# Date 2008-01-16 Time 05:14:41 PST -0800 (1200489281.28 s)
#phil __OFF__

Command line arguments: "../657.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30807
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 657

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.9921
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9921

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.9921
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2624 [2141/2165]  1923   218  10.2%
  bin  2:  4.2624 -  3.3960 [2042/2062]  1842   200   9.8%
  bin  3:  3.3960 -  2.9705 [2019/2038]  1816   203  10.1%
  bin  4:  2.9705 -  2.7006 [1996/2026]  1794   202  10.1%
  bin  5:  2.7006 -  2.5080 [2004/2023]  1806   198   9.9%
  bin  6:  2.5080 -  2.3607 [1985/2010]  1783   202  10.2%
  bin  7:  2.3607 -  2.2429 [1960/1988]  1767   193   9.8%
  bin  8:  2.2429 -  2.1455 [1964/2000]  1768   196  10.0%
  bin  9:  2.1455 -  2.0631 [1946/1988]  1755   191   9.8%
  bin 10:  2.0631 -  1.9921 [1532/2013]  1376   156  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_657/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2180
        3.04 -     3.66: 4653
        3.66 -     4.28: 8975
        4.28 -     4.90: 12332
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.863 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.904 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.007 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.116 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28150 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_657/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_657/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 87.68585 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: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3018   r_free= 0.2962   ksol= 0.00   Bsol= 0.00   scale= 0.975    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.991701                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7540 0.99   1389  152 0.2724 0.2595      6.3273      6.2169|
|  2:  4.7540 -  3.7933 0.99   1331  152 0.2288 0.2368      6.3461      6.3627|
|  3:  3.7933 -  3.3196 0.99   1299  143 0.2551 0.2468      6.2818      6.3046|
|  4:  3.3196 -  3.0188 0.99   1306  145 0.2769 0.2984      6.1846      6.2252|
|  5:  3.0188 -  2.8039 0.99   1282  145 0.3113 0.2491      6.0553      5.9258|
|  6:  2.8039 -  2.6395 0.99   1291  141 0.3032 0.3414      5.9419      5.9178|
|  7:  2.6395 -  2.5080 0.99   1283  143 0.3115 0.3117       5.933      5.9217|
|  8:  2.5080 -  2.3992 0.98   1273  137 0.3375 0.2988      5.9495      5.9201|
|  9:  2.3992 -  2.3072 0.98   1262  144 0.3300 0.3253      5.8733      5.8374|
| 10:  2.3072 -  2.2279 1.00   1279  143 0.3589 0.3345      5.9085      5.8042|
| 11:  2.2279 -  2.1584 0.97   1254  137 0.3565 0.3634      5.8308       5.891|
| 12:  2.1584 -  2.0969 0.98   1251  142 0.3459 0.3339      5.7675      5.7998|
| 13:  2.0969 -  2.0418 0.99   1278  135 0.3584 0.3349      5.6721      5.6372|
| 14:  2.0418 -  1.9921 0.66    852  100 0.3340 0.3720        5.63       5.601|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7540  1389   152  0.82  23.11   0.86     0.84      34623.16|
|  2:  4.7540 -  3.7933  1331   152  0.86  19.89   0.98     0.93      39068.65|
|  3:  3.7933 -  3.3196  1299   143  0.84  23.04   0.99     0.96      37167.02|
|  4:  3.3196 -  3.0188  1306   145  0.82  24.83   0.99     0.95      31413.43|
|  5:  3.0188 -  2.8039  1282   145  0.77  29.01   1.01     0.92      24690.98|
|  6:  2.8039 -  2.6395  1291   141  0.76  30.24   0.99     0.90      22519.19|
|  7:  2.6395 -  2.5080  1283   143  0.75  31.32   1.02     0.91      21520.03|
|  8:  2.5080 -  2.3992  1273   137  0.74  31.81   1.00     0.92      20461.77|
|  9:  2.3992 -  2.3072  1262   144  0.75  31.20   1.04     0.94      18917.26|
| 10:  2.3072 -  2.2279  1279   143  0.73  33.26   1.05     0.94      18168.18|
| 11:  2.2279 -  2.1584  1254   137  0.72  34.43   1.03     0.95      18683.10|
| 12:  2.1584 -  2.0969  1251   142  0.70  35.58   1.06     0.95      18143.00|
| 13:  2.0969 -  2.0418  1278   135  0.68  37.76   1.03     0.93      16098.10|
| 14:  2.0418 -  1.9921   852   100  0.71  34.85   1.07     0.89      12832.02|
|alpha:            min =        0.84 max =            0.96 mean =         0.92|
|beta:             min =    12832.02 max =        39068.65 mean =     24306.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.86 mean =        29.80|
|phase err.(test): min =        0.00 max =           89.34 mean =        29.52|
|-----------------------------------------------------------------------------|

============================== 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 = 3.179439              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.299   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.516329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.069   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      197 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1983 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2812 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4612 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4363 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5670 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6662 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.178 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    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: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3018   r_free= 0.2962   ksol= 0.00   Bsol= 0.00   scale= 0.975    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.991701                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2849   r_free= 0.2815   ksol= 0.32   Bsol= 50.00   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,-2.26,2.55,-0.00,0.00,0.00); trace/3= -0.97                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.961450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.759443              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.180   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.286779              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.876   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2849      final r-factor (work) = 0.1725          |
| start r-factor (free) = 0.2815      final r-factor (free) = 0.1972          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3952 = 2.76 * 0.50 * 5.9665 + 1.00 * 0.1631                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8644 = 2.76 * 0.50 * 5.6563 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1725      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.1972      final r-factor (free) = 0.1978          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6295 = 0.29 * 1.00 * 5.6563 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7249 = 0.29 * 1.00 * 5.4329 + 1.00 * 0.1669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.47   16.18    None  None   None       |
|    all(noH): 2823   0      0.00    83.47   16.18    None  None   None       |
|    Sol.    : 438    0      5.96    62.57   37.07    None  None   None       |
