# Date 2008-01-16 Time 05:34:44 PST -0800 (1200490484.51 s)
#phil __OFF__

Command line arguments: "../790.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21932
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 790

-------------------------------------------------------------------------------
  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, 46.93, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


================================== 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, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.00211
Completeness in resolution range: 0.964453
Completeness with d_max=infinity: 0.961471

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1289
                             d_min =   2.0021

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, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.00211
Completeness in resolution range: 0.964453
Completeness with d_max=infinity: 0.961471

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1294 -  4.2838 [2140/2164]  1922   218  10.2%
  bin  2:  4.2838 -  3.4130 [2041/2061]  1841   200   9.8%
  bin  3:  3.4130 -  2.9854 [2021/2040]  1818   203  10.0%
  bin  4:  2.9854 -  2.7141 [1995/2025]  1793   202  10.1%
  bin  5:  2.7141 -  2.5206 [2003/2022]  1805   198   9.9%
  bin  6:  2.5206 -  2.3725 [1986/2011]  1784   202  10.2%
  bin  7:  2.3725 -  2.2541 [1959/1987]  1766   193   9.9%
  bin  8:  2.2541 -  2.1563 [1965/2001]  1770   195   9.9%
  bin  9:  2.1563 -  2.0735 [1947/1989]  1755   192   9.9%
  bin 10:  2.0735 -  2.0021 [1532/2011]  1376   156  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_790/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 11
        2.38 -     3.01: 1948
        3.01 -     3.64: 4524
        3.64 -     4.27: 8980
        4.27 -     4.90: 12464
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.746 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.930 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.930 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.952 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27922 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_790/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_790/model_refine_001.geo

