# Date 2008-01-16 Time 04:39:12 PST -0800 (1200487152.21 s)
#phil __OFF__

Command line arguments: "../410.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9215
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 410

-------------------------------------------------------------------------------
  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: (69.5475, 46.6953, 85.5261, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98044
Completeness in resolution range: 0.98156
Completeness with d_max=infinity: 0.978423

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9804

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: (69.5475, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98044
Completeness in resolution range: 0.98156
Completeness with d_max=infinity: 0.978423

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.2367 [2093/2118]  1884   209  10.0%
  bin  2:  4.2367 -  3.3758 [2024/2042]  1822   202  10.0%
  bin  3:  3.3758 -  2.9529 [1983/2002]  1784   199  10.0%
  bin  4:  2.9529 -  2.6847 [1956/1986]  1761   195  10.0%
  bin  5:  2.6847 -  2.4932 [1960/1979]  1764   196  10.0%
  bin  6:  2.4932 -  2.3468 [1949/1974]  1751   198  10.2%
  bin  7:  2.3468 -  2.2297 [1944/1972]  1755   189   9.7%
  bin  8:  2.2297 -  2.1329 [1941/1977]  1744   197  10.1%
  bin  9:  2.1329 -  2.0510 [1902/1944]  1711   191  10.0%
  bin 10:  2.0510 -  1.9804 [1837/1963]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_410/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: 0.15 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: 18
        2.38 -     3.01: 2018
        3.01 -     3.64: 4668
        3.64 -     4.27: 9247
        4.27 -     4.90: 12700
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.748 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  37 " - " O   HOH Z 416 "  2.016 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.024 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.070 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28646 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_410/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_410/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 69.5475 46.69535 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2971   r_free= 0.2990   ksol= 0.00   Bsol= 0.00   scale= 0.995    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.949697                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7250 0.99   1370  153 0.2738 0.2698      6.3185      6.2925|
|  2:  4.7250 -  3.7706 0.99   1303  145 0.2353 0.2321      6.3244      6.3257|
|  3:  3.7706 -  3.3000 0.99   1281  142 0.2507 0.2539      6.2309      6.3217|
|  4:  3.3000 -  3.0010 0.99   1280  140 0.2653 0.2783      6.1087      6.1516|
|  5:  3.0010 -  2.7874 0.99   1257  142 0.2881 0.2901      5.9885      5.9646|
|  6:  2.7874 -  2.6240 0.99   1274  140 0.3080 0.3144      5.9535      5.9204|
|  7:  2.6240 -  2.4932 0.99   1250  139 0.3154 0.2834      5.9165      5.8022|
|  8:  2.4932 -  2.3851 0.98   1254  140 0.3203 0.3316      5.8878      5.9484|
|  9:  2.3851 -  2.2937 0.98   1241  140 0.3337 0.3268       5.853      5.7976|
| 10:  2.2937 -  2.2148 0.99   1237  137 0.3264 0.3664      5.8065      5.8762|
| 11:  2.2148 -  2.1457 0.98   1252  137 0.3393 0.3435      5.7766      5.8301|
| 12:  2.1457 -  2.0846 0.97   1236  138 0.3436 0.3129      5.7596      5.7313|
| 13:  2.0846 -  2.0298 1.00   1230  134 0.3453 0.3440      5.6582      5.6486|
| 14:  2.0298 -  1.9804 0.91   1165  132 0.3483 0.3353      5.6198      5.4866|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7250  1370   153  0.79  25.87   0.87     0.80      41978.01|
|  2:  4.7250 -  3.7706  1303   145  0.86  20.55   0.99     0.94      40221.49|
|  3:  3.7706 -  3.3000  1281   142  0.84  22.85   1.02     0.99      36529.06|
|  4:  3.3000 -  3.0010  1280   140  0.82  24.92   1.02     0.99      31363.66|
|  5:  3.0010 -  2.7874  1257   142  0.78  28.17   1.01     0.97      25641.98|
|  6:  2.7874 -  2.6240  1274   140  0.78  28.57   1.02     0.99      22108.21|
|  7:  2.6240 -  2.4932  1250   139  0.78  28.91   1.02     1.00      19939.03|
|  8:  2.4932 -  2.3851  1254   140  0.77  29.97   1.04     0.99      19647.92|
|  9:  2.3851 -  2.2937  1241   140  0.75  31.36   1.05     0.96      18836.09|
| 10:  2.2937 -  2.2148  1237   137  0.73  33.16   1.09     0.96      18441.29|
| 11:  2.2148 -  2.1457  1252   137  0.73  33.08   1.07     0.98      17066.08|
| 12:  2.1457 -  2.0846  1236   138  0.74  32.07   1.09     1.01      15332.28|
| 13:  2.0846 -  2.0298  1230   134  0.74  32.24   1.08     1.00      12763.39|
| 14:  2.0298 -  1.9804  1165   132  0.76  30.31   1.08     0.97       9696.36|
|alpha:            min =        0.80 max =            1.01 mean =         0.97|
|beta:             min =     9696.36 max =        41978.01 mean =     23841.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.78|
|phase err.(work): min =        0.00 max =           89.93 mean =        28.64|
|phase err.(test): min =        0.00 max =           89.19 mean =        28.64|
|-----------------------------------------------------------------------------|

============================== 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 = 2.197940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.356   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.515276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.480   (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 |  1.748 -  2.063:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.063 -  2.378:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.378 -  2.693:      132 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.693 -  3.009:     1886 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.009 -  3.324:     1895 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.324 -  3.639:     2773 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.639 -  3.954:     4775 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.954 -  4.270:     4472 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.270 -  4.585:     5793 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.585 -  4.900:     6907 |
|-----------------------------------------------------------------------------|
|-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 |   4.111    4.900  1.748 |       0.228 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2971   r_free= 0.2990   ksol= 0.00   Bsol= 0.00   scale= 0.995    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.949697                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2819   r_free= 0.2790   ksol= 0.32   Bsol= 27.15   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.96,-0.31,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.923104                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.923964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.343   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268591              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.404   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2819      final r-factor (work) = 0.1690          |
| start r-factor (free) = 0.2790      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8843 = 1.92 * 0.50 * 5.9462 + 1.00 * 0.1642                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4678 = 1.92 * 0.50 * 5.6272 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1690      final r-factor (work) = 0.1574          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1931          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5177 = 0.27 * 1.00 * 5.6272 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5014 = 0.27 * 1.00 * 5.3983 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.18   16.44    None  None   None       |
|    all(noH): 2823   0      0.00    78.18   16.44    None  None   None       |
|    Sol.    : 438    0      7.10    62.27   37.24    None  None   None       |
