       4109.15|
| 13:  2.1058 -  2.0505  1260   141  0.90  15.81   0.99     0.97       3408.12|
| 14:  2.0505 -  2.0006   910   103  0.91  15.06   0.97     0.93       2684.94|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2684.94 max =        10109.54 mean =      6453.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.16|
|phase err.(test): min =        0.00 max =           88.03 mean =        13.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.24   16.60    None  None   None       |
|    all(noH): 2823   0      0.00    99.24   16.60    None  None   None       |
|    Sol.    : 438    0      5.19    86.60   40.31    None  None   None       |
|    Mac.    : 2385   0      0.00    99.24   12.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.926: 1215   |   5:    49.619 -  59.542:   92        |
|      1:     9.926 -  19.849:  977   |   6:    59.542 -  69.465:   54        |
|      2:    19.849 -  29.773:  215   |   7:    69.465 -  79.389:   16        |
|      3:    29.773 -  39.696:  130   |   8:    79.389 -  89.312:    6        |
|      4:    39.696 -  49.619:  114   |   9:    89.312 -  99.235:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.468 - 4.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 300
   mapped sites are within: 0.757 - 4.875

peak=    5.823 closest distance to " NH2 ARG A  56 " =    2.367
peak=    5.227 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.208 closest distance to " CG  PRO A  54 " =    1.265
peak=    4.996 closest distance to " CB  GLN A 183 " =    1.315
peak=    4.969 closest distance to " CB  ARG A 275 " =    0.949
peak=    4.839 closest distance to " CB  SER A  63 " =    1.190
peak=    4.755 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.665 closest distance to " CG  PRO A 213 " =    1.200
peak=    4.610 closest distance to " C   PRO A 198 " =    1.472
peak=    4.566 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.555 closest distance to " CB  ARG A 190 " =    1.693
peak=    4.555 closest distance to " O   HOH Z 126 " =    1.845
peak=    4.490 closest distance to " O   HOH Z 298 " =    1.846
peak=    4.402 closest distance to " NE2 GLN A  11 " =    1.018
peak=    4.364 closest distance to " CB  ARG A  79 " =    1.339
peak=    4.362 closest distance to " O   HOH Z 203 " =    1.768
peak=    4.263 closest distance to " O   HOH Z 369 " =    2.260
peak=    4.255 closest distance to " CB  TYR A 169 " =    0.837
peak=    4.237 closest distance to " CB  PRO A  54 " =    0.878
peak=    4.235 closest distance to " O   HOH Z 142 " =    1.552
peak=    4.231 closest distance to " O   HOH Z  15 " =    2.141
peak=    4.206 closest distance to " CB  ASN A 148 " =    1.438
peak=    4.169 closest distance to " CB  GLU A 152 " =    1.110
peak=    4.161 closest distance to " O   HOH Z 403 " =    1.685
peak=    4.151 closest distance to " OD1 ASN A  69 " =    2.509
peak=    4.117 closest distance to " O   HOH Z 427 " =    2.995
peak=    4.116 closest distance to " CA  ALA A  51 " =    0.940
peak=    4.115 closest distance to " NZ  LYS A 117 " =    3.273
peak=    4.112 closest distance to " CB  GLU A 128 " =    1.138
peak=    4.099 closest distance to " O   HOH Z 234 " =    3.757
peak=    4.089 closest distance to " CB  ASP A 140 " =    1.027
peak=    4.089 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.071 closest distance to " O   HOH Z 236 " =    2.081
peak=    4.070 closest distance to " CZ  PHE A 218 " =    1.126
peak=    4.067 closest distance to " O   HOH Z 158 " =    3.093
peak=    4.062 closest distance to " O   HOH Z 180 " =    2.238
peak=    4.061 closest distance to " O   HOH Z 280 " =    3.012
peak=    4.050 closest distance to " CA  ARG A 195 " =    1.329
peak=    4.038 closest distance to " O   HOH Z 303 " =    2.194
peak=    4.025 closest distance to " O   HOH Z 423 " =    2.002
peak=    4.008 closest distance to " C   ILE A 106 " =    1.885
peak=    4.005 closest distance to " O   HOH Z 209 " =    2.263
peak=    3.995 closest distance to " CA  ALA A  21 " =    1.258
peak=    3.995 closest distance to " CG  PRO A  90 " =    1.136
peak=    3.991 closest distance to " O   HOH Z  97 " =    1.941
peak=    3.983 closest distance to " CB  GLU A 277 " =    3.685
peak=    3.970 closest distance to " CB  TRP A 266 " =    0.977
peak=    3.967 closest distance to " O   HOH Z  78 " =    1.656
peak=    3.962 closest distance to " O   HOH Z 193 " =    1.831
peak=    3.962 closest distance to " CG1 ILE A  33 " =    1.179
peak=    3.957 closest distance to " O   HOH Z 133 " =    2.625
peak=    3.950 closest distance to " CB  LEU A 228 " =    1.096
peak=    3.949 closest distance to " O   HOH Z 272 " =    1.861
peak=    3.945 closest distance to " O   HOH Z 147 " =    1.830
peak=    3.941 closest distance to " O   HOH Z 346 " =    1.667
peak=    3.935 closest distance to " CA  ARG A  36 " =    1.130
peak=    3.925 closest distance to " CB  ARG A  79 " =    0.918
peak=    3.913 closest distance to " CG  ARG A  66 " =    2.489
peak=    3.899 closest distance to " O   HOH Z  40 " =    1.825
peak=    3.897 closest distance to " CD2 LEU A 297 " =    0.842
peak=    3.880 closest distance to " O   HOH Z 250 " =    1.460
peak=    3.878 closest distance to " O   HOH Z 214 " =    2.204
peak=    3.862 closest distance to " O   SER A  87 " =    2.242
peak=    3.860 closest distance to " O   HOH Z 368 " =    2.152
peak=    3.857 closest distance to " O   HOH Z 359 " =    1.538
