# Date 2008-01-16 Time 05:36:15 PST -0800 (1200490575.25 s)
#phil __OFF__

Command line arguments: "../802.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24117
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 802

-------------------------------------------------------------------------------
  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: (70.6012, 47.1647, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.74, per 1000 atoms: 0.97


================================== 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: (70.6012, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01033
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964405

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   2.0103

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: (70.6012, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01033
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964405

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.3012 [2138/2162]  1920   218  10.2%
  bin  2:  4.3012 -  3.4270 [2036/2056]  1838   198   9.7%
  bin  3:  3.4270 -  2.9976 [2019/2038]  1816   203  10.1%
  bin  4:  2.9976 -  2.7253 [1980/2010]  1776   204  10.3%
  bin  5:  2.7253 -  2.5309 [2002/2021]  1806   196   9.8%
  bin  6:  2.5309 -  2.3823 [1977/2002]  1778   199  10.1%
  bin  7:  2.3823 -  2.2634 [1960/1988]  1766   194   9.9%
  bin  8:  2.2634 -  2.1651 [1962/1998]  1766   196  10.0%
  bin  9:  2.1651 -  2.0820 [1946/1988]  1754   192   9.9%
  bin 10:  2.0820 -  2.0103 [1569/1986]  1410   159  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_802/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: 0.12 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:
        1.54 -     2.21: 7
        2.21 -     2.88: 1252
        2.88 -     3.56: 4351
        3.56 -     4.23: 9046
        4.23 -     4.90: 13156
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.540 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.713 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.713 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.802 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27807 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_802/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_802/model_refine_001.geo