|    Mac.    : 2385   0      0.00    78.18   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.818:  440   |   5:    39.089 -  46.906:  118        |
|      1:     7.818 -  15.635: 1469   |   6:    46.906 -  54.724:   80        |
|      2:    15.635 -  23.453:  420   |   7:    54.724 -  62.542:   39        |
|      3:    23.453 -  31.271:  138   |   8:    62.542 -  70.359:    0        |
|      4:    31.271 -  39.089:  118   |   9:    70.359 -  78.177:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1574 r_free = 0.1931             target_work(ml) = 5.408         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1570 r_free = 0.1933             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1570   r_free= 0.1933   ksol= 0.32   Bsol= 27.15   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.96,-0.31,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.405919                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1562   r_free= 0.1934   ksol= 0.32   Bsol= 34.08   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.60,-1.49,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.405743                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.412832              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.826   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.302097              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.479   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1562      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1934      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8758 = 1.41 * 0.50 * 5.4094 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7893 = 1.41 * 0.50 * 5.2958 + 1.00 * 0.0483                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6460 = 0.30 * 1.00 * 5.2958 + 1.00 * 0.0462                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5675 = 0.30 * 1.00 * 5.1629 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    73.07   16.93    None  None   None       |
|    all(noH): 2823   0      0.48    73.07   16.93    None  None   None       |
|    Sol.    : 438    0      5.05    70.64   38.60    None  None   None       |
|    Mac.    : 2385   0      0.48    73.07   12.95    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:     0.477 -   7.736:  438   |   5:    36.775 -  44.034:  112        |
|      1:     7.736 -  14.996: 1405   |   6:    44.034 -  51.294:  103        |
|      2:    14.996 -  22.255:  420   |   7:    51.294 -  58.553:   71        |
|      3:    22.255 -  29.515:  132   |   8:    58.553 -  65.813:   23        |
|      4:    29.515 -  36.775:  107   |   9:    65.813 -  73.072:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1560             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1560             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1560   ksol= 0.32   Bsol= 34.08   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.60,-1.49,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1559   ksol= 0.32   Bsol= 38.31   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.38,-1.43,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156106                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.286078              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.021  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.293531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.104  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3691 = 1.29 * 0.50 * 5.1643 + 1.00 * 0.0483                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3452 = 1.29 * 0.50 * 5.1284 + 1.00 * 0.0474                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1518          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5132 = 0.29 * 1.00 * 5.1284 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5093 = 0.29 * 1.00 * 5.1153 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    76.91   16.78    None  None   None       |
|    all(noH): 2823   0      1.06    76.91   16.78    None  None   None       |
|    Sol.    : 438    0      4.43    73.81   38.27    None  None   None       |
|    Mac.    : 2385   0      1.06    76.91   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.058 -   8.643:  684   |   5:    38.983 -  46.569:  115        |
|      1:     8.643 -  16.228: 1271   |   6:    46.569 -  54.154:   92        |
|      2:    16.228 -  23.813:  354   |   7:    54.154 -  61.739:   50        |
|      3:    23.813 -  31.398:  122   |   8:    61.739 -  69.324:   16        |
|      4:    31.398 -  38.983:  113   |   9:    69.324 -  76.909:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1109 r_free = 0.1518             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1109 r_free = 0.1517             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1517   ksol= 0.32   Bsol= 38.31   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.38,-1.43,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113788                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1516   ksol= 0.32   Bsol= 39.40   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-2.29,-1.38,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113592                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.320532              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.300  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.118080              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.932  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1503          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9825 = 2.32 * 0.50 * 5.1153 + 1.00 * 0.0474                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9670 = 2.32 * 0.50 * 5.0907 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1055      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1503      final r-factor (free) = 0.1503          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6089 = 0.12 * 1.00 * 5.0907 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6075 = 0.12 * 1.00 * 5.0907 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.93    74.67   16.25    None  None   None       |
|    all(noH): 2823   0      1.93    74.67   16.25    None  None   None       |
|    Sol.    : 438    0      6.08    74.35   36.03    None  None   None       |
|    Mac.    : 2385   0      1.93    74.67   12.61    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:     1.925 -   9.200:  823   |   5:    38.297 -  45.571:  104        |
|      1:     9.200 -  16.474: 1186   |   6:    45.571 -  52.845:   85        |
|      2:    16.474 -  23.748:  315   |   7:    52.845 -  60.119:   32        |
|      3:    23.748 -  31.022:  128   |   8:    60.119 -  67.393:   10        |
|      4:    31.022 -  38.297:  134   |   9:    67.393 -  74.668:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1066 r_free = 0.1503             target_work(ml) = 5.089         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1503             target_work(ml) = 5.089         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1503   ksol= 0.32   Bsol= 39.40   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-2.29,-1.38,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.089391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1503   ksol= 0.32   Bsol= 39.40   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.22,-1.28,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.089656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.247351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.967  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.763561              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.595  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1065      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1503      final r-factor (free) = 0.1512          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7810 = 2.25 * 0.50 * 5.0909 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7758 = 2.25 * 0.50 * 5.0883 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1052          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8917 = 0.76 * 1.00 * 5.0883 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8907 = 0.76 * 1.00 * 5.0852 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    77.34   16.39    None  None   None       |