peak=    3.856 closest distance to " O   HOH Z 128 " =    2.022
peak=    3.855 closest distance to " CD  ARG A 269 " =    0.970
peak=    3.838 closest distance to " O   HOH Z  43 " =    1.955
peak=    3.829 closest distance to " O   HOH Z 126 " =    1.554
peak=    3.804 closest distance to " CB  VAL A 202 " =    1.523
peak=    3.803 closest distance to " CA  ASN A 176 " =    1.710
peak=    3.801 closest distance to " O   HOH Z 316 " =    3.131
peak=    3.793 closest distance to " O   HOH Z 189 " =    2.516
peak=    3.792 closest distance to " OG BSER A 164 " =    2.304
peak=    3.788 closest distance to " OD2 ASP A 298 " =    3.884
peak=    3.787 closest distance to " O   HOH Z 412 " =    3.762
peak=    3.782 closest distance to " ND2 ASN A 187 " =    1.409
peak=    3.764 closest distance to " CD1 LEU A 300 " =    1.178
peak=    3.759 closest distance to " O   HOH Z  44 " =    1.837
peak=    3.757 closest distance to " CB  VAL A 265 " =    1.229
peak=    3.752 closest distance to " O   HOH Z  68 " =    1.818
peak=    3.746 closest distance to " CB  SER A   3 " =    1.306
peak=    3.740 closest distance to " O   HOH Z 271 " =    2.833
peak=    3.734 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.730 closest distance to " O   HOH Z 406 " =    1.577
peak=    3.725 closest distance to " O   HOH Z 426 " =    1.608
peak=    3.716 closest distance to " CD2 TRP A 179 " =    1.350
peak=    3.713 closest distance to " NH2 ARG A 156 " =    1.170
peak=    3.703 closest distance to " O   HOH Z 183 " =    1.520
peak=    3.690 closest distance to " O   HOH Z 197 " =    2.816
peak=    3.684 closest distance to " O   HOH Z 371 " =    3.227
peak=    3.672 closest distance to " CD  LYS A 166 " =    1.327
peak=    3.672 closest distance to " CG2 ILE A 120 " =    1.025
peak=    3.671 closest distance to " O   HOH Z 126 " =    1.950
peak=    3.655 closest distance to " OG1 THR A 294 " =    2.449
peak=    3.654 closest distance to " CA  PRO A  54 " =    1.349
peak=    3.646 closest distance to " NH2BARG A 145 " =    2.201
peak=    3.642 closest distance to " CB  TRP A 179 " =    1.393
peak=    3.642 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.636 closest distance to " CG  PRO A 243 " =    1.093
peak=    3.629 closest distance to " CA  ASN A 215 " =    1.119
peak=    3.625 closest distance to " CA  THR A 221 " =    0.942
peak=    3.619 closest distance to " O   HOH Z 389 " =    1.937
peak=    3.619 closest distance to " CD BLYS A 290 " =    1.026
peak=    3.619 closest distance to " O   HOH Z 291 " =    1.508
peak=    3.616 closest distance to " CG1BVAL A  72 " =    1.719
peak=    3.614 closest distance to " O   HOH Z 261 " =    1.807
peak=    3.599 closest distance to " OD2 ASP A 286 " =    2.852
peak=    3.596 closest distance to " O   HOH Z 245 " =    1.295
peak=    3.590 closest distance to " CA  ALA A 160 " =    0.881
peak=    3.590 closest distance to " O   HOH Z 402 " =    1.421
peak=    3.589 closest distance to " O   HOH Z 279 " =    2.251
peak=    3.571 closest distance to " CB  ASN A  39 " =    0.823
peak=    3.569 closest distance to " O   HOH Z  19 " =    1.810
peak=    3.567 closest distance to " NH1AARG A 145 " =    1.251
peak=    3.561 closest distance to " ND1 HIS A  81 " =    1.664
peak=    3.561 closest distance to " CG2 VAL A 257 " =    0.878
peak=    3.560 closest distance to " O   HOH Z 391 " =    2.910
peak=    3.557 closest distance to " O   HOH Z  97 " =    2.405
peak=    3.557 closest distance to " O   HOH Z 285 " =    2.808
peak=    3.543 closest distance to " CG2 ILE A  20 " =    1.294
peak=    3.536 closest distance to " O   HOH Z 185 " =    1.743
peak=    3.533 closest distance to " CG  GLN A  58 " =    2.699
peak=    3.529 closest distance to " O   HOH Z 403 " =    1.380
peak=    3.524 closest distance to " CB  ASN A 215 " =    1.191
peak=    3.515 closest distance to " O   HOH Z 383 " =    2.197
peak=    3.515 closest distance to " O   HOH Z 305 " =    3.679
peak=    3.515 closest distance to " O   HOH Z  80 " =    1.675
peak=    3.513 closest distance to " O   HOH Z 258 " =    2.087
peak=    3.512 closest distance to " O   HOH Z  21 " =    1.825
peak=    3.511 closest distance to " O   HOH Z 299 " =    4.482
peak=    3.508 closest distance to " CD  ARG A 159 " =    0.821
peak=    3.507 closest distance to " CG2 THR A 221 " =    1.128
peak=    3.507 closest distance to " O   HOH Z 265 " =    2.195
peak=    3.503 closest distance to " O   HOH Z 421 " =    1.603
peak=    3.497 closest distance to " O   HOH Z  20 " =    1.471
peak=    3.489 closest distance to " CD  LYS A  76 " =    1.980
peak=    3.484 closest distance to " O   HOH Z  59 " =    2.377
peak=    3.483 closest distance to " O   HOH Z 425 " =    1.986
peak=    3.480 closest distance to " CA  ALA A  84 " =    1.278
peak=    3.478 closest distance to " CA  MET A  40 " =    1.140
peak=    3.475 closest distance to " O   HOH Z   1 " =    2.209
peak=    3.475 closest distance to " O   HOH Z 171 " =    1.831
peak=    3.469 closest distance to " NE2 GLN A  77 " =    3.259
peak=    3.469 closest distance to " CG2 VAL A 197 " =    1.134
peak=    3.468 closest distance to " CD1 ILE A 106 " =    0.826
peak=    3.463 closest distance to " CA  ALA A 291 " =    0.827
peak=    3.462 closest distance to " OG  SER A  22 " =    2.710
peak=    3.461 closest distance to " O   ASN A  74 " =    1.597
peak=    3.461 closest distance to " O   HOH Z 163 " =    1.489