CPU time processing inputs: 9.79


============================ 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 46.93 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3294   r_free= 0.3200   ksol= 0.00   Bsol= 0.00   scale= 0.954    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.073702                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7779 0.99   1389  152 0.2876 0.2749      6.3693      6.2585|
|  2:  4.7779 -  3.8123 0.99   1331  152 0.2548 0.2552      6.4771      6.5024|
|  3:  3.8123 -  3.3363 0.99   1298  143 0.2899 0.2613      6.4071      6.3526|
|  4:  3.3363 -  3.0339 0.99   1306  144 0.3043 0.3258      6.2803      6.2935|
|  5:  3.0339 -  2.8180 0.99   1283  146 0.3394 0.2872       6.152      6.0792|
|  6:  2.8180 -  2.6528 0.99   1290  141 0.3362 0.3747      6.0435      6.0162|
|  7:  2.6528 -  2.5206 0.99   1282  143 0.3498 0.3457      6.0319      6.0357|
|  8:  2.5206 -  2.4113 0.98   1275  137 0.3691 0.3313      6.0288      5.9939|
|  9:  2.4113 -  2.3188 0.98   1262  144 0.3592 0.3464      5.9365      5.9139|
| 10:  2.3188 -  2.2390 1.00   1278  143 0.3868 0.3603      5.9782      5.8904|
| 11:  2.2390 -  2.1692 0.97   1250  137 0.3914 0.3853      5.8967      5.9552|
| 12:  2.1692 -  2.1074 0.98   1256  142 0.3732 0.3597      5.8317      5.8789|
| 13:  2.1074 -  2.0521 0.99   1277  134 0.3839 0.3731      5.7352      5.7031|
| 14:  2.0521 -  2.0021 0.67    853  101 0.3428 0.3780      5.6658      5.6523|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7779  1389   152  0.81  24.48   0.85     0.82      38745.65|
|  2:  4.7779 -  3.8123  1331   152  0.84  21.90   0.96     0.91      46926.68|
|  3:  3.8123 -  3.3363  1298   143  0.80  25.98   0.96     0.92      45752.93|
|  4:  3.3363 -  3.0339  1306   144  0.77  29.04   0.97     0.89      40099.66|
|  5:  3.0339 -  2.8180  1283   146  0.72  33.86   0.99     0.86      32439.52|
|  6:  2.8180 -  2.6528  1290   141  0.69  36.17   0.97     0.84      30660.10|
|  7:  2.6528 -  2.5206  1282   143  0.68  37.06   0.99     0.84      28824.26|
|  8:  2.5206 -  2.4113  1275   137  0.69  36.83   0.97     0.86      26296.59|
|  9:  2.4113 -  2.3188  1262   144  0.70  36.07   1.01     0.88      23896.27|
| 10:  2.3188 -  2.2390  1278   143  0.68  37.37   1.03     0.88      22019.34|
| 11:  2.2390 -  2.1692  1250   137  0.67  38.83   1.00     0.88      22764.43|
| 12:  2.1692 -  2.1074  1256   142  0.66  39.50   1.02     0.88      21556.86|
| 13:  2.1074 -  2.0521  1277   134  0.62  42.27   1.00     0.87      19637.53|
| 14:  2.0521 -  2.0021   853   101  0.66  39.37   1.04     0.84      16215.58|
|alpha:            min =        0.82 max =            0.92 mean =         0.87|
|beta:             min =    16215.58 max =        46926.68 mean =     30199.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.90 mean =        33.94|
|phase err.(test): min =        0.00 max =           89.91 mean =        33.54|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.098174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.152   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.667656              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.175   (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 |  1.746 -  2.061:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.061 -  2.377:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.377 -  2.692:       92 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.692 -  3.007:     1856 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.007 -  3.323:     1837 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.323 -  3.638:     2687 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.638 -  3.954:     4638 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.954 -  4.269:     4342 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.269 -  4.585:     5681 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.585 -  4.900:     6783 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.746 |       0.180 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3294   r_free= 0.3200   ksol= 0.00   Bsol= 0.00   scale= 0.954    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.073702                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3108   r_free= 0.3061   ksol= 0.32   Bsol= 61.15   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-3.23,4.54,-0.00,0.00,0.00); trace/3= -0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.043365                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.445355              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.944   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.376994              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.893   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3108      final r-factor (work) = 0.1810          |
| start r-factor (free) = 0.3061      final r-factor (free) = 0.2081          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6216 = 5.45 * 0.50 * 6.0445 + 1.00 * 0.1643                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7216 = 5.45 * 0.50 * 5.7446 + 1.00 * 0.0810                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1810      final r-factor (work) = 0.1704          |
| start r-factor (free) = 0.2081      final r-factor (free) = 0.2084          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1730 = 0.38 * 1.00 * 5.7446 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2146 = 0.38 * 1.00 * 5.4777 + 1.00 * 0.1495                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.17   16.21    None  None   None       |
|    all(noH): 2823   0      0.00    88.17   16.21    None  None   None       |
|    Sol.    : 438    0      4.10    62.95   37.25    None  None   None       |
|    Mac.    : 2385   0      0.00    88.17   12.35    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 -   8.817:  645   |   5:    44.086 -  52.904:   94        |
|      1:     8.817 -  17.635: 1472   |   6:    52.904 -  61.721:   50        |
|      2:    17.635 -  26.452:  275   |   7:    61.721 -  70.538:    3        |
|      3:    26.452 -  35.269:  150   |   8:    70.538 -  79.356:    0        |
|      4:    35.269 -  44.086:  133   |   9:    79.356 -  88.173:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1704 r_free = 0.2084             target_work(ml) = 5.480         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1699 r_free = 0.2084             target_work(ml) = 5.478         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1699   r_free= 0.2084   ksol= 0.32   Bsol= 61.15   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-3.23,4.54,-0.00,0.00,0.00); trace/3= -0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.478466                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1651   r_free= 0.2035   ksol= 0.34   Bsol= 68.02   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.69,0.40,-0.00,0.00,0.00); trace/3= -1.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.454961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.792174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.838   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.913541              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.206   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1651      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.2035      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9876 = 1.79 * 0.50 * 5.4756 + 1.00 * 0.0810                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8594 = 1.79 * 0.50 * 5.3609 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1358      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9164 = 0.91 * 1.00 * 5.3609 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7875 = 0.91 * 1.00 * 5.2292 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    83.71   17.30    None  None   None       |
|    all(noH): 2823   0      0.36    83.71   17.30    None  None   None       |
|    Sol.    : 438    0      5.55    83.71   41.68    None  None   None       |
|    Mac.    : 2385   0      0.36    80.55   12.82    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:     0.362 -   8.697:  770   |   5:    42.037 -  50.372:   92        |
|      1:     8.697 -  17.032: 1267   |   6:    50.372 -  58.706:   80        |
|      2:    17.032 -  25.367:  282   |   7:    58.706 -  67.041:   61        |
|      3:    25.367 -  33.702:  133   |   8:    67.041 -  75.376:   30        |
|      4:    33.702 -  42.037:  101   |   9:    75.376 -  83.711:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1263 r_free = 0.1683             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1262 r_free = 0.1682             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1682   ksol= 0.34   Bsol= 68.02   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.69,0.40,-0.00,0.00,0.00); trace/3= -1.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1674   ksol= 0.33   Bsol= 69.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.28,-0.08,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.229465                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.469480              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.851  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.149158              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.352  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8968 = 1.47 * 0.50 * 5.2280 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8778 = 1.47 * 0.50 * 5.2041 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7866 = 0.15 * 1.00 * 5.2041 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7828 = 0.15 * 1.00 * 5.1963 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    78.85   16.43    None  None   None       |
|    all(noH): 2823   0      1.42    78.85   16.43    None  None   None       |
|    Sol.    : 438    0      2.59    78.85   38.03    None  None   None       |
|    Mac.    : 2385   0      1.42    77.04   12.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.416 -   9.160:  900   |   5:    40.134 -  47.878:   81        |
|      1:     9.160 -  16.904: 1150   |   6:    47.878 -  55.621:   80        |
|      2:    16.904 -  24.647:  283   |   7:    55.621 -  63.365:   41        |
|      3:    24.647 -  32.391:  132   |   8:    63.365 -  71.109:   17        |