|    all(noH): 2823   0      0.68    77.34   16.39    None  None   None       |
|    Sol.    : 438    0      6.11    74.95   37.39    None  None   None       |
|    Mac.    : 2385   0      0.68    77.34   12.54    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:     0.678 -   8.344:  665   |   5:    39.009 -  46.675:  122        |
|      1:     8.344 -  16.010: 1308   |   6:    46.675 -  54.341:   90        |
|      2:    16.010 -  23.677:  341   |   7:    54.341 -  62.007:   36        |
|      3:    23.677 -  31.343:  124   |   8:    62.007 -  69.673:   11        |
|      4:    31.343 -  39.009:  121   |   9:    69.673 -  77.340:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1052 r_free = 0.1522             target_work(ml) = 5.091         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1052 r_free = 0.1522             target_work(ml) = 5.091         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1522   ksol= 0.32   Bsol= 39.40   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.22,-1.28,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090738                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7250 0.99   1370  153 0.0994 0.1232      5.3709       5.492|
|  2:  4.7250 -  3.7706 0.99   1303  145 0.0838 0.1132      5.4221      5.6312|
|  3:  3.7706 -  3.3000 0.99   1281  142 0.1018 0.1485      5.4492       5.835|
|  4:  3.3000 -  3.0010 0.99   1280  140 0.1145 0.1465      5.4172      5.5596|
|  5:  3.0010 -  2.7874 0.99   1257  142 0.1193 0.1688      5.2663      5.5062|
|  6:  2.7874 -  2.6240 0.99   1274  140 0.1132 0.1650      5.1607      5.3679|
|  7:  2.6240 -  2.4932 0.99   1250  139 0.1169 0.1611      5.0982       5.353|
|  8:  2.4932 -  2.3851 0.98   1254  140 0.1075 0.1708        5.02      5.3343|
|  9:  2.3851 -  2.2937 0.98   1241  140 0.1085 0.1645      4.9755      5.2097|
| 10:  2.2937 -  2.2148 0.99   1237  137 0.1036 0.1784      4.9242      5.2212|
| 11:  2.2148 -  2.1457 0.98   1252  137 0.1045 0.1640       4.888      5.1973|
| 12:  2.1457 -  2.0846 0.97   1236  138 0.1041 0.1614      4.8329      5.1791|
| 13:  2.0846 -  2.0298 1.00   1230  134 0.0993 0.1571      4.7342      5.0132|
| 14:  2.0298 -  1.9804 0.91   1165  132 0.0957 0.1705      4.6076      4.9095|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7250  1370   153  0.94   8.90   0.98     0.96       6683.46|
|  2:  4.7250 -  3.7706  1303   145  0.95   7.68   1.02     1.01       8669.42|
|  3:  3.7706 -  3.3000  1281   142  0.94  10.62   1.03     1.02       9852.66|
|  4:  3.3000 -  3.0010  1280   140  0.93  12.77   1.01     1.00       9667.85|
|  5:  3.0010 -  2.7874  1257   142  0.91  14.54   0.99     0.96       7456.76|
|  6:  2.7874 -  2.6240  1274   140  0.91  14.84   0.99     0.96       6390.05|
|  7:  2.6240 -  2.4932  1250   139  0.91  14.65   0.98     0.96       5460.42|
|  8:  2.4932 -  2.3851  1254   140  0.92  13.59   0.99     0.98       4771.47|
|  9:  2.3851 -  2.2937  1241   140  0.92  14.39   1.01     0.98       4503.93|
| 10:  2.2937 -  2.2148  1237   137  0.91  14.53   1.00     0.96       4067.55|
| 11:  2.2148 -  2.1457  1252   137  0.91  15.30   1.00     0.97       4048.12|
| 12:  2.1457 -  2.0846  1236   138  0.92  14.36   1.01     0.99       3624.53|
| 13:  2.0846 -  2.0298  1230   134  0.92  14.27   1.01     1.00       3048.57|
| 14:  2.0298 -  1.9804  1165   132  0.92  13.57   0.98     0.95       2283.43|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2283.43 max =         9852.66 mean =      5805.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.09|
|phase err.(test): min =        0.00 max =           88.80 mean =        12.73|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1051   r_free= 0.1521   ksol= 0.32   Bsol= 39.37   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.01,-1.08,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090634                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1051   r_free= 0.1521   ksol= 0.32   Bsol= 39.37   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.01,-1.08,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090634                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7250 0.99   1370  153 0.0994 0.1233        5.37      5.4905|
|  2:  4.7250 -  3.7706 0.99   1303  145 0.0839 0.1133      5.4224      5.6313|
|  3:  3.7706 -  3.3000 0.99   1281  142 0.1018 0.1485      5.4494      5.8354|
|  4:  3.3000 -  3.0010 0.99   1280  140 0.1145 0.1465      5.4171      5.5595|
|  5:  3.0010 -  2.7874 0.99   1257  142 0.1193 0.1688       5.266      5.5058|
|  6:  2.7874 -  2.6240 0.99   1274  140 0.1132 0.1650      5.1605      5.3677|
|  7:  2.6240 -  2.4932 0.99   1250  139 0.1169 0.1611      5.0981       5.353|
|  8:  2.4932 -  2.3851 0.98   1254  140 0.1075 0.1707      5.0199       5.334|
|  9:  2.3851 -  2.2937 0.98   1241  140 0.1085 0.1645      4.9755      5.2096|
| 10:  2.2937 -  2.2148 0.99   1237  137 0.1036 0.1784      4.9242      5.2211|
| 11:  2.2148 -  2.1457 0.98   1252  137 0.1044 0.1640      4.8879      5.1971|
| 12:  2.1457 -  2.0846 0.97   1236  138 0.1041 0.1614      4.8328       5.179|
| 13:  2.0846 -  2.0298 1.00   1230  134 0.0993 0.1571       4.734      5.0131|
| 14:  2.0298 -  1.9804 0.91   1165  132 0.0957 0.1705      4.6076      4.9096|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7250  1370   153  0.94   8.88   0.99     0.96       6657.58|
|  2:  4.7250 -  3.7706  1303   145  0.95   7.68   1.03     1.02       8661.88|
|  3:  3.7706 -  3.3000  1281   142  0.94  10.62   1.03     1.02       9856.64|
|  4:  3.3000 -  3.0010  1280   140  0.93  12.77   1.01     1.00       9664.13|
|  5:  3.0010 -  2.7874  1257   142  0.91  14.54   1.00     0.97       7452.77|
|  6:  2.7874 -  2.6240  1274   140  0.91  14.83   0.99     0.97       6386.46|
|  7:  2.6240 -  2.4932  1250   139  0.91  14.65   0.99     0.96       5458.83|
|  8:  2.4932 -  2.3851  1254   140  0.92  13.59   1.00     0.99       4770.04|
|  9:  2.3851 -  2.2937  1241   140  0.92  14.39   1.01     0.99       4504.03|
| 10:  2.2937 -  2.2148  1237   137  0.91  14.53   1.01     0.97       4067.15|
| 11:  2.2148 -  2.1457  1252   137  0.91  15.30   1.01     0.98       4047.00|
| 12:  2.1457 -  2.0846  1236   138  0.92  14.36   1.02     1.00       3623.15|
| 13:  2.0846 -  2.0298  1230   134  0.92  14.27   1.02     1.01       3047.58|
| 14:  2.0298 -  1.9804  1165   132  0.92  13.57   0.99     0.96       2283.30|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2283.30 max =         9856.64 mean =      5801.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.09|
|phase err.(test): min =        0.00 max =           88.76 mean =        12.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    77.32   16.37    None  None   None       |
|    all(noH): 2823   0      0.66    77.32   16.37    None  None   None       |
|    Sol.    : 438    0      6.09    74.93   37.36    None  None   None       |
|    Mac.    : 2385   0      0.66    77.32   12.52    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:     0.656 -   8.322:  665   |   5:    38.986 -  46.653:  122        |
|      1:     8.322 -  15.988: 1308   |   6:    46.653 -  54.319:   90        |
|      2:    15.988 -  23.654:  341   |   7:    54.319 -  61.985:   36        |
|      3:    23.654 -  31.320:  124   |   8:    61.985 -  69.651:   11        |
|      4:    31.320 -  38.986:  121   |   9:    69.651 -  77.317:    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)= 266         
Filter by distance & map next to the model:
   mapped sites are within: 0.460 - 3.798
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 261 from: 266
   mapped sites are within: 0.706 - 3.798

peak=    5.786 closest distance to " O   HOH Z 126 " =    1.910