peak=    3.459 closest distance to " O   HOH Z 148 " =    3.305
peak=    3.450 closest distance to " OE1 GLU A   2 " =    2.196
peak=    3.449 closest distance to " CA  ALA A 248 " =    1.216
peak=    3.443 closest distance to " CB  SER A 212 " =    1.055
peak=    3.442 closest distance to " CA  ALA A 295 " =    1.086
peak=    3.439 closest distance to " CA  MET A 105 " =    1.056
peak=    3.437 closest distance to " O   HOH Z 325 " =    2.372
peak=    3.437 closest distance to " O   HOH Z 361 " =    3.417
peak=    3.435 closest distance to " O   HOH Z 417 " =    3.064
peak=    3.435 closest distance to " O   HOH Z  54 " =    1.702
peak=    3.433 closest distance to " O   HOH Z 365 " =    2.915
peak=    3.432 closest distance to " CB  GLN A 103 " =    0.879
peak=    3.428 closest distance to " CB  ARG A 139 " =    0.925
peak=    3.426 closest distance to " CA  TYR A 116 " =    1.404
peak=    3.426 closest distance to " CB  GLU A  46 " =    1.007
peak=    3.420 closest distance to " O   HOH Z 411 " =    1.752
peak=    3.419 closest distance to " N   ASN A  39 " =    1.343
peak=    3.412 closest distance to " CB  ALA A 291 " =    1.335
peak=    3.410 closest distance to " O   HOH Z  10 " =    1.791
peak=    3.409 closest distance to " CB  THR A  31 " =    1.764
peak=    3.409 closest distance to " O   HOH Z 345 " =    1.637
peak=    3.404 closest distance to " CB  ALA A 248 " =    1.314
peak=    3.404 closest distance to " O   HOH Z 353 " =    2.786
peak=    3.404 closest distance to " CB  MET A  47 " =    1.001
peak=    3.403 closest distance to " O   HOH Z 193 " =    2.207
peak=    3.400 closest distance to " CA  LYS A 117 " =    1.254
peak=    3.398 closest distance to " O   ALA A 165 " =    1.476
peak=    3.396 closest distance to " O   HOH Z 132 " =    2.646
peak=    3.393 closest distance to " O   ALA A 158 " =    1.187
peak=    3.390 closest distance to " O   HOH Z 374 " =    2.715
peak=    3.384 closest distance to " CG1 VAL A 153 " =    0.990
peak=    3.378 closest distance to " O   HOH Z  66 " =    2.134
peak=    3.375 closest distance to " O   HOH Z 357 " =    2.058
peak=    3.371 closest distance to " CB  ILE A 120 " =    1.250
peak=    3.357 closest distance to " CB  MET A  40 " =    0.844
peak=    3.356 closest distance to " O   THR A 251 " =    1.149
peak=    3.353 closest distance to " NZ  LYS A  48 " =    1.299
peak=    3.349 closest distance to " O  BHOH Z 338 " =    2.313
peak=    3.348 closest distance to " OG BSER A 134 " =    2.938
peak=    3.347 closest distance to " CB  TYR A 169 " =    0.965
peak=    3.345 closest distance to " O   HOH Z  35 " =    2.468
peak=    3.341 closest distance to " CB  SER A  62 " =    0.805
peak=    3.340 closest distance to " CA  ASP A 140 " =    1.141
peak=    3.335 closest distance to " O   HOH Z 313 " =    1.915
peak=    3.334 closest distance to " CG BARG A 275 " =    1.389
peak=    3.332 closest distance to " CA  THR A 264 " =    0.893
peak=    3.330 closest distance to " O   THR A 220 " =    1.255
peak=    3.326 closest distance to " O   HOH Z 344 " =    3.176
peak=    3.325 closest distance to " NH2AARG A 275 " =    3.661
peak=    3.322 closest distance to " CB  SER A 141 " =    0.984
peak=    3.321 closest distance to " CB  TYR A 116 " =    0.792
peak=    3.320 closest distance to " O   HOH Z 380 " =    2.015
peak=    3.318 closest distance to " N   ASN A 127 " =    1.302
peak=    3.318 closest distance to " CA  ASP A 191 " =    0.881
peak=    3.318 closest distance to " O   HOH Z  88 " =    3.398
peak=    3.316 closest distance to " O   HOH Z 294 " =    1.478
peak=    3.314 closest distance to " CG  MET A 185 " =    1.126
peak=    3.308 closest distance to " CA  THR A 221 " =    1.324
peak=    3.305 closest distance to " O   HOH Z 345 " =    3.106
peak=    3.305 closest distance to " ND2 ASN A 110 " =    1.562
peak=    3.302 closest distance to " O   HOH Z 166 " =    3.773
peak=    3.302 closest distance to " CE1 TYR A 186 " =    1.279
peak=    3.301 closest distance to " O   HOH Z  64 " =    1.987
peak=    3.300 closest distance to " O   HOH Z 135 " =    1.753
peak=    3.296 closest distance to " O   HOH Z 173 " =    2.147
peak=    3.295 closest distance to " N   CYS A 260 " =    0.832
peak=    3.294 closest distance to " CD  GLU A 152 " =    0.757
peak=    3.293 closest distance to " O   HOH Z 422 " =    2.633
peak=    3.292 closest distance to " O   HOH Z 327 " =    1.550
peak=    3.287 closest distance to " N   ARG A 156 " =    1.430
peak=    3.286 closest distance to " CG  GLU A  37 " =    0.902
peak=    3.280 closest distance to " O   HOH Z 128 " =    2.341
peak=    3.276 closest distance to " CB  ALA A   1 " =    4.875
peak=    3.273 closest distance to " CB  GLN A  88 " =    1.195
peak=    3.268 closest distance to " CB  ASN A 142 " =    1.121
peak=    3.267 closest distance to " O   HOH Z  62 " =    2.178
peak=    3.262 closest distance to " O   HOH Z 134 " =    1.233
peak=    3.257 closest distance to " CB  SER A  26 " =    1.707
peak=    3.251 closest distance to " O   HOH Z 271 " =    2.188
peak=    3.249 closest distance to " CZ2 TRP A 179 " =    1.692
peak=    3.247 closest distance to " O   HOH Z 393 " =    3.202
peak=    3.246 closest distance to " CZ  PHE A  38 " =    1.284
peak=    3.238 closest distance to " CB  GLU A 236 " =    1.109
peak=    3.238 closest distance to " CA  MET A 188 " =    0.943
peak=    3.232 closest distance to " CB  THR A  52 " =    0.823