|      4:    32.391 -  40.134:  131   |   9:    71.109 -  78.852:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1198 r_free = 0.1604             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1604             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1604   ksol= 0.33   Bsol= 69.92   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.28,-0.08,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187736                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1603   ksol= 0.34   Bsol= 69.92   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.05,-0.19,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187596                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.242078              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.557  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.133979              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.853  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4780 = 3.24 * 0.50 * 5.1966 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4342 = 3.24 * 0.50 * 5.1543 + 1.00 * 0.0789                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6983 = 0.13 * 1.00 * 5.1543 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6962 = 0.13 * 1.00 * 5.1446 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    76.09   16.06    None  None   None       |
|    all(noH): 2823   0      1.75    76.09   16.06    None  None   None       |
|    Sol.    : 438    0      4.29    76.09   36.67    None  None   None       |
|    Mac.    : 2385   0      1.75    73.98   12.27    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:     1.747 -   9.181:  907   |   5:    38.918 -  46.352:   98        |
|      1:     9.181 -  16.616: 1149   |   6:    46.352 -  53.786:   78        |
|      2:    16.616 -  24.050:  281   |   7:    53.786 -  61.220:   36        |
|      3:    24.050 -  31.484:  127   |   8:    61.220 -  68.654:   13        |
|      4:    31.484 -  38.918:  125   |   9:    68.654 -  76.088:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1117 r_free = 0.1571             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1116 r_free = 0.1571             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1571   ksol= 0.34   Bsol= 69.92   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.05,-0.19,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142027                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1572   ksol= 0.32   Bsol= 56.51   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.93,-0.14,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142043                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.312347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.876  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.422796              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.392  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5995 = 3.31 * 0.50 * 5.1446 + 1.00 * 0.0792                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5884 = 3.31 * 0.50 * 5.1374 + 1.00 * 0.0800                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3164 = 1.42 * 1.00 * 5.1374 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3107 = 1.42 * 1.00 * 5.1317 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.25    81.64   16.41    None  None   None       |
|    all(noH): 2823   0      0.25    81.64   16.41    None  None   None       |
|    Sol.    : 438    0      5.40    81.64   38.91    None  None   None       |
|    Mac.    : 2385   0      0.25    81.27   12.27    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:     0.246 -   8.385:  790   |   5:    40.942 -  49.081:   90        |
|      1:     8.385 -  16.524: 1242   |   6:    49.081 -  57.221:   85        |
|      2:    16.524 -  24.664:  301   |   7:    57.221 -  65.360:   48        |
|      3:    24.664 -  32.803:  127   |   8:    65.360 -  73.499:   17        |
|      4:    32.803 -  40.942:  118   |   9:    73.499 -  81.639:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1588             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1589             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1589   ksol= 0.32   Bsol= 56.51   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.93,-0.14,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.135735                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7779 0.99   1389  152 0.1019 0.1383      5.4253       5.568|
|  2:  4.7779 -  3.8123 0.99   1331  152 0.0855 0.1142      5.4536      5.6631|
|  3:  3.8123 -  3.3363 0.99   1298  143 0.1031 0.1493      5.4718      5.8351|
|  4:  3.3363 -  3.0339 0.99   1306  144 0.1170 0.1640      5.4292      5.5894|
|  5:  3.0339 -  2.8180 0.99   1283  146 0.1282 0.1599      5.3129      5.5369|
|  6:  2.8180 -  2.6528 0.99   1290  141 0.1183 0.2140      5.2066      5.5387|
|  7:  2.6528 -  2.5206 0.99   1282  143 0.1254 0.1558      5.1636      5.3098|
|  8:  2.5206 -  2.4113 0.98   1275  137 0.1098 0.1640      5.0523      5.3351|
|  9:  2.4113 -  2.3188 0.98   1262  144 0.1120 0.1799      5.0217      5.3014|
| 10:  2.3188 -  2.2390 1.00   1278  143 0.1086 0.1787      4.9364      5.2144|
| 11:  2.2390 -  2.1692 0.97   1250  137 0.1106 0.1641      4.9282      5.2008|
| 12:  2.1692 -  2.1074 0.98   1256  142 0.1072 0.1782      4.8678      5.2582|
| 13:  2.1074 -  2.0521 0.99   1277  134 0.1052 0.1692      4.7712      5.0335|
| 14:  2.0521 -  2.0021 0.67    853  101 0.0916 0.1670      4.6286      4.9093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7779  1389   152  0.94   9.81   0.97     0.94       8078.11|
|  2:  4.7779 -  3.8123  1331   152  0.95   8.22   1.00     0.99       9722.92|
|  3:  3.8123 -  3.3363  1298   143  0.94  11.09   1.01     1.01      10395.02|
|  4:  3.3363 -  3.0339  1306   144  0.92  13.37   0.99     0.97       9967.20|
|  5:  3.0339 -  2.8180  1283   146  0.90  15.49   0.99     0.97       8247.94|
|  6:  2.8180 -  2.6528  1290   141  0.90  16.31   0.97     0.95       7186.46|
|  7:  2.6528 -  2.5206  1282   143  0.90  15.75   0.98     0.95       6284.21|
|  8:  2.5206 -  2.4113  1275   137  0.91  14.96   0.98     0.96       5271.47|
|  9:  2.4113 -  2.3188  1262   144  0.91  14.99   0.99     0.95       4972.84|
| 10:  2.3188 -  2.2390  1278   143  0.90  15.62   0.98     0.95       4279.82|
| 11:  2.2390 -  2.1692  1250   137  0.90  15.90   0.98     0.94       4341.39|
| 12:  2.1692 -  2.1074  1256   142  0.91  15.63   0.99     0.98       3980.32|
| 13:  2.1074 -  2.0521  1277   134  0.90  16.02   0.98     0.95       3374.18|
| 14:  2.0521 -  2.0021   853   101  0.92  13.58   0.95     0.92       2475.73|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2475.73 max =        10395.02 mean =      6460.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.01|
|phase err.(test): min =        0.00 max =           89.28 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1587   ksol= 0.31   Bsol= 56.51   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.67,0.06,-0.00,0.00,0.00); trace/3= -1.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.135633                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1587   ksol= 0.31   Bsol= 56.51   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.67,0.06,-0.00,0.00,0.00); trace/3= -1.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.135633                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7779 0.99   1389  152 0.1017 0.1385      5.4239       5.568|
|  2:  4.7779 -  3.8123 0.99   1331  152 0.0856 0.1143      5.4545      5.6638|
|  3:  3.8123 -  3.3363 0.99   1298  143 0.1031 0.1493      5.4719      5.8351|
|  4:  3.3363 -  3.0339 0.99   1306  144 0.1170 0.1640      5.4289      5.5892|
|  5:  3.0339 -  2.8180 0.99   1283  146 0.1281 0.1599      5.3124      5.5363|
|  6:  2.8180 -  2.6528 0.99   1290  141 0.1183 0.2141      5.2065      5.5388|
|  7:  2.6528 -  2.5206 0.99   1282  143 0.1254 0.1558      5.1635      5.3096|
|  8:  2.5206 -  2.4113 0.98   1275  137 0.1098 0.1639      5.0523      5.3349|
|  9:  2.4113 -  2.3188 0.98   1262  144 0.1119 0.1800      5.0216      5.3015|
| 10:  2.3188 -  2.2390 1.00   1278  143 0.1086 0.1786      4.9364      5.2137|
| 11:  2.2390 -  2.1692 0.97   1250  137 0.1106 0.1639       4.928      5.2002|
| 12:  2.1692 -  2.1074 0.98   1256  142 0.1072 0.1780      4.8676      5.2577|
| 13:  2.1074 -  2.0521 0.99   1277  134 0.1051 0.1694      4.7713       5.034|
| 14:  2.0521 -  2.0021 0.67    853  101 0.0916 0.1670      4.6291      4.9093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7779  1389   152  0.94   9.81   0.97     0.94       8072.87|
|  2:  4.7779 -  3.8123  1331   152  0.95   8.23   1.01     0.99       9729.36|
|  3:  3.8123 -  3.3363  1298   143  0.94  11.10   1.02     1.01      10397.91|
|  4:  3.3363 -  3.0339  1306   144  0.92  13.36   1.00     0.98       9960.86|
|  5:  3.0339 -  2.8180  1283   146  0.90  15.48   1.00     0.98       8243.92|
|  6:  2.8180 -  2.6528  1290   141  0.90  16.30   0.98     0.95       7181.52|
|  7:  2.6528 -  2.5206  1282   143  0.90  15.75   0.99     0.96       6282.88|
|  8:  2.5206 -  2.4113  1275   137  0.91  14.96   0.99     0.97       5271.00|
|  9:  2.4113 -  2.3188  1262   144  0.91  14.99   1.00     0.96       4973.12|
| 10:  2.3188 -  2.2390  1278   143  0.90  15.62   1.00     0.96       4277.38|
| 11:  2.2390 -  2.1692  1250   137  0.90  15.89   0.99     0.95       4337.54|
| 12:  2.1692 -  2.1074  1256   142  0.91  15.62   1.01     0.99       3977.89|
| 13:  2.1074 -  2.0521  1277   134  0.90  16.03   0.99     0.97       3374.35|
| 14:  2.0521 -  2.0021   853   101  0.92  13.59   0.97     0.93       2478.27|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2478.27 max =        10397.91 mean =      6458.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.01|
|phase err.(test): min =        0.00 max =           89.29 mean =        13.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.24    81.63   16.40    None  None   None       |
|    all(noH): 2823   0      0.24    81.63   16.40    None  None   None       |
|    Sol.    : 438    0      5.40    81.63   38.91    None  None   None       |
|    Mac.    : 2385   0      0.24    81.27   12.27    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:     0.239 -   8.379:  790   |   5:    40.936 -  49.075:   90        |
|      1:     8.379 -  16.518: 1242   |   6:    49.075 -  57.214:   85        |
|      2:    16.518 -  24.657:  301   |   7:    57.214 -  65.354:   48        |
|      3:    24.657 -  32.797:  127   |   8:    65.354 -  73.493:   17        |
|      4:    32.797 -  40.936:  118   |   9:    73.493 -  81.632:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 276         
Filter by distance & map next to the model:
   mapped sites are within: 0.439 - 4.852
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 276
   mapped sites are within: 0.708 - 4.852