|    Mac.    : 2385   0      0.00    83.47   12.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.347:  515   |   5:    41.734 -  50.081:   99        |
|      1:     8.347 -  16.694: 1557   |   6:    50.081 -  58.428:   69        |
|      2:    16.694 -  25.041:  293   |   7:    58.428 -  66.775:   11        |
|      3:    25.041 -  33.387:  155   |   8:    66.775 -  75.122:    0        |
|      4:    33.387 -  41.734:  123   |   9:    75.122 -  83.469:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1629 r_free = 0.1978             target_work(ml) = 5.434         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1623 r_free = 0.1973             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1623   r_free= 0.1973   ksol= 0.32   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,-2.26,2.55,-0.00,0.00,0.00); trace/3= -0.97                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.432189                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1600   r_free= 0.1945   ksol= 0.33   Bsol= 59.35   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-2.81,-0.37,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.422399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.575552              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.368  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.992282              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.984   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1600      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1945      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0675 = 2.58 * 0.50 * 5.4413 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8898 = 2.58 * 0.50 * 5.3014 + 1.00 * 0.0627                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3174 = 0.99 * 1.00 * 5.3014 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1252 = 0.99 * 1.00 * 5.1556 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    78.10   17.18    None  None   None       |
|    all(noH): 2823   0      0.76    78.10   17.18    None  None   None       |
|    Sol.    : 438    0      2.95    78.10   40.45    None  None   None       |
|    Mac.    : 2385   0      0.76    77.43   12.91    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:     0.763 -   8.496:  659   |   5:    39.431 -  47.165:  100        |
|      1:     8.496 -  16.230: 1321   |   6:    47.165 -  54.899:   76        |
|      2:    16.230 -  23.964:  322   |   7:    54.899 -  62.633:   77        |
|      3:    23.964 -  31.698:  130   |   8:    62.633 -  70.366:   29        |
|      4:    31.698 -  39.431:   97   |   9:    70.366 -  78.100:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1583             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1582             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1582   ksol= 0.33   Bsol= 59.35   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-2.81,-0.37,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161536                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1575   ksol= 0.33   Bsol= 59.79   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.47,-0.54,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159145                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.473224              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.276  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.090  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8601 = 1.47 * 0.50 * 5.1552 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8525 = 1.47 * 0.50 * 5.1559 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5509 = 0.30 * 1.00 * 5.1559 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5494 = 0.30 * 1.00 * 5.1531 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.67    80.80   16.82    None  None   None       |
|    all(noH): 2823   0      0.67    80.80   16.82    None  None   None       |
|    Sol.    : 438    0      0.67    76.50   39.22    None  None   None       |
|    Mac.    : 2385   0      0.86    80.80   12.70    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:     0.672 -   8.685:  743   |   5:    40.738 -  48.751:   93        |
|      1:     8.685 -  16.698: 1271   |   6:    48.751 -  56.765:   83        |
|      2:    16.698 -  24.712:  310   |   7:    56.765 -  64.778:   43        |
|      3:    24.712 -  32.725:  126   |   8:    64.778 -  72.791:   23        |
|      4:    32.725 -  40.738:  124   |   9:    72.791 -  80.804:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1146 r_free = 0.1554             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1145 r_free = 0.1554             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1554   ksol= 0.33   Bsol= 59.79   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.47,-0.54,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150710                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1554   ksol= 0.33   Bsol= 56.14   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.27,-0.50,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150810                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.351832              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.536  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.196512              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.828  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1148 = 2.35 * 0.50 * 5.1536 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0978 = 2.35 * 0.50 * 5.1297 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0166 = 0.20 * 1.00 * 5.1297 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0151 = 0.20 * 1.00 * 5.1264 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.67    79.86   16.39    None  None   None       |
|    all(noH): 2823   0      0.67    79.86   16.39    None  None   None       |
|    Sol.    : 438    0      0.67    73.79   37.63    None  None   None       |
|    Mac.    : 2385   0      1.23    79.86   12.49    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:     0.671 -   8.590:  747   |   5:    40.264 -  48.182:  100        |
|      1:     8.590 -  16.508: 1275   |   6:    48.182 -  56.101:   85        |
|      2:    16.508 -  24.427:  308   |   7:    56.101 -  64.019:   30        |
|      3:    24.427 -  32.345:  132   |   8:    64.019 -  71.938:   14        |
|      4:    32.345 -  40.264:  125   |   9:    71.938 -  79.856:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1541             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1542             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1542   ksol= 0.33   Bsol= 56.14   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.27,-0.50,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125253                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1542   ksol= 0.33   Bsol= 56.14   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.13,-0.43,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125277                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.262522              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.669  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.763395              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.817  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8654 = 2.26 * 0.50 * 5.1267 + 1.00 * 0.0657                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8601 = 2.26 * 0.50 * 5.1256 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9205 = 0.76 * 1.00 * 5.1256 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9214 = 0.76 * 1.00 * 5.1254 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.51    81.45   16.37    None  None   None       |