peak=    3.229 closest distance to " CB  SER A 273 " =    0.856
peak=    3.226 closest distance to " O   HOH Z 199 " =    1.535
peak=    3.226 closest distance to " CD1AILE A 234 " =    0.905
peak=    3.219 closest distance to " OD1BASN A 224 " =    2.279
peak=    3.218 closest distance to " CA  ALA A 158 " =    1.245
peak=    3.213 closest distance to " CA  ALA A 154 " =    0.999
peak=    3.213 closest distance to " CG  MET A 185 " =    1.018
peak=    3.212 closest distance to " CB  GLN A  89 " =    1.311
peak=    3.212 closest distance to " O   HOH Z 248 " =    1.726
peak=    3.209 closest distance to " O   HOH Z  44 " =    3.374
peak=    3.209 closest distance to " O   HOH Z 407 " =    2.849
peak=    3.205 closest distance to " CD2 HIS A  81 " =    1.052
peak=    3.197 closest distance to " O   HOH Z 361 " =    2.493
peak=    3.193 closest distance to " O   HOH Z 285 " =    1.458
peak=    3.191 closest distance to " O   ASP A 124 " =    1.236
peak=    3.189 closest distance to " CB  ALA A 248 " =    0.923
peak=    3.188 closest distance to " O   HOH Z 213 " =    1.721
peak=    3.184 closest distance to " O   HOH Z 171 " =    3.947
peak=    3.184 closest distance to " CG1 ILE A 151 " =    1.013
peak=    3.180 closest distance to " CA  VAL A 125 " =    1.141
peak=    3.175 closest distance to " CB  ALA A 227 " =    1.074
peak=    3.172 closest distance to " CA  SER A  87 " =    1.096
peak=    3.171 closest distance to " C   TYR A 214 " =    1.437
peak=    3.165 closest distance to " O   HOH Z 417 " =    2.107
peak=    3.164 closest distance to " CG  ARG A 219 " =    1.101
peak=    3.163 closest distance to " O   HOH Z  61 " =    1.482
peak=    3.160 closest distance to " CA  LEU A  83 " =    1.371
peak=    3.159 closest distance to " O   HOH Z 261 " =    1.540
peak=    3.156 closest distance to " O   TRP A 274 " =    1.969
peak=    3.155 closest distance to " NE2 GLN A  58 " =    3.088
peak=    3.149 closest distance to " O   HOH Z 273 " =    2.941
peak=    3.144 closest distance to " C   SER A  32 " =    1.076
peak=    3.141 closest distance to " N   VAL A 126 " =    1.476
peak=    3.139 closest distance to " CG  LYS A  76 " =    1.038
peak=    3.138 closest distance to " O   GLU A   2 " =    1.765
peak=    3.132 closest distance to " CD  LYS A 119 " =    1.359
peak=    3.131 closest distance to " CB  PHE A 204 " =    0.921
peak=    3.129 closest distance to " CE  LYS A  48 " =    1.020
peak=    3.127 closest distance to " O   HOH Z  48 " =    1.774
peak=    3.117 closest distance to " CG  LEU A 167 " =    1.215
peak=    3.113 closest distance to " O   HOH Z 293 " =    1.961
peak=    3.112 closest distance to " O   GLN A  88 " =    1.777
peak=    3.112 closest distance to " O   HOH Z 250 " =    1.547
peak=    3.109 closest distance to " NE2 HIS A 115 " =    1.028
peak=    3.107 closest distance to " OG  SER A 245 " =    1.605
peak=    3.102 closest distance to " CZ3 TRP A  85 " =    0.888
peak=    3.100 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.098 closest distance to " CB  GLN A 205 " =    1.034
peak=    3.089 closest distance to " O   HOH Z 387 " =    2.893
peak=    3.075 closest distance to " CG2BVAL A  72 " =    1.714
peak=    3.073 closest distance to " CB  ARG A 138 " =    0.952
peak=    3.068 closest distance to " OG  SER A  62 " =    2.856
peak=    3.042 closest distance to " CD  ARG A  66 " =    2.470
peak=    3.035 closest distance to " O   HOH Z 430 " =    1.554
peak=    3.034 closest distance to " O   HOH Z 383 " =    1.612
peak=    3.016 closest distance to " O   ALA A 242 " =    1.147
peak=    3.010 closest distance to " CA  LEU A 101 " =    1.714
peak=    3.005 closest distance to " O   HOH Z 374 " =    3.049

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.835 - 5.337
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.835 - 5.337

peak=   -4.815 closest distance to " O   HOH Z 266 " =    4.963
peak=   -4.482 closest distance to " CB  PRO A 243 " =    2.683
peak=   -4.437 closest distance to " CD  GLN A  58 " =    1.048
peak=   -4.420 closest distance to " C   HIS A 108 " =    1.102
peak=   -4.292 closest distance to " CD  ARG A 156 " =    2.087
peak=   -4.277 closest distance to " CD  ARG A  14 " =    3.390
peak=   -4.192 closest distance to " O   HOH Z 231 " =    2.355
peak=   -4.160 closest distance to " O   HOH Z  10 " =    1.559
peak=   -4.159 closest distance to " O   HOH Z 377 " =    2.074
peak=   -4.157 closest distance to " O   HOH Z 196 " =    1.977
peak=   -4.156 closest distance to " O   VAL A  67 " =    2.792
peak=   -4.121 closest distance to " CA  ASP A 298 " =    1.041
peak=   -4.117 closest distance to " OXT GLY A 302 " =    2.853
peak=   -4.106 closest distance to " CB  ALA A 161 " =    2.618
peak=   -4.079 closest distance to " O   HOH Z 198 " =    2.187
peak=   -4.060 closest distance to " CD1 LEU A 101 " =    2.424
peak=   -4.047 closest distance to " OE1 GLN A 223 " =    2.079
peak=   -4.046 closest distance to " O   HOH Z 372 " =    2.408
peak=   -4.007 closest distance to " CB  ASP A 132 " =    2.393
peak=   -3.993 closest distance to " CG1 VAL A 112 " =    2.583
peak=   -3.951 closest distance to " CG1 VAL A 250 " =    2.635
peak=   -3.922 closest distance to " O   HOH Z 394 " =    1.538
peak=   -3.907 closest distance to " OG BSER A 134 " =    1.296
peak=   -3.879 closest distance to " NE2 GLN A  88 " =    1.846
peak=   -3.870 closest distance to " O   HOH Z 292 " =    4.670