peak=    5.661 closest distance to " NH2 ARG A  56 " =    2.222
peak=    5.064 closest distance to " CB  GLN A 223 " =    1.446
peak=    4.994 closest distance to " O   HOH Z 126 " =    1.900
peak=    4.983 closest distance to " CB  ARG A  79 " =    1.333
peak=    4.902 closest distance to " CG  PRO A  54 " =    1.296
peak=    4.823 closest distance to " NE2 GLN A  11 " =    1.114
peak=    4.767 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.748 closest distance to " O   HOH Z 298 " =    1.999
peak=    4.735 closest distance to " CB  SER A  63 " =    1.181
peak=    4.688 closest distance to " O   HOH Z 142 " =    1.703
peak=    4.673 closest distance to " CB  ARG A 275 " =    0.900
peak=    4.614 closest distance to " CZ  PHE A 218 " =    1.095
peak=    4.594 closest distance to " CB  ARG A 190 " =    1.669
peak=    4.555 closest distance to " O   HOH Z 232 " =    2.385
peak=    4.531 closest distance to " O   HOH Z  78 " =    1.735
peak=    4.523 closest distance to " O   HOH Z  15 " =    2.082
peak=    4.429 closest distance to " CA  TYR A  30 " =    0.976
peak=    4.414 closest distance to " O   HOH Z  53 " =    2.524
peak=    4.324 closest distance to " CG  PRO A 213 " =    1.136
peak=    4.299 closest distance to " CD  ARG A 159 " =    0.791
peak=    4.298 closest distance to " CB  PRO A  54 " =    0.923
peak=    4.291 closest distance to " O   HOH Z 303 " =    2.088
peak=    4.259 closest distance to " CB  GLU A 152 " =    1.231
peak=    4.253 closest distance to " O   HOH Z 158 " =    3.142
peak=    4.210 closest distance to " C   PRO A 198 " =    1.436
peak=    4.207 closest distance to " CB  LEU A 228 " =    1.082
peak=    4.193 closest distance to " O   HOH Z 346 " =    1.769
peak=    4.190 closest distance to " O   HOH Z 236 " =    2.196
peak=    4.173 closest distance to " O   HOH Z 313 " =    2.044
peak=    4.170 closest distance to " CG  PRO A 198 " =    1.250
peak=    4.147 closest distance to " O   HOH Z 189 " =    2.832
peak=    4.138 closest distance to " O   HOH Z 392 " =    3.024
peak=    4.136 closest distance to " CE  LYS A  76 " =    0.860
peak=    4.131 closest distance to " CB  ASN A 148 " =    1.461
peak=    4.121 closest distance to " O   HOH Z 423 " =    1.913
peak=    4.106 closest distance to " O   HOH Z 126 " =    1.948
peak=    4.098 closest distance to " O   HOH Z 369 " =    2.233
peak=    4.062 closest distance to " O   HOH Z 427 " =    2.987
peak=    4.026 closest distance to " O   HOH Z 250 " =    1.479
peak=    3.992 closest distance to " CA  ALA A  51 " =    0.942
peak=    3.989 closest distance to " CB  VAL A 265 " =    1.255
peak=    3.971 closest distance to " CG2 VAL A 257 " =    0.848
peak=    3.969 closest distance to " O  BHOH Z 338 " =    2.346
peak=    3.964 closest distance to " CB  GLU A 277 " =    3.660
peak=    3.952 closest distance to " NZ  LYS A 117 " =    3.295
peak=    3.941 closest distance to " CB  TYR A 169 " =    0.777
peak=    3.934 closest distance to " O   SER A  87 " =    2.325
peak=    3.927 closest distance to " O   HOH Z 272 " =    1.842
peak=    3.919 closest distance to " CA  ASN A 215 " =    1.103
peak=    3.919 closest distance to " O   HOH Z 180 " =    2.136
peak=    3.900 closest distance to " CD2 TRP A 179 " =    1.340
peak=    3.899 closest distance to " O   HOH Z 403 " =    1.495
peak=    3.897 closest distance to " O   HOH Z 234 " =    3.840
peak=    3.892 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.890 closest distance to " CD  LYS A 166 " =    1.249
peak=    3.875 closest distance to " O   HOH Z 406 " =    1.682
peak=    3.862 closest distance to " OD1 ASN A  69 " =    2.658
peak=    3.837 closest distance to " NH1AARG A 145 " =    1.365
peak=    3.835 closest distance to " O   HOH Z 389 " =    1.912
peak=    3.814 closest distance to " CB  ASN A  39 " =    0.934
peak=    3.812 closest distance to " CA  ARG A 195 " =    1.241
peak=    3.808 closest distance to " O   HOH Z 316 " =    3.165
peak=    3.808 closest distance to " O   HOH Z  61 " =    1.580
peak=    3.804 closest distance to " O   HOH Z 214 " =    2.167
peak=    3.801 closest distance to " CB  ASP A 140 " =    1.079
peak=    3.787 closest distance to " O   HOH Z 193 " =    1.924
peak=    3.778 closest distance to " O   HOH Z 368 " =    2.211
peak=    3.768 closest distance to " O   HOH Z 172 " =    3.288
peak=    3.757 closest distance to " ND2 ASN A 187 " =    1.414
peak=    3.745 closest distance to " O   HOH Z  10 " =    1.820
peak=    3.742 closest distance to " CG  LEU A 167 " =    1.278
peak=    3.740 closest distance to " CA  ARG A  36 " =    1.047
peak=    3.730 closest distance to " O   HOH Z 133 " =    2.554
peak=    3.719 closest distance to " CB  ASN A 142 " =    1.031
peak=    3.709 closest distance to " OG BSER A 164 " =    2.331
peak=    3.695 closest distance to " O   HOH Z 291 " =    1.582
peak=    3.688 closest distance to " CB  GLU A  46 " =    0.960
peak=    3.680 closest distance to " CG  PRO A 243 " =    1.073
peak=    3.679 closest distance to " O   HOH Z   1 " =    2.127
peak=    3.678 closest distance to " CB  VAL A 202 " =    1.575
peak=    3.677 closest distance to " O   HOH Z 248 " =    1.653
peak=    3.677 closest distance to " CB  GLU A 128 " =    0.919
peak=    3.676 closest distance to " O   HOH Z  43 " =    1.961
peak=    3.671 closest distance to " O   HOH Z 185 " =    1.871
peak=    3.664 closest distance to " CB  PRO A  90 " =    1.169
peak=    3.663 closest distance to " O   HOH Z  40 " =    1.884
peak=    3.654 closest distance to " CA  PRO A  54 " =    1.362
peak=    3.649 closest distance to " CG1 VAL A 153 " =    1.018
peak=    3.642 closest distance to " CG  MET A 185 " =    1.134
peak=    3.636 closest distance to " CD1 LEU A 300 " =    1.208
peak=    3.631 closest distance to " CA  THR A 264 " =    0.910
peak=    3.623 closest distance to " O   HOH Z 209 " =    2.312
peak=    3.618 closest distance to " O   HOH Z 265 " =    2.225
peak=    3.612 closest distance to " CG2AVAL A  72 " =    1.677
peak=    3.608 closest distance to " CB  ASN A 110 " =    1.087
peak=    3.598 closest distance to " O   HOH Z 371 " =    2.999
peak=    3.595 closest distance to " O   HOH Z 280 " =    2.969
peak=    3.592 closest distance to " O   HOH Z 417 " =    3.473
peak=    3.589 closest distance to " CD2 LEU A 297 " =    0.830
peak=    3.586 closest distance to " CD  ARG A  66 " =    2.417
peak=    3.582 closest distance to " O   ASN A  74 " =    1.407
peak=    3.574 closest distance to " O   HOH Z 411 " =    3.933
peak=    3.559 closest distance to " CB  ASN A 187 " =    1.074
peak=    3.557 closest distance to " O   HOH Z 148 " =    3.407
peak=    3.553 closest distance to " CD1 LEU A  96 " =    0.720
peak=    3.549 closest distance to " CZ3 TRP A 266 " =    1.146
peak=    3.545 closest distance to " CD  ARG A 269 " =    0.942
peak=    3.542 closest distance to " CB  SER A 212 " =    1.158
peak=    3.541 closest distance to " O   HOH Z  21 " =    1.811
peak=    3.538 closest distance to " O   HOH Z 147 " =    1.869
peak=    3.524 closest distance to " CG2 ILE A 234 " =    0.816
peak=    3.521 closest distance to " N   ARG A 156 " =    1.374
peak=    3.521 closest distance to " O   HOH Z  88 " =    3.292
peak=    3.516 closest distance to " CZ2 TRP A 179 " =    1.758
peak=    3.501 closest distance to " CB  SER A   3 " =    1.298
peak=    3.500 closest distance to " O   HOH Z 359 " =    1.527
peak=    3.493 closest distance to " NE2 HIS A 207 " =    1.228
peak=    3.492 closest distance to " O   HOH Z 166 " =    3.962
peak=    3.491 closest distance to " CE1 TYR A 186 " =    1.379
peak=    3.487 closest distance to " CA  ALA A 158 " =    1.271
peak=    3.486 closest distance to " CB  THR A  31 " =    1.582
peak=    3.485 closest distance to " O   HOH Z 245 " =    1.249
peak=    3.481 closest distance to " O   HOH Z 368 " =    3.563
peak=    3.477 closest distance to " O   HOH Z 294 " =    1.556
peak=    3.470 closest distance to " CE1 PHE A  38 " =    1.197
peak=    3.469 closest distance to " O   HOH Z 285 " =    2.355
peak=    3.468 closest distance to " CG  GLN A  11 " =    1.688
peak=    3.467 closest distance to " O   HOH Z 325 " =    4.040
peak=    3.463 closest distance to " CA  TYR A 116 " =    1.362
peak=    3.461 closest distance to " O   HOH Z 421 " =    2.080
peak=    3.451 closest distance to " CA  SER A  87 " =    1.002
peak=    3.440 closest distance to " O   HOH Z 116 " =    3.172
peak=    3.435 closest distance to " O   HOH Z 419 " =    2.095
peak=    3.435 closest distance to " O   THR A 220 " =    1.265
peak=    3.418 closest distance to " ND2 ASN A 249 " =    0.866