|    all(noH): 2823   0      0.51    81.45   16.37    None  None   None       |
|    Sol.    : 438    0      1.85    74.89   38.23    None  None   None       |
|    Mac.    : 2385   0      0.51    81.45   12.36    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:     0.509 -   8.603:  814   |   5:    40.977 -  49.071:   99        |
|      1:     8.603 -  16.697: 1223   |   6:    49.071 -  57.164:   85        |
|      2:    16.697 -  24.790:  294   |   7:    57.164 -  65.258:   31        |
|      3:    24.790 -  32.884:  128   |   8:    65.258 -  73.352:   16        |
|      4:    32.884 -  40.977:  129   |   9:    73.352 -  81.445:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1559             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1559             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1559   ksol= 0.33   Bsol= 56.14   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.13,-0.43,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130344                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7540 0.99   1389  152 0.1004 0.1287      5.3975       5.529|
|  2:  4.7540 -  3.7933 0.99   1331  152 0.0854 0.1107      5.4407      5.6319|
|  3:  3.7933 -  3.3196 0.99   1299  143 0.1043 0.1482      5.4695      5.8379|
|  4:  3.3196 -  3.0188 0.99   1306  145 0.1173 0.1641      5.4278      5.5899|
|  5:  3.0188 -  2.8039 0.99   1282  145 0.1283 0.1574      5.3095      5.5219|
|  6:  2.8039 -  2.6395 0.99   1291  141 0.1171 0.2103      5.1939      5.5255|
|  7:  2.6395 -  2.5080 0.99   1283  143 0.1250 0.1525      5.1583       5.298|
|  8:  2.5080 -  2.3992 0.98   1273  137 0.1118 0.1634      5.0496      5.3238|
|  9:  2.3992 -  2.3072 0.98   1262  144 0.1131 0.1767      5.0193      5.2849|
| 10:  2.3072 -  2.2279 1.00   1279  143 0.1093 0.1762      4.9364      5.2135|
| 11:  2.2279 -  2.1584 0.97   1254  137 0.1107 0.1661       4.927      5.2101|
| 12:  2.1584 -  2.0969 0.98   1251  142 0.1087 0.1727      4.8667      5.2379|
| 13:  2.0969 -  2.0418 0.99   1278  135 0.1068 0.1685      4.7701      5.0338|
| 14:  2.0418 -  1.9921 0.66    852  100 0.0935 0.1661      4.6319      4.9005|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7540  1389   152  0.94   9.35   0.97     0.94       7371.27|
|  2:  4.7540 -  3.7933  1331   152  0.95   7.89   1.01     0.99       9134.39|
|  3:  3.7933 -  3.3196  1299   143  0.94  10.99   1.02     1.01      10154.15|
|  4:  3.3196 -  3.0188  1306   145  0.92  13.25   1.00     0.98       9856.66|
|  5:  3.0188 -  2.8039  1282   145  0.91  15.35   0.99     0.97       8102.26|
|  6:  2.8039 -  2.6395  1291   141  0.90  16.00   0.98     0.95       6951.12|
|  7:  2.6395 -  2.5080  1283   143  0.91  15.43   0.98     0.95       6117.57|
|  8:  2.5080 -  2.3992  1273   137  0.91  14.77   0.98     0.96       5130.46|
|  9:  2.3992 -  2.3072  1262   144  0.91  14.83   1.00     0.96       4900.27|
| 10:  2.3072 -  2.2279  1279   143  0.90  15.55   0.99     0.95       4248.85|
| 11:  2.2279 -  2.1584  1254   137  0.90  15.76   0.98     0.95       4290.45|
| 12:  2.1584 -  2.0969  1251   142  0.91  15.52   1.00     0.98       3928.90|
| 13:  2.0969 -  2.0418  1278   135  0.91  15.78   0.98     0.96       3308.58|
| 14:  2.0418 -  1.9921   852   100  0.93  13.49   0.96     0.93       2451.03|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2451.03 max =        10154.15 mean =      6263.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.00 mean =        13.35|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1558   ksol= 0.32   Bsol= 56.12   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.94,-0.26,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.130346                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1558   ksol= 0.32   Bsol= 56.12   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.94,-0.26,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.130346                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7540 0.99   1389  152 0.1003 0.1288       5.397      5.5289|
|  2:  4.7540 -  3.7933 0.99   1331  152 0.0855 0.1107      5.4411      5.6321|
|  3:  3.7933 -  3.3196 0.99   1299  143 0.1044 0.1482      5.4695      5.8382|
|  4:  3.3196 -  3.0188 0.99   1306  145 0.1173 0.1641      5.4277      5.5898|
|  5:  3.0188 -  2.8039 0.99   1282  145 0.1283 0.1573      5.3094      5.5216|
|  6:  2.8039 -  2.6395 0.99   1291  141 0.1171 0.2103      5.1939      5.5255|
|  7:  2.6395 -  2.5080 0.99   1283  143 0.1250 0.1525      5.1583       5.298|
|  8:  2.5080 -  2.3992 0.98   1273  137 0.1118 0.1634      5.0496      5.3236|
|  9:  2.3992 -  2.3072 0.98   1262  144 0.1131 0.1768      5.0193      5.2849|
| 10:  2.3072 -  2.2279 1.00   1279  143 0.1093 0.1762      4.9365      5.2133|
| 11:  2.2279 -  2.1584 0.97   1254  137 0.1107 0.1660       4.927      5.2099|
| 12:  2.1584 -  2.0969 0.98   1251  142 0.1087 0.1726      4.8666      5.2377|
| 13:  2.0969 -  2.0418 0.99   1278  135 0.1068 0.1686      4.7702       5.034|
| 14:  2.0418 -  1.9921 0.66    852  100 0.0935 0.1661      4.6322      4.9005|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7540  1389   152  0.94   9.33   0.97     0.94       7364.68|
|  2:  4.7540 -  3.7933  1331   152  0.95   7.89   1.01     1.00       9136.20|
|  3:  3.7933 -  3.3196  1299   143  0.94  10.99   1.02     1.01      10156.57|
|  4:  3.3196 -  3.0188  1306   145  0.92  13.25   1.00     0.98       9854.06|
|  5:  3.0188 -  2.8039  1282   145  0.91  15.35   1.00     0.97       8100.14|
|  6:  2.8039 -  2.6395  1291   141  0.90  16.00   0.98     0.96       6949.00|
|  7:  2.6395 -  2.5080  1283   143  0.91  15.43   0.99     0.95       6117.14|
|  8:  2.5080 -  2.3992  1273   137  0.91  14.77   0.99     0.97       5130.13|
|  9:  2.3992 -  2.3072  1262   144  0.91  14.83   1.00     0.97       4900.57|
| 10:  2.3072 -  2.2279  1279   143  0.90  15.55   1.00     0.96       4248.06|
| 11:  2.2279 -  2.1584  1254   137  0.90  15.76   0.99     0.95       4289.16|
| 12:  2.1584 -  2.0969  1251   142  0.91  15.52   1.01     0.99       3928.09|
| 13:  2.0969 -  2.0418  1278   135  0.91  15.79   0.99     0.97       3308.64|
| 14:  2.0418 -  1.9921   852   100  0.93  13.49   0.97     0.94       2452.19|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2452.19 max =        10156.57 mean =      6262.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.81|
|phase err.(test): min =        0.00 max =           88.94 mean =        13.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    81.43   16.35    None  None   None       |
|    all(noH): 2823   0      0.49    81.43   16.35    None  None   None       |
|    Sol.    : 438    0      1.83    74.87   38.22    None  None   None       |