peak=   -3.859 closest distance to " O   HOH Z 283 " =    2.233
peak=   -3.858 closest distance to " OG  SER A  97 " =    2.270
peak=   -3.854 closest distance to " O   HOH Z  52 " =    1.463
peak=   -3.835 closest distance to " ND2 ASN A  45 " =    1.801
peak=   -3.822 closest distance to " N   ALA A  43 " =    2.731
peak=   -3.817 closest distance to " O   HOH Z  13 " =    1.724
peak=   -3.805 closest distance to " CD1 PHE A  59 " =    1.966
peak=   -3.804 closest distance to " CE2 TYR A  30 " =    2.725
peak=   -3.794 closest distance to " CE2 PHE A  61 " =    2.538
peak=   -3.789 closest distance to " CG2 ILE A 263 " =    2.334
peak=   -3.775 closest distance to " CZ3 TRP A 179 " =    1.197
peak=   -3.755 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.754 closest distance to " CG1 VAL A 112 " =    2.799
peak=   -3.751 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.737 closest distance to " O   PRO A 163 " =    2.144
peak=   -3.717 closest distance to " N   MET A 188 " =    1.937
peak=   -3.709 closest distance to " O   HOH Z 353 " =    2.248
peak=   -3.680 closest distance to " ND2 ASN A  45 " =    1.099
peak=   -3.655 closest distance to " CD1 LEU A  25 " =    2.480
peak=   -3.654 closest distance to " CB  ALA A 291 " =    2.346
peak=   -3.654 closest distance to " CB  PHE A 192 " =    2.064
peak=   -3.650 closest distance to " CB  ASN A  39 " =    2.397
peak=   -3.644 closest distance to " NH2 ARG A 159 " =    2.368
peak=   -3.640 closest distance to " O   HOH Z 311 " =    3.763
peak=   -3.637 closest distance to " CB  PHE A 208 " =    2.276
peak=   -3.634 closest distance to " O   HOH Z 114 " =    3.235
peak=   -3.634 closest distance to " O   HOH Z 166 " =    1.755
peak=   -3.632 closest distance to " O   VAL A  67 " =    2.960
peak=   -3.628 closest distance to " CB  TRP A  85 " =    2.449
peak=   -3.628 closest distance to " CD  GLN A 223 " =    1.495
peak=   -3.627 closest distance to " O   HOH Z 165 " =    1.922
peak=   -3.607 closest distance to " CD  ARG A 139 " =    1.604
peak=   -3.602 closest distance to " CD2 TYR A 293 " =    2.041
peak=   -3.587 closest distance to " ND2 ASN A 249 " =    2.435
peak=   -3.574 closest distance to " O   SER A 210 " =    1.845
peak=   -3.574 closest distance to " CE  MET A 105 " =    2.317
peak=   -3.569 closest distance to " O   HOH Z 389 " =    1.844
peak=   -3.561 closest distance to " NH2 ARG A  79 " =    2.059
peak=   -3.553 closest distance to " OD1 ASN A 148 " =    1.510
peak=   -3.551 closest distance to " O   HOH Z 211 " =    1.577
peak=   -3.547 closest distance to " C   LEU A 143 " =    1.085
peak=   -3.547 closest distance to " ND2 ASN A 187 " =    1.620
peak=   -3.537 closest distance to " O   HOH Z 171 " =    1.977
peak=   -3.528 closest distance to " CD  LYS A 289 " =    2.470
peak=   -3.525 closest distance to " CB  ALA A  43 " =    2.607
peak=   -3.521 closest distance to " CA  GLY A 203 " =    2.404
peak=   -3.514 closest distance to " O   HOH Z 393 " =    1.430
peak=   -3.508 closest distance to " CZ  TYR A 169 " =    1.805
peak=   -3.507 closest distance to " OG BSER A 134 " =    1.849
peak=   -3.503 closest distance to " O   HOH Z 407 " =    3.137
peak=   -3.497 closest distance to " CD  PRO A 213 " =    2.218
peak=   -3.493 closest distance to " O   HOH Z 166 " =    1.622
peak=   -3.491 closest distance to " OG BSER A 210 " =    2.146
peak=   -3.477 closest distance to " CD1 LEU A 228 " =    2.254
peak=   -3.465 closest distance to " OD1 ASP A 171 " =    1.587
peak=   -3.459 closest distance to " O   HOH Z 123 " =    2.313
peak=   -3.457 closest distance to " O   HOH Z   6 " =    1.611
peak=   -3.457 closest distance to " O   HOH Z 111 " =    1.563
peak=   -3.453 closest distance to " O   PHE A 218 " =    1.603
peak=   -3.448 closest distance to " NE2 GLN A 103 " =    1.750
peak=   -3.447 closest distance to " O   HOH Z 243 " =    1.992
peak=   -3.444 closest distance to " O   HOH Z   6 " =    2.213
peak=   -3.443 closest distance to " CG1 VAL A 112 " =    2.866
peak=   -3.438 closest distance to " O   HOH Z  37 " =    1.809
peak=   -3.436 closest distance to " CD1 ILE A 151 " =    2.356
peak=   -3.435 closest distance to " CD  ARG A 195 " =    5.183
peak=   -3.427 closest distance to " CE3 TRP A 150 " =    2.236
peak=   -3.424 closest distance to " OG  SER A  62 " =    1.764
peak=   -3.422 closest distance to " NH2 ARG A  79 " =    1.565
peak=   -3.419 closest distance to " CB  PHE A  16 " =    2.642
peak=   -3.418 closest distance to " N   THR A  52 " =    1.671
peak=   -3.415 closest distance to " CG2 VAL A 189 " =    2.240
peak=   -3.413 closest distance to " O   HOH Z 185 " =    2.385
peak=   -3.412 closest distance to " C   SER A 206 " =    1.532
peak=   -3.411 closest distance to " CB  ALA A 248 " =    2.273
peak=   -3.411 closest distance to " CG  GLU A   2 " =    1.861
peak=   -3.408 closest distance to " NE2 GLN A 194 " =    1.831
peak=   -3.405 closest distance to " CB  ASP A 286 " =    1.873
peak=   -3.403 closest distance to " CD2 TYR A 247 " =    2.424
peak=   -3.403 closest distance to " N   TYR A  68 " =    2.989
peak=   -3.402 closest distance to " O   HOH Z 177 " =    1.798
peak=   -3.396 closest distance to " O   HOH Z 193 " =    1.804
peak=   -3.395 closest distance to " O   HOH Z  71 " =    1.807
peak=   -3.394 closest distance to " O   HOH Z  43 " =    1.577
peak=   -3.386 closest distance to " CZ  PHE A  59 " =    1.777