CPU time processing inputs: 7.92


============================ 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 = 70.60125 47.16465 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3787   r_free= 0.3711   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.168837                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7971 0.99   1388  152 0.3134 0.3014       6.436       6.333|
|  2:  4.7971 -  3.8278 0.99   1319  152 0.3018 0.3067      6.6232      6.6927|
|  3:  3.8278 -  3.3499 0.99   1300  142 0.3446 0.2968      6.5422      6.4709|
|  4:  3.3499 -  3.0464 0.99   1308  142 0.3563 0.3734      6.3938      6.3697|
|  5:  3.0464 -  2.8295 0.99   1278  144 0.3911 0.3356      6.2541      6.2093|
|  6:  2.8295 -  2.6636 0.99   1286  143 0.3916 0.4542      6.1533      6.1319|
|  7:  2.6636 -  2.5309 0.99   1277  144 0.4039 0.3901      6.1291      6.0976|
|  8:  2.5309 -  2.4212 0.98   1270  138 0.4290 0.3837      6.1085       6.078|
|  9:  2.4212 -  2.3283 0.98   1266  143 0.4101 0.4108      6.0185      6.0212|
| 10:  2.3283 -  2.2482 1.00   1276  142 0.4428 0.4148      6.0537      6.0193|
| 11:  2.2482 -  2.1781 0.97   1249  134 0.4474 0.4454      5.9705       6.022|
| 12:  2.1781 -  2.1161 0.98   1244  141 0.4312 0.4306      5.9055      5.9902|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.4401 0.4415      5.8282      5.7815|
| 14:  2.0605 -  2.0103 0.71    904  106 0.4042 0.4115      5.7619      5.6929|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7971  1388   152  0.78  26.92   0.84     0.80      45818.19|
|  2:  4.7971 -  3.8278  1319   152  0.81  25.30   0.94     0.88      61922.83|
|  3:  3.8278 -  3.3499  1300   142  0.75  30.96   0.93     0.88      62656.29|
|  4:  3.3499 -  3.0464  1308   142  0.69  35.88   0.94     0.82      56661.46|
|  5:  3.0464 -  2.8295  1278   144  0.63  41.32   0.96     0.77      46166.70|
|  6:  2.8295 -  2.6636  1286   143  0.59  44.47   0.93     0.74      44181.25|
|  7:  2.6636 -  2.5309  1277   144  0.59  45.03   0.96     0.75      40469.42|
|  8:  2.5309 -  2.4212  1270   138  0.59  44.72   0.93     0.77      36714.03|
|  9:  2.4212 -  2.3283  1266   143  0.60  44.52   0.96     0.79      33460.32|
| 10:  2.3283 -  2.2482  1276   142  0.58  46.00   0.99     0.77      31245.68|
| 11:  2.2482 -  2.1781  1249   134  0.55  48.02   0.96     0.76      31825.97|
| 12:  2.1781 -  2.1161  1244   141  0.54  48.79   0.97     0.76      29591.65|
| 13:  2.1161 -  2.0605  1265   136  0.53  49.73   0.96     0.75      25937.46|
| 14:  2.0605 -  2.0103   904   106  0.57  47.07   1.00     0.72      20456.51|
|alpha:            min =        0.72 max =            0.88 mean =         0.78|
|beta:             min =    20456.51 max =        62656.29 mean =     41126.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.98 mean =        41.03|
|phase err.(test): min =        0.00 max =           89.91 mean =        40.81|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.151242              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.166   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.034646              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.427   (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 |  1.540 -  1.876:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.876 -  2.212:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.212 -  2.548:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.548 -  2.884:     1230 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.884 -  3.220:     1876 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.220 -  3.556:     2475 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.556 -  3.892:     4594 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.892 -  4.228:     4452 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.228 -  4.564:     5996 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7160 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.540 |       0.224 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3787   r_free= 0.3711   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.168837                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3630   r_free= 0.3557   ksol= 0.31   Bsol= 60.33   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-2.24,6.04,-0.00,0.00,0.00); trace/3= 0.26                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.146182                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.972722              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.877   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.569283              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.047   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3630      final r-factor (work) = 0.2239          |
| start r-factor (free) = 0.3557      final r-factor (free) = 0.2523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.6633 = 7.97 * 0.50 * 6.1448 + 1.00 * 0.1678                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6141 = 7.97 * 0.50 * 5.8972 + 1.00 * 0.1056                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2239      final r-factor (work) = 0.2062          |
| start r-factor (free) = 0.2523      final r-factor (free) = 0.2559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3642 = 0.57 * 1.00 * 5.8972 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3330 = 0.57 * 1.00 * 5.6553 + 1.00 * 0.1135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.31   16.80    None  None   None       |
|    all(noH): 2823   0      0.00    96.31   16.80    None  None   None       |
|    Sol.    : 438    0      4.65    64.23   38.34    None  None   None       |
|    Mac.    : 2385   0      0.00    96.31   12.84    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 -   9.631:  874   |   5:    48.154 -  57.785:   93        |
|      1:     9.631 -  19.262: 1204   |   6:    57.785 -  67.416:   19        |
|      2:    19.262 -  28.892:  336   |   7:    67.416 -  77.047:    0        |
|      3:    28.892 -  38.523:  146   |   8:    77.047 -  86.677:    0        |
|      4:    38.523 -  48.154:  150   |   9:    86.677 -  96.308:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2062 r_free = 0.2559             target_work(ml) = 5.661         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2058 r_free = 0.2560             target_work(ml) = 5.661         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2058   r_free= 0.2560   ksol= 0.31   Bsol= 60.33   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-2.24,6.04,-0.00,0.00,0.00); trace/3= 0.26                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.660693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2011   r_free= 0.2526   ksol= 0.34   Bsol= 73.70   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.33,1.24,-0.00,0.00,0.00); trace/3= -1.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.646642                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.328671              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.055   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.846506              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.075   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2011      final r-factor (work) = 0.1489          |
| start r-factor (free) = 0.2526      final r-factor (free) = 0.1889          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5204 = 3.33 * 0.50 * 5.6568 + 1.00 * 0.1056                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2573 = 3.33 * 0.50 * 5.5200 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1489      final r-factor (work) = 0.1359          |
| start r-factor (free) = 0.1889      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6975 = 0.85 * 1.00 * 5.5200 + 1.00 * 0.0247                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5172 = 0.85 * 1.00 * 5.3223 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.64   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    84.64   17.74    None  None   None       |
|    Sol.    : 438    0      5.18    84.64   43.27    None  None   None       |
|    Mac.    : 2385   0      0.00    79.94   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.464:  724   |   5:    42.318 -  50.782:   81        |
|      1:     8.464 -  16.927: 1270   |   6:    50.782 -  59.245:   94        |
|      2:    16.927 -  25.391:  311   |   7:    59.245 -  67.709:   66        |
|      3:    25.391 -  33.854:  135   |   8:    67.709 -  76.172:   30        |
|      4:    33.854 -  42.318:   98   |   9:    76.172 -  84.636:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1359 r_free = 0.1817             target_work(ml) = 5.303         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1358 r_free = 0.1815             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1815   ksol= 0.34   Bsol= 73.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.33,1.24,-0.00,0.00,0.00); trace/3= -1.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.302333                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1353   r_free= 0.1803   ksol= 0.34   Bsol= 79.25   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.10,0.22,-0.00,0.00,0.00); trace/3= -1.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.297335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.693717              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.861  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.730510              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.451  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1353      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2362 = 2.69 * 0.50 * 5.3206 + 1.00 * 0.0701                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1440 = 2.69 * 0.50 * 5.2516 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1668          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8481 = 0.73 * 1.00 * 5.2516 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8132 = 0.73 * 1.00 * 5.2042 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.96   17.43    None  None   None       |
|    all(noH): 2823   0      0.00    91.96   17.43    None  None   None       |
|    Sol.    : 438    0      0.00    91.96   42.76    None  None   None       |
|    Mac.    : 2385   0      0.00    87.66   12.78    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 -   9.196:  938   |   5:    45.981 -  55.177:   88        |
|      1:     9.196 -  18.392: 1162   |   6:    55.177 -  64.374:   81        |
|      2:    18.392 -  27.589:  257   |   7:    64.374 -  73.570:   33        |
|      3:    27.589 -  36.785:  126   |   8:    73.570 -  82.766:   24        |