|    Mac.    : 2385   0      0.49    81.43   12.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.493 -   8.587:  814   |   5:    40.961 -  49.055:   99        |
|      1:     8.587 -  16.680: 1223   |   6:    49.055 -  57.148:   85        |
|      2:    16.680 -  24.774:  294   |   7:    57.148 -  65.242:   31        |
|      3:    24.774 -  32.868:  128   |   8:    65.242 -  73.335:   16        |
|      4:    32.868 -  40.961:  129   |   9:    73.335 -  81.429:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 269         
Filter by distance & map next to the model:
   mapped sites are within: 0.521 - 4.809
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 265 from: 269
   mapped sites are within: 0.722 - 4.809

peak=    5.656 closest distance to " NH2 ARG A  56 " =    2.234
peak=    5.380 closest distance to " CG  PRO A  54 " =    1.360
peak=    5.177 closest distance to " O   HOH Z 144 " =    1.790
peak=    5.177 closest distance to " CB  GLN A 223 " =    1.447
peak=    5.096 closest distance to " O   HOH Z 126 " =    1.929
peak=    5.024 closest distance to " NE2 GLN A  11 " =    1.132
peak=    4.949 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.845 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.795 closest distance to " CB  ARG A  79 " =    1.335
peak=    4.678 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.612 closest distance to " CB  PRO A  54 " =    0.959
peak=    4.606 closest distance to " O   HOH Z  78 " =    1.747
peak=    4.591 closest distance to " O   HOH Z 232 " =    2.422
peak=    4.568 closest distance to " CB  ARG A 190 " =    1.654
peak=    4.555 closest distance to " O   HOH Z 298 " =    1.967
peak=    4.505 closest distance to " O   HOH Z 189 " =    2.576
peak=    4.491 closest distance to " O   HOH Z  15 " =    2.198
peak=    4.457 closest distance to " O   HOH Z 369 " =    2.128
peak=    4.429 closest distance to " CB  SER A  63 " =    1.188
peak=    4.393 closest distance to " CZ  PHE A 218 " =    1.055
peak=    4.380 closest distance to " CB  GLU A 152 " =    1.228
peak=    4.370 closest distance to " O   HOH Z 303 " =    2.133
peak=    4.357 closest distance to " ND2 ASN A 187 " =    1.526
peak=    4.339 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.309 closest distance to " CG2 VAL A 257 " =    0.855
peak=    4.291 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.246 closest distance to " O   HOH Z 158 " =    3.072
peak=    4.246 closest distance to " O   HOH Z 287 " =    2.196
peak=    4.244 closest distance to " C   PRO A 198 " =    1.461
peak=    4.227 closest distance to " CB  LEU A 228 " =    1.091
peak=    4.198 closest distance to " O   HOH Z 427 " =    2.954
peak=    4.189 closest distance to " O   HOH Z 250 " =    1.496
peak=    4.186 closest distance to " CE  LYS A  76 " =    0.855
peak=    4.183 closest distance to " CB  VAL A 265 " =    1.261
peak=    4.157 closest distance to " CB  ASN A 148 " =    1.392
peak=    4.139 closest distance to " O   HOH Z 126 " =    2.065
peak=    4.113 closest distance to " CD2 TRP A 179 " =    1.308
peak=    4.107 closest distance to " O   HOH Z 346 " =    1.669
peak=    4.100 closest distance to " CA  ASN A 215 " =    1.101
peak=    4.087 closest distance to " CD  ARG A 159 " =    0.744
peak=    4.073 closest distance to " CB  TRP A 266 " =    1.018
peak=    4.069 closest distance to " NZ  LYS A 117 " =    3.190
peak=    4.055 closest distance to " OD1 ASN A  69 " =    2.629
peak=    4.054 closest distance to " O   SER A  87 " =    2.255
peak=    4.045 closest distance to " O   HOH Z  61 " =    1.640
peak=    4.028 closest distance to " CB  TYR A 169 " =    0.731
peak=    3.964 closest distance to " O   HOH Z 272 " =    1.856
peak=    3.954 closest distance to " O   HOH Z 392 " =    3.091
peak=    3.925 closest distance to " CG  PRO A 243 " =    1.031
peak=    3.906 closest distance to " O   HOH Z  40 " =    1.721
peak=    3.897 closest distance to " O   HOH Z 313 " =    1.985
peak=    3.880 closest distance to " CB  GLU A 277 " =    3.634
peak=    3.877 closest distance to " O   HOH Z 234 " =    3.749
peak=    3.873 closest distance to " OG ASER A 258 " =    3.142
peak=    3.861 closest distance to " NH1AARG A 145 " =    1.263
peak=    3.860 closest distance to " O   HOH Z  53 " =    2.550
peak=    3.849 closest distance to " O   HOH Z 406 " =    1.622
peak=    3.848 closest distance to " O   HOH Z 214 " =    2.150
peak=    3.841 closest distance to " O   HOH Z 193 " =    1.911
peak=    3.837 closest distance to " O   HOH Z 209 " =    2.294
peak=    3.835 closest distance to " CB  ASN A  39 " =    0.910
peak=    3.829 closest distance to " O   HOH Z 389 " =    1.866
peak=    3.825 closest distance to " O   HOH Z 265 " =    2.337
peak=    3.810 closest distance to " CB  SER A 212 " =    1.186
peak=    3.776 closest distance to " CB  ASN A 142 " =    1.013
peak=    3.767 closest distance to " ND2 ASN A 249 " =    0.860
peak=    3.752 closest distance to " CB  ASP A 124 " =    0.792
peak=    3.752 closest distance to " CA  THR A 264 " =    0.893
peak=    3.744 closest distance to " O  BHOH Z 338 " =    2.320
peak=    3.742 closest distance to " O   HOH Z 368 " =    2.119
peak=    3.742 closest distance to " CD  ARG A  66 " =    2.539
peak=    3.738 closest distance to " CB  GLU A 128 " =    0.937
peak=    3.724 closest distance to " O   HOH Z  21 " =    1.777
peak=    3.723 closest distance to " O   HOH Z   1 " =    1.875
peak=    3.717 closest distance to " CB  ASP A 140 " =    1.010
peak=    3.704 closest distance to " O   HOH Z  10 " =    1.832
peak=    3.703 closest distance to " O   HOH Z 180 " =    2.132
peak=    3.699 closest distance to " CB  ASN A 110 " =    1.071
peak=    3.686 closest distance to " O   HOH Z 353 " =    2.650
peak=    3.683 closest distance to " CB  VAL A 202 " =    1.603
peak=    3.681 closest distance to " CA  ARG A 195 " =    1.218
peak=    3.674 closest distance to " CA  ALA A  51 " =    0.924
peak=    3.669 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.668 closest distance to " O   HOH Z  43 " =    1.897
peak=    3.657 closest distance to " O   HOH Z 368 " =    3.585
peak=    3.656 closest distance to " CB  GLU A  46 " =    0.972
peak=    3.655 closest distance to " OG BSER A 164 " =    2.327
peak=    3.653 closest distance to " O   HOH Z 261 " =    2.005
peak=    3.651 closest distance to " O   ASN A  74 " =    1.413
peak=    3.643 closest distance to " O   HOH Z 419 " =    2.123
peak=    3.639 closest distance to " O   HOH Z 172 " =    3.133
peak=    3.638 closest distance to " O   HOH Z 423 " =    1.865
peak=    3.629 closest distance to " CA  ARG A  36 " =    1.042
peak=    3.621 closest distance to " O   HOH Z 371 " =    2.969
peak=    3.620 closest distance to " O   HOH Z 371 " =    1.814
peak=    3.619 closest distance to " O   HOH Z 403 " =    1.486
peak=    3.617 closest distance to " CA  SER A  87 " =    1.040
peak=    3.606 closest distance to " O   HOH Z 248 " =    1.556
peak=    3.605 closest distance to " CD  LYS A 166 " =    1.253
peak=    3.604 closest distance to " N   ASN A  39 " =    1.254
peak=    3.593 closest distance to " O   HOH Z 128 " =    2.156
peak=    3.588 closest distance to " CE1 PHE A 218 " =    1.085
peak=    3.587 closest distance to " O   HOH Z 402 " =    1.409
peak=    3.577 closest distance to " CB  ARG A 139 " =    1.018