peak=    3.417 closest distance to " O   HOH Z 299 " =    4.499
peak=    3.414 closest distance to " CB  ILE A 120 " =    1.254
peak=    3.414 closest distance to " CB  TYR A 116 " =    0.786
peak=    3.413 closest distance to " O   HOH Z 273 " =    2.938
peak=    3.412 closest distance to " CG2 ILE A  20 " =    1.255
peak=    3.410 closest distance to " O   HOH Z 329 " =    4.123
peak=    3.410 closest distance to " CA  MET A 105 " =    1.011
peak=    3.409 closest distance to " N   ASN A  39 " =    1.328
peak=    3.399 closest distance to " O   HOH Z 325 " =    2.424
peak=    3.394 closest distance to " CB  ALA A 291 " =    1.253
peak=    3.392 closest distance to " NH2BARG A 145 " =    2.158
peak=    3.387 closest distance to " CB  ASP A 298 " =    1.180
peak=    3.386 closest distance to " CA  THR A 221 " =    1.000
peak=    3.383 closest distance to " O   HOH Z 305 " =    3.603
peak=    3.381 closest distance to " O   HOH Z 258 " =    1.596
peak=    3.381 closest distance to " O   HOH Z 337 " =    3.642
peak=    3.379 closest distance to " O   HOH Z   9 " =    2.022
peak=    3.378 closest distance to " NH2 ARG A 156 " =    1.182
peak=    3.375 closest distance to " CB  LEU A  83 " =    0.781
peak=    3.375 closest distance to " O   HOH Z  97 " =    2.488
peak=    3.370 closest distance to " O   HOH Z 353 " =    2.653
peak=    3.370 closest distance to " O   HOH Z 213 " =    2.027
peak=    3.370 closest distance to " O   HOH Z 384 " =    3.029
peak=    3.365 closest distance to " O   MET A 105 " =    1.952
peak=    3.364 closest distance to " OG BSER A  99 " =    2.317
peak=    3.363 closest distance to " CG2 ILE A 120 " =    1.119
peak=    3.363 closest distance to " CB  TRP A 179 " =    1.464
peak=    3.359 closest distance to " O   HOH Z 403 " =    1.578
peak=    3.357 closest distance to " O   HOH Z 425 " =    2.027
peak=    3.356 closest distance to " O   HOH Z 402 " =    1.382
peak=    3.356 closest distance to " CA  VAL A 125 " =    1.096
peak=    3.349 closest distance to " NZ  LYS A  48 " =    1.286
peak=    3.346 closest distance to " CB  ARG A 139 " =    1.039
peak=    3.345 closest distance to " CB  THR A  82 " =    1.436
peak=    3.342 closest distance to " CA  ALA A 291 " =    0.813
peak=    3.341 closest distance to " CB  GLN A  88 " =    1.225
peak=    3.335 closest distance to " CG1 ILE A  49 " =    1.543
peak=    3.328 closest distance to " CA  ILE A 234 " =    0.964
peak=    3.325 closest distance to " O   HOH Z 128 " =    2.375
peak=    3.321 closest distance to " O   HOH Z 365 " =    2.913
peak=    3.321 closest distance to " O   ALA A 165 " =    1.598
peak=    3.319 closest distance to " O   HOH Z 261 " =    1.921
peak=    3.317 closest distance to " CA  ALA A 154 " =    1.033
peak=    3.315 closest distance to " O   HOH Z  62 " =    2.065
peak=    3.310 closest distance to " O   HOH Z 426 " =    1.937
peak=    3.306 closest distance to " CG2 VAL A 197 " =    1.097
peak=    3.303 closest distance to " CA  ARG A 159 " =    1.263
peak=    3.302 closest distance to " CB  MET A  47 " =    1.027
peak=    3.299 closest distance to " N   ASN A 127 " =    1.302
peak=    3.297 closest distance to " CB  MET A  40 " =    0.795
peak=    3.296 closest distance to " OG  SER A  22 " =    2.722
peak=    3.295 closest distance to " O   HOH Z 261 " =    1.655
peak=    3.291 closest distance to " O   HOH Z 248 " =    1.660
peak=    3.291 closest distance to " CE  LYS A  48 " =    1.070
peak=    3.290 closest distance to " CG  LYS A  76 " =    0.966
peak=    3.290 closest distance to " O   HOH Z 345 " =    1.694
peak=    3.287 closest distance to " CG1 ILE A  33 " =    1.217
peak=    3.287 closest distance to " CB  ALA A 248 " =    0.908
peak=    3.281 closest distance to " N   PHE A 130 " =    1.259
peak=    3.279 closest distance to " CA  ALA A 129 " =    1.237
peak=    3.278 closest distance to " CA  ALA A 160 " =    0.943
peak=    3.275 closest distance to " CB  PHE A 204 " =    0.708
peak=    3.275 closest distance to " CA  ARG A 102 " =    1.097
peak=    3.271 closest distance to " CB  LYS A 117 " =    1.193
peak=    3.270 closest distance to " CG2 THR A 221 " =    1.087
peak=    3.270 closest distance to " O   HOH Z 132 " =    2.827
peak=    3.270 closest distance to " O   HOH Z 383 " =    2.280
peak=    3.269 closest distance to " OD2 ASP A 286 " =    2.899
peak=    3.263 closest distance to " OG1 THR A 294 " =    2.430
peak=    3.260 closest distance to " O   HOH Z 203 " =    1.629
peak=    3.256 closest distance to " O   HOH Z 218 " =    4.654
peak=    3.252 closest distance to " CD BLYS A 290 " =    0.956
peak=    3.246 closest distance to " O   HOH Z 234 " =    1.870
peak=    3.243 closest distance to " CD1 LEU A 228 " =    2.022
peak=    3.235 closest distance to " CG  GLU A  37 " =    0.873
peak=    3.233 closest distance to " O   HOH Z  59 " =    2.016
peak=    3.233 closest distance to " CA  ALA A  84 " =    1.363
peak=    3.231 closest distance to " O   HOH Z 175 " =    2.077
peak=    3.231 closest distance to " OD2 ASP A 286 " =    3.245
peak=    3.229 closest distance to " CB  ARG A 138 " =    0.961
peak=    3.224 closest distance to " CB  GLN A 103 " =    0.840
peak=    3.223 closest distance to " CA  ALA A  43 " =    1.311
peak=    3.223 closest distance to " O   HOH Z 407 " =    2.540
peak=    3.223 closest distance to " O   HOH Z 188 " =    2.005
peak=    3.222 closest distance to " O   HOH Z 128 " =    2.138
peak=    3.220 closest distance to " CB  ALA A 114 " =    1.092
peak=    3.215 closest distance to " O   HOH Z 193 " =    1.804
peak=    3.210 closest distance to " O   HOH Z 422 " =    2.713
peak=    3.209 closest distance to " O   HOH Z 285 " =    1.990
peak=    3.209 closest distance to " N   GLY A  98 " =    1.099
peak=    3.207 closest distance to " CB  ALA A   1 " =    4.852
peak=    3.207 closest distance to " ND1 HIS A  86 " =    1.727
peak=    3.199 closest distance to " CA  ASN A 217 " =    1.234
peak=    3.193 closest distance to " O   HOH Z 287 " =    2.286
peak=    3.191 closest distance to " CB  ALA A   9 " =    1.560
peak=    3.190 closest distance to " O   ALA A   1 " =    1.619
peak=    3.188 closest distance to " O   SER A 164 " =    1.305
peak=    3.184 closest distance to " CB  LEU A  96 " =    1.340
peak=    3.181 closest distance to " CA  ALA A 233 " =    1.338
peak=    3.180 closest distance to " O   TYR A 116 " =    1.342
peak=    3.176 closest distance to " N   TYR A 247 " =    1.304
peak=    3.172 closest distance to " CB  ALA A 291 " =    0.757
peak=    3.171 closest distance to " CE1 TYR A 116 " =    1.264
peak=    3.168 closest distance to " CB  GLN A  89 " =    1.309
peak=    3.167 closest distance to " NE  ARG A  79 " =    1.092
peak=    3.166 closest distance to " CD1 ILE A 106 " =    0.734
peak=    3.164 closest distance to " CB  ASN A 224 " =    0.986
peak=    3.157 closest distance to " CB  SER A 210 " =    0.740
peak=    3.156 closest distance to " O   HOH Z 302 " =    2.051
peak=    3.150 closest distance to " O   HOH Z 193 " =    2.112
peak=    3.144 closest distance to " ND2 ASN A 110 " =    1.639
peak=    3.135 closest distance to " O   HOH Z 391 " =    2.955
peak=    3.134 closest distance to " OG BSER A 134 " =    2.960
peak=    3.127 closest distance to " CD  LYS A  76 " =    2.013
peak=    3.122 closest distance to " CB  ASN A 215 " =    1.104
peak=    3.121 closest distance to " CA  ASP A 162 " =    1.038
peak=    3.118 closest distance to " CB  SER A 216 " =    0.868
peak=    3.113 closest distance to " O   PHE A  61 " =    1.395
peak=    3.106 closest distance to " CD1 ILE A 263 " =    1.320
peak=    3.103 closest distance to " O   HOH Z  88 " =    2.730
peak=    3.103 closest distance to " O   HOH Z  80 " =    1.606
peak=    3.102 closest distance to " O   HOH Z 171 " =    3.960
peak=    3.100 closest distance to " CB  GLN A 205 " =    1.062
peak=    3.097 closest distance to " ND1 HIS A  81 " =    1.718
peak=    3.090 closest distance to " O   HOH Z 258 " =    1.975
peak=    3.086 closest distance to " O   HOH Z  88 " =    2.631
peak=    3.084 closest distance to " O   HOH Z 409 " =    3.021
peak=    3.079 closest distance to " O   HOH Z  97 " =    1.946
peak=    3.068 closest distance to " O   HOH Z 130 " =    2.183
peak=    3.066 closest distance to " O   ALA A 158 " =    1.282
peak=    3.065 closest distance to " CD1 ILE A 199 " =    0.852
peak=    3.058 closest distance to " O   GLN A 278 " =    1.517
peak=    3.053 closest distance to " CD  LYS A 119 " =    1.381
peak=    3.048 closest distance to " CA  GLY A 211 " =    1.325