peak=    5.739 closest distance to " NH2 ARG A  56 " =    2.225
peak=    5.627 closest distance to " O   HOH Z 142 " =    1.803
peak=    5.602 closest distance to " CB  ARG A 275 " =    0.935
peak=    5.232 closest distance to " NE2 GLN A  11 " =    1.112
peak=    5.216 closest distance to " CG  PRO A  54 " =    1.225
peak=    5.163 closest distance to " CB  GLN A 223 " =    1.461
peak=    5.019 closest distance to " CB  GLU A 152 " =    1.202
peak=    4.917 closest distance to " CB  SER A  63 " =    1.146
peak=    4.888 closest distance to " O   HOH Z  78 " =    1.797
peak=    4.844 closest distance to " CB  GLN A 183 " =    1.207
peak=    4.838 closest distance to " CG  PRO A 213 " =    1.243
peak=    4.789 closest distance to " O   HOH Z 250 " =    2.423
peak=    4.631 closest distance to " O   HOH Z 236 " =    1.977
peak=    4.521 closest distance to " O   HOH Z 427 " =    2.792
peak=    4.490 closest distance to " C   PRO A 198 " =    1.424
peak=    4.484 closest distance to " O   HOH Z 209 " =    2.239
peak=    4.462 closest distance to " O   HOH Z 193 " =    1.808
peak=    4.440 closest distance to " O   HOH Z 369 " =    2.079
peak=    4.411 closest distance to " CB  ASN A 148 " =    1.760
peak=    4.387 closest distance to " CB  ARG A  79 " =    1.418
peak=    4.378 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.352 closest distance to " O   HOH Z  44 " =    1.852
peak=    4.324 closest distance to " O   HOH Z  78 " =    2.085
peak=    4.313 closest distance to " O   HOH Z 234 " =    3.614
peak=    4.278 closest distance to " CG2 VAL A 257 " =    0.890
peak=    4.273 closest distance to " O   HOH Z 402 " =    1.455
peak=    4.235 closest distance to " CB  PRO A  54 " =    0.929
peak=    4.225 closest distance to " O   HOH Z 303 " =    2.024
peak=    4.221 closest distance to " CB  VAL A 265 " =    1.268
peak=    4.183 closest distance to " ND2 ASN A 187 " =    1.481
peak=    4.180 closest distance to " O   HOH Z 298 " =    1.839
peak=    4.164 closest distance to " O   HOH Z  66 " =    2.160
peak=    4.151 closest distance to " O   HOH Z 316 " =    3.025
peak=    4.144 closest distance to " O   HOH Z 250 " =    1.440
peak=    4.144 closest distance to " O   HOH Z  15 " =    2.258
peak=    4.143 closest distance to " O   HOH Z 203 " =    1.739
peak=    4.141 closest distance to " O   HOH Z  93 " =    2.441
peak=    4.130 closest distance to " O   HOH Z 346 " =    1.719
peak=    4.105 closest distance to " O   HOH Z  54 " =    1.698
peak=    4.093 closest distance to " NZ  LYS A 117 " =    3.217
peak=    4.083 closest distance to " OD1 ASN A  69 " =    2.593
peak=    4.080 closest distance to " O   HOH Z  40 " =    1.617
peak=    4.071 closest distance to " CB  SER A   3 " =    1.282
peak=    4.032 closest distance to " CD2 TRP A 179 " =    1.381
peak=    4.029 closest distance to " O   HOH Z 189 " =    2.048
peak=    4.029 closest distance to " CA  ASN A 215 " =    1.189
peak=    4.015 closest distance to " O   HOH Z 144 " =    2.176
peak=    4.013 closest distance to " O   HOH Z 403 " =    1.696
peak=    4.012 closest distance to " O   HOH Z 392 " =    3.143
peak=    4.001 closest distance to " CG1 ILE A  33 " =    1.210
peak=    3.996 closest distance to " O   HOH Z 132 " =    2.416
peak=    3.993 closest distance to " O   HOH Z 407 " =    2.386
peak=    3.975 closest distance to " O   HOH Z 158 " =    2.986
peak=    3.955 closest distance to " O   HOH Z  43 " =    1.945
peak=    3.950 closest distance to " O   SER A  87 " =    2.275
peak=    3.947 closest distance to " O   HOH Z 344 " =    3.191
peak=    3.937 closest distance to " O   HOH Z 389 " =    1.804
peak=    3.933 closest distance to " O   HOH Z 245 " =    1.311
peak=    3.921 closest distance to " CB  ARG A 190 " =    1.678
peak=    3.918 closest distance to " O   HOH Z  61 " =    1.620
peak=    3.885 closest distance to " OD2 ASP A 286 " =    2.738
peak=    3.879 closest distance to " CB  LEU A 228 " =    1.089
peak=    3.878 closest distance to " O   HOH Z 128 " =    2.132
peak=    3.875 closest distance to " O   HOH Z 272 " =    1.845
peak=    3.875 closest distance to " CB  TRP A 266 " =    0.991
peak=    3.872 closest distance to " CE  LYS A  76 " =    0.832
peak=    3.859 closest distance to " CB  SER A  26 " =    1.579
peak=    3.831 closest distance to " O   HOH Z 425 " =    2.049
peak=    3.827 closest distance to " O   HOH Z  97 " =    1.944
peak=    3.823 closest distance to " O   HOH Z 248 " =    1.677
peak=    3.820 closest distance to " O   HOH Z 368 " =    1.941
peak=    3.820 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.805 closest distance to " CB  ARG A 139 " =    1.001
peak=    3.804 closest distance to " CG2 ILE A 120 " =    1.069
peak=    3.798 closest distance to " CG  PRO A  90 " =    1.046
peak=    3.797 closest distance to " CG  PRO A 243 " =    1.034
peak=    3.790 closest distance to " CG  ARG A  66 " =    2.450
peak=    3.766 closest distance to " CA  ALA A  21 " =    1.115
peak=    3.760 closest distance to " O   HOH Z   6 " =    2.143
peak=    3.753 closest distance to " O   HOH Z  10 " =    1.821
peak=    3.749 closest distance to " O   HOH Z 371 " =    3.151
peak=    3.738 closest distance to " OG BSER A 164 " =    2.334
peak=    3.736 closest distance to " O   HOH Z 173 " =    1.920
peak=    3.734 closest distance to " CD1 ILE A 106 " =    0.881
peak=    3.733 closest distance to " CG1BVAL A  72 " =    1.522
peak=    3.732 closest distance to " CG  PRO A 198 " =    1.242
peak=    3.729 closest distance to " CB  GLU A 128 " =    1.033
peak=    3.683 closest distance to " O   HOH Z 417 " =    3.207
peak=    3.681 closest distance to " O   HOH Z   1 " =    1.950
peak=    3.680 closest distance to " O   HOH Z 327 " =    1.631
peak=    3.651 closest distance to " CB  ILE A 120 " =    1.240
peak=    3.643 closest distance to " CB  TRP A 179 " =    1.235
peak=    3.616 closest distance to " O   HOH Z  21 " =    1.749
peak=    3.609 closest distance to " O   HOH Z  61 " =    1.484
peak=    3.603 closest distance to " O   HOH Z 419 " =    2.029
peak=    3.596 closest distance to " N   ASN A  39 " =    1.206
peak=    3.592 closest distance to " CB  GLU A 277 " =    3.481
peak=    3.587 closest distance to " CB  ALA A 291 " =    1.311
peak=    3.578 closest distance to " O   HOH Z  71 " =    2.131
peak=    3.578 closest distance to " O   HOH Z  64 " =    2.287
peak=    3.576 closest distance to " O   HOH Z 371 " =    1.658
peak=    3.576 closest distance to " CZ  PHE A 218 " =    1.022
peak=    3.576 closest distance to " O   HOH Z   9 " =    2.096
peak=    3.574 closest distance to " CB  VAL A 202 " =    1.553
peak=    3.568 closest distance to " CB  ASP A 140 " =    0.922
peak=    3.567 closest distance to " O   HOH Z 147 " =    1.776
peak=    3.565 closest distance to " O   HOH Z  59 " =    1.839
peak=    3.555 closest distance to " O   HOH Z 433 " =    1.801
peak=    3.555 closest distance to " NH1AARG A 145 " =    1.146
peak=    3.554 closest distance to " NH2BARG A 145 " =    1.945
peak=    3.553 closest distance to " O   HOH Z 250 " =    1.928
peak=    3.548 closest distance to " O   HOH Z 368 " =    3.595
peak=    3.542 closest distance to " O   HOH Z 284 " =    2.923
peak=    3.533 closest distance to " O   HOH Z  88 " =    2.661
peak=    3.530 closest distance to " O   MET A 105 " =    1.820
peak=    3.529 closest distance to " O   HOH Z 207 " =    1.785
peak=    3.523 closest distance to " O   HOH Z 423 " =    1.901
peak=    3.523 closest distance to " CB  ASN A  39 " =    0.850
peak=    3.516 closest distance to " O   HOH Z 291 " =    1.556
peak=    3.512 closest distance to " O   ALA A   1 " =    1.700
peak=    3.495 closest distance to " N   ARG A 156 " =    1.299
peak=    3.493 closest distance to " O   HOH Z 234 " =    1.829
peak=    3.491 closest distance to " O   HOH Z 148 " =    3.293
peak=    3.488 closest distance to " CG2 ILE A  20 " =    1.474
peak=    3.485 closest distance to " CA  THR A 264 " =    0.884
peak=    3.483 closest distance to " CB  SER A 216 " =    0.750