|      4:    36.785 -  45.981:  108   |   9:    82.766 -  91.962:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1668             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1668             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1668   ksol= 0.34   Bsol= 79.25   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.10,0.22,-0.00,0.00,0.00); trace/3= -1.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.197248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1665   ksol= 0.33   Bsol= 71.35   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-1.72,0.26,-0.00,0.00,0.00); trace/3= -1.17                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.196887                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.937707              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.853  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.188481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.480  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1665      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7168 = 2.94 * 0.50 * 5.2054 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6864 = 2.94 * 0.50 * 5.1815 + 1.00 * 0.0756                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9879 = 0.19 * 1.00 * 5.1815 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9847 = 0.19 * 1.00 * 5.1800 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.19    84.52   16.40    None  None   None       |
|    all(noH): 2823   0      1.19    84.52   16.40    None  None   None       |
|    Sol.    : 438    0      1.74    84.52   38.48    None  None   None       |
|    Mac.    : 2385   0      1.19    79.43   12.34    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:     1.192 -   9.524: 1023   |   5:    42.854 -  51.187:   89        |
|      1:     9.524 -  17.857: 1088   |   6:    51.187 -  59.519:   71        |
|      2:    17.857 -  26.189:  248   |   7:    59.519 -  67.852:   30        |
|      3:    26.189 -  34.522:  129   |   8:    67.852 -  76.184:    9        |
|      4:    34.522 -  42.854:  130   |   9:    76.184 -  84.517:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1616             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1153 r_free = 0.1614             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1614   ksol= 0.33   Bsol= 71.35   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-1.72,0.26,-0.00,0.00,0.00); trace/3= -1.17                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170650                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1615   ksol= 0.32   Bsol= 61.20   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.74,0.08,-0.00,0.00,0.00); trace/3= -1.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170574                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.039683              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.110  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205046              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.578  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3577 = 2.04 * 0.50 * 5.1793 + 1.00 * 0.0756                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3427 = 2.04 * 0.50 * 5.1746 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0693 = 0.21 * 1.00 * 5.1746 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0696 = 0.21 * 1.00 * 5.1773 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    81.81   16.11    None  None   None       |
|    all(noH): 2823   0      1.21    81.81   16.11    None  None   None       |
|    Sol.    : 438    0      3.43    81.81   37.60    None  None   None       |
|    Mac.    : 2385   0      1.21    78.01   12.16    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:     1.207 -   9.268: 1002   |   5:    41.509 -  49.569:   95        |
|      1:     9.268 -  17.328: 1088   |   6:    49.569 -  57.629:   73        |
|      2:    17.328 -  25.388:  264   |   7:    57.629 -  65.689:   29        |
|      3:    25.388 -  33.448:  133   |   8:    65.689 -  73.750:   11        |
|      4:    33.448 -  41.509:  122   |   9:    73.750 -  81.810:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1624             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1624             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1624   ksol= 0.32   Bsol= 61.20   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.74,0.08,-0.00,0.00,0.00); trace/3= -1.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178329                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7971 0.99   1388  152 0.1052 0.1389      5.4438      5.5801|
|  2:  4.7971 -  3.8278 0.99   1319  152 0.0898 0.1194      5.4882      5.7002|
|  3:  3.8278 -  3.3499 0.99   1300  142 0.1077 0.1487      5.5027      5.8377|
|  4:  3.3499 -  3.0464 0.99   1308  142 0.1239 0.1633      5.4683      5.6167|
|  5:  3.0464 -  2.8295 0.99   1278  144 0.1394 0.1703      5.3642      5.5719|
|  6:  2.8295 -  2.6636 0.99   1286  143 0.1273 0.2134      5.2581      5.5607|
|  7:  2.6636 -  2.5309 0.99   1277  144 0.1339 0.1682      5.2177      5.3732|
|  8:  2.5309 -  2.4212 0.98   1270  138 0.1215 0.1659      5.1229       5.365|
|  9:  2.4212 -  2.3283 0.98   1266  143 0.1200 0.1895      5.0675      5.3357|
| 10:  2.3283 -  2.2482 1.00   1276  142 0.1195 0.1763      4.9922      5.2141|
| 11:  2.2482 -  2.1781 0.97   1249  134 0.1183 0.1677       4.961      5.2115|
| 12:  2.1781 -  2.1161 0.98   1244  141 0.1186 0.1808      4.9082      5.3001|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.1136 0.1771       4.816      5.0588|
| 14:  2.0605 -  2.0103 0.71    904  106 0.1022 0.1697      4.6755      4.9373|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7971  1388   152  0.94   9.86   0.97     0.94       8204.36|
|  2:  4.7971 -  3.8278  1319   152  0.95   8.55   1.00     0.98      10062.94|
|  3:  3.8278 -  3.3499  1300   142  0.93  11.41   1.01     1.00      10844.83|
|  4:  3.3499 -  3.0464  1308   142  0.92  13.77   0.99     0.98      10483.22|
|  5:  3.0464 -  2.8295  1278   144  0.90  15.91   0.99     0.96       8523.26|
|  6:  2.8295 -  2.6636  1286   143  0.89  16.88   0.97     0.95       7723.61|
|  7:  2.6636 -  2.5309  1277   144  0.90  16.37   0.98     0.95       6810.46|
|  8:  2.5309 -  2.4212  1270   138  0.90  15.86   0.98     0.96       5864.65|
|  9:  2.4212 -  2.3283  1266   143  0.91  15.75   0.99     0.96       5422.07|
| 10:  2.3283 -  2.2482  1276   142  0.90  16.24   0.99     0.95       4534.89|
| 11:  2.2482 -  2.1781  1249   134  0.90  16.06   0.98     0.94       4457.02|
| 12:  2.1781 -  2.1161  1244   141  0.90  16.24   0.99     0.97       4144.19|
| 13:  2.1161 -  2.0605  1265   136  0.90  16.16   0.98     0.96       3538.70|
| 14:  2.0605 -  2.0103   904   106  0.92  14.15   0.95     0.92       2555.98|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2555.98 max =        10844.83 mean =      6783.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.47|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.90|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1613   ksol= 0.32   Bsol= 61.33   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.66,0.13,-0.00,0.00,0.00); trace/3= -1.17                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.175111                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1613   ksol= 0.32   Bsol= 61.33   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.66,0.13,-0.00,0.00,0.00); trace/3= -1.17                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.175111                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7971 0.99   1388  152 0.1044 0.1305      5.4173      5.5304|
|  2:  4.7971 -  3.8278 0.99   1319  152 0.0902 0.1161      5.4754      5.6807|
|  3:  3.8278 -  3.3499 0.99   1300  142 0.1078 0.1476      5.4996       5.829|
|  4:  3.3499 -  3.0464 0.99   1308  142 0.1238 0.1646       5.468      5.6232|
|  5:  3.0464 -  2.8295 0.99   1278  144 0.1396 0.1704      5.3653        5.57|
|  6:  2.8295 -  2.6636 0.99   1286  143 0.1269 0.2142      5.2573      5.5627|
|  7:  2.6636 -  2.5309 0.99   1277  144 0.1338 0.1683      5.2182      5.3743|
|  8:  2.5309 -  2.4212 0.98   1270  138 0.1216 0.1661      5.1231      5.3646|
|  9:  2.4212 -  2.3283 0.98   1266  143 0.1201 0.1896      5.0676      5.3366|
| 10:  2.3283 -  2.2482 1.00   1276  142 0.1195 0.1764      4.9923      5.2146|
| 11:  2.2482 -  2.1781 0.97   1249  134 0.1183 0.1674      4.9608      5.2112|
| 12:  2.1781 -  2.1161 0.98   1244  141 0.1185 0.1805      4.9077      5.2989|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.1135 0.1774      4.8161      5.0596|
| 14:  2.0605 -  2.0103 0.71    904  106 0.1022 0.1697      4.6761       4.938|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7971  1388   152  0.94   9.35   0.96     0.94       7404.73|
|  2:  4.7971 -  3.8278  1319   152  0.95   8.14   1.00     0.98       9405.58|
|  3:  3.8278 -  3.3499  1300   142  0.93  11.25   1.01     1.01      10591.53|
|  4:  3.3499 -  3.0464  1308   142  0.92  13.78   0.99     0.98      10489.83|
|  5:  3.0464 -  2.8295  1278   144  0.90  15.97   0.99     0.96       8559.37|
|  6:  2.8295 -  2.6636  1286   143  0.89  16.88   0.97     0.95       7725.55|
|  7:  2.6636 -  2.5309  1277   144  0.90  16.39   0.98     0.95       6822.94|
|  8:  2.5309 -  2.4212  1270   138  0.90  15.86   0.98     0.96       5866.28|
|  9:  2.4212 -  2.3283  1266   143  0.91  15.76   1.00     0.96       5428.20|
| 10:  2.3283 -  2.2482  1276   142  0.90  16.24   0.99     0.95       4531.56|
| 11:  2.2482 -  2.1781  1249   134  0.90  16.06   0.98     0.94       4455.79|
| 12:  2.1781 -  2.1161  1244   141  0.90  16.23   0.99     0.98       4139.08|
| 13:  2.1161 -  2.0605  1265   136  0.90  16.17   0.98     0.96       3541.08|
| 14:  2.0605 -  2.0103   904   106  0.92  14.18   0.95     0.92       2562.53|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2562.53 max =        10591.53 mean =      6657.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.39|
|phase err.(test): min =        0.00 max =           88.26 mean =        13.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    81.77   16.07    None  None   None       |
|    all(noH): 2823   0      1.17    81.77   16.07    None  None   None       |
|    Sol.    : 438    0      3.39    81.77   37.56    None  None   None       |
|    Mac.    : 2385   0      1.17    77.97   12.12    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:     1.165 -   9.225: 1002   |   5:    41.466 -  49.527:   95        |
|      1:     9.225 -  17.286: 1088   |   6:    49.527 -  57.587:   73        |
|      2:    17.286 -  25.346:  264   |   7:    57.587 -  65.647:   29        |
|      3:    25.346 -  33.406:  133   |   8:    65.647 -  73.707:   11        |
|      4:    33.406 -  41.466:  122   |   9:    73.707 -  81.768:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 287         
Filter by distance & map next to the model:
   mapped sites are within: 0.515 - 4.900
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 287
   mapped sites are within: 0.710 - 4.900