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.775 - 5.777
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.775 - 5.777

peak=   -4.822 closest distance to " CD  ARG A  14 " =    3.482
peak=   -4.771 closest distance to " CG1 VAL A 112 " =    2.641
peak=   -4.574 closest distance to " CD  GLN A  58 " =    0.932
peak=   -4.405 closest distance to " CD  ARG A 156 " =    2.089
peak=   -4.382 closest distance to " O   VAL A  67 " =    2.767
peak=   -4.298 closest distance to " CZ3 TRP A 179 " =    1.163
peak=   -4.279 closest distance to " O   HOH Z 231 " =    2.203
peak=   -4.273 closest distance to " O   HOH Z 377 " =    2.173
peak=   -4.219 closest distance to " CB  PRO A 243 " =    2.655
peak=   -4.167 closest distance to " O   PRO A 198 " =    1.334
peak=   -4.160 closest distance to " O   HOH Z 266 " =    5.437
peak=   -4.159 closest distance to " C   HIS A 108 " =    1.107
peak=   -4.108 closest distance to " O   HOH Z  73 " =    2.283
peak=   -4.107 closest distance to " N   ALA A  43 " =    2.674
peak=   -4.103 closest distance to " OG BSER A 134 " =    1.340
peak=   -4.041 closest distance to " CG  GLN A 223 " =    2.089
peak=   -3.987 closest distance to " O   HOH Z 372 " =    2.340
peak=   -3.982 closest distance to " O   HOH Z  10 " =    1.499
peak=   -3.976 closest distance to " CG1 VAL A 112 " =    2.841
peak=   -3.959 closest distance to " CE  MET A 105 " =    2.500
peak=   -3.956 closest distance to " CD2 PHE A 192 " =    2.035
peak=   -3.949 closest distance to " OG  SER A  97 " =    2.295
peak=   -3.949 closest distance to " O   HOH Z 198 " =    2.080
peak=   -3.932 closest distance to " CA  VAL A  67 " =    2.938
peak=   -3.915 closest distance to " O   HOH Z 185 " =    2.261
peak=   -3.897 closest distance to " O   HOH Z 196 " =    1.979
peak=   -3.886 closest distance to " CB  ALA A  43 " =    2.603
peak=   -3.835 closest distance to " NE2 GLN A 194 " =    1.842
peak=   -3.834 closest distance to " CB  ALA A 291 " =    2.291
peak=   -3.814 closest distance to " CD1 PHE A  59 " =    1.978
peak=   -3.812 closest distance to " O   HOH Z 389 " =    1.916
peak=   -3.768 closest distance to " CD2 TYR A 293 " =    2.011
peak=   -3.764 closest distance to " OXT GLY A 302 " =    2.903
peak=   -3.751 closest distance to " CE BMET A  47 " =    1.537
peak=   -3.750 closest distance to " CE2 PHE A  61 " =    2.658
peak=   -3.743 closest distance to " CG  ARG A 269 " =    2.533
peak=   -3.732 closest distance to " O   HOH Z 394 " =    1.537
peak=   -3.727 closest distance to " O   HOH Z 313 " =    1.945
peak=   -3.726 closest distance to " OD1 ASN A 148 " =    1.479
peak=   -3.726 closest distance to " CB  ALA A 161 " =    2.587
peak=   -3.725 closest distance to " CE2 TYR A  30 " =    2.755
peak=   -3.717 closest distance to " O   HOH Z 114 " =    3.084
peak=   -3.701 closest distance to " O   HOH Z 407 " =    3.169
peak=   -3.701 closest distance to " CA  ASP A 298 " =    1.084
peak=   -3.694 closest distance to " O   HOH Z  51 " =    1.620
peak=   -3.675 closest distance to " CG2 ILE A 263 " =    2.343
peak=   -3.672 closest distance to " NH2AARG A 275 " =    5.423
peak=   -3.667 closest distance to " OD1 ASP A 171 " =    1.677
peak=   -3.649 closest distance to " CA  GLY A 203 " =    2.430
peak=   -3.630 closest distance to " N   ALA A 248 " =    1.655
peak=   -3.629 closest distance to " O   PRO A 163 " =    2.096
peak=   -3.625 closest distance to " O   HOH Z 351 " =    1.507
peak=   -3.621 closest distance to " CB  ASN A  39 " =    2.316
peak=   -3.582 closest distance to " NE2 GLN A  88 " =    1.843
peak=   -3.579 closest distance to " CG1 VAL A 250 " =    2.675
peak=   -3.577 closest distance to " O   HOH Z 311 " =    3.802
peak=   -3.574 closest distance to " CB  ALA A 291 " =    2.343
peak=   -3.563 closest distance to " ND2 ASN A 249 " =    2.373
peak=   -3.560 closest distance to " CG2 ILE A  49 " =    2.761
peak=   -3.547 closest distance to " CZ  PHE A 155 " =    1.365
peak=   -3.542 closest distance to " CD1 LEU A 101 " =    2.405
peak=   -3.535 closest distance to " O   HOH Z 198 " =    1.364
peak=   -3.527 closest distance to " O   HOH Z 435 " =    2.913
peak=   -3.524 closest distance to " C   LEU A 143 " =    1.075
peak=   -3.508 closest distance to " CB  ASP A 286 " =    2.067
peak=   -3.504 closest distance to " CG  PHE A 283 " =    2.702
peak=   -3.500 closest distance to " O   HOH Z   6 " =    1.437
peak=   -3.497 closest distance to " O   VAL A 189 " =    2.661
peak=   -3.491 closest distance to " O   HOH Z  37 " =    1.784
peak=   -3.488 closest distance to " CB  ASP A 132 " =    2.325
peak=   -3.487 closest distance to " ND2 ASN A  45 " =    1.155
peak=   -3.480 closest distance to " CE3 TRP A 150 " =    2.228
peak=   -3.473 closest distance to " O   HOH Z  38 " =    1.504
peak=   -3.471 closest distance to " O   HOH Z 290 " =    1.447
peak=   -3.471 closest distance to " O   HOH Z  60 " =    1.890
peak=   -3.464 closest distance to " CG  HIS A  86 " =    1.081
peak=   -3.460 closest distance to " CD  ARG A 139 " =    1.649
peak=   -3.452 closest distance to " ND2 ASN A  60 " =    1.373
peak=   -3.444 closest distance to " O   HOH Z 166 " =    2.003
peak=   -3.433 closest distance to " CA  GLY A 241 " =    3.299
peak=   -3.432 closest distance to " CB  ALA A 248 " =    2.411
peak=   -3.427 closest distance to " NE2 GLN A  11 " =    1.800
peak=   -3.423 closest distance to " O   HOH Z 211 " =    1.554
peak=   -3.414 closest distance to " ND2 ASN A  45 " =    1.874
peak=   -3.413 closest distance to " O   HOH Z 134 " =    3.104
peak=   -3.401 closest distance to " CD2 LEU A 237 " =    2.884
peak=   -3.399 closest distance to " O   PHE A 218 " =    1.517
peak=   -3.397 closest distance to " O   HOH Z 216 " =    1.407
peak=   -3.390 closest distance to " O   ALA A  10 " =    1.679
peak=   -3.389 closest distance to " O   HOH Z  44 " =    2.406
peak=   -3.388 closest distance to " CB  ALA A 129 " =    2.431
peak=   -3.387 closest distance to " O   HOH Z  52 " =    1.460
peak=   -3.386 closest distance to " CB  TRP A  85 " =    2.550
peak=   -3.385 closest distance to " CG  ARG A  66 " =    2.292
peak=   -3.381 closest distance to " N   THR A  52 " =    1.698
peak=   -3.375 closest distance to " C   ASN A 285 " =    2.434
peak=   -3.373 closest distance to " O   HOH Z 357 " =    2.120
peak=   -3.365 closest distance to " O   HOH Z 174 " =    2.630
peak=   -3.364 closest distance to " NH2 ARG A 159 " =    2.394