peak=    3.575 closest distance to " CG2 ILE A 120 " =    1.185
peak=    3.566 closest distance to " CE1 PHE A  38 " =    1.235
peak=    3.562 closest distance to " N   ARG A 156 " =    1.362
peak=    3.552 closest distance to " CG  MET A 185 " =    1.151
peak=    3.551 closest distance to " CG2AVAL A  72 " =    1.675
peak=    3.547 closest distance to " CB  TYR A 116 " =    0.781
peak=    3.539 closest distance to " O   HOH Z 245 " =    1.259
peak=    3.539 closest distance to " CG1 VAL A 153 " =    1.035
peak=    3.536 closest distance to " O   HOH Z 203 " =    1.768
peak=    3.534 closest distance to " CB  SER A   3 " =    1.311
peak=    3.532 closest distance to " O   HOH Z 359 " =    1.499
peak=    3.530 closest distance to " O   HOH Z 133 " =    2.620
peak=    3.514 closest distance to " CB  MET A  47 " =    1.128
peak=    3.513 closest distance to " CD1 LEU A 300 " =    1.191
peak=    3.508 closest distance to " CG  LEU A 167 " =    1.265
peak=    3.494 closest distance to " O   HOH Z 234 " =    1.917
peak=    3.493 closest distance to " N   PHE A 130 " =    1.241
peak=    3.490 closest distance to " NE2 HIS A 207 " =    1.264
peak=    3.490 closest distance to " O   HOH Z 337 " =    3.653
peak=    3.485 closest distance to " CB  ALA A 291 " =    1.277
peak=    3.477 closest distance to " CD  ARG A  66 " =    2.354
peak=    3.468 closest distance to " CZ3 TRP A 266 " =    1.120
peak=    3.467 closest distance to " CG  GLN A  11 " =    1.685
peak=    3.463 closest distance to " O   HOH Z 305 " =    3.540
peak=    3.458 closest distance to " CA  TYR A 116 " =    1.351
peak=    3.452 closest distance to " O   HOH Z 280 " =    2.983
peak=    3.452 closest distance to " CD2 LEU A 297 " =    0.836
peak=    3.450 closest distance to " O   HOH Z 425 " =    2.052
peak=    3.449 closest distance to " O   HOH Z 294 " =    1.496
peak=    3.448 closest distance to " O   HOH Z  97 " =    2.591
peak=    3.445 closest distance to " O   HOH Z 147 " =    1.857
peak=    3.436 closest distance to " CD  ARG A 269 " =    0.924
peak=    3.426 closest distance to " CZ2 TRP A 179 " =    1.789
peak=    3.417 closest distance to " CD1 LEU A  96 " =    0.766
peak=    3.414 closest distance to " O   HOH Z  68 " =    2.229
peak=    3.410 closest distance to " CB  PRO A  90 " =    1.164
peak=    3.408 closest distance to " O   HOH Z 411 " =    3.913
peak=    3.407 closest distance to " O   HOH Z 417 " =    3.357
peak=    3.405 closest distance to " O   HOH Z 148 " =    3.433
peak=    3.403 closest distance to " O   HOH Z 261 " =    1.683
peak=    3.398 closest distance to " CB  THR A  31 " =    1.588
peak=    3.390 closest distance to " O   HOH Z 285 " =    2.487
peak=    3.390 closest distance to " CB  ALA A  34 " =    0.958
peak=    3.386 closest distance to " CG1 ILE A  33 " =    1.230
peak=    3.384 closest distance to " O   HOH Z 329 " =    4.049
peak=    3.384 closest distance to " CB  LYS A 117 " =    1.230
peak=    3.383 closest distance to " CB  ASN A 215 " =    1.099
peak=    3.378 closest distance to " CB  LYS A 290 " =    1.060
peak=    3.378 closest distance to " O   HOH Z 193 " =    1.703
peak=    3.376 closest distance to " O   HOH Z 132 " =    2.566
peak=    3.369 closest distance to " CB  GLN A  88 " =    1.208
peak=    3.369 closest distance to " O   HOH Z  59 " =    1.861
peak=    3.367 closest distance to " CB  SER A 210 " =    0.753
peak=    3.366 closest distance to " OG  SER A  22 " =    2.722
peak=    3.365 closest distance to " O   HOH Z 426 " =    1.947
peak=    3.362 closest distance to " CB  ILE A 120 " =    1.253
peak=    3.359 closest distance to " O   HOH Z 128 " =    2.286
peak=    3.348 closest distance to " ND1 HIS A  86 " =    1.638
peak=    3.344 closest distance to " CA  ASN A 217 " =    1.195
peak=    3.342 closest distance to " CB  LEU A  83 " =    0.780
peak=    3.335 closest distance to " NE2 GLN A  73 " =    3.854
peak=    3.333 closest distance to " O   HOH Z 218 " =    4.648
peak=    3.328 closest distance to " CB  TRP A 179 " =    1.355
peak=    3.326 closest distance to " CA  MET A 105 " =    0.985
peak=    3.325 closest distance to " O   HOH Z 213 " =    1.922
peak=    3.324 closest distance to " CB  ALA A 242 " =    0.895
peak=    3.321 closest distance to " CB  MET A  40 " =    0.791
peak=    3.321 closest distance to " O   HOH Z 403 " =    1.553
peak=    3.318 closest distance to " CG1 VAL A 189 " =    2.048
peak=    3.313 closest distance to " CB  ALA A 114 " =    1.075
peak=    3.311 closest distance to " O   ALA A 165 " =    1.573
peak=    3.307 closest distance to " O   HOH Z 365 " =    2.834
peak=    3.303 closest distance to " CA  ALA A 291 " =    0.792
peak=    3.297 closest distance to " O   HOH Z 188 " =    1.931
peak=    3.295 closest distance to " CB  GLN A  89 " =    1.322
peak=    3.295 closest distance to " CE1 TYR A 186 " =    1.376
peak=    3.294 closest distance to " O   HOH Z  88 " =    3.178
peak=    3.293 closest distance to " O   HOH Z 325 " =    4.008
peak=    3.288 closest distance to " CB  PHE A 204 " =    0.722
peak=    3.283 closest distance to " CB  SER A 141 " =    0.991
peak=    3.275 closest distance to " CD BLYS A 290 " =    1.062
peak=    3.274 closest distance to " O   HOH Z 273 " =    2.881
peak=    3.273 closest distance to " CA  THR A 221 " =    1.076
peak=    3.270 closest distance to " NH2BARG A 145 " =    2.114
peak=    3.270 closest distance to " O   HOH Z  62 " =    1.997
peak=    3.262 closest distance to " CA  ILE A 234 " =    0.954
peak=    3.261 closest distance to " O   HOH Z 421 " =    1.985
peak=    3.257 closest distance to " CG2 ILE A  20 " =    1.439
peak=    3.255 closest distance to " CA  VAL A 125 " =    1.096
peak=    3.254 closest distance to " CD1 ILE A 106 " =    0.792
peak=    3.254 closest distance to " OG BSER A  99 " =    2.255
peak=    3.250 closest distance to " O   MET A 105 " =    1.894
peak=    3.245 closest distance to " O   HOH Z   1 " =    1.656
peak=    3.244 closest distance to " O   HOH Z 175 " =    2.048
peak=    3.243 closest distance to " O   HOH Z 185 " =    1.832
peak=    3.238 closest distance to " O   HOH Z 325 " =    2.494
peak=    3.236 closest distance to " CD1 ILE A 263 " =    1.314
peak=    3.231 closest distance to " CA  ALA A 158 " =    1.294
peak=    3.222 closest distance to " CB  ARG A 138 " =    0.952
peak=    3.221 closest distance to " CB  ASN A 224 " =    0.972
peak=    3.220 closest distance to " CG2 VAL A 197 " =    1.092
peak=    3.218 closest distance to " O   HOH Z 433 " =    1.781
peak=    3.217 closest distance to " OG BSER A 134 " =    2.946
peak=    3.214 closest distance to " CA  ALA A  21 " =    1.164
peak=    3.212 closest distance to " O   THR A 251 " =    1.137
peak=    3.211 closest distance to " O   HOH Z 116 " =    3.145
peak=    3.211 closest distance to " CA  ALA A 129 " =    1.310
peak=    3.207 closest distance to " N   TYR A 116 " =    1.525
peak=    3.206 closest distance to " O  BHOH Z  74 " =    1.247
peak=    3.205 closest distance to " O   THR A 220 " =    1.249
peak=    3.205 closest distance to " CG  GLU A  37 " =    0.876
peak=    3.203 closest distance to " O   HOH Z  44 " =    2.868
peak=    3.203 closest distance to " N   ASN A 127 " =    1.272
peak=    3.202 closest distance to " CG2 THR A 221 " =    1.037