peak=    3.480 closest distance to " CD  ARG A 159 " =    0.706
peak=    3.475 closest distance to " O   HOH Z   3 " =    1.839
peak=    3.475 closest distance to " CG  LYS A  76 " =    0.997
peak=    3.471 closest distance to " CA  ALA A  84 " =    1.318
peak=    3.447 closest distance to " NH1BARG A 145 " =    1.299
peak=    3.446 closest distance to " O   HOH Z 337 " =    3.598
peak=    3.444 closest distance to " CA  THR A 221 " =    0.970
peak=    3.436 closest distance to " O   HOH Z 305 " =    3.597
peak=    3.435 closest distance to " O   HOH Z 366 " =    3.162
peak=    3.431 closest distance to " CD BLYS A 290 " =    1.264
peak=    3.426 closest distance to " CG  GLN A  77 " =    2.003
peak=    3.422 closest distance to " CA  ARG A  36 " =    1.012
peak=    3.414 closest distance to " CB  LYS A 290 " =    1.098
peak=    3.409 closest distance to " O   HOH Z 172 " =    3.470
peak=    3.390 closest distance to " CD2 LEU A 297 " =    0.878
peak=    3.385 closest distance to " O   HOH Z 286 " =    2.221
peak=    3.382 closest distance to " CB  LYS A 117 " =    1.197
peak=    3.376 closest distance to " O   HOH Z 298 " =    2.523
peak=    3.371 closest distance to " O   HOH Z 128 " =    2.084
peak=    3.367 closest distance to " O   HOH Z 421 " =    1.705
peak=    3.364 closest distance to " O   HOH Z 214 " =    2.160
peak=    3.363 closest distance to " CA  ASP A 162 " =    1.089
peak=    3.359 closest distance to " CA  ALA A 233 " =    1.159
peak=    3.355 closest distance to " CB  THR A 157 " =    1.062
peak=    3.354 closest distance to " CZ2 TRP A 179 " =    1.735
peak=    3.347 closest distance to " CB  GLN A 278 " =    0.858
peak=    3.346 closest distance to " O   HOH Z  19 " =    2.380
peak=    3.342 closest distance to " O   HOH Z   1 " =    1.629
peak=    3.340 closest distance to " O   HOH Z 426 " =    1.485
peak=    3.338 closest distance to " OG  SER A  22 " =    2.599
peak=    3.335 closest distance to " O   HOH Z  89 " =    2.155
peak=    3.333 closest distance to " O   HOH Z 366 " =    2.832
peak=    3.329 closest distance to " O   HOH Z 219 " =    2.093
peak=    3.325 closest distance to " O   HOH Z 193 " =    1.898
peak=    3.321 closest distance to " CG2BVAL A  41 " =    0.898
peak=    3.316 closest distance to " CA  MET A  40 " =    1.046
peak=    3.315 closest distance to " CB  ALA A  34 " =    1.106
peak=    3.310 closest distance to " O   HOH Z  66 " =    2.059
peak=    3.307 closest distance to " O   HOH Z 411 " =    3.782
peak=    3.306 closest distance to " O   HOH Z 163 " =    1.767
peak=    3.304 closest distance to " CB  ASN A 224 " =    0.978
peak=    3.296 closest distance to " O   HOH Z 336 " =    1.860
peak=    3.289 closest distance to " CB  GLN A  89 " =    1.365
peak=    3.286 closest distance to " CG1 VAL A 153 " =    1.001
peak=    3.283 closest distance to " CB  ASN A 110 " =    1.072
peak=    3.278 closest distance to " CB  THR A  31 " =    1.682
peak=    3.276 closest distance to " O   HOH Z 345 " =    3.321
peak=    3.275 closest distance to " O   HOH Z 313 " =    1.934
peak=    3.273 closest distance to " ND1 HIS A  86 " =    1.774
peak=    3.271 closest distance to " O   HOH Z  47 " =    1.778
peak=    3.269 closest distance to " N   PHE A 130 " =    1.318
peak=    3.269 closest distance to " O   HOH Z 423 " =    2.960
peak=    3.269 closest distance to " CD  LYS A 166 " =    1.229
peak=    3.267 closest distance to " CG  MET A 113 " =    1.106
peak=    3.267 closest distance to " CB  ALA A   9 " =    1.561
peak=    3.266 closest distance to " O   HOH Z 193 " =    1.602
peak=    3.264 closest distance to " CD2 LEU A 255 " =    1.366
peak=    3.263 closest distance to " O   HOH Z 227 " =    1.545
peak=    3.260 closest distance to " CG  MET A 185 " =    1.127
peak=    3.260 closest distance to " CB  THR A 294 " =    1.657
peak=    3.258 closest distance to " CD1 LEU A 300 " =    1.328
peak=    3.258 closest distance to " O   HOH Z 357 " =    1.793
peak=    3.255 closest distance to " O   HOH Z 265 " =    2.470
peak=    3.253 closest distance to " O   HOH Z 329 " =    3.798
peak=    3.253 closest distance to " O   HOH Z 273 " =    2.645
peak=    3.252 closest distance to " O   HOH Z 359 " =    1.400
peak=    3.251 closest distance to " CG AARG A 275 " =    1.109
peak=    3.246 closest distance to " CA  ALA A 291 " =    0.887
peak=    3.245 closest distance to " CB  ASN A 215 " =    1.128
peak=    3.245 closest distance to " CB  SER A 212 " =    1.055
peak=    3.244 closest distance to " CA  ILE A  33 " =    1.408
peak=    3.242 closest distance to " CA  ASP A 140 " =    1.098
peak=    3.237 closest distance to " O   HOH Z 253 " =    2.307
peak=    3.231 closest distance to " CA  ASN A 176 " =    1.176
peak=    3.230 closest distance to " OG1 THR A 294 " =    2.369
peak=    3.230 closest distance to " CB  SER A  62 " =    1.296
peak=    3.225 closest distance to " OE2 GLU A  53 " =    2.150
peak=    3.223 closest distance to " O   HOH Z 108 " =    2.374
peak=    3.223 closest distance to " CE1 TYR A 186 " =    1.330
peak=    3.214 closest distance to " O   HOH Z 406 " =    1.595
peak=    3.211 closest distance to " N   TYR A 116 " =    1.572
peak=    3.193 closest distance to " CA  ALA A  51 " =    0.915
peak=    3.192 closest distance to " O   HOH Z 236 " =    1.402
peak=    3.190 closest distance to " O   HOH Z 180 " =    2.227
peak=    3.188 closest distance to " OD1BASN A 224 " =    2.287
peak=    3.185 closest distance to " CA  MET A 105 " =    0.936
peak=    3.178 closest distance to " O   TRP A 274 " =    1.845
peak=    3.176 closest distance to " OG  SER A 206 " =    1.350
peak=    3.170 closest distance to " O   HOH Z 124 " =    1.289
peak=    3.168 closest distance to " O   HOH Z 188 " =    2.004
peak=    3.163 closest distance to " O   HOH Z 213 " =    1.772
peak=    3.163 closest distance to " O   HOH Z 222 " =    2.473
peak=    3.162 closest distance to " CE AMET A  47 " =    1.286
peak=    3.161 closest distance to " O   HOH Z 435 " =    1.871
peak=    3.160 closest distance to " CG2 THR A 221 " =    1.139
peak=    3.156 closest distance to " O   HOH Z 261 " =    1.512
peak=    3.155 closest distance to " O   HOH Z 199 " =    1.556
peak=    3.151 closest distance to " CD1AILE A 234 " =    0.943
peak=    3.149 closest distance to " O  BHOH Z  74 " =    1.339
peak=    3.147 closest distance to " O   HOH Z 218 " =    2.438
peak=    3.137 closest distance to " CB  HIS A 108 " =    0.821
peak=    3.135 closest distance to " O   HOH Z  44 " =    3.244
peak=    3.135 closest distance to " CA  ASN A 217 " =    1.238
peak=    3.134 closest distance to " O   HOH Z 144 " =    1.832
peak=    3.132 closest distance to " CD  LYS A 119 " =    1.292
peak=    3.132 closest distance to " CB  TYR A 116 " =    0.759
peak=    3.127 closest distance to " CG  ARG A 269 " =    1.291
peak=    3.124 closest distance to " CA  ALA A 158 " =    1.264
peak=    3.124 closest distance to " O   HOH Z 256 " =    1.491
peak=    3.118 closest distance to " CD2 HIS A  81 " =    1.151
peak=    3.116 closest distance to " CB  MET A  40 " =    0.858
peak=    3.114 closest distance to " O   HOH Z 175 " =    2.048
peak=    3.113 closest distance to " CG  GLN A  89 " =    1.489
peak=    3.111 closest distance to " OG  SER A  62 " =    2.784
peak=    3.110 closest distance to " CD  ARG A  66 " =    2.412
peak=    3.109 closest distance to " OD1 ASP A 231 " =    1.915
peak=    3.108 closest distance to " O   HOH Z 279 " =    2.100
peak=    3.107 closest distance to " CD  ARG A  36 " =    1.008
peak=    3.106 closest distance to " O   HOH Z  49 " =    2.105
peak=    3.104 closest distance to " O   HOH Z 132 " =    2.739
peak=    3.095 closest distance to " CB  LEU A 255 " =    0.770
peak=    3.087 closest distance to " O   HOH Z 291 " =    1.769
peak=    3.084 closest distance to " O   HOH Z 342 " =    0.804
peak=    3.082 closest distance to " CE  LYS A 119 " =    1.127
peak=    3.072 closest distance to " CA  ARG A 195 " =    1.170
peak=    3.072 closest distance to " CB  ALA A 114 " =    1.183