peak=   -3.362 closest distance to " CA  GLY A 241 " =    2.321
peak=   -3.362 closest distance to " O   HOH Z 426 " =    1.583
peak=   -3.361 closest distance to " ND2BASN A 224 " =    1.813
peak=   -3.361 closest distance to " CG  LEU A  83 " =    1.972
peak=   -3.340 closest distance to " NH2BARG A 275 " =    1.884
peak=   -3.337 closest distance to " CA  SER A 135 " =    1.342
peak=   -3.332 closest distance to " NH2 ARG A  79 " =    1.539
peak=   -3.329 closest distance to " O   HOH Z  11 " =    1.663
peak=   -3.323 closest distance to " CD2 PHE A  61 " =    2.062
peak=   -3.323 closest distance to " O   HOH Z 243 " =    1.924
peak=   -3.323 closest distance to " OD2 ASP A 191 " =    1.499
peak=   -3.321 closest distance to " CG1 VAL A 125 " =    1.887
peak=   -3.320 closest distance to " OD1 ASN A 187 " =    1.574
peak=   -3.308 closest distance to " C   MET A 188 " =    1.314
peak=   -3.307 closest distance to " N   THR A 157 " =    1.552
peak=   -3.303 closest distance to " O   HOH Z 353 " =    2.173
peak=   -3.302 closest distance to " O   HOH Z 132 " =    1.566
peak=   -3.301 closest distance to " CA  PRO A 243 " =    2.346
peak=   -3.300 closest distance to " O   HOH Z 351 " =    1.605
peak=   -3.293 closest distance to " C   SER A 206 " =    1.486
peak=   -3.291 closest distance to " O   HOH Z 295 " =    1.630
peak=   -3.290 closest distance to " O   VAL A 189 " =    1.571
peak=   -3.286 closest distance to " O   ARG A 145 " =    1.579
peak=   -3.285 closest distance to " NH2 ARG A  24 " =    1.911
peak=   -3.283 closest distance to " O   HOH Z 298 " =    1.288
peak=   -3.281 closest distance to " CB  ASN A 252 " =    1.567
peak=   -3.278 closest distance to " O   HOH Z  71 " =    1.939
peak=   -3.276 closest distance to " O   HOH Z 429 " =    2.160
peak=   -3.276 closest distance to " O   HOH Z 262 " =    2.872
peak=   -3.271 closest distance to " CA  GLY A 241 " =    2.874
peak=   -3.270 closest distance to " O   TRP A  70 " =    1.430
peak=   -3.269 closest distance to " CG2 ILE A  20 " =    2.875
peak=   -3.266 closest distance to " O   HOH Z 128 " =    2.647
peak=   -3.266 closest distance to " CD1 ILE A 239 " =    2.402
peak=   -3.258 closest distance to " O   SER A 210 " =    2.015
peak=   -3.257 closest distance to " O   HOH Z 322 " =    1.660
peak=   -3.257 closest distance to " CD  ARG A 195 " =    5.199
peak=   -3.248 closest distance to " OE2 GLU A 152 " =    1.238
peak=   -3.248 closest distance to " OH  TYR A 247 " =    2.078
peak=   -3.247 closest distance to " CD  GLN A 223 " =    0.993
peak=   -3.247 closest distance to " O   HOH Z 232 " =    1.575
peak=   -3.238 closest distance to " OG BSER A 134 " =    1.781
peak=   -3.232 closest distance to " O   GLY A  17 " =    1.149
peak=   -3.232 closest distance to " CG  GLU A 277 " =    1.171
peak=   -3.226 closest distance to " O   HOH Z  43 " =    1.642
peak=   -3.224 closest distance to " O   HOH Z 348 " =    2.232
peak=   -3.221 closest distance to " CG2 VAL A 189 " =    2.145
peak=   -3.220 closest distance to " CB  ALA A 100 " =    2.133
peak=   -3.214 closest distance to " CD2 HIS A 207 " =    2.374
peak=   -3.212 closest distance to " CE3 TRP A 274 " =    2.443
peak=   -3.211 closest distance to " O   HOH Z 177 " =    1.772
peak=   -3.211 closest distance to " CD1 LEU A   5 " =    2.626
peak=   -3.210 closest distance to " O   HOH Z 191 " =    5.733
peak=   -3.208 closest distance to " O   SER A  95 " =    1.669
peak=   -3.207 closest distance to " OE1 GLN A  88 " =    1.132
peak=   -3.206 closest distance to " OD2 ASP A 171 " =    1.813
peak=   -3.204 closest distance to " O   HOH Z  13 " =    1.556
peak=   -3.204 closest distance to " O   HOH Z 241 " =    1.417
peak=   -3.201 closest distance to " CA  GLY A 133 " =    2.072
peak=   -3.198 closest distance to " O   ALA A 292 " =    2.267
peak=   -3.192 closest distance to " O   HOH Z 189 " =    1.946
peak=   -3.188 closest distance to " O   HOH Z 278 " =    1.636
peak=   -3.187 closest distance to " CZ  TYR A 169 " =    1.782
peak=   -3.186 closest distance to " SD  MET A 188 " =    2.234
peak=   -3.180 closest distance to " CG1 VAL A 197 " =    2.298
peak=   -3.180 closest distance to " C   ASP A 272 " =    2.344
peak=   -3.177 closest distance to " O   PRO A 198 " =    1.375
peak=   -3.169 closest distance to " CB  PRO A 163 " =    2.478
peak=   -3.167 closest distance to " O   HOH Z 175 " =    4.144
peak=   -3.164 closest distance to " CD1 TRP A  70 " =    1.081
peak=   -3.162 closest distance to " OD2 ASP A 171 " =    2.501
peak=   -3.154 closest distance to " CG  TRP A 266 " =    1.826
peak=   -3.153 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.151 closest distance to " O   HOH Z 106 " =    1.821
peak=   -3.149 closest distance to " O   ALA A 161 " =    1.838
peak=   -3.148 closest distance to " O   SER A 135 " =    1.467
peak=   -3.148 closest distance to " CZ  PHE A  38 " =    2.007
peak=   -3.148 closest distance to " O   HOH Z  55 " =    1.242
peak=   -3.147 closest distance to " OD1AASN A 224 " =    1.765
peak=   -3.146 closest distance to " O   HOH Z 111 " =    1.576
peak=   -3.144 closest distance to " CE1 PHE A 218 " =    2.709
peak=   -3.144 closest distance to " O   HOH Z 193 " =    1.668
peak=   -3.139 closest distance to " SG BCYS A 201 " =    1.956
peak=   -3.137 closest distance to " NE2 GLN A 278 " =    1.688
peak=   -3.131 closest distance to " OD2 ASP A  27 " =    1.573
peak=   -3.123 closest distance to " O   ARG A  24 " =    1.720
peak=   -3.122 closest distance to " CG  PRO A 243 " =    1.850
peak=   -3.120 closest distance to " O   HOH Z 339 " =    1.924
peak=   -3.115 closest distance to " O   HOH Z 421 " =    3.074
peak=   -3.115 closest distance to " O   HOH Z 174 " =    3.038
peak=   -3.107 closest distance to " CD1 LEU A 228 " =    2.321
peak=   -3.097 closest distance to " C   ALA A 158 " =    1.401
peak=   -3.091 closest distance to " CB  TYR A  15 " =    2.207
peak=   -3.088 closest distance to " O   HOH Z 283 " =    5.777
peak=   -3.086 closest distance to " CG  PRO A 163 " =    2.509
peak=   -3.084 closest distance to " CE2 PHE A 218 " =    2.437
peak=   -3.073 closest distance to " SG ACYS A 201 " =    2.005
peak=   -3.073 closest distance to " N   SER A   3 " =    2.041
peak=   -3.068 closest distance to " CA  GLY A 133 " =    2.280
peak=   -3.067 closest distance to " O   HOH Z 281 " =    2.746
peak=   -3.020 closest distance to " O   HOH Z 265 " =    1.836