peak=    3.195 closest distance to " CA  ALA A 233 " =    1.247
peak=    3.194 closest distance to " CB  ALA A   1 " =    4.809
peak=    3.189 closest distance to " CB  SER A 216 " =    0.834
peak=    3.184 closest distance to " OG1 THR A 294 " =    2.428
peak=    3.183 closest distance to " CG1 ILE A  49 " =    1.505
peak=    3.181 closest distance to " CD1 ILE A 199 " =    0.966
peak=    3.179 closest distance to " O   TYR A 116 " =    1.370
peak=    3.179 closest distance to " O   HOH Z  97 " =    2.005
peak=    3.178 closest distance to " CB  THR A 157 " =    1.138
peak=    3.175 closest distance to " O   HOH Z 193 " =    2.012
peak=    3.172 closest distance to " O   HOH Z 407 " =    2.443
peak=    3.166 closest distance to " CG  LYS A  76 " =    0.922
peak=    3.165 closest distance to " NH1BARG A 145 " =    1.019
peak=    3.162 closest distance to " NZ  LYS A  48 " =    1.210
peak=    3.161 closest distance to " O   HOH Z 391 " =    2.914
peak=    3.159 closest distance to " CD  ARG A 219 " =    1.173
peak=    3.156 closest distance to " CG2 ILE A 234 " =    0.765
peak=    3.153 closest distance to " O   HOH Z 233 " =    1.763
peak=    3.151 closest distance to " OE2 GLU A  53 " =    2.045
peak=    3.147 closest distance to " CB  ALA A   9 " =    1.548
peak=    3.141 closest distance to " O   HOH Z 116 " =    1.775
peak=    3.138 closest distance to " O   HOH Z 332 " =    1.482
peak=    3.136 closest distance to " O   SER A 164 " =    1.352
peak=    3.133 closest distance to " O   HOH Z 287 " =    2.318
peak=    3.133 closest distance to " O   HOH Z  88 " =    1.925
peak=    3.132 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.130 closest distance to " CA  LYS A 290 " =    1.246
peak=    3.130 closest distance to " CB  ASP A 298 " =    1.158
peak=    3.128 closest distance to " O   PHE A 192 " =    1.400
peak=    3.126 closest distance to " O   HOH Z 383 " =    1.892
peak=    3.117 closest distance to " CA  ARG A 159 " =    1.252
peak=    3.115 closest distance to " CA  ASP A 162 " =    0.983
peak=    3.110 closest distance to " CB  ALA A  43 " =    0.754
peak=    3.109 closest distance to " CB  SER A  62 " =    1.114
peak=    3.106 closest distance to " O   HOH Z 344 " =    3.195
peak=    3.106 closest distance to " O   HOH Z 336 " =    1.769
peak=    3.104 closest distance to " CB  THR A 235 " =    1.232
peak=    3.102 closest distance to " O   HOH Z 327 " =    1.647
peak=    3.102 closest distance to " N   GLY A  98 " =    1.074
peak=    3.094 closest distance to " O   HOH Z 298 " =    2.381
peak=    3.083 closest distance to " O   ALA A   1 " =    1.610
peak=    3.082 closest distance to " O   HOH Z 384 " =    2.948
peak=    3.080 closest distance to " ND2 ASN A 110 " =    1.643
peak=    3.075 closest distance to " O   HOH Z 409 " =    2.865
peak=    3.064 closest distance to " O   HOH Z 345 " =    3.452
peak=    3.053 closest distance to " O   HOH Z 421 " =    2.899
peak=    3.041 closest distance to " O   HOH Z 171 " =    4.052

                           ----------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: 0.771 - 5.611
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.771 - 5.611

peak=   -4.669 closest distance to " CD  ARG A  14 " =    3.505
peak=   -4.594 closest distance to " CD  GLN A  58 " =    0.981
peak=   -4.427 closest distance to " CD  ARG A 156 " =    2.069
peak=   -4.389 closest distance to " CB  PRO A 243 " =    2.677
peak=   -4.381 closest distance to " O   HOH Z 231 " =    2.286
peak=   -4.364 closest distance to " O   HOH Z 266 " =    5.375
peak=   -4.358 closest distance to " O   HOH Z 377 " =    2.124
peak=   -4.331 closest distance to " CZ3 TRP A 179 " =    1.187
peak=   -4.281 closest distance to " CG1 VAL A 112 " =    2.644
peak=   -4.251 closest distance to " CD2 PHE A 192 " =    2.016
peak=   -4.201 closest distance to " O   VAL A  67 " =    2.699
peak=   -4.193 closest distance to " OG BSER A 134 " =    1.293
peak=   -4.158 closest distance to " CG  GLN A 223 " =    2.026
peak=   -4.132 closest distance to " N   ALA A  43 " =    2.652
peak=   -4.122 closest distance to " C   HIS A 108 " =    1.117
peak=   -4.053 closest distance to " CG1 VAL A 112 " =    2.891
peak=   -4.030 closest distance to " O   PRO A 198 " =    1.293
peak=   -4.017 closest distance to " CE  MET A 105 " =    2.489
peak=   -3.971 closest distance to " O   HOH Z 372 " =    2.398
peak=   -3.967 closest distance to " O   HOH Z 389 " =    2.012
peak=   -3.921 closest distance to " O   HOH Z  73 " =    2.284
peak=   -3.889 closest distance to " CE BMET A  47 " =    1.379
peak=   -3.879 closest distance to " O   HOH Z 198 " =    1.949
peak=   -3.874 closest distance to " CA  VAL A  67 " =    2.952
peak=   -3.835 closest distance to " OG  SER A  97 " =    2.250
peak=   -3.818 closest distance to " CE2 TYR A  30 " =    2.736
peak=   -3.808 closest distance to " O   HOH Z 290 " =    1.194
peak=   -3.807 closest distance to " CB  ALA A  43 " =    2.552
peak=   -3.788 closest distance to " O   HOH Z 313 " =    1.903
peak=   -3.779 closest distance to " CG2 ILE A 263 " =    2.336
peak=   -3.777 closest distance to " O   HOH Z 407 " =    3.121
peak=   -3.773 closest distance to " O   HOH Z 114 " =    3.057
peak=   -3.762 closest distance to " O   HOH Z 185 " =    2.271
peak=   -3.762 closest distance to " ND2 ASN A  45 " =    1.883
peak=   -3.758 closest distance to " CB  ASN A  39 " =    2.320
peak=   -3.755 closest distance to " O   HOH Z 196 " =    2.049
peak=   -3.754 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.751 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.722 closest distance to " O   HOH Z 351 " =    1.515
peak=   -3.714 closest distance to " N   SER A 212 " =    2.037
peak=   -3.686 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.685 closest distance to " CD2 TYR A 293 " =    1.986
peak=   -3.678 closest distance to " N   ALA A 248 " =    1.606
peak=   -3.667 closest distance to " CE2 PHE A  61 " =    2.602
peak=   -3.638 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.636 closest distance to " CG  ARG A 269 " =    2.353
peak=   -3.615 closest distance to " OD1 ASP A 171 " =    1.637
peak=   -3.606 closest distance to " ND2 ASN A 249 " =    2.213
peak=   -3.597 closest distance to " CD1 LEU A 255 " =    2.896
peak=   -3.576 closest distance to " CD  ARG A 139 " =    1.575
peak=   -3.575 closest distance to " CD2 PHE A  61 " =    2.075
peak=   -3.573 closest distance to " O   HOH Z  10 " =    1.504
peak=   -3.569 closest distance to " CG1 VAL A 250 " =    2.688
peak=   -3.558 closest distance to " NH2AARG A 275 " =    5.365
peak=   -3.548 closest distance to " CB  ALA A 248 " =    2.414
peak=   -3.536 closest distance to " CG  ASP A 132 " =    2.293
peak=   -3.531 closest distance to " CA  GLY A 203 " =    2.394
peak=   -3.526 closest distance to " O   PHE A 218 " =    1.547
peak=   -3.522 closest distance to " O   HOH Z  51 " =    1.627
peak=   -3.510 closest distance to " OD2 ASP A 191 " =    1.426
peak=   -3.502 closest distance to " OXT GLY A 302 " =    2.852
peak=   -3.502 closest distance to " O   ALA A  10 " =    1.664
peak=   -3.495 closest distance to " CA  GLY A 241 " =    2.316
peak=   -3.494 closest distance to " CD2 LEU A 237 " =    2.867