peak=   -3.385 closest distance to " NH2AARG A 275 " =    5.337
peak=   -3.383 closest distance to " O   PRO A 198 " =    1.925
peak=   -3.381 closest distance to " O   ALA A  10 " =    1.749
peak=   -3.378 closest distance to " C   ALA A 158 " =    1.288
peak=   -3.373 closest distance to " O   HOH Z 234 " =    4.237
peak=   -3.369 closest distance to " CG2 ILE A  49 " =    2.749
peak=   -3.367 closest distance to " N   ALA A 248 " =    1.707
peak=   -3.352 closest distance to " CA  GLY A 133 " =    2.338
peak=   -3.345 closest distance to " CE BMET A  47 " =    1.987
peak=   -3.340 closest distance to " O   HOH Z  60 " =    2.165
peak=   -3.337 closest distance to " O   SER A 135 " =    1.546
peak=   -3.334 closest distance to " O   HOH Z 102 " =    1.508
peak=   -3.333 closest distance to " O   HOH Z 377 " =    1.799
peak=   -3.333 closest distance to " SG ACYS A 201 " =    2.014
peak=   -3.320 closest distance to " CG  ASP A 231 " =    0.835
peak=   -3.319 closest distance to " O   HOH Z 350 " =    2.093
peak=   -3.306 closest distance to " CZ2 TRP A 274 " =    1.075
peak=   -3.297 closest distance to " OD1 ASN A 187 " =    1.709
peak=   -3.290 closest distance to " CD2 LEU A 300 " =    2.873
peak=   -3.290 closest distance to " CG  GLU A 277 " =    1.084
peak=   -3.289 closest distance to " CB  TYR A  15 " =    2.217
peak=   -3.288 closest distance to " ND2 ASN A  60 " =    1.893
peak=   -3.286 closest distance to " O   HOH Z 134 " =    2.840
peak=   -3.285 closest distance to " CZ  PHE A 155 " =    1.266
peak=   -3.283 closest distance to " O   VAL A 189 " =    2.627
peak=   -3.278 closest distance to " N   ALA A 226 " =    2.098
peak=   -3.277 closest distance to " CG  PRO A 243 " =    1.860
peak=   -3.255 closest distance to " O   HOH Z 351 " =    1.493
peak=   -3.254 closest distance to " O   HOH Z 252 " =    3.994
peak=   -3.250 closest distance to " O   ASN A 187 " =    1.548
peak=   -3.244 closest distance to " NH2 ARG A  66 " =    2.067
peak=   -3.242 closest distance to " O   HOH Z  38 " =    1.549
peak=   -3.235 closest distance to " OD2 ASP A 171 " =    1.762
peak=   -3.235 closest distance to " CG  PRO A 163 " =    2.553
peak=   -3.234 closest distance to " CE3 TRP A 274 " =    2.523
peak=   -3.225 closest distance to " CG1AVAL A  41 " =    2.898
peak=   -3.223 closest distance to " CA  GLY A 241 " =    3.130
peak=   -3.222 closest distance to " OG ASER A 134 " =    1.340
peak=   -3.221 closest distance to " O   HOH Z  44 " =    2.108
peak=   -3.220 closest distance to " N   GLN A  58 " =    1.585
peak=   -3.218 closest distance to " O   ALA A 161 " =    1.716
peak=   -3.218 closest distance to " O   HOH Z 275 " =    1.486
peak=   -3.213 closest distance to " O   HOH Z 414 " =    1.596
peak=   -3.207 closest distance to " CA  GLY A 241 " =    2.325
peak=   -3.207 closest distance to " CG1 VAL A  78 " =    2.980
peak=   -3.205 closest distance to " OD1 ASP A 191 " =    1.663
peak=   -3.205 closest distance to " ND2BASN A 224 " =    1.725
peak=   -3.201 closest distance to " NH1 ARG A 195 " =    2.637
peak=   -3.196 closest distance to " O   HOH Z 290 " =    1.332
peak=   -3.194 closest distance to " CG  PHE A 283 " =    2.571
peak=   -3.194 closest distance to " CG  GLU A  53 " =    1.553
peak=   -3.189 closest distance to " CE2 PHE A 218 " =    2.447
peak=   -3.188 closest distance to " O   HOH Z 264 " =    1.780
peak=   -3.184 closest distance to " CB  ALA A  10 " =    2.192
peak=   -3.183 closest distance to " CE  MET A  93 " =    1.294
peak=   -3.179 closest distance to " O   HOH Z 149 " =    2.160
peak=   -3.178 closest distance to " CD2 LEU A 237 " =    2.186
peak=   -3.176 closest distance to " N   SER A 276 " =    1.426
peak=   -3.175 closest distance to " CB  ALA A 248 " =    2.134
peak=   -3.173 closest distance to " N   MET A 105 " =    2.580
peak=   -3.171 closest distance to " O   HOH Z 426 " =    1.574
peak=   -3.157 closest distance to " O   HOH Z 396 " =    1.842
peak=   -3.153 closest distance to " CG  LEU A  83 " =    1.974
peak=   -3.153 closest distance to " O   HOH Z  77 " =    2.019
peak=   -3.144 closest distance to " O   ASN A 301 " =    1.409
peak=   -3.143 closest distance to " O   HOH Z 128 " =    2.621
peak=   -3.140 closest distance to " CB  GLN A  11 " =    1.845
peak=   -3.139 closest distance to " O   HOH Z 106 " =    1.874
peak=   -3.129 closest distance to " O   GLY A 196 " =    1.162
peak=   -3.128 closest distance to " O   HOH Z 435 " =    2.612
peak=   -3.123 closest distance to " O   HOH Z 377 " =    1.846
peak=   -3.122 closest distance to " NH1BARG A 275 " =    2.223
peak=   -3.122 closest distance to " O   PRO A 198 " =    1.351
peak=   -3.116 closest distance to " O   MET A  40 " =    2.793
peak=   -3.106 closest distance to " O   HOH Z 385 " =    1.933
peak=   -3.104 closest distance to " O   HOH Z 256 " =    2.410
peak=   -3.103 closest distance to " O   ALA A  34 " =    2.346
peak=   -3.102 closest distance to " CD2 LEU A 237 " =    2.764
peak=   -3.091 closest distance to " CG  TRP A 266 " =    1.918
peak=   -3.080 closest distance to " O   HOH Z 357 " =    2.042
peak=   -3.079 closest distance to " CE3 TRP A  70 " =    1.877
peak=   -3.079 closest distance to " O   HOH Z 353 " =    2.184
peak=   -3.077 closest distance to " O   HOH Z 139 " =    3.021
peak=   -3.076 closest distance to " O   HOH Z 126 " =    1.803
peak=   -3.070 closest distance to " CD1 TYR A 247 " =    2.600