peak=    3.070 closest distance to " O   HOH Z 409 " =    2.945
peak=    3.070 closest distance to " O   HOH Z 353 " =    2.624
peak=    3.069 closest distance to " CB  ALA A 248 " =    1.528
peak=    3.062 closest distance to " CB  VAL A 126 " =    1.036
peak=    3.048 closest distance to " O   THR A 220 " =    1.333
peak=    3.045 closest distance to " O   HOH Z 112 " =    2.692
peak=    3.012 closest distance to " CA  LYS A 290 " =    1.212
peak=    2.994 closest distance to " O   HOH Z 175 " =    2.095

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.641 - 5.992
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.783 - 5.992

peak=   -4.828 closest distance to " O   HOH Z 266 " =    4.769
peak=   -4.516 closest distance to " CB  PRO A 243 " =    2.603
peak=   -4.500 closest distance to " O   VAL A  67 " =    2.716
peak=   -4.442 closest distance to " O   HOH Z 290 " =    1.071
peak=   -4.440 closest distance to " CD  ARG A 156 " =    2.033
peak=   -4.380 closest distance to " C   HIS A 108 " =    1.079
peak=   -4.339 closest distance to " CA  VAL A  67 " =    2.720
peak=   -4.175 closest distance to " OG BSER A 134 " =    1.212
peak=   -4.164 closest distance to " CG  GLN A 223 " =    1.898
peak=   -4.159 closest distance to " CG1 VAL A 112 " =    2.820
peak=   -4.154 closest distance to " O   HOH Z 377 " =    2.161
peak=   -4.132 closest distance to " SG  CYS A 254 " =    3.459
peak=   -4.124 closest distance to " CD  GLN A  58 " =    1.088
peak=   -4.100 closest distance to " O   HOH Z 372 " =    2.335
peak=   -4.088 closest distance to " O   HOH Z 389 " =    1.851
peak=   -4.056 closest distance to " CD  ARG A 139 " =    1.465
peak=   -4.054 closest distance to " N   GLN A  58 " =    1.660
peak=   -4.031 closest distance to " O   HOH Z 435 " =    2.750
peak=   -4.019 closest distance to " ND2 ASN A  45 " =    1.551
peak=   -4.017 closest distance to " CE2 TYR A  30 " =    2.781
peak=   -4.009 closest distance to " CE2 PHE A 218 " =    2.467
peak=   -4.002 closest distance to " CB  ALA A 161 " =    2.493
peak=   -3.959 closest distance to " O   HOH Z 198 " =    1.893
peak=   -3.940 closest distance to " CZ3 TRP A 179 " =    1.204
peak=   -3.930 closest distance to " O   HOH Z 126 " =    1.826
peak=   -3.911 closest distance to " OD1 ASN A 187 " =    1.608
peak=   -3.911 closest distance to " CZ  TYR A 169 " =    1.718
peak=   -3.909 closest distance to " CZ  PHE A  59 " =    1.488
peak=   -3.904 closest distance to " O   PRO A 198 " =    1.271
peak=   -3.895 closest distance to " O   HOH Z 185 " =    2.180
peak=   -3.878 closest distance to " CE  MET A 105 " =    2.327
peak=   -3.873 closest distance to " CG  PHE A 283 " =    2.722
peak=   -3.861 closest distance to " O   HOH Z 313 " =    1.898
peak=   -3.861 closest distance to " OG  SER A  97 " =    2.144
peak=   -3.858 closest distance to " OXT GLY A 302 " =    2.745
peak=   -3.850 closest distance to " CB  ASN A  39 " =    2.273
peak=   -3.837 closest distance to " O   HOH Z 114 " =    3.109
peak=   -3.834 closest distance to " CG  ASP A 231 " =    0.783
peak=   -3.813 closest distance to " O   HOH Z 231 " =    2.223
peak=   -3.802 closest distance to " O   ALA A 161 " =    1.587
peak=   -3.797 closest distance to " CB  PHE A 192 " =    1.956
peak=   -3.772 closest distance to " O   HOH Z 407 " =    2.902
peak=   -3.767 closest distance to " O   HOH Z 353 " =    2.168
peak=   -3.758 closest distance to " O   ARG A 145 " =    1.559
peak=   -3.742 closest distance to " OD2 ASP A 171 " =    2.270
peak=   -3.739 closest distance to " CD1 PHE A  59 " =    1.864
peak=   -3.736 closest distance to " NE  ARG A 156 " =    1.863
peak=   -3.720 closest distance to " CB  ALA A 291 " =    2.401
peak=   -3.719 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.713 closest distance to " N   SER A 212 " =    2.005
peak=   -3.684 closest distance to " O   HOH Z 351 " =    1.452
peak=   -3.676 closest distance to " CG2 ILE A 263 " =    2.228
peak=   -3.659 closest distance to " ND2 ASN A  45 " =    1.026
peak=   -3.658 closest distance to " O   HOH Z  13 " =    1.526
peak=   -3.658 closest distance to " N   ALA A  43 " =    2.531
peak=   -3.651 closest distance to " CA  GLY A 203 " =    2.241
peak=   -3.643 closest distance to " CG1 VAL A 230 " =    1.949
peak=   -3.634 closest distance to " OD1 ASP A 171 " =    1.628
peak=   -3.632 closest distance to " CB  ASP A 132 " =    2.264
peak=   -3.623 closest distance to " O   HOH Z 211 " =    1.693
peak=   -3.622 closest distance to " O   HOH Z 298 " =    1.264
peak=   -3.616 closest distance to " O   HOH Z 385 " =    2.000
peak=   -3.586 closest distance to " OD1 ASN A 148 " =    1.598
peak=   -3.580 closest distance to " CB  ALA A 248 " =    2.093
peak=   -3.563 closest distance to " O   MET A  40 " =    2.677
peak=   -3.554 closest distance to " O   HOH Z  43 " =    1.688
peak=   -3.547 closest distance to " CB  ASP A 132 " =    2.365
peak=   -3.532 closest distance to " O   HOH Z 102 " =    1.536
peak=   -3.530 closest distance to " CD2 LEU A 300 " =    2.897
peak=   -3.521 closest distance to " N   ALA A 248 " =    1.585
peak=   -3.514 closest distance to " OD1 ASP A 191 " =    1.454
peak=   -3.513 closest distance to " NH1 ARG A 195 " =    2.551
peak=   -3.502 closest distance to " OD2 ASP A 191 " =    1.445
peak=   -3.492 closest distance to " O   HOH Z 362 " =    5.992
peak=   -3.487 closest distance to " N   HIS A 115 " =    2.026
peak=   -3.482 closest distance to " NH2AARG A 275 " =    5.152
peak=   -3.476 closest distance to " N   ASP A 286 " =    2.383
peak=   -3.467 closest distance to " O   SER A 135 " =    1.468
peak=   -3.465 closest distance to " O   HOH Z 244 " =    2.067
peak=   -3.458 closest distance to " CD1 LEU A 228 " =    2.095
peak=   -3.457 closest distance to " N   THR A 235 " =    1.405
peak=   -3.456 closest distance to " CD1 LEU A 101 " =    2.278
peak=   -3.455 closest distance to " CB  ALA A 248 " =    2.299
peak=   -3.450 closest distance to " C   MET A 188 " =    1.449
peak=   -3.440 closest distance to " CG  GLU A   2 " =    1.973
peak=   -3.439 closest distance to " O   SER A  95 " =    1.495
peak=   -3.437 closest distance to " O   PRO A 163 " =    1.971
peak=   -3.437 closest distance to " CB  TYR A  15 " =    2.180
peak=   -3.435 closest distance to " O   HOH Z  10 " =    1.439
peak=   -3.433 closest distance to " CG  ARG A  66 " =    2.426
peak=   -3.424 closest distance to " OXT GLY A 302 " =    3.380
peak=   -3.419 closest distance to " CB  PRO A 163 " =    2.458
peak=   -3.418 closest distance to " OD1 ASN A 176 " =    1.283
peak=   -3.417 closest distance to " CG  GLU A 152 " =    0.981
peak=   -3.416 closest distance to " C   PRO A  90 " =    1.507
peak=   -3.399 closest distance to " O   HOH Z 166 " =    1.430
peak=   -3.398 closest distance to " C   ASP A 231 " =    2.604
peak=   -3.396 closest distance to " SG ACYS A 201 " =    1.885
peak=   -3.396 closest distance to " O   HOH Z  63 " =    1.646
peak=   -3.393 closest distance to " CB  ALA A  43 " =    2.378
peak=   -3.384 closest distance to " O   PHE A 218 " =    1.619
peak=   -3.383 closest distance to " O   HOH Z  37 " =    1.771
peak=   -3.380 closest distance to " O   HOH Z  24 " =    1.413
peak=   -3.377 closest distance to " CA  GLY A  98 " =    1.885
peak=   -3.369 closest distance to " OH  TYR A 214 " =    1.214
peak=   -3.367 closest distance to " NZ  LYS A 119 " =    3.372
peak=   -3.367 closest distance to " O   HOH Z 198 " =    1.409
peak=   -3.366 closest distance to " O   HOH Z 253 " =    3.663
peak=   -3.365 closest distance to " O   HOH Z  11 " =    1.750
peak=   -3.364 closest distance to " C   ALA A 158 " =    1.270
peak=   -3.363 closest distance to " OG1 THR A 178 " =    1.270
peak=   -3.357 closest distance to " O   HOH Z 263 " =    2.886
peak=   -3.357 closest distance to " O   HOH Z  52 " =    1.327
peak=   -3.348 closest distance to " CD1 ILE A 239 " =    2.593
peak=   -3.348 closest distance to " CD  ARG A 195 " =    5.202