peak=   -3.489 closest distance to " O   HOH Z 211 " =    1.572
peak=   -3.480 closest distance to " O   PRO A 163 " =    2.037
peak=   -3.473 closest distance to " O   VAL A 189 " =    2.652
peak=   -3.471 closest distance to " O   HOH Z 429 " =    2.201
peak=   -3.470 closest distance to " CG2 THR A 178 " =    2.333
peak=   -3.459 closest distance to " CD1 PHE A  59 " =    1.984
peak=   -3.457 closest distance to " O   HOH Z 394 " =    1.479
peak=   -3.454 closest distance to " O   HOH Z 253 " =    3.938
peak=   -3.452 closest distance to " CZ  TYR A 169 " =    1.748
peak=   -3.442 closest distance to " ND2 ASN A  45 " =    1.209
peak=   -3.431 closest distance to " O   HOH Z 348 " =    2.231
peak=   -3.430 closest distance to " CG  PHE A 283 " =    2.733
peak=   -3.428 closest distance to " CD1 LEU A 101 " =    2.336
peak=   -3.424 closest distance to " CG  GLU A 277 " =    1.225
peak=   -3.421 closest distance to " NE2 GLN A 194 " =    1.828
peak=   -3.419 closest distance to " O   HOH Z  11 " =    1.729
peak=   -3.417 closest distance to " O   VAL A 189 " =    1.608
peak=   -3.410 closest distance to " O   HOH Z 298 " =    1.277
peak=   -3.408 closest distance to " CA  GLY A 241 " =    3.117
peak=   -3.405 closest distance to " O   HOH Z 166 " =    2.101
peak=   -3.402 closest distance to " CZ  PHE A 155 " =    1.245
peak=   -3.401 closest distance to " C   MET A 188 " =    1.382
peak=   -3.397 closest distance to " O   HOH Z  13 " =    1.675
peak=   -3.395 closest distance to " NH2BARG A 275 " =    1.897
peak=   -3.395 closest distance to " O   HOH Z  38 " =    1.524
peak=   -3.391 closest distance to " CB  TRP A  85 " =    2.490
peak=   -3.390 closest distance to " CB  ASP A 286 " =    2.068
peak=   -3.387 closest distance to " NE2 GLN A 278 " =    1.704
peak=   -3.384 closest distance to " CG  ARG A  66 " =    2.237
peak=   -3.381 closest distance to " CA  ASN A 110 " =    2.415
peak=   -3.376 closest distance to " O   HOH Z 243 " =    1.915
peak=   -3.376 closest distance to " CE2 PHE A 218 " =    2.455
peak=   -3.372 closest distance to " CG  HIS A  86 " =    1.099
peak=   -3.363 closest distance to " CG1 VAL A 125 " =    1.861
peak=   -3.356 closest distance to " CB  PRO A 163 " =    2.475
peak=   -3.354 closest distance to " O   HOH Z 359 " =    3.181
peak=   -3.352 closest distance to " OD1 ASN A 187 " =    1.552
peak=   -3.350 closest distance to " CB  GLN A  11 " =    1.763
peak=   -3.336 closest distance to " O   HOH Z 134 " =    3.167
peak=   -3.333 closest distance to " CE3 TRP A 150 " =    2.181
peak=   -3.333 closest distance to " O   HOH Z 353 " =    2.175
peak=   -3.332 closest distance to " O   HOH Z 357 " =    2.045
peak=   -3.332 closest distance to " O   ALA A 161 " =    1.705
peak=   -3.331 closest distance to " O   HOH Z 351 " =    1.621
peak=   -3.326 closest distance to " CZ  PHE A  59 " =    1.537
peak=   -3.318 closest distance to " C   ASP A 231 " =    2.667
peak=   -3.315 closest distance to " CG1BVAL A  41 " =    2.823
peak=   -3.308 closest distance to " CB  TYR A  15 " =    2.209
peak=   -3.307 closest distance to " ND2 ASN A 187 " =    1.480
peak=   -3.307 closest distance to " CA  GLY A 241 " =    2.860
peak=   -3.304 closest distance to " O   HOH Z 316 " =    1.836
peak=   -3.303 closest distance to " O   ARG A 145 " =    1.578
peak=   -3.303 closest distance to " CG  LEU A  83 " =    1.918
peak=   -3.301 closest distance to " OD2 ASP A 171 " =    2.372
peak=   -3.298 closest distance to " N   THR A  52 " =    1.690
peak=   -3.297 closest distance to " NH2 ARG A  79 " =    1.539
peak=   -3.292 closest distance to " O   ALA A  51 " =    1.308
peak=   -3.290 closest distance to " O   HOH Z 426 " =    1.583
peak=   -3.285 closest distance to " N   GLN A  58 " =    1.739
peak=   -3.282 closest distance to " C   ALA A 158 " =    1.438
peak=   -3.281 closest distance to " O   GLN A 240 " =    2.079
peak=   -3.279 closest distance to " O   HOH Z 311 " =    3.759
peak=   -3.276 closest distance to " O   HOH Z  37 " =    1.822
peak=   -3.271 closest distance to " N   THR A 157 " =    1.526
peak=   -3.271 closest distance to " O   HOH Z 126 " =    1.911
peak=   -3.270 closest distance to " O   HOH Z 102 " =    1.586
peak=   -3.267 closest distance to " CD  ARG A 195 " =    5.211
peak=   -3.265 closest distance to " O   HOH Z 174 " =    2.616
peak=   -3.263 closest distance to " O   HOH Z 421 " =    3.087
peak=   -3.261 closest distance to " CE3 TRP A 274 " =    2.396
peak=   -3.258 closest distance to " NE2 GLN A  88 " =    1.839
peak=   -3.242 closest distance to " OE1 GLN A  88 " =    1.076
peak=   -3.240 closest distance to " OH  TYR A 247 " =    2.102
peak=   -3.238 closest distance to " O   HOH Z 244 " =    2.009
peak=   -3.234 closest distance to " O   ILE A 106 " =    2.046
peak=   -3.233 closest distance to " O   HOH Z  71 " =    2.072
peak=   -3.232 closest distance to " O   HOH Z 191 " =    5.611
peak=   -3.231 closest distance to " CD1 ILE A 239 " =    2.349
peak=   -3.229 closest distance to " OD2 ASP A  50 " =    1.692
peak=   -3.229 closest distance to " O   HOH Z   6 " =    1.373
peak=   -3.228 closest distance to " N   ASP A 286 " =    2.359
peak=   -3.225 closest distance to " CD  GLU A 236 " =    1.080
peak=   -3.223 closest distance to " CA  GLY A 133 " =    2.054
peak=   -3.223 closest distance to " O   ALA A 180 " =    1.306
peak=   -3.221 closest distance to " CZ  PHE A  38 " =    1.984
peak=   -3.212 closest distance to " O   ALA A  34 " =    2.561
peak=   -3.209 closest distance to " CB  ALA A 114 " =    2.568
peak=   -3.208 closest distance to " C   LEU A 143 " =    1.097
peak=   -3.208 closest distance to " ND2 ASN A  60 " =    1.341
peak=   -3.207 closest distance to " O   SER A  95 " =    1.612
peak=   -3.197 closest distance to " CA  PRO A 243 " =    2.293
peak=   -3.196 closest distance to " CA  SER A 135 " =    1.306
peak=   -3.192 closest distance to " C   PHE A  59 " =    1.372
peak=   -3.192 closest distance to " O   HOH Z 365 " =    1.947
peak=   -3.191 closest distance to " O   HOH Z  43 " =    1.674
peak=   -3.188 closest distance to " O   HOH Z 317 " =    1.498
peak=   -3.187 closest distance to " O   SER A 135 " =    1.408
peak=   -3.182 closest distance to " CD  GLN A 223 " =    0.794
peak=   -3.181 closest distance to " O   HOH Z 298 " =    2.464
peak=   -3.179 closest distance to " CG1 VAL A 197 " =    2.294
peak=   -3.177 closest distance to " CG  ASP A 231 " =    0.771
peak=   -3.175 closest distance to " CD2 HIS A 207 " =    2.336
peak=   -3.168 closest distance to " O   HOH Z  60 " =    1.927
peak=   -3.167 closest distance to " O   HOH Z 262 " =    2.912
peak=   -3.167 closest distance to " O   VAL A 174 " =    2.087
peak=   -3.164 closest distance to " O   ALA A 292 " =    2.125
peak=   -3.157 closest distance to " C   SER A 206 " =    1.524
peak=   -3.156 closest distance to " O   HOH Z  63 " =    1.809
peak=   -3.155 closest distance to " O   TRP A  70 " =    1.425
peak=   -3.144 closest distance to " OD2 ASP A 171 " =    1.832
peak=   -3.144 closest distance to " CD  ARG A  79 " =    1.186
peak=   -3.143 closest distance to " CD1 LEU A   5 " =    2.554
peak=   -3.135 closest distance to " OE2 GLU A 152 " =    1.206
peak=   -3.135 closest distance to " CG  TRP A 266 " =    1.893