peak=   -3.070 closest distance to " CA  GLY A  98 " =    2.157
peak=   -3.036 closest distance to " CD2 TYR A 293 " =    2.153

================= 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    :  0.3353 0.3251   6.092415e+00   6.055202e+00
   1_bss:  0.3197 0.3090   6.067102e+00   6.023700e+00
   1_xyz:  0.1847 0.2046   5.537783e+00   5.638130e+00
   1_adp:  0.1668 0.2065   5.476579e+00   5.653015e+00
   1_occ:  0.1665 0.2064   5.475601e+00   5.652469e+00
   2_bss:  0.1629 0.2019   5.459252e+00   5.636817e+00
   2_xyz:  0.1284 0.1648   5.240286e+00   5.441482e+00
   2_adp:  0.1231 0.1602   5.204766e+00   5.410985e+00
   2_occ:  0.1229 0.1602   5.204073e+00   5.410819e+00
   3_bss:  0.1228 0.1598   5.201755e+00   5.407986e+00
   3_xyz:  0.1120 0.1564   5.144406e+00   5.382814e+00
   3_adp:  0.1110 0.1557   5.137216e+00   5.378010e+00
   3_occ:  0.1110 0.1557   5.137206e+00   5.378378e+00
   4_bss:  0.1109 0.1557   5.136743e+00   5.378153e+00
   4_xyz:  0.1104 0.1568   5.137817e+00   5.383554e+00
   4_adp:  0.1096 0.1577   5.138189e+00   5.390206e+00
   4_occ:  0.1096 0.1578   5.138379e+00   5.390745e+00
   5_bss:  0.1095 0.1577   5.138415e+00   5.390797e+00
   5_xyz:  0.1083 0.1585   5.135007e+00   5.393144e+00
   5_adp:  0.1081 0.1596   5.136364e+00   5.398013e+00
   5_occ:  0.1081 0.1597   5.136487e+00   5.398381e+00
   5_bss:  0.1079 0.1595   5.136520e+00   5.398401e+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:  0.307  50.001  -3.394   3.559  -1.032   0.000  -0.000  -0.000
   1_xyz:  0.307  50.001  -3.394   3.559  -1.032   0.000  -0.000  -0.000
   1_adp:  0.307  50.001  -3.394   3.559  -1.032   0.000  -0.000  -0.000
   1_occ:  0.307  50.001  -3.394   3.559  -1.032   0.000  -0.000  -0.000
   2_bss:  0.329  66.351  -3.101  -0.287  -1.183  -0.000  -0.000  -0.000
   2_xyz:  0.329  66.351  -3.101  -0.287  -1.183  -0.000  -0.000  -0.000
   2_adp:  0.329  66.351  -3.101  -0.287  -1.183  -0.000  -0.000  -0.000
   2_occ:  0.329  66.351  -3.101  -0.287  -1.183  -0.000  -0.000  -0.000
   3_bss:  0.327  62.188  -2.654  -1.167  -0.974  -0.000  -0.000  -0.000
   3_xyz:  0.327  62.188  -2.654  -1.167  -0.974  -0.000  -0.000  -0.000
   3_adp:  0.327  62.188  -2.654  -1.167  -0.974  -0.000  -0.000  -0.000
   3_occ:  0.327  62.188  -2.654  -1.167  -0.974  -0.000  -0.000  -0.000
   4_bss:  0.323  58.097  -2.359  -1.316  -0.755  -0.000  -0.000  -0.000
   4_xyz:  0.323  58.097  -2.359  -1.316  -0.755  -0.000  -0.000  -0.000
   4_adp:  0.323  58.097  -2.359  -1.316  -0.755  -0.000  -0.000  -0.000
   4_occ:  0.323  58.097  -2.359  -1.316  -0.755  -0.000  -0.000  -0.000
   5_bss:  0.323  58.097  -2.075  -1.186  -0.509  -0.000  -0.000  -0.000
   5_xyz:  0.323  58.097  -2.075  -1.186  -0.509  -0.000  -0.000  -0.000
   5_adp:  0.323  58.097  -2.075  -1.186  -0.509  -0.000  -0.000  -0.000
   5_occ:  0.323  58.097  -2.075  -1.186  -0.509  -0.000  -0.000  -0.000
   5_bss:  0.320  58.743  -1.740  -0.911  -0.217  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.290 0.7007  0.8616    32073.196
   1_bss:  34.124 0.7123  0.8645    28644.695
   1_xyz:  19.955 0.8625  0.9954    10847.297
   1_adp:  20.421 0.8571  0.9845    11012.352
   1_occ:  20.415 0.8571  0.9842    10996.453
   2_bss:  19.856 0.8628  0.9515    10588.198
   2_xyz:  15.291 0.9039  0.9728     6940.233
   2_adp:  14.602 0.9099  0.9672     6620.706
   2_occ:  14.590 0.9100  0.9671     6616.930
   3_bss:  14.526 0.9106  0.9660     6596.213
   3_xyz:  13.919 0.9157  0.9702     6281.819
   3_adp:  13.786 0.9169  0.9639     6251.731
   3_occ:  13.791 0.9169  0.9637     6253.251
   4_bss:  13.785 0.9170  0.9684     6251.364
   4_xyz:  13.842 0.9166  0.9673     6301.869
   4_adp:  13.964 0.9156  0.9584     6357.392
   4_occ:  13.970 0.9156  0.9582     6362.100
   5_bss:  13.971 0.9156  0.9659     6363.869
   5_xyz:  13.999 0.9154  0.9667     6407.552
   5_adp:  14.110 0.9145  0.9577     6446.984
   5_occ:  14.114 0.9145  0.9577     6451.237
   5_bss:  14.116 0.9145  0.9681     6452.765
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6146e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6146e-01
   1_xyz:   1.364  0.013  0.081 15.143  0.005  4.115   1.0512e-01
   1_adp:   1.364  0.013  0.081 15.143  0.005  4.115   1.0512e-01
   1_occ:   1.364  0.013  0.081 15.143  0.005  4.115   1.0512e-01
   2_bss:   1.364  0.013  0.081 15.143  0.005  4.115   1.0512e-01
   2_xyz:   1.053  0.008  0.077 14.691  0.004  4.129   6.4133e-02
   2_adp:   1.053  0.008  0.077 14.691  0.004  4.129   6.4133e-02
   2_occ:   1.053  0.008  0.077 14.691  0.004  4.129   6.4133e-02
   3_bss:   1.053  0.008  0.077 14.691  0.004  4.129   6.4133e-02
   3_xyz:   1.110  0.011  0.085 14.890  0.005  4.115   7.6594e-02
   3_adp:   1.110  0.011  0.085 14.890  0.005  4.115   7.6594e-02
   3_occ:   1.110  0.011  0.085 14.890  0.005  4.115   7.6594e-02
   4_bss:   1.110  0.011  0.085 14.890  0.005  4.115   7.6594e-02
   4_xyz:   1.072  0.010  0.082 14.674  0.004  4.117   6.9737e-02
   4_adp:   1.072  0.010  0.082 14.674  0.004  4.117   6.9737e-02
   4_occ:   1.072  0.010  0.082 14.674  0.004  4.117   6.9737e-02
   5_bss:   1.072  0.010  0.082 14.674  0.004  4.117   6.9737e-02
   5_xyz:   1.099  0.010  0.084 14.734  0.004  4.118   7.3523e-02
   5_adp:   1.099  0.010  0.084 14.734  0.004  4.118   7.3523e-02
   5_occ:   1.099  0.010  0.084 14.734  0.004  4.118   7.3523e-02