peak=    5.392 closest distance to " CB  GLN A 223 " =    1.461
peak=    5.341 closest distance to " O   HOH Z 113 " =    2.179
peak=    5.101 closest distance to " CZ  PHE A 218 " =    1.127
peak=    5.018 closest distance to " CG  PRO A  54 " =    1.440
peak=    4.745 closest distance to " CB  PRO A  54 " =    0.983
peak=    4.687 closest distance to " CB  ARG A 190 " =    1.518
peak=    4.610 closest distance to " CG  PRO A 198 " =    1.372
peak=    4.598 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.580 closest distance to " CB  ARG A  79 " =    1.308
peak=    4.547 closest distance to " CB  GLN A 183 " =    1.225
peak=    4.530 closest distance to " CB  SER A  63 " =    1.172
peak=    4.508 closest distance to " O   HOH Z 232 " =    2.298
peak=    4.502 closest distance to " O   HOH Z 126 " =    1.817
peak=    4.485 closest distance to " O   HOH Z 188 " =    3.013
peak=    4.460 closest distance to " O   HOH Z 369 " =    2.105
peak=    4.429 closest distance to " ND2 ASN A 187 " =    1.522
peak=    4.408 closest distance to " O   HOH Z 298 " =    1.977
peak=    4.400 closest distance to " NE2 GLN A  11 " =    1.148
peak=    4.392 closest distance to " CB  ASN A 148 " =    1.471
peak=    4.368 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.283 closest distance to " CA  TYR A  30 " =    0.985
peak=    4.240 closest distance to " CB  GLU A 152 " =    1.233
peak=    4.239 closest distance to " O   HOH Z 142 " =    1.697
peak=    4.185 closest distance to " CG  PRO A 243 " =    1.067
peak=    4.170 closest distance to " O   HOH Z 368 " =    2.111
peak=    4.153 closest distance to " CG2 VAL A 257 " =    0.835
peak=    4.149 closest distance to " CB  GLU A 277 " =    3.726
peak=    4.140 closest distance to " CB  GLU A  46 " =    0.950
peak=    4.098 closest distance to " O   HOH Z  19 " =    2.459
peak=    4.090 closest distance to " O   HOH Z 406 " =    1.724
peak=    4.081 closest distance to " CD  LYS A 166 " =    1.279
peak=    4.079 closest distance to " CZ  PHE A  38 " =    1.280
peak=    4.078 closest distance to " CB  TYR A 169 " =    0.753
peak=    4.069 closest distance to " O   HOH Z  63 " =    2.013
peak=    4.064 closest distance to " CA  PRO A  54 " =    1.387
peak=    4.064 closest distance to " O   HOH Z 303 " =    2.142
peak=    4.052 closest distance to " O   SER A  87 " =    2.287
peak=    4.048 closest distance to " CB  LEU A  83 " =    0.756
peak=    4.011 closest distance to " O   HOH Z  15 " =    2.126
peak=    4.001 closest distance to " C   PRO A 198 " =    1.456
peak=    3.999 closest distance to " CD2 TRP A 179 " =    1.301
peak=    3.999 closest distance to " CB  VAL A 265 " =    1.271
peak=    3.996 closest distance to " CB  ASN A 142 " =    0.983
peak=    3.991 closest distance to " CB  ASP A 124 " =    0.794
peak=    3.990 closest distance to " CB  ASN A  39 " =    0.886
peak=    3.986 closest distance to " O   HOH Z 214 " =    2.232
peak=    3.981 closest distance to " CZ3 TRP A 266 " =    1.093
peak=    3.976 closest distance to " CG  MET A 185 " =    1.161
peak=    3.973 closest distance to " CB  ASN A 187 " =    1.212
peak=    3.971 closest distance to " CB  VAL A 202 " =    1.529
peak=    3.966 closest distance to " CB  TRP A 266 " =    1.003
peak=    3.965 closest distance to " CB  LEU A 228 " =    1.061
peak=    3.943 closest distance to " CA  ALA A  51 " =    0.920
peak=    3.932 closest distance to " CB  PRO A  90 " =    1.181
peak=    3.923 closest distance to " NH1AARG A 145 " =    1.373
peak=    3.912 closest distance to " O   HOH Z  21 " =    1.821
peak=    3.910 closest distance to " CE  LYS A  76 " =    0.923
peak=    3.906 closest distance to " O   HOH Z  40 " =    1.800
peak=    3.890 closest distance to " O   HOH Z 313 " =    2.019
peak=    3.884 closest distance to " CD  ARG A 269 " =    0.903
peak=    3.884 closest distance to " O   HOH Z 265 " =    2.158
peak=    3.880 closest distance to " CD  ARG A 159 " =    0.760
peak=    3.874 closest distance to " O   HOH Z 158 " =    3.150
peak=    3.870 closest distance to " CB  ALA A 104 " =    0.719
peak=    3.866 closest distance to " CA  THR A 264 " =    0.907
peak=    3.843 closest distance to " CD1 LEU A 300 " =    1.184
peak=    3.831 closest distance to " O   HOH Z  78 " =    1.628
peak=    3.825 closest distance to " O  BHOH Z 338 " =    2.313
peak=    3.818 closest distance to " O   HOH Z 180 " =    2.157
peak=    3.818 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.816 closest distance to " O   HOH Z  43 " =    2.006
peak=    3.798 closest distance to " O   HOH Z 427 " =    3.112
peak=    3.796 closest distance to " O   HOH Z 248 " =    1.602
peak=    3.771 closest distance to " CA  SER A  87 " =    1.012
peak=    3.766 closest distance to " O   HOH Z 403 " =    1.539
peak=    3.752 closest distance to " CG2 ILE A 120 " =    1.163
peak=    3.750 closest distance to " ND2 ASN A 249 " =    0.877
peak=    3.744 closest distance to " O   HOH Z 294 " =    1.587
peak=    3.740 closest distance to " O   HOH Z 261 " =    1.935
peak=    3.731 closest distance to " O   HOH Z 423 " =    1.946
peak=    3.729 closest distance to " CG1 VAL A 153 " =    1.009
peak=    3.728 closest distance to " O   HOH Z 148 " =    3.421
peak=    3.724 closest distance to " CG  LEU A 167 " =    1.263
peak=    3.713 closest distance to " O   ASN A  74 " =    1.427
peak=    3.703 closest distance to " CB  SER A 210 " =    0.778
peak=    3.695 closest distance to " O   HOH Z 236 " =    2.199
peak=    3.695 closest distance to " O   HOH Z 250 " =    1.481
peak=    3.694 closest distance to " O   HOH Z 193 " =    1.790
peak=    3.693 closest distance to " N   ASN A  39 " =    1.258
peak=    3.692 closest distance to " CB  GLU A 128 " =    0.894
peak=    3.676 closest distance to " O   HOH Z  88 " =    1.724
peak=    3.675 closest distance to " O   HOH Z 234 " =    3.890
peak=    3.665 closest distance to " O   HOH Z 128 " =    2.188
peak=    3.664 closest distance to " O   HOH Z 128 " =    2.158
peak=    3.649 closest distance to " O   HOH Z 172 " =    3.682
peak=    3.641 closest distance to " CA  ASP A 162 " =    0.966
peak=    3.641 closest distance to " O   HOH Z  62 " =    2.202
peak=    3.631 closest distance to " O   HOH Z 285 " =    2.228
peak=    3.631 closest distance to " O   HOH Z 346 " =    1.652
peak=    3.630 closest distance to " O   HOH Z 203 " =    1.742
peak=    3.620 closest distance to " O   HOH Z 209 " =    2.264
peak=    3.613 closest distance to " O   THR A 220 " =    1.220
peak=    3.612 closest distance to " CB  ASN A 110 " =    1.070
peak=    3.608 closest distance to " O   HOH Z 133 " =    2.798
peak=    3.604 closest distance to " CH2 TRP A  70 " =    0.951
peak=    3.604 closest distance to " CG2AVAL A  72 " =    1.716
peak=    3.601 closest distance to " CB  ASP A 140 " =    1.054
peak=    3.598 closest distance to " CB  MET A  40 " =    0.873
peak=    3.598 closest distance to " CA  ASN A 215 " =    1.079
peak=    3.595 closest distance to " O   HOH Z 316 " =    3.171
peak=    3.591 closest distance to " O   HOH Z 272 " =    1.896
peak=    3.574 closest distance to " CG  GLN A  11 " =    1.673
peak=    3.571 closest distance to " OG BSER A 134 " =    2.887
peak=    3.570 closest distance to " O   HOH Z 280 " =    2.967
peak=    3.565 closest distance to " O  BHOH Z  74 " =    1.251
peak=    3.552 closest distance to " CA  ARG A  36 " =    1.079
peak=    3.551 closest distance to " ND2 ASN A 249 " =    1.907
peak=    3.538 closest distance to " CD1 LEU A  96 " =    0.754
peak=    3.538 closest distance to " NE2 HIS A 207 " =    1.112
peak=    3.534 closest distance to " O   HOH Z 353 " =    2.605
peak=    3.529 closest distance to " CB  ILE A 120 " =    1.199
peak=    3.526 closest distance to " NZ  LYS A 117 " =    3.234
peak=    3.524 closest distance to " CB  GLN A  88 " =    1.184
peak=    3.521 closest distance to " CB  SER A   3 " =    1.421
peak=    3.520 closest distance to " CA  MET A 105 " =    0.981
peak=    3.515 closest distance to " O   HOH Z 419 " =    2.035
peak=    3.509 closest distance to " O   HOH Z 183 " =    1.441
peak=    3.509 closest distance to " CG AARG A 275 " =    1.194
peak=    3.503 closest distance to " O   HOH Z 368 " =    3.555
peak=    3.492 closest distance to " O   HOH Z 392 " =    2.809
peak=    3.490 closest distance to " O   HOH Z 383 " =    2.113
peak=    3.486 closest distance to " CB  ALA A 291 " =    1.119
peak=    3.480 closest distance to " O   HOH Z 394 " =    4.097
peak=    3.478 closest distance to " CA  ALA A 154 " =    1.042
peak=    3.477 closest distance to " NH2 ARG A 156 " =    1.100
peak=    3.472 closest distance to " CG2 ILE A 239 " =    0.712
peak=    3.470 closest distance to " O   HOH Z 291 " =    1.559
peak=    3.468 closest distance to " CA  ILE A 234 " =    0.924
peak=    3.458 closest distance to " O   HOH Z 163 " =    1.956
peak=    3.455 closest distance to " O   HOH Z 412 " =    3.998
peak=    3.449 closest distance to " O   HOH Z  10 " =    1.787