peak=   -3.346 closest distance to " CG  ARG A 269 " =    2.323
peak=   -3.344 closest distance to " O   HOH Z 196 " =    2.104
peak=   -3.340 closest distance to " O   HOH Z 165 " =    2.034
peak=   -3.338 closest distance to " N   ALA A 226 " =    2.001
peak=   -3.335 closest distance to " CG1 VAL A  78 " =    3.093
peak=   -3.334 closest distance to " O   SER A  22 " =    2.346
peak=   -3.315 closest distance to " NH2 ARG A  79 " =    1.945
peak=   -3.310 closest distance to " CA  GLY A 133 " =    1.954
peak=   -3.309 closest distance to " O   HOH Z  44 " =    2.259
peak=   -3.308 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.307 closest distance to " CB  ASP A 286 " =    2.213
peak=   -3.305 closest distance to " C   LEU A 143 " =    0.994
peak=   -3.304 closest distance to " O   PRO A  90 " =    1.807
peak=   -3.300 closest distance to " CD2 LEU A 237 " =    2.672
peak=   -3.290 closest distance to " O   TRP A  70 " =    1.510
peak=   -3.290 closest distance to " ND2 ASN A 187 " =    1.524
peak=   -3.289 closest distance to " O   SER A 146 " =    1.107
peak=   -3.276 closest distance to " O   VAL A 174 " =    2.048
peak=   -3.269 closest distance to " O   ALA A  51 " =    1.313
peak=   -3.268 closest distance to " OG  SER A  62 " =    1.521
peak=   -3.260 closest distance to " O   GLN A 240 " =    1.841
peak=   -3.257 closest distance to " O   VAL A 189 " =    2.613
peak=   -3.257 closest distance to " OG  SER A 206 " =    1.631
peak=   -3.251 closest distance to " O   HOH Z 377 " =    1.743
peak=   -3.241 closest distance to " O   ASN A 249 " =    1.412
peak=   -3.241 closest distance to " O   LYS A 117 " =    1.607
peak=   -3.239 closest distance to " OG BSER A 134 " =    1.655
peak=   -3.231 closest distance to " NE2 GLN A  88 " =    1.856
peak=   -3.231 closest distance to " CA  GLY A 241 " =    3.052
peak=   -3.223 closest distance to " N   PRO A 163 " =    1.495
peak=   -3.220 closest distance to " ND2 ASN A 249 " =    2.117
peak=   -3.219 closest distance to " O   ALA A  34 " =    2.415
peak=   -3.217 closest distance to " O   VAL A 153 " =    2.374
peak=   -3.216 closest distance to " O   HOH Z 166 " =    2.055
peak=   -3.215 closest distance to " CG  GLU A 277 " =    1.239
peak=   -3.213 closest distance to " NE2 GLN A 278 " =    1.728
peak=   -3.211 closest distance to " O   HOH Z 421 " =    3.152
peak=   -3.211 closest distance to " CD  GLU A 152 " =    2.541
peak=   -3.210 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.209 closest distance to " O   HOH Z 243 " =    2.013
peak=   -3.208 closest distance to " CB  GLN A  11 " =    1.750
peak=   -3.207 closest distance to " O   HOH Z 322 " =    1.670
peak=   -3.207 closest distance to " O   ALA A  10 " =    1.702
peak=   -3.207 closest distance to " OD2 ASP A  50 " =    1.483
peak=   -3.206 closest distance to " O   HOH Z   6 " =    1.447
peak=   -3.206 closest distance to " OE1 GLN A  88 " =    1.112
peak=   -3.202 closest distance to " O   HOH Z   6 " =    2.049
peak=   -3.200 closest distance to " NH2BARG A 275 " =    1.993
peak=   -3.200 closest distance to " O   HOH Z 311 " =    3.599
peak=   -3.198 closest distance to " N   PHE A  59 " =    2.128
peak=   -3.198 closest distance to " CB  LEU A  83 " =    2.354
peak=   -3.196 closest distance to " O   LEU A 167 " =    1.462
peak=   -3.190 closest distance to " O   HOH Z 281 " =    2.705
peak=   -3.188 closest distance to " O   HOH Z 250 " =    1.377
peak=   -3.188 closest distance to " O   HOH Z 148 " =    1.918
peak=   -3.181 closest distance to " C   TRP A 274 " =    1.468
peak=   -3.180 closest distance to " O   HOH Z 134 " =    2.971
peak=   -3.179 closest distance to " CB  PHE A 208 " =    2.219
peak=   -3.179 closest distance to " O   ILE A 120 " =    1.450
peak=   -3.174 closest distance to " CA  GLY A  57 " =    2.134
peak=   -3.169 closest distance to " OE2 GLU A 152 " =    1.175
peak=   -3.162 closest distance to " OD1 ASP A 191 " =    1.763
peak=   -3.157 closest distance to " O   ASP A 162 " =    2.223
peak=   -3.152 closest distance to " O   HOH Z 394 " =    1.459
peak=   -3.151 closest distance to " O   HOH Z 265 " =    1.994
peak=   -3.144 closest distance to " O   HOH Z 427 " =    1.482
peak=   -3.129 closest distance to " O   HOH Z 351 " =    1.326
peak=   -3.125 closest distance to " OG1 THR A 246 " =    1.404
peak=   -3.124 closest distance to " O   HOH Z 137 " =    1.462
peak=   -3.121 closest distance to " O   HOH Z 111 " =    2.488
peak=   -3.119 closest distance to " NH2 ARG A  79 " =    1.630
peak=   -3.113 closest distance to " O   HOH Z 282 " =    1.297
peak=   -3.111 closest distance to " O   HOH Z 385 " =    1.889
peak=   -3.110 closest distance to " O   HOH Z 361 " =    3.473
peak=   -3.106 closest distance to " CD2 TYR A 293 " =    1.990
peak=   -3.106 closest distance to " O   GLY A  80 " =    2.478
peak=   -3.105 closest distance to " O   HOH Z 298 " =    2.345
peak=   -3.098 closest distance to " O   HOH Z  91 " =    1.607
peak=   -3.094 closest distance to " CG1AVAL A  41 " =    2.777
peak=   -3.088 closest distance to " CB  TRP A  85 " =    2.580
peak=   -3.085 closest distance to " CE  MET A  93 " =    1.220
peak=   -3.085 closest distance to " CD  GLN A  88 " =    0.887
peak=   -3.078 closest distance to " CG  MET A 105 " =    0.938
peak=   -3.057 closest distance to " O   HOH Z  60 " =    2.195
peak=   -3.042 closest distance to " OD2 ASP A  50 " =    2.344
peak=   -3.034 closest distance to " CG1 VAL A 197 " =    2.151

================= 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    :  0.2971 0.2990   5.949697e+00   5.942563e+00
   1_bss:  0.2819 0.2790   5.923104e+00   5.898192e+00
   1_xyz:  0.1690 0.1894   5.452623e+00   5.546762e+00
   1_adp:  0.1574 0.1931   5.407569e+00   5.570162e+00
   1_occ:  0.1570 0.1933   5.405919e+00   5.569643e+00
   2_bss:  0.1562 0.1934   5.405743e+00   5.568932e+00
   2_xyz:  0.1248 0.1581   5.193922e+00   5.378393e+00
   2_adp:  0.1182 0.1560   5.155688e+00   5.360984e+00
   2_occ:  0.1180 0.1560   5.155169e+00   5.360689e+00
   3_bss:  0.1183 0.1559   5.156106e+00   5.360156e+00
   3_xyz:  0.1120 0.1523   5.119881e+00   5.344955e+00
   3_adp:  0.1109 0.1518   5.113884e+00   5.342356e+00
   3_occ:  0.1109 0.1517   5.113788e+00   5.342347e+00
   4_bss:  0.1108 0.1516   5.113592e+00   5.342056e+00
   4_xyz:  0.1055 0.1503   5.085213e+00   5.335427e+00
   4_adp:  0.1066 0.1503   5.089422e+00   5.333742e+00
   4_occ:  0.1065 0.1503   5.089391e+00   5.333915e+00
   5_bss:  0.1065 0.1503   5.089656e+00   5.334238e+00
   5_xyz:  0.1062 0.1512   5.091924e+00   5.341784e+00
   5_adp:  0.1052 0.1522   5.090785e+00   5.349339e+00
   5_occ:  0.1052 0.1522   5.090738e+00   5.349262e+00
   5_bss:  0.1051 0.1521   5.090634e+00   5.349078e+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:  0.322  27.146  -2.036  -1.958  -0.308  -0.000  -0.000  -0.000
   1_xyz:  0.322  27.146  -2.036  -1.958  -0.308  -0.000  -0.000  -0.000
   1_adp:  0.322  27.146  -2.036  -1.958  -0.308  -0.000  -0.000  -0.000
   1_occ:  0.322  27.146  -2.036  -1.958  -0.308  -0.000  -0.000  -0.000
   2_bss:  0.320  34.081  -2.931  -2.604  -1.488  -0.000  -0.000  -0.000
   2_xyz:  0.320  34.081  -2.931  -2.604  -1.488  -0.000  -0.000  -0.000
   2_adp:  0.320  34.081  -2.931  -2.604  -1.488  -0.000  -0.000  -0.000
   2_occ:  0.320  34.081  -2.931  -2.604  -1.488  -0.000  -0.000  -0.000
   3_bss:  0.321  38.312  -2.780  -2.378  -1.435  -0.000  -0.000  -0.000
   3_xyz:  0.321  38.312  -2.780  -2.378  -1.435  -0.000  -0.000  -0.000
   3_adp:  0.321  38.312  -2.780  -2.378  -1.435  -0.000  -0.000  -0.000
   3_occ:  0.321  38.312  -2.780  -2.378  -1.435  -0.000  -0.000  -0.000
   4_bss:  0.320  39.396  -2.707  -2.287  -1.385  -0.000  -0.000  -0.000
   4_xyz:  0.320  39.396  -2.707  -2.287  -1.385  -0.000  -0.000  -0.000
   4_adp:  0.320  39.396  -2.707  -2.287  -1.385  -0.000  -0.000  -0.000
   4_occ:  0.320  39.396  -2.707  -2.287  -1.385  -0.000  -0.000  -0.000
   5_bss:  0.324  39.395  -2.650  -2.221  -1.285  -0.000  -0.000  -0.000