   5_bss:   1.099  0.010  0.084 14.734  0.004  4.118   7.3523e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4266e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4266e-01
   1_xyz:   9.057  0.077  0.317 85.781  0.024  2.257   2.0007e-01
   1_adp:   9.057  0.077  0.317 85.781  0.024  2.257   2.0007e-01
   1_occ:   9.057  0.077  0.317 85.781  0.024  2.257   2.0007e-01
   2_bss:   9.057  0.077  0.317 85.781  0.024  2.257   2.0007e-01
   2_xyz:   7.390  0.056  0.237 82.891  0.046  2.318   5.3685e-02
   2_adp:   7.390  0.056  0.237 82.891  0.046  2.318   5.3685e-02
   2_occ:   7.390  0.056  0.237 82.891  0.046  2.318   5.3685e-02
   3_bss:   7.390  0.056  0.237 82.891  0.046  2.318   5.3685e-02
   3_xyz:   8.212  0.051  0.298 82.897  0.041  2.310   6.4004e-02
   3_adp:   8.212  0.051  0.298 82.897  0.041  2.310   6.4004e-02
   3_occ:   8.212  0.051  0.298 82.897  0.041  2.310   6.4004e-02
   4_bss:   8.212  0.051  0.298 82.897  0.041  2.310   6.4004e-02
   4_xyz:   7.918  0.052  0.271 81.760  0.041  2.352   5.1161e-02
   4_adp:   7.918  0.052  0.271 81.760  0.041  2.352   5.1161e-02
   4_occ:   7.918  0.052  0.271 81.760  0.041  2.352   5.1161e-02
   5_bss:   7.918  0.052  0.271 81.760  0.041  2.352   5.1161e-02
   5_xyz:   7.963  0.052  0.280 82.336  0.039  2.315   5.6856e-02
   5_adp:   7.963  0.052  0.280 82.336  0.039  2.315   5.6856e-02
   5_occ:   7.963  0.052  0.280 82.336  0.039  2.315   5.6856e-02
   5_bss:   7.963  0.052  0.280 82.336  0.039  2.315   5.6856e-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:  77.82   0.00  17.11  73.31   0.00  12.96  77.82   6.12  39.67
   1_occ:  77.82   0.00  17.11  73.31   0.00  12.96  77.82   6.12  39.67
   2_bss:  77.82   0.00  17.11  73.31   0.00  12.96  77.82   6.12  39.67
   2_xyz:  77.82   0.00  17.11  73.31   0.00  12.96  77.82   6.12  39.67
   2_adp:  80.99   0.00  16.74  80.99   0.00  12.67  78.07   5.68  38.88
   2_occ:  80.99   0.00  16.74  80.99   0.00  12.67  78.07   5.68  38.88
   3_bss:  80.99   0.00  16.74  80.99   0.00  12.67  78.07   5.68  38.88
   3_xyz:  80.99   0.00  16.74  80.99   0.00  12.67  78.07   5.68  38.88
   3_adp:  81.69   1.09  16.48  81.69   1.09  12.45  77.65   5.44  38.43
   3_occ:  81.69   1.09  16.48  81.69   1.09  12.45  77.65   5.44  38.43
   4_bss:  81.69   1.09  16.48  81.69   1.09  12.45  77.65   5.44  38.43
   4_xyz:  81.69   1.09  16.48  81.69   1.09  12.45  77.65   5.44  38.43
   4_adp:  85.15   0.00  16.42  85.15   0.00  12.30  77.31   5.53  38.91
   4_occ:  85.15   0.00  16.42  85.15   0.00  12.30  77.31   5.53  38.91
   5_bss:  85.15   0.00  16.42  85.15   0.00  12.30  77.31   5.53  38.91
   5_xyz:  85.15   0.00  16.42  85.15   0.00  12.30  77.31   5.53  38.91
   5_adp:  99.23   0.00  16.59  99.23   0.00  12.24  86.60   5.19  40.31
   5_occ:  99.23   0.00  16.59  99.23   0.00  12.24  86.60   5.19  40.31
   5_bss:  99.24   0.00  16.60  99.24   0.00  12.24  86.60   5.19  40.31
------------------------------------------------------------------------
 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:    1.013    0.026    0.387
   1_adp:    1.013    0.026    0.387
   1_occ:    1.013    0.026    0.387
   2_bss:    1.013    0.026    0.387
   2_xyz:    0.982    0.026    0.427
   2_adp:    0.982    0.026    0.427
   2_occ:    0.982    0.026    0.427
   3_bss:    0.982    0.026    0.427
   3_xyz:    0.986    0.055    0.464
   3_adp:    0.986    0.055    0.464
   3_occ:    0.986    0.055    0.464
   4_bss:    0.986    0.055    0.464
   4_xyz:    1.058    0.040    0.476
   4_adp:    1.058    0.040    0.476
   4_occ:    1.058    0.040    0.476
   5_bss:    1.058    0.040    0.476
   5_xyz:    1.091    0.034    0.481
   5_adp:    1.091    0.034    0.481
   5_occ:    1.091    0.034    0.481
   5_bss:    1.091    0.034    0.481
------------------------------------------------------------------------

CPU time actual refinement: 276.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_699/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_699/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_699/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_699/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_699/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 276.40 
  Macro-tasks:
    bulk solvent and scale       = 33.35  
    individual site refinement   = 116.92 
    weights calculation          = 23.88  
    collect and process          = 5.40   
    model show statistics        = 0.07   
    TOTAL for macro-tasks        = 179.62 
  Micro-tasks:
    mask                            = 1.01   
    f_calc                          = 87.51  
    alpha_beta                      = 6.62   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 96.45  
    fmodel                         = 5.26   
    r_factors                      = 0.12   
    phase_errors                   = 9.12   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 207.27 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.864 micro seconds
Total CPU time: 4.80 minutes
from_scatterers_fft:    660 calls, 87.17 s
gradients_fft:          605 calls, 84.21 s

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

# Date 2008-01-16 Time 05:26:09 PST -0800 (1200489969.41 s)
Start R-work = 0.3353, R-free = 0.3251 (no bulk solvent and anisotropic scale)
Final R-work = 0.1273, R-free = 0.1745 (no bulk solvent and anisotropic scale)

Start R-work = 0.3197, R-free = 0.3090
Final R-work = 0.1079, R-free = 0.1595