peak=    3.448 closest distance to " O   THR A 182 " =    1.336
peak=    3.448 closest distance to " CG  PHE A 204 " =    0.877
peak=    3.442 closest distance to " CA  TYR A 116 " =    1.411
peak=    3.441 closest distance to " O   HOH Z 147 " =    1.913
peak=    3.439 closest distance to " N   ARG A 156 " =    1.409
peak=    3.434 closest distance to " OD1 ASN A  69 " =    2.538
peak=    3.434 closest distance to " CD1 ILE A 199 " =    0.911
peak=    3.426 closest distance to " CA  VAL A 125 " =    1.197
peak=    3.424 closest distance to " O   HOH Z 251 " =    1.732
peak=    3.422 closest distance to " O   HOH Z 213 " =    1.956
peak=    3.415 closest distance to " O   HOH Z  68 " =    2.124
peak=    3.410 closest distance to " CA  GLN A  94 " =    0.775
peak=    3.407 closest distance to " O   HOH Z  61 " =    1.650
peak=    3.405 closest distance to " O   ALA A 165 " =    1.542
peak=    3.401 closest distance to " CB  PHE A 204 " =    0.726
peak=    3.390 closest distance to " O   HOH Z  48 " =    1.586
peak=    3.388 closest distance to " CA  ALA A 160 " =    1.054
peak=    3.382 closest distance to " CG2 ILE A  20 " =    1.357
peak=    3.381 closest distance to " O   HOH Z  97 " =    2.425
peak=    3.378 closest distance to " CB  GLU A  37 " =    1.044
peak=    3.370 closest distance to " CG  GLU A  37 " =    0.893
peak=    3.368 closest distance to " O   HOH Z 337 " =    3.592
peak=    3.366 closest distance to " O   HOH Z 273 " =    2.751
peak=    3.365 closest distance to " NE2 GLN A  77 " =    3.419
peak=    3.363 closest distance to " O   HOH Z 192 " =    2.058
peak=    3.361 closest distance to " O   HOH Z 126 " =    1.638
peak=    3.358 closest distance to " CB  TYR A 116 " =    0.789
peak=    3.358 closest distance to " CB  SER A 141 " =    1.047
peak=    3.354 closest distance to " O   HOH Z   1 " =    2.209
peak=    3.340 closest distance to " CA  ASN A 127 " =    1.150
peak=    3.340 closest distance to " CA  ALA A 233 " =    1.480
peak=    3.339 closest distance to " O   HOH Z 199 " =    1.597
peak=    3.336 closest distance to " CB  PRO A 198 " =    1.067
peak=    3.336 closest distance to " O   HOH Z 166 " =    3.944
peak=    3.331 closest distance to " O   PRO A 213 " =    1.510
peak=    3.331 closest distance to " CG2AVAL A 121 " =    2.301
peak=    3.328 closest distance to " O   HOH Z 359 " =    1.599
peak=    3.326 closest distance to " O   ASP A 191 " =    1.445
peak=    3.323 closest distance to " O   TYR A 116 " =    1.333
peak=    3.322 closest distance to " CB  GLN A 205 " =    1.109
peak=    3.321 closest distance to " CB  ALA A 114 " =    1.041
peak=    3.320 closest distance to " CD  ARG A  66 " =    2.392
peak=    3.319 closest distance to " N   PHE A 130 " =    1.193
peak=    3.314 closest distance to " N   TYR A 116 " =    1.443
peak=    3.311 closest distance to " OG BSER A 164 " =    2.402
peak=    3.311 closest distance to " CB  ASP A 298 " =    1.167
peak=    3.307 closest distance to " CA  ALA A 100 " =    0.856
peak=    3.306 closest distance to " O   HOH Z 305 " =    3.791
peak=    3.302 closest distance to " CB  ALA A 242 " =    0.792
peak=    3.302 closest distance to " O   HOH Z  78 " =    2.156
peak=    3.300 closest distance to " CB  ASN A 215 " =    1.134
peak=    3.299 closest distance to " O   ASN A  74 " =    2.130
peak=    3.293 closest distance to " O   HOH Z 116 " =    1.791
peak=    3.283 closest distance to " O   HOH Z 417 " =    3.462
peak=    3.283 closest distance to " O   HOH Z 325 " =    2.396
peak=    3.282 closest distance to " CD1 LEU A 261 " =    1.289
peak=    3.281 closest distance to " O   HOH Z 340 " =    2.131
peak=    3.281 closest distance to " O   HOH Z  66 " =    2.236
peak=    3.278 closest distance to " O   HOH Z  80 " =    1.692
peak=    3.275 closest distance to " O   HOH Z  94 " =    2.454
peak=    3.273 closest distance to " O   HOH Z 118 " =    1.834
peak=    3.271 closest distance to " CA  ARG A 139 " =    1.051
peak=    3.267 closest distance to " OE1 GLN A  11 " =    2.119
peak=    3.266 closest distance to " O   HOH Z 384 " =    2.994
peak=    3.261 closest distance to " N   GLY A  98 " =    1.119
peak=    3.260 closest distance to " O   HOH Z 271 " =    2.574
peak=    3.258 closest distance to " OE2 GLU A  53 " =    1.206
peak=    3.258 closest distance to " O   HOH Z 152 " =    2.074
peak=    3.256 closest distance to " CG  ARG A 138 " =    1.245
peak=    3.254 closest distance to " O   THR A 251 " =    1.095
peak=    3.249 closest distance to " CB  TRP A 179 " =    1.436
peak=    3.247 closest distance to " CB  ALA A 299 " =    0.948
peak=    3.244 closest distance to " CA  ASN A 217 " =    1.298
peak=    3.243 closest distance to " O   SER A 164 " =    1.441
peak=    3.243 closest distance to " CB  GLN A  89 " =    1.282
peak=    3.240 closest distance to " CG2 THR A 220 " =    0.859
peak=    3.237 closest distance to " CB  MET A  47 " =    0.976
peak=    3.236 closest distance to " NE  ARG A  79 " =    1.091
peak=    3.235 closest distance to " CB  ARG A 138 " =    1.037
peak=    3.234 closest distance to " O   PHE A 192 " =    1.409
peak=    3.233 closest distance to " O   HOH Z 365 " =    2.890
peak=    3.232 closest distance to " CB  SER A 212 " =    1.346
peak=    3.226 closest distance to " O   HOH Z 421 " =    1.996
peak=    3.225 closest distance to " CB  ALA A  34 " =    0.974
peak=    3.225 closest distance to " O   HOH Z 171 " =    4.056
peak=    3.222 closest distance to " CB  THR A  31 " =    1.550
peak=    3.221 closest distance to " CB  LYS A 117 " =    1.195
peak=    3.220 closest distance to " CG BARG A 275 " =    1.339
peak=    3.217 closest distance to " CA  ALA A 158 " =    1.275
peak=    3.212 closest distance to " CD BLYS A 290 " =    0.949
peak=    3.209 closest distance to " CB  PRO A 243 " =    1.389
peak=    3.207 closest distance to " CA  THR A 221 " =    0.975
peak=    3.205 closest distance to " OG  SER A  22 " =    2.700
peak=    3.199 closest distance to " CG1 ILE A  49 " =    1.546
peak=    3.193 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.191 closest distance to " OE2 GLU A  53 " =    1.878
peak=    3.189 closest distance to " CA  GLU A 152 " =    0.907
peak=    3.187 closest distance to " CA  GLY A 241 " =    0.838
peak=    3.186 closest distance to " O   HOH Z 299 " =    4.537
peak=    3.185 closest distance to " CD  ARG A 219 " =    1.111
peak=    3.183 closest distance to " CG BARG A 102 " =    1.875
peak=    3.178 closest distance to " O   GLY A  91 " =    1.420
peak=    3.173 closest distance to " CG2 ILE A 234 " =    0.839
peak=    3.170 closest distance to " CB  GLN A 103 " =    0.844
peak=    3.169 closest distance to " O   HOH Z 298 " =    2.455
peak=    3.169 closest distance to " CG2 THR A 221 " =    1.067
peak=    3.168 closest distance to " O   HOH Z 234 " =    1.810
peak=    3.164 closest distance to " CG  MET A 185 " =    0.988
peak=    3.163 closest distance to " CA  ASP A 191 " =    1.199
peak=    3.155 closest distance to " CA  ILE A 106 " =    0.810
peak=    3.154 closest distance to " OD1 ASN A 217 " =    1.694
peak=    3.148 closest distance to " CE3 TRP A 150 " =    1.074
peak=    3.140 closest distance to " O   PHE A  61 " =    1.414
peak=    3.130 closest distance to " O   HOH Z 120 " =    3.362
peak=    3.128 closest distance to " CB  ALA A   1 " =    4.900
peak=    3.125 closest distance to " N   ASN A 127 " =    1.242
peak=    3.123 closest distance to " CZ  PHE A 192 " =    1.012
peak=    3.121 closest distance to " CB  PHE A 283 " =    0.710
peak=    3.119 closest distance to " O   HOH Z 371 " =    2.899
peak=    3.114 closest distance to " CA  ALA A 129 " =    1.229
peak=    3.114 closest distance to " O   MET A 105 " =    1.912
peak=    3.110 closest distance to " CA  ALA A 248 " =    1.185
peak=    3.109 closest distance to " CE  MET A 113 " =    1.723
peak=    3.106 closest distance to " O   HOH Z  47 " =    1.812
peak=    3.096 closest distance to " OH  TYR A 116 " =    1.106
peak=    3.095 closest distance to " O   HOH Z 425 " =    1.313
peak=    3.091 closest distance to " OG1 THR A 294 " =    2.479
peak=    3.088 closest distance to " O   HOH Z 327 " =    2.034
peak=    3.087 closest distance to " CA  GLU A  46 " =    1.084
peak=    3.081 closest distance to " CB  ARG A 156 " =    1.169
peak=    3.076 closest distance to " O   HOH Z  59 " =    2.094
peak=    3.069 closest distance to " CA  GLY A 211 " =    1.335
peak=    3.068 closest distance to " CB  ALA A  43 " =    0.820
peak=    3.061 closest distance to " O   HOH Z   9 " =    1.989
peak=    3.058 closest distance to " O   HOH Z 421 " =    2.980
peak=    3.057 closest distance to " CG  ARG A 159 " =    0.877
peak=    3.042 closest distance to " O   ALA A 158 " =    1.228
peak=    3.040 closest distance to " O   HOH Z 358 " =    2.240
peak=    3.020 closest distance to " CB  PHE A 204 " =    0.716
peak=    3.009 closest distance to " O   THR A 220 " =    1.043