   5_xyz:  0.324  39.395  -2.650  -2.221  -1.285  -0.000  -0.000  -0.000
   5_adp:  0.324  39.395  -2.650  -2.221  -1.285  -0.000  -0.000  -0.000
   5_occ:  0.324  39.395  -2.650  -2.221  -1.285  -0.000  -0.000  -0.000
   5_bss:  0.321  39.373  -2.428  -2.014  -1.084  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.638 0.7769  0.9666    23840.770
   1_bss:  27.010 0.7925  0.9346    19991.800
   1_xyz:  17.017 0.8908  1.0045     8779.427
   1_adp:  17.591 0.8853  0.9987     9145.455
   1_occ:  17.572 0.8855  0.9987     9115.891
   2_bss:  17.543 0.8857  0.9668     9094.340
   2_xyz:  13.796 0.9164  0.9816     6143.095
   2_adp:  13.473 0.9190  0.9806     5954.825
   2_occ:  13.464 0.9191  0.9805     5949.720
   3_bss:  13.451 0.9192  0.9863     5944.046
   3_xyz:  13.095 0.9221  0.9870     5741.412
   3_adp:  13.010 0.9228  0.9830     5717.078
   3_occ:  13.011 0.9228  0.9829     5716.129
   4_bss:  13.006 0.9228  0.9855     5712.107
   4_xyz:  12.857 0.9239  0.9855     5637.076
   4_adp:  12.787 0.9245  0.9824     5639.200
   4_occ:  12.794 0.9244  0.9822     5641.096
   5_bss:  12.801 0.9244  0.9849     5647.791
   5_xyz:  12.908 0.9237  0.9845     5749.833
   5_adp:  13.053 0.9226  0.9781     5804.629
   5_occ:  13.054 0.9226  0.9780     5805.091
   5_bss:  13.052 0.9226  0.9848     5801.508
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6422e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6422e-01
   1_xyz:   0.936  0.006  0.062 14.794  0.004  4.110   5.4552e-02
   1_adp:   0.936  0.006  0.062 14.794  0.004  4.110   5.4552e-02
   1_occ:   0.936  0.006  0.062 14.794  0.004  4.110   5.4552e-02
   2_bss:   0.936  0.006  0.062 14.794  0.004  4.110   5.4552e-02
   2_xyz:   0.900  0.004  0.065 14.351  0.004  4.111   4.8255e-02
   2_adp:   0.900  0.004  0.065 14.351  0.004  4.111   4.8255e-02
   2_occ:   0.900  0.004  0.065 14.351  0.004  4.111   4.8255e-02
   3_bss:   0.900  0.004  0.065 14.351  0.004  4.111   4.8255e-02
   3_xyz:   0.868  0.005  0.066 14.459  0.004  4.110   4.7409e-02
   3_adp:   0.868  0.005  0.066 14.459  0.004  4.110   4.7409e-02
   3_occ:   0.868  0.005  0.066 14.459  0.004  4.110   4.7409e-02
   4_bss:   0.868  0.005  0.066 14.459  0.004  4.110   4.7409e-02
   4_xyz:   1.007  0.007  0.075 14.776  0.004  4.111   6.0454e-02
   4_adp:   1.007  0.007  0.075 14.776  0.004  4.111   6.0454e-02
   4_occ:   1.007  0.007  0.075 14.776  0.004  4.111   6.0454e-02
   5_bss:   1.007  0.007  0.075 14.776  0.004  4.111   6.0454e-02
   5_xyz:   0.978  0.007  0.074 14.655  0.004  4.110   5.8157e-02
   5_adp:   0.978  0.007  0.074 14.655  0.004  4.110   5.8157e-02
   5_occ:   0.978  0.007  0.074 14.655  0.004  4.110   5.8157e-02
   5_bss:   0.978  0.007  0.074 14.655  0.004  4.110   5.8157e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.748   2.3866e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.748   2.3866e-01
   1_xyz:   8.118  0.038  0.247 86.963  0.041  2.306   5.5568e-02
   1_adp:   8.118  0.038  0.247 86.963  0.041  2.306   5.5568e-02
   1_occ:   8.118  0.038  0.247 86.963  0.041  2.306   5.5568e-02
   2_bss:   8.118  0.038  0.247 86.963  0.041  2.306   5.5568e-02
   2_xyz:   6.368  0.033  0.202 83.810  0.041  2.359   4.3609e-02
   2_adp:   6.368  0.033  0.202 83.810  0.041  2.359   4.3609e-02
   2_occ:   6.368  0.033  0.202 83.810  0.041  2.359   4.3609e-02
   3_bss:   6.368  0.033  0.202 83.810  0.041  2.359   4.3609e-02
   3_xyz:   6.146  0.034  0.213 83.286  0.038  2.352   2.8934e-02
   3_adp:   6.146  0.034  0.213 83.286  0.038  2.352   2.8934e-02
   3_occ:   6.146  0.034  0.213 83.286  0.038  2.352   2.8934e-02
   4_bss:   6.146  0.034  0.213 83.286  0.038  2.352   2.8934e-02
   4_xyz:   6.424  0.043  0.252 82.959  0.040  2.264   5.1681e-02
   4_adp:   6.424  0.043  0.252 82.959  0.040  2.264   5.1681e-02
   4_occ:   6.424  0.043  0.252 82.959  0.040  2.264   5.1681e-02
   5_bss:   6.424  0.043  0.252 82.959  0.040  2.264   5.1681e-02
   5_xyz:   6.475  0.044  0.242 83.508  0.040  2.287   4.4445e-02
   5_adp:   6.475  0.044  0.242 83.508  0.040  2.287   4.4445e-02
   5_occ:   6.475  0.044  0.242 83.508  0.040  2.287   4.4445e-02
   5_bss:   6.475  0.044  0.242 83.508  0.040  2.287   4.4445e-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:  78.18   0.00  16.44  78.18   0.00  12.62  62.27   7.10  37.24
   1_occ:  78.18   0.00  16.44  78.18   0.00  12.62  62.27   7.10  37.24
   2_bss:  78.18   0.00  16.44  78.18   0.00  12.62  62.27   7.10  37.24
   2_xyz:  78.18   0.00  16.44  78.18   0.00  12.62  62.27   7.10  37.24
   2_adp:  73.07   0.48  16.93  73.07   0.48  12.95  70.64   5.05  38.60
   2_occ:  73.07   0.48  16.93  73.07   0.48  12.95  70.64   5.05  38.60
   3_bss:  73.07   0.48  16.93  73.07   0.48  12.95  70.64   5.05  38.60
   3_xyz:  73.07   0.48  16.93  73.07   0.48  12.95  70.64   5.05  38.60
   3_adp:  76.91   1.06  16.78  76.91   1.06  12.84  73.81   4.43  38.27
   3_occ:  76.91   1.06  16.78  76.91   1.06  12.84  73.81   4.43  38.27
   4_bss:  76.91   1.06  16.78  76.91   1.06  12.84  73.81   4.43  38.27
   4_xyz:  76.91   1.06  16.78  76.91   1.06  12.84  73.81   4.43  38.27
   4_adp:  74.67   1.93  16.25  74.67   1.93  12.61  74.35   6.08  36.03
   4_occ:  74.67   1.93  16.25  74.67   1.93  12.61  74.35   6.08  36.03
   5_bss:  74.67   1.93  16.25  74.67   1.93  12.61  74.35   6.08  36.03
   5_xyz:  74.67   1.93  16.25  74.67   1.93  12.61  74.35   6.08  36.03
   5_adp:  77.34   0.68  16.39  77.34   0.68  12.54  74.95   6.11  37.39
   5_occ:  77.34   0.68  16.39  77.34   0.68  12.54  74.95   6.11  37.39
   5_bss:  77.32   0.66  16.37  77.32   0.66  12.52  74.93   6.09  37.36
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.236    0.013    0.221
   1_adp:    1.236    0.013    0.221
   1_occ:    1.236    0.013    0.221
   2_bss:    1.236    0.013    0.221
   2_xyz:    0.916    0.008    0.285
   2_adp:    0.916    0.008    0.285
   2_occ:    0.916    0.008    0.285
   3_bss:    0.916    0.008    0.285
   3_xyz:    0.995    0.024    0.311
   3_adp:    0.995    0.024    0.311
   3_occ:    0.995    0.024    0.311
   4_bss:    0.995    0.024    0.311
   4_xyz:    0.937    0.049    0.328
   4_adp:    0.937    0.049    0.328
   4_occ:    0.937    0.049    0.328
   5_bss:    0.937    0.049    0.328
   5_xyz:    1.069    0.067    0.333
   5_adp:    1.069    0.067    0.333
   5_occ:    1.069    0.067    0.333
   5_bss:    1.069    0.067    0.333
------------------------------------------------------------------------

CPU time actual refinement: 321.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_410/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_410/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_410/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_410/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_410/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.21 
  Macro-tasks:
    bulk solvent and scale       = 37.76  
    individual site refinement   = 129.90 
    weights calculation          = 28.87  
    collect and process          = 6.46   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 203.09 
  Micro-tasks:
    mask                            = 1.19   
    f_calc                          = 102.46 
    alpha_beta                      = 7.94   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 111.07 
    fmodel                         = 6.46   
    r_factors                      = 0.19   
    phase_errors                   = 11.19  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 241.92 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.577 micro seconds
Total CPU time: 5.58 minutes
from_scatterers_fft:    647 calls, 102.20 s
gradients_fft:          592 calls,  97.90 s

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

# Date 2008-01-16 Time 04:44:46 PST -0800 (1200487486.83 s)
Start R-work = 0.2971, R-free = 0.2990 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1723 (no bulk solvent and anisotropic scale)

Start R-work = 0.2819, R-free = 0.2790
Final R-work = 0.1051, R-free = 0.1521