================= 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    :  0.3294 0.3200   6.073702e+00   6.051111e+00
   1_bss:  0.3108 0.3061   6.043365e+00   6.020570e+00
   1_xyz:  0.1810 0.2081   5.520831e+00   5.624676e+00
   1_adp:  0.1704 0.2084   5.479522e+00   5.632629e+00
   1_occ:  0.1699 0.2084   5.478466e+00   5.633378e+00
   2_bss:  0.1651 0.2035   5.454961e+00   5.611891e+00
   2_xyz:  0.1358 0.1669   5.271966e+00   5.439262e+00
   2_adp:  0.1263 0.1683   5.232624e+00   5.441277e+00
   2_occ:  0.1262 0.1682   5.232055e+00   5.440921e+00
   3_bss:  0.1258 0.1674   5.229465e+00   5.437204e+00
   3_xyz:  0.1192 0.1637   5.192198e+00   5.417835e+00
   3_adp:  0.1198 0.1604   5.187713e+00   5.403652e+00
   3_occ:  0.1197 0.1604   5.187736e+00   5.404282e+00
   4_bss:  0.1196 0.1603   5.187596e+00   5.404283e+00
   4_xyz:  0.1113 0.1575   5.142669e+00   5.385256e+00
   4_adp:  0.1117 0.1571   5.141935e+00   5.381238e+00
   4_occ:  0.1116 0.1571   5.142027e+00   5.381720e+00
   5_bss:  0.1115 0.1572   5.142043e+00   5.382234e+00
   5_xyz:  0.1103 0.1578   5.140568e+00   5.388074e+00
   5_adp:  0.1088 0.1588   5.135631e+00   5.392436e+00
   5_occ:  0.1088 0.1589   5.135735e+00   5.392815e+00
   5_bss:  0.1086 0.1587   5.135633e+00   5.392716e+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:  0.319  61.151  -2.979  -3.226   4.543  -0.000   0.000   0.000
   1_xyz:  0.319  61.151  -2.979  -3.226   4.543  -0.000   0.000   0.000
   1_adp:  0.319  61.151  -2.979  -3.226   4.543  -0.000   0.000   0.000
   1_occ:  0.319  61.151  -2.979  -3.226   4.543  -0.000   0.000   0.000
   2_bss:  0.336  68.020  -2.819  -2.692   0.400  -0.000   0.000   0.000
   2_xyz:  0.336  68.020  -2.819  -2.692   0.400  -0.000   0.000   0.000
   2_adp:  0.336  68.020  -2.819  -2.692   0.400  -0.000   0.000   0.000
   2_occ:  0.336  68.020  -2.819  -2.692   0.400  -0.000   0.000   0.000
   3_bss:  0.333  69.919  -2.487  -2.283  -0.078  -0.000  -0.000  -0.000
   3_xyz:  0.333  69.919  -2.487  -2.283  -0.078  -0.000  -0.000  -0.000
   3_adp:  0.333  69.919  -2.487  -2.283  -0.078  -0.000  -0.000  -0.000
   3_occ:  0.333  69.919  -2.487  -2.283  -0.078  -0.000  -0.000  -0.000
   4_bss:  0.336  69.919  -2.257  -2.048  -0.187  -0.000  -0.000  -0.000
   4_xyz:  0.336  69.919  -2.257  -2.048  -0.187  -0.000  -0.000  -0.000
   4_adp:  0.336  69.919  -2.257  -2.048  -0.187  -0.000  -0.000  -0.000
   4_occ:  0.336  69.919  -2.257  -2.048  -0.187  -0.000  -0.000  -0.000
   5_bss:  0.322  56.514  -2.122  -1.927  -0.144  -0.000  -0.000  -0.000
   5_xyz:  0.322  56.514  -2.122  -1.927  -0.144  -0.000  -0.000  -0.000
   5_adp:  0.322  56.514  -2.122  -1.927  -0.144  -0.000  -0.000  -0.000
   5_occ:  0.322  56.514  -2.122  -1.927  -0.144  -0.000  -0.000  -0.000
   5_bss:  0.314  56.507  -1.860  -1.669   0.063  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.900 0.7173  0.8705    30199.931
   1_bss:  32.650 0.7300  0.8704    27259.613
   1_xyz:  19.475 0.8675  0.9918    10757.082
   1_adp:  19.724 0.8648  0.9836    10908.093
   1_occ:  19.747 0.8645  0.9831    10913.660
   2_bss:  19.003 0.8721  0.9533    10504.002
   2_xyz:  15.100 0.9062  0.9664     7124.904
   2_adp:  15.123 0.9060  0.9577     7083.625
   2_occ:  15.113 0.9061  0.9577     7073.853
   3_bss:  15.021 0.9068  0.9613     7006.586
   3_xyz:  14.536 0.9110  0.9650     6744.734
   3_adp:  14.204 0.9138  0.9615     6587.467
   3_occ:  14.215 0.9137  0.9613     6592.008
   4_bss:  14.212 0.9137  0.9656     6593.583
   4_xyz:  13.889 0.9160  0.9684     6362.472
   4_adp:  13.771 0.9172  0.9647     6328.335
   4_occ:  13.778 0.9171  0.9645     6330.107
   5_bss:  13.788 0.9170  0.9678     6327.750
   5_xyz:  13.868 0.9166  0.9674     6449.162
   5_adp:  13.961 0.9158  0.9598     6456.032
   5_occ:  13.965 0.9158  0.9597     6460.249
   5_bss:  13.965 0.9158  0.9677     6458.816
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6430e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6430e-01
   1_xyz:   1.205  0.010  0.076 15.415  0.005  4.118   8.0980e-02
   1_adp:   1.205  0.010  0.076 15.415  0.005  4.118   8.0980e-02
   1_occ:   1.205  0.010  0.076 15.415  0.005  4.118   8.0980e-02
   2_bss:   1.205  0.010  0.076 15.415  0.005  4.118   8.0980e-02
   2_xyz:   0.960  0.007  0.074 14.931  0.004  4.128   5.5608e-02
   2_adp:   0.960  0.007  0.074 14.931  0.004  4.128   5.5608e-02
   2_occ:   0.960  0.007  0.074 14.931  0.004  4.128   5.5608e-02
   3_bss:   0.960  0.007  0.074 14.931  0.004  4.128   5.5608e-02
   3_xyz:   0.942  0.007  0.073 14.691  0.003  4.131   5.4115e-02
   3_adp:   0.942  0.007  0.073 14.691  0.003  4.131   5.4115e-02
   3_occ:   0.942  0.007  0.073 14.691  0.003  4.131   5.4115e-02
   4_bss:   0.942  0.007  0.073 14.691  0.003  4.131   5.4115e-02
   4_xyz:   1.134  0.011  0.087 15.056  0.004  4.136   7.8852e-02
   4_adp:   1.134  0.011  0.087 15.056  0.004  4.136   7.8852e-02
   4_occ:   1.134  0.011  0.087 15.056  0.004  4.136   7.8852e-02
   5_bss:   1.134  0.011  0.087 15.056  0.004  4.136   7.8852e-02
   5_xyz:   1.124  0.012  0.088 15.010  0.004  4.127   7.9982e-02
   5_adp:   1.124  0.012  0.088 15.010  0.004  4.127   7.9982e-02
   5_occ:   1.124  0.012  0.088 15.010  0.004  4.127   7.9982e-02
   5_bss:   1.124  0.012  0.088 15.010  0.004  4.127   7.9982e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.746   2.4349e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.746   2.4349e-01
   1_xyz:  10.760  0.058  0.231 81.466  0.040  2.267   9.6929e-02
   1_adp:  10.760  0.058  0.231 81.466  0.040  2.267   9.6929e-02
   1_occ:  10.760  0.058  0.231 81.466  0.040  2.267   9.6929e-02
   2_bss:  10.760  0.058  0.231 81.466  0.040  2.267   9.6929e-02
   2_xyz:   6.744  0.038  0.221 82.650  0.039  2.364   4.4492e-02
   2_adp:   6.744  0.038  0.221 82.650  0.039  2.364   4.4492e-02
   2_occ:   6.744  0.038  0.221 82.650  0.039  2.364   4.4492e-02
   3_bss:   6.744  0.038  0.221 82.650  0.039  2.364   4.4492e-02
   3_xyz:   7.054  0.043  0.223 82.351  0.036  2.419   3.0979e-02
   3_adp:   7.054  0.043  0.223 82.351  0.036  2.419   3.0979e-02
   3_occ:   7.054  0.043  0.223 82.351  0.036  2.419   3.0979e-02
   4_bss:   7.054  0.043  0.223 82.351  0.036  2.419   3.0979e-02
   4_xyz:   7.437  0.056  0.298 83.026  0.035  2.250   5.9176e-02
   4_adp:   7.437  0.056  0.298 83.026  0.035  2.250   5.9176e-02
   4_occ:   7.437  0.056  0.298 83.026  0.035  2.250   5.9176e-02
   5_bss:   7.437  0.056  0.298 83.026  0.035  2.250   5.9176e-02
   5_xyz:   7.270  0.059  0.285 83.454  0.034  2.279   6.2991e-02
   5_adp:   7.270  0.059  0.285 83.454  0.034  2.279   6.2991e-02
   5_occ:   7.270  0.059  0.285 83.454  0.034  2.279   6.2991e-02
   5_bss:   7.270  0.059  0.285 83.454  0.034  2.279   6.2991e-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:  88.17   0.00  16.21  88.17   0.00  12.35  62.95   4.10  37.25
   1_occ:  88.17   0.00  16.21  88.17   0.00  12.35  62.95   4.10  37.25
   2_bss:  88.17   0.00  16.21  88.17   0.00  12.35  62.95   4.10  37.25
   2_xyz:  88.17   0.00  16.21  88.17   0.00  12.35  62.95   4.10  37.25
   2_adp:  83.71   0.36  17.30  80.55   0.36  12.82  83.71   5.55  41.68
   2_occ:  83.71   0.36  17.30  80.55   0.36  12.82  83.71   5.55  41.68
   3_bss:  83.71   0.36  17.30  80.55   0.36  12.82  83.71   5.55  41.68
   3_xyz:  83.71   0.36  17.30  80.55   0.36  12.82  83.71   5.55  41.68
   3_adp:  78.85   1.42  16.43  77.04   1.42  12.47  78.85   2.59  38.03
   3_occ:  78.85   1.42  16.43  77.04   1.42  12.47  78.85   2.59  38.03
   4_bss:  78.85   1.42  16.43  77.04   1.42  12.47  78.85   2.59  38.03
   4_xyz:  78.85   1.42  16.43  77.04   1.42  12.47  78.85   2.59  38.03
   4_adp:  76.09   1.75  16.06  73.98   1.75  12.27  76.09   4.29  36.67
   4_occ:  76.09   1.75  16.06  73.98   1.75  12.27  76.09   4.29  36.67
   5_bss:  76.09   1.75  16.06  73.98   1.75  12.27  76.09   4.29  36.67
   5_xyz:  76.09   1.75  16.06  73.98   1.75  12.27  76.09   4.29  36.67
   5_adp:  81.64   0.25  16.41  81.27   0.25  12.27  81.64   5.40  38.91
   5_occ:  81.64   0.25  16.41  81.27   0.25  12.27  81.64   5.40  38.91
   5_bss:  81.63   0.24  16.40  81.27   0.24  12.27  81.63   5.40  38.91
------------------------------------------------------------------------
 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:    1.139    0.012    0.335
   1_adp:    1.139    0.012    0.335
   1_occ:    1.139    0.012    0.335
   2_bss:    1.139    0.012    0.335
   2_xyz:    0.918    0.021    0.362
   2_adp:    0.918    0.021    0.362
   2_occ:    0.918    0.021    0.362
   3_bss:    0.918    0.021    0.362
   3_xyz:    1.074    0.016    0.390
   3_adp:    1.074    0.016    0.390
   3_occ:    1.074    0.016    0.390
   4_bss:    1.074    0.016    0.390
   4_xyz:    1.309    0.015    0.402
   4_adp:    1.309    0.015    0.402
   4_occ:    1.309    0.015    0.402
   5_bss:    1.309    0.015    0.402
   5_xyz:    1.465    0.016    0.413
   5_adp:    1.465    0.016    0.413
   5_occ:    1.465    0.016    0.413
   5_bss:    1.465    0.016    0.413
------------------------------------------------------------------------

CPU time actual refinement: 319.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_790/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_790/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_790/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_790/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_790/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.77 
  Macro-tasks:
    bulk solvent and scale       = 37.19  
    individual site refinement   = 132.74 
    weights calculation          = 29.16  
    collect and process          = 6.48   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 205.67 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 101.47 
    alpha_beta                      = 8.18   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.88 
    fmodel                         = 6.15   
    r_factors                      = 0.24   
    phase_errors                   = 10.90  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 240.45 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.529 micro seconds
Total CPU time: 5.56 minutes
from_scatterers_fft:    647 calls, 101.22 s
gradients_fft:          592 calls,  97.21 s

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

# Date 2008-01-16 Time 05:40:16 PST -0800 (1200490816.07 s)
Start R-work = 0.3294, R-free = 0.3200 (no bulk solvent and anisotropic scale)
Final R-work = 0.1299, R-free = 0.1756 (no bulk solvent and anisotropic scale)

Start R-work = 0.3108, R-free = 0.3061
Final R-work = 0.1086, R-free = 0.1587