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.738 - 5.609
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 194
   mapped sites are within: 0.738 - 5.609

peak=   -4.869 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -4.810 closest distance to " CD  GLN A  58 " =    0.881
peak=   -4.699 closest distance to " CD  ARG A  14 " =    3.433
peak=   -4.524 closest distance to " O   HOH Z 211 " =    1.137
peak=   -4.368 closest distance to " O   PRO A 198 " =    1.272
peak=   -4.331 closest distance to " CZ3 TRP A 179 " =    1.221
peak=   -4.286 closest distance to " O   HOH Z 290 " =    1.049
peak=   -4.273 closest distance to " OG  SER A  97 " =    2.349
peak=   -4.258 closest distance to " CD  ARG A 156 " =    2.075
peak=   -4.204 closest distance to " CB  PRO A 243 " =    2.697
peak=   -4.149 closest distance to " O   VAL A  67 " =    2.724
peak=   -4.147 closest distance to " CD2 TYR A 293 " =    2.038
peak=   -4.135 closest distance to " C   HIS A 108 " =    1.122
peak=   -4.076 closest distance to " O   HOH Z 266 " =    5.609
peak=   -4.039 closest distance to " CA  VAL A  67 " =    2.978
peak=   -4.024 closest distance to " CG1 VAL A 112 " =    2.865
peak=   -4.024 closest distance to " O   HOH Z 196 " =    2.006
peak=   -3.994 closest distance to " O   HOH Z 231 " =    2.318
peak=   -3.946 closest distance to " CA  GLY A 241 " =    3.360
peak=   -3.915 closest distance to " CG1 VAL A 250 " =    2.751
peak=   -3.905 closest distance to " O   HOH Z 394 " =    1.547
peak=   -3.895 closest distance to " OD1 ASN A 148 " =    1.388
peak=   -3.879 closest distance to " CE2 PHE A  61 " =    2.676
peak=   -3.863 closest distance to " O   ALA A  10 " =    1.641
peak=   -3.859 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.850 closest distance to " O   HOH Z  73 " =    2.438
peak=   -3.846 closest distance to " CA  GLY A 241 " =    2.400
peak=   -3.788 closest distance to " NH2 ARG A  79 " =    1.542
peak=   -3.782 closest distance to " O   HOH Z 377 " =    2.041
peak=   -3.776 closest distance to " CA  ASP A 298 " =    1.151
peak=   -3.769 closest distance to " O   HOH Z  10 " =    1.538
peak=   -3.735 closest distance to " CD1 LEU A 101 " =    2.407
peak=   -3.722 closest distance to " CD2 PHE A 192 " =    2.054
peak=   -3.712 closest distance to " CG  GLN A 223 " =    2.002
peak=   -3.704 closest distance to " CB  ALA A  43 " =    2.634
peak=   -3.699 closest distance to " O   HOH Z 216 " =    1.038
peak=   -3.695 closest distance to " OG BSER A 134 " =    1.363
peak=   -3.678 closest distance to " O   HOH Z 166 " =    1.860
peak=   -3.667 closest distance to " NH2AARG A 275 " =    5.491
peak=   -3.652 closest distance to " O   HOH Z 372 " =    2.404
peak=   -3.648 closest distance to " CD  GLN A 223 " =    0.753
peak=   -3.648 closest distance to " N   THR A  52 " =    1.621
peak=   -3.646 closest distance to " O   SER A 210 " =    1.980
peak=   -3.646 closest distance to " C   MET A 188 " =    1.322
peak=   -3.645 closest distance to " CE BMET A  47 " =    1.642
peak=   -3.641 closest distance to " N   ALA A  43 " =    2.555
peak=   -3.637 closest distance to " O   HOH Z 185 " =    2.341
peak=   -3.635 closest distance to " O   ILE A 109 " =    2.568
peak=   -3.625 closest distance to " O   VAL A 189 " =    2.652
peak=   -3.619 closest distance to " O   HOH Z 174 " =    3.908
peak=   -3.617 closest distance to " CG  ARG A 269 " =    2.518
peak=   -3.604 closest distance to " CG2 ILE A  49 " =    2.892
peak=   -3.592 closest distance to " CG  MET A 105 " =    1.000
peak=   -3.584 closest distance to " CZ  PHE A 155 " =    1.186
peak=   -3.583 closest distance to " CB  HIS A  86 " =    1.173
peak=   -3.583 closest distance to " OD1 ASP A 171 " =    1.623
peak=   -3.576 closest distance to " CE  MET A 105 " =    2.352
peak=   -3.569 closest distance to " O   HOH Z 359 " =    3.068
peak=   -3.559 closest distance to " O   HOH Z  38 " =    1.534
peak=   -3.553 closest distance to " O   HOH Z 198 " =    1.959
peak=   -3.553 closest distance to " CG  GLU A 277 " =    1.235
peak=   -3.550 closest distance to " O   HOH Z 351 " =    1.554
peak=   -3.525 closest distance to " CB  ALA A 291 " =    2.332
peak=   -3.514 closest distance to " OXT GLY A 302 " =    2.993
peak=   -3.508 closest distance to " CE3 TRP A 150 " =    2.274
peak=   -3.499 closest distance to " ND2 ASN A  60 " =    1.311
peak=   -3.490 closest distance to " O   HOH Z  37 " =    1.801
peak=   -3.486 closest distance to " CB  ALA A 291 " =    2.396
peak=   -3.480 closest distance to " CD1 LEU A 255 " =    2.941
peak=   -3.476 closest distance to " CG  GLN A  11 " =    1.666
peak=   -3.471 closest distance to " CB  ASN A  39 " =    2.276
peak=   -3.464 closest distance to " ND2 ASN A 249 " =    2.446
peak=   -3.461 closest distance to " CD  PRO A 243 " =    2.177
peak=   -3.461 closest distance to " O   HOH Z 128 " =    2.641
peak=   -3.456 closest distance to " O   TYR A 247 " =    2.854
peak=   -3.448 closest distance to " NE2 GLN A 194 " =    1.949
peak=   -3.447 closest distance to " CG1 VAL A 125 " =    1.811
peak=   -3.441 closest distance to " O   HOH Z 176 " =    0.738
peak=   -3.440 closest distance to " CD  GLN A  88 " =    0.819
peak=   -3.440 closest distance to " O   HOH Z 407 " =    3.212
peak=   -3.438 closest distance to " CB  ASP A 286 " =    2.018
peak=   -3.433 closest distance to " CB  ALA A 129 " =    2.468
peak=   -3.426 closest distance to " O   VAL A 189 " =    1.594
peak=   -3.421 closest distance to " O   HOH Z 421 " =    3.209
peak=   -3.417 closest distance to " O   HOH Z 313 " =    1.898
peak=   -3.413 closest distance to " O   HOH Z 393 " =    1.306
peak=   -3.410 closest distance to " N   ALA A 248 " =    1.748
peak=   -3.399 closest distance to " CD  ARG A  79 " =    1.173
peak=   -3.393 closest distance to " CG2 ILE A 263 " =    2.348
peak=   -3.385 closest distance to " CG1BVAL A  41 " =    2.752
peak=   -3.379 closest distance to " O   ILE A 106 " =    1.935
peak=   -3.365 closest distance to " O   GLY A 211 " =    1.352
peak=   -3.359 closest distance to " O   HOH Z 174 " =    2.611
peak=   -3.359 closest distance to " CZ  PHE A  38 " =    2.066
peak=   -3.358 closest distance to " CA  GLY A 241 " =    2.891
peak=   -3.357 closest distance to " NE2 GLN A 278 " =    1.549
peak=   -3.350 closest distance to " O   HOH Z 134 " =    3.141
peak=   -3.349 closest distance to " ND2 ASN A  45 " =    1.878
peak=   -3.347 closest distance to " CG  GLU A  53 " =    1.583
peak=   -3.346 closest distance to " C   ASN A 285 " =    2.407
peak=   -3.342 closest distance to " O   HOH Z 232 " =    1.629
peak=   -3.341 closest distance to " O   HOH Z 149 " =    2.234
peak=   -3.333 closest distance to " CB  TRP A  85 " =    2.583
peak=   -3.333 closest distance to " O   HOH Z 102 " =    1.600
peak=   -3.331 closest distance to " C   ALA A 158 " =    1.451
peak=   -3.329 closest distance to " O   HOH Z  60 " =    1.964
peak=   -3.328 closest distance to " O   HOH Z  60 " =    1.305
peak=   -3.327 closest distance to " C   LEU A 143 " =    1.084
peak=   -3.324 closest distance to " O   PHE A 218 " =    1.506
peak=   -3.324 closest distance to " CD  GLN A 223 " =    0.811
peak=   -3.309 closest distance to " O   HOH Z 106 " =    1.960
peak=   -3.308 closest distance to " O   HOH Z 278 " =    1.152
peak=   -3.298 closest distance to " CG2 VAL A 189 " =    2.180
peak=   -3.295 closest distance to " O   HOH Z  51 " =    1.806
peak=   -3.294 closest distance to " CG  LEU A  83 " =    1.991
peak=   -3.292 closest distance to " O   HOH Z 311 " =    3.810
peak=   -3.289 closest distance to " OH  TYR A 247 " =    2.201
peak=   -3.287 closest distance to " CB  PRO A 163 " =    2.477
peak=   -3.287 closest distance to " CD  GLN A  73 " =    0.805
peak=   -3.285 closest distance to " CB  ALA A 100 " =    2.185
peak=   -3.284 closest distance to " O   HOH Z 114 " =    3.140
peak=   -3.283 closest distance to " CG  PHE A 283 " =    2.664
peak=   -3.282 closest distance to " O   PRO A 163 " =    2.013
peak=   -3.281 closest distance to " O   HOH Z 100 " =    1.145
peak=   -3.278 closest distance to " O   HOH Z 389 " =    2.051
peak=   -3.278 closest distance to " NE2 GLN A  88 " =    1.959
peak=   -3.265 closest distance to " CB  ALA A 248 " =    2.450
peak=   -3.265 closest distance to " O   GLY A  17 " =    1.219
peak=   -3.264 closest distance to " ND2 ASN A  60 " =    4.168
peak=   -3.260 closest distance to " CZ3 TRP A 274 " =    1.069
peak=   -3.258 closest distance to " C   GLY A 262 " =    1.979
peak=   -3.256 closest distance to " C   SER A 206 " =    1.460
peak=   -3.255 closest distance to " CG  ASP A 132 " =    2.361
peak=   -3.254 closest distance to " O   HOH Z 429 " =    1.930
peak=   -3.250 closest distance to " CA  GLY A 203 " =    2.525
peak=   -3.243 closest distance to " CG1AVAL A  41 " =    2.774
peak=   -3.243 closest distance to " CE3 TRP A 274 " =    2.527
peak=   -3.239 closest distance to " CB  PHE A  16 " =    2.503
peak=   -3.237 closest distance to " O   HOH Z  53 " =    1.640
peak=   -3.235 closest distance to " O   SER A  95 " =    1.734
peak=   -3.233 closest distance to " CB  ALA A  10 " =    2.254
peak=   -3.229 closest distance to " O   ALA A  34 " =    2.603
peak=   -3.227 closest distance to " O   HOH Z 111 " =    1.774
peak=   -3.223 closest distance to " NE1 TRP A 266 " =    2.326
peak=   -3.221 closest distance to " O   HOH Z  52 " =    1.642
peak=   -3.220 closest distance to " O   GLN A  94 " =    2.189
peak=   -3.213 closest distance to " O   HOH Z 396 " =    2.182
peak=   -3.211 closest distance to " CA  GLY A 287 " =    1.641
peak=   -3.211 closest distance to " O   HOH Z 275 " =    1.555
peak=   -3.208 closest distance to " OD2 ASP A 171 " =    1.884
peak=   -3.207 closest distance to " O   HOH Z 298 " =    2.538
peak=   -3.207 closest distance to " O   HOH Z 193 " =    1.469
peak=   -3.202 closest distance to " O   LEU A 300 " =    2.462
peak=   -3.200 closest distance to " N   ALA A 226 " =    2.152
peak=   -3.198 closest distance to " O   HOH Z  47 " =    1.651
peak=   -3.197 closest distance to " CE3 TRP A  70 " =    1.892
peak=   -3.195 closest distance to " CD1 LEU A   5 " =    2.562
peak=   -3.194 closest distance to " CG  ARG A  66 " =    2.336
peak=   -3.191 closest distance to " O   HOH Z 114 " =    1.444
peak=   -3.182 closest distance to " CD  GLN A  11 " =    0.750
peak=   -3.182 closest distance to " O   GLY A 196 " =    1.232
peak=   -3.181 closest distance to " CD2 PHE A  61 " =    2.069
peak=   -3.177 closest distance to " O   HOH Z 326 " =    5.073
peak=   -3.174 closest distance to " O   HOH Z 357 " =    2.141
peak=   -3.172 closest distance to " CG1 VAL A 265 " =    2.806
peak=   -3.172 closest distance to " OE1 GLU A  44 " =    0.969
peak=   -3.162 closest distance to " C   GLY A  13 " =    0.830
peak=   -3.161 closest distance to " CG  TRP A 266 " =    1.878
peak=   -3.153 closest distance to " N   GLN A  58 " =    1.748
peak=   -3.146 closest distance to " O   ASP A 270 " =    2.056
peak=   -3.146 closest distance to " CD1 ILE A 239 " =    2.093
peak=   -3.144 closest distance to " O   HOH Z 198 " =    1.202
peak=   -3.144 closest distance to " O   HOH Z 323 " =    1.403
peak=   -3.141 closest distance to " O   HOH Z 198 " =    1.409
peak=   -3.135 closest distance to " O   HOH Z   6 " =    1.275
peak=   -3.135 closest distance to " O   ALA A 292 " =    2.066
peak=   -3.133 closest distance to " O   HOH Z 139 " =    4.868
peak=   -3.129 closest distance to " O   HOH Z 281 " =    2.617
peak=   -3.129 closest distance to " O   GLN A 240 " =    2.630
peak=   -3.127 closest distance to " O   SER A 135 " =    1.489
peak=   -3.125 closest distance to " OD1 ASN A 173 " =    1.337
peak=   -3.124 closest distance to " O   HOH Z 371 " =    1.691
peak=   -3.123 closest distance to " O   HOH Z  71 " =    2.502
peak=   -3.115 closest distance to " N   ASP A 171 " =    2.318
peak=   -3.114 closest distance to " OG BSER A 134 " =    1.935
peak=   -3.107 closest distance to " O   HOH Z  63 " =    1.854
peak=   -3.106 closest distance to " OE1 GLN A  88 " =    0.992
peak=   -3.103 closest distance to " OD2 ASP A 191 " =    1.490
peak=   -3.102 closest distance to " CA  GLY A 133 " =    2.295
peak=   -3.073 closest distance to " O   HOH Z 353 " =    2.236
peak=   -3.053 closest distance to " CD1 TRP A  70 " =    1.049
peak=   -3.050 closest distance to " O   HOH Z 241 " =    1.311
peak=   -3.029 closest distance to " C   LEU A 222 " =    0.892
peak=   -3.027 closest distance to " O   HOH Z 348 " =    2.250

================= 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    :  0.3787 0.3711   6.168837e+00   6.150154e+00
   1_bss:  0.3630 0.3557   6.146182e+00   6.126988e+00
   1_xyz:  0.2239 0.2523   5.710744e+00   5.802304e+00
   1_adp:  0.2062 0.2559   5.660807e+00   5.815341e+00
   1_occ:  0.2058 0.2560   5.660693e+00   5.816879e+00
   2_bss:  0.2011 0.2526   5.646642e+00   5.806641e+00
   2_xyz:  0.1489 0.1889   5.368359e+00   5.556524e+00
   2_adp:  0.1359 0.1817   5.303290e+00   5.519748e+00
   2_occ:  0.1358 0.1815   5.302333e+00   5.518985e+00
   3_bss:  0.1353 0.1803   5.297335e+00   5.512469e+00
   3_xyz:  0.1215 0.1690   5.212768e+00   5.448428e+00
   3_adp:  0.1192 0.1668   5.197388e+00   5.434786e+00
   3_occ:  0.1190 0.1668   5.197248e+00   5.435126e+00
   4_bss:  0.1188 0.1665   5.196887e+00   5.435079e+00
   4_xyz:  0.1148 0.1645   5.175665e+00   5.424236e+00
   4_adp:  0.1154 0.1616   5.171152e+00   5.410877e+00
   4_occ:  0.1153 0.1614   5.170650e+00   5.410905e+00
   5_bss:  0.1152 0.1615   5.170574e+00   5.411128e+00
   5_xyz:  0.1161 0.1623   5.177481e+00   5.416685e+00
   5_adp:  0.1162 0.1624   5.178191e+00   5.417191e+00
   5_occ:  0.1161 0.1624   5.178329e+00   5.417666e+00
   5_bss:  0.1161 0.1613   5.175111e+00   5.412284e+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:  0.313  60.330  -3.030  -2.241   6.037  -0.000   0.000   0.000
   1_xyz:  0.313  60.330  -3.030  -2.241   6.037  -0.000   0.000   0.000
   1_adp:  0.313  60.330  -3.030  -2.241   6.037  -0.000   0.000   0.000
   1_occ:  0.313  60.330  -3.030  -2.241   6.037  -0.000   0.000   0.000
   2_bss:  0.339  73.702  -2.949  -2.334   1.243  -0.000   0.000   0.000
   2_xyz:  0.339  73.702  -2.949  -2.334   1.243  -0.000   0.000   0.000
   2_adp:  0.339  73.702  -2.949  -2.334   1.243  -0.000   0.000   0.000
   2_occ:  0.339  73.702  -2.949  -2.334   1.243  -0.000   0.000   0.000
   3_bss:  0.337  79.248  -2.632  -2.104   0.216  -0.000   0.000   0.000
   3_xyz:  0.337  79.248  -2.632  -2.104   0.216  -0.000   0.000   0.000
   3_adp:  0.337  79.248  -2.632  -2.104   0.216  -0.000   0.000   0.000
   3_occ:  0.337  79.248  -2.632  -2.104   0.216  -0.000   0.000   0.000
   4_bss:  0.330  71.351  -2.067  -1.717   0.264  -0.000   0.000   0.000
   4_xyz:  0.330  71.351  -2.067  -1.717   0.264  -0.000   0.000   0.000
   4_adp:  0.330  71.351  -2.067  -1.717   0.264  -0.000   0.000   0.000
   4_occ:  0.330  71.351  -2.067  -1.717   0.264  -0.000   0.000   0.000
   5_bss:  0.319  61.201  -2.082  -1.740   0.077  -0.000   0.000   0.000
   5_xyz:  0.319  61.201  -2.082  -1.740   0.077  -0.000   0.000   0.000
   5_adp:  0.319  61.201  -2.082  -1.740   0.077  -0.000   0.000   0.000
   5_occ:  0.319  61.201  -2.082  -1.740   0.077  -0.000   0.000   0.000
   5_bss:  0.321  61.328  -1.995  -1.655   0.127  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.011 0.6329  0.7833    41124.795
   1_bss:  39.734 0.6468  0.8102    38049.878
   1_xyz:  24.710 0.8154  0.9798    16156.261
   1_adp:  25.316 0.8084  0.9768    16708.458
   1_occ:  25.381 0.8077  0.9757    16762.242
   2_bss:  24.667 0.8157  0.9338    16330.983
   2_xyz:  17.956 0.8805  0.9693     9082.343
   2_adp:  16.940 0.8899  0.9620     8380.011
   2_occ:  16.916 0.8901  0.9621     8361.375
   3_bss:  16.752 0.8915  0.9579     8224.020
   3_xyz:  15.273 0.9044  0.9664     7198.764
   3_adp:  14.901 0.9079  0.9580     7008.376
   3_occ:  14.906 0.9078  0.9577     7010.591
   4_bss:  14.904 0.9079  0.9693     7012.620
   4_xyz:  14.669 0.9099  0.9718     6851.584
   4_adp:  14.329 0.9127  0.9675     6696.403
   4_occ:  14.327 0.9127  0.9674     6690.134
   5_bss:  14.330 0.9127  0.9648     6689.602
   5_xyz:  14.412 0.9122  0.9638     6765.624
   5_adp:  14.404 0.9123  0.9578     6780.691
   5_occ:  14.411 0.9122  0.9577     6783.481
   5_bss:  14.334 0.9127  0.9590     6657.142
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6784e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6784e-01
   1_xyz:   1.415  0.012  0.087 15.574  0.006  4.120   1.0562e-01
   1_adp:   1.415  0.012  0.087 15.574  0.006  4.120   1.0562e-01
   1_occ:   1.415  0.012  0.087 15.574  0.006  4.120   1.0562e-01
   2_bss:   1.415  0.012  0.087 15.574  0.006  4.120   1.0562e-01
   2_xyz:   1.085  0.009  0.079 15.130  0.005  4.116   7.0085e-02
   2_adp:   1.085  0.009  0.079 15.130  0.005  4.116   7.0085e-02
   2_occ:   1.085  0.009  0.079 15.130  0.005  4.116   7.0085e-02
   3_bss:   1.085  0.009  0.079 15.130  0.005  4.116   7.0085e-02
   3_xyz:   1.095  0.010  0.080 14.934  0.004  4.124   7.0824e-02
   3_adp:   1.095  0.010  0.080 14.934  0.004  4.124   7.0824e-02
   3_occ:   1.095  0.010  0.080 14.934  0.004  4.124   7.0824e-02
   4_bss:   1.095  0.010  0.080 14.934  0.004  4.124   7.0824e-02
   4_xyz:   1.110  0.011  0.085 14.943  0.004  4.118   7.5595e-02
   4_adp:   1.110  0.011  0.085 14.943  0.004  4.118   7.5595e-02
   4_occ:   1.110  0.011  0.085 14.943  0.004  4.118   7.5595e-02
   5_bss:   1.110  0.011  0.085 14.943  0.004  4.118   7.5595e-02
   5_xyz:   1.033  0.009  0.079 14.728  0.003  4.119   6.5402e-02
   5_adp:   1.033  0.009  0.079 14.728  0.003  4.119   6.5402e-02
   5_occ:   1.033  0.009  0.079 14.728  0.003  4.119   6.5402e-02
   5_bss:   1.033  0.009  0.079 14.728  0.003  4.119   6.5402e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.540   2.4448e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.540   2.4448e-01
   1_xyz:   9.150  0.060  0.297 81.707  0.044  2.148   1.0638e-01
   1_adp:   9.150  0.060  0.297 81.707  0.044  2.148   1.0638e-01
   1_occ:   9.150  0.060  0.297 81.707  0.044  2.148   1.0638e-01
   2_bss:   9.150  0.060  0.297 81.707  0.044  2.148   1.0638e-01
   2_xyz:   6.865  0.054  0.237 85.690  0.052  2.357   9.3771e-02
   2_adp:   6.865  0.054  0.237 85.690  0.052  2.357   9.3771e-02
   2_occ:   6.865  0.054  0.237 85.690  0.052  2.357   9.3771e-02
   3_bss:   6.865  0.054  0.237 85.690  0.052  2.357   9.3771e-02
   3_xyz:   7.668  0.053  0.254 83.161  0.038  2.375   4.6247e-02
   3_adp:   7.668  0.053  0.254 83.161  0.038  2.375   4.6247e-02
   3_occ:   7.668  0.053  0.254 83.161  0.038  2.375   4.6247e-02
   4_bss:   7.668  0.053  0.254 83.161  0.038  2.375   4.6247e-02
   4_xyz:   7.601  0.058  0.281 83.992  0.037  2.348   5.5061e-02
   4_adp:   7.601  0.058  0.281 83.992  0.037  2.348   5.5061e-02
   4_occ:   7.601  0.058  0.281 83.992  0.037  2.348   5.5061e-02
   5_bss:   7.601  0.058  0.281 83.992  0.037  2.348   5.5061e-02
   5_xyz:   7.080  0.051  0.248 82.641  0.034  2.390   4.1868e-02
   5_adp:   7.080  0.051  0.248 82.641  0.034  2.390   4.1868e-02
   5_occ:   7.080  0.051  0.248 82.641  0.034  2.390   4.1868e-02
   5_bss:   7.080  0.051  0.248 82.641  0.034  2.390   4.1868e-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:  96.31   0.00  16.80  96.31   0.00  12.84  64.23   4.65  38.34
   1_occ:  96.31   0.00  16.80  96.31   0.00  12.84  64.23   4.65  38.34
   2_bss:  96.31   0.00  16.80  96.31   0.00  12.84  64.23   4.65  38.34
   2_xyz:  96.31   0.00  16.80  96.31   0.00  12.84  64.23   4.65  38.34
   2_adp:  84.64   0.00  17.74  79.94   0.00  13.05  84.64   5.18  43.27
   2_occ:  84.64   0.00  17.74  79.94   0.00  13.05  84.64   5.18  43.27
   3_bss:  84.64   0.00  17.74  79.94   0.00  13.05  84.64   5.18  43.27
   3_xyz:  84.64   0.00  17.74  79.94   0.00  13.05  84.64   5.18  43.27
   3_adp:  91.96   0.00  17.43  87.66   0.00  12.78  91.96   0.00  42.76
   3_occ:  91.96   0.00  17.43  87.66   0.00  12.78  91.96   0.00  42.76
   4_bss:  91.96   0.00  17.43  87.66   0.00  12.78  91.96   0.00  42.76
   4_xyz:  91.96   0.00  17.43  87.66   0.00  12.78  91.96   0.00  42.76
   4_adp:  84.52   1.19  16.40  79.43   1.19  12.34  84.52   1.74  38.48
   4_occ:  84.52   1.19  16.40  79.43   1.19  12.34  84.52   1.74  38.48
   5_bss:  84.52   1.19  16.40  79.43   1.19  12.34  84.52   1.74  38.48
   5_xyz:  84.52   1.19  16.40  79.43   1.19  12.34  84.52   1.74  38.48
   5_adp:  81.81   1.21  16.11  78.01   1.21  12.16  81.81   3.43  37.60
   5_occ:  81.81   1.21  16.11  78.01   1.21  12.16  81.81   3.43  37.60
   5_bss:  81.77   1.17  16.07  77.97   1.17  12.12  81.77   3.39  37.56
------------------------------------------------------------------------
 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:    1.300    0.021    0.410
   1_adp:    1.300    0.021    0.410
   1_occ:    1.300    0.021    0.410
   2_bss:    1.300    0.021    0.410
   2_xyz:    1.184    0.046    0.475
   2_adp:    1.184    0.046    0.475
   2_occ:    1.184    0.046    0.475
   3_bss:    1.184    0.046    0.475
   3_xyz:    1.109    0.031    0.510
   3_adp:    1.109    0.031    0.510
   3_occ:    1.109    0.031    0.510
   4_bss:    1.109    0.031    0.510
   4_xyz:    1.371    0.055    0.528
   4_adp:    1.371    0.055    0.528
   4_occ:    1.371    0.055    0.528
   5_bss:    1.371    0.055    0.528
   5_xyz:    1.499    0.040    0.533
   5_adp:    1.499    0.040    0.533
   5_occ:    1.499    0.040    0.533
   5_bss:    1.499    0.040    0.533
------------------------------------------------------------------------

CPU time actual refinement: 270.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_802/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_802/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_802/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_802/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_802/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 270.30 
  Macro-tasks:
    bulk solvent and scale       = 37.37  
    individual site refinement   = 109.87 
    weights calculation          = 23.67  
    collect and process          = 5.43   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 176.43 
  Micro-tasks:
    mask                            = 1.43   
    f_calc                          = 83.24  
    alpha_beta                      = 6.79   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 91.06  
    fmodel                         = 5.94   
    r_factors                      = 0.15   
    phase_errors                   = 9.06   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 198.90 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.845 micro seconds
Total CPU time: 4.70 minutes
from_scatterers_fft:    632 calls, 82.93 s
gradients_fft:          577 calls, 79.75 s

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

# Date 2008-01-16 Time 05:40:55 PST -0800 (1200490855.61 s)
Start R-work = 0.3787, R-free = 0.3711 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1785 (no bulk solvent and anisotropic scale)

Start R-work = 0.3630, R-free = 0.3557
Final R-work = 0.1161, R-free = 0.1613