peak=   -3.125 closest distance to " CG2 VAL A 189 " =    2.002
peak=   -3.124 closest distance to " O   PRO A 198 " =    1.334
peak=   -3.116 closest distance to " O   GLN A 240 " =    2.519
peak=   -3.115 closest distance to " CB  ASP A 132 " =    2.397
peak=   -3.115 closest distance to " CG1 VAL A  67 " =    3.089
peak=   -3.115 closest distance to " OG BSER A 134 " =    1.761
peak=   -3.114 closest distance to " O   HOH Z  52 " =    1.369
peak=   -3.114 closest distance to " O   HOH Z 174 " =    4.208
peak=   -3.110 closest distance to " O   GLU A 152 " =    1.382
peak=   -3.109 closest distance to " CA  TRP A 274 " =    1.408
peak=   -3.106 closest distance to " CB  ALA A 129 " =    2.432
peak=   -3.098 closest distance to " O   HOH Z 128 " =    2.639
peak=   -3.082 closest distance to " C   ALA A 114 " =    2.339
peak=   -3.081 closest distance to " O   SER A  22 " =    2.416
peak=   -3.076 closest distance to " CB  ALA A 100 " =    2.177
peak=   -3.068 closest distance to " O   HOH Z 189 " =    1.967
peak=   -3.068 closest distance to " CD1 LEU A 228 " =    2.227
peak=   -3.066 closest distance to " CE  LYS A  76 " =    2.737
peak=   -3.065 closest distance to " O   HOH Z 281 " =    2.713
peak=   -3.053 closest distance to " O   HOH Z 283 " =    5.581
peak=   -3.046 closest distance to " CD1 ILE A 199 " =    2.552
peak=   -3.031 closest distance to " CD1 TRP A  70 " =    1.059
peak=   -3.030 closest distance to " OD1AASN A 224 " =    1.757
peak=   -2.958 closest distance to " CB  SER A  97 " =    2.401

================= 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    :  0.3018 0.2962   5.991701e+00   5.967407e+00
   1_bss:  0.2849 0.2815   5.961450e+00   5.932019e+00
   1_xyz:  0.1725 0.1972   5.475151e+00   5.573515e+00
   1_adp:  0.1629 0.1978   5.434495e+00   5.581431e+00
   1_occ:  0.1623 0.1973   5.432189e+00   5.579926e+00
   2_bss:  0.1600 0.1945   5.422399e+00   5.569587e+00
   2_xyz:  0.1246 0.1555   5.195208e+00   5.376580e+00
   2_adp:  0.1163 0.1583   5.161814e+00   5.385182e+00
   2_occ:  0.1161 0.1582   5.161536e+00   5.385117e+00
   3_bss:  0.1158 0.1575   5.159145e+00   5.381261e+00
   3_xyz:  0.1147 0.1565   5.154496e+00   5.378914e+00
   3_adp:  0.1146 0.1554   5.150634e+00   5.374019e+00
   3_occ:  0.1145 0.1554   5.150710e+00   5.374454e+00
   4_bss:  0.1144 0.1554   5.150810e+00   5.374743e+00
   4_xyz:  0.1094 0.1545   5.125331e+00   5.369244e+00
   4_adp:  0.1096 0.1541   5.124950e+00   5.366493e+00
   4_occ:  0.1095 0.1542   5.125253e+00   5.367326e+00
   5_bss:  0.1095 0.1542   5.125277e+00   5.367366e+00
   5_xyz:  0.1096 0.1549   5.129498e+00   5.375263e+00
   5_adp:  0.1091 0.1559   5.130041e+00   5.380906e+00
   5_occ:  0.1091 0.1559   5.130344e+00   5.381467e+00
   5_bss:  0.1090 0.1558   5.130346e+00   5.381419e+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:  0.324  50.000  -3.215  -2.265   2.555  -0.000   0.000   0.000
   1_xyz:  0.324  50.000  -3.215  -2.265   2.555  -0.000   0.000   0.000
   1_adp:  0.324  50.000  -3.215  -2.265   2.555  -0.000   0.000   0.000
   1_occ:  0.324  50.000  -3.215  -2.265   2.555  -0.000   0.000   0.000
   2_bss:  0.330  59.348  -3.265  -2.807  -0.375  -0.000  -0.000  -0.000
   2_xyz:  0.330  59.348  -3.265  -2.807  -0.375  -0.000  -0.000  -0.000
   2_adp:  0.330  59.348  -3.265  -2.807  -0.375  -0.000  -0.000  -0.000
   2_occ:  0.330  59.348  -3.265  -2.807  -0.375  -0.000  -0.000  -0.000
   3_bss:  0.329  59.787  -2.769  -2.467  -0.544  -0.000  -0.000  -0.000
   3_xyz:  0.329  59.787  -2.769  -2.467  -0.544  -0.000  -0.000  -0.000
   3_adp:  0.329  59.787  -2.769  -2.467  -0.544  -0.000  -0.000  -0.000
   3_occ:  0.329  59.787  -2.769  -2.467  -0.544  -0.000  -0.000  -0.000
   4_bss:  0.326  56.137  -2.515  -2.266  -0.498  -0.000  -0.000  -0.000
   4_xyz:  0.326  56.137  -2.515  -2.266  -0.498  -0.000  -0.000  -0.000
   4_adp:  0.326  56.137  -2.515  -2.266  -0.498  -0.000  -0.000  -0.000
   4_occ:  0.326  56.137  -2.515  -2.266  -0.498  -0.000  -0.000  -0.000
   5_bss:  0.326  56.137  -2.349  -2.134  -0.435  -0.000  -0.000  -0.000
   5_xyz:  0.326  56.137  -2.349  -2.134  -0.435  -0.000  -0.000  -0.000
   5_adp:  0.326  56.137  -2.349  -2.134  -0.435  -0.000  -0.000  -0.000
   5_occ:  0.326  56.137  -2.349  -2.134  -0.435  -0.000  -0.000  -0.000
   5_bss:  0.323  56.121  -2.141  -1.935  -0.255  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  29.773 0.7641  0.9233    24306.799
   1_bss:  28.359 0.7776  0.9094    21289.698
   1_xyz:  18.107 0.8804  0.9939     9520.907
   1_adp:  18.286 0.8784  0.9903     9623.290
   1_occ:  18.262 0.8786  0.9902     9578.860
   2_bss:  17.912 0.8822  0.9543     9430.213
   2_xyz:  13.825 0.9163  0.9691     6243.006
   2_adp:  13.989 0.9150  0.9631     6288.080
   2_occ:  13.983 0.9150  0.9629     6282.376
   3_bss:  13.915 0.9156  0.9706     6224.185
   3_xyz:  13.787 0.9169  0.9712     6223.851
   3_adp:  13.682 0.9178  0.9652     6165.954
   3_occ:  13.689 0.9177  0.9651     6170.319
   4_bss:  13.693 0.9177  0.9709     6173.938
   4_xyz:  13.562 0.9187  0.9727     6117.723
   4_adp:  13.486 0.9194  0.9678     6089.852
   4_occ:  13.504 0.9193  0.9676     6096.956
   5_bss:  13.505 0.9193  0.9719     6098.344
   5_xyz:  13.637 0.9183  0.9713     6210.967
   5_adp:  13.752 0.9174  0.9638     6258.615
   5_occ:  13.762 0.9173  0.9636     6263.938
   5_bss:  13.762 0.9173  0.9698     6263.054
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6311e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6311e-01
   1_xyz:   1.002  0.007  0.071 15.312  0.004  4.111   6.0297e-02
   1_adp:   1.002  0.007  0.071 15.312  0.004  4.111   6.0297e-02
   1_occ:   1.002  0.007  0.071 15.312  0.004  4.111   6.0297e-02
   2_bss:   1.002  0.007  0.071 15.312  0.004  4.111   6.0297e-02
   2_xyz:   1.021  0.008  0.077 15.090  0.004  4.123   6.2743e-02
   2_adp:   1.021  0.008  0.077 15.090  0.004  4.123   6.2743e-02
   2_occ:   1.021  0.008  0.077 15.090  0.004  4.123   6.2743e-02
   3_bss:   1.021  0.008  0.077 15.090  0.004  4.123   6.2743e-02
   3_xyz:   0.937  0.007  0.073 14.913  0.003  4.112   5.4577e-02
   3_adp:   0.937  0.007  0.073 14.913  0.003  4.112   5.4577e-02
   3_occ:   0.937  0.007  0.073 14.913  0.003  4.112   5.4577e-02
   4_bss:   0.937  0.007  0.073 14.913  0.003  4.112   5.4577e-02
   4_xyz:   1.035  0.009  0.081 14.972  0.004  4.115   6.5710e-02
   4_adp:   1.035  0.009  0.081 14.972  0.004  4.115   6.5710e-02
   4_occ:   1.035  0.009  0.081 14.972  0.004  4.115   6.5710e-02
   5_bss:   1.035  0.009  0.081 14.972  0.004  4.115   6.5710e-02
   5_xyz:   0.995  0.008  0.078 14.828  0.004  4.116   6.1697e-02
   5_adp:   0.995  0.008  0.078 14.828  0.004  4.116   6.1697e-02
   5_occ:   0.995  0.008  0.078 14.828  0.004  4.116   6.1697e-02
   5_bss:   0.995  0.008  0.078 14.828  0.004  4.116   6.1697e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4188e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4188e-01
   1_xyz:   7.155  0.036  0.257 83.832  0.039  2.240   5.8693e-02
   1_adp:   7.155  0.036  0.257 83.832  0.039  2.240   5.8693e-02
   1_occ:   7.155  0.036  0.257 83.832  0.039  2.240   5.8693e-02
   2_bss:   7.155  0.036  0.257 83.832  0.039  2.240   5.8693e-02
   2_xyz:   6.876  0.046  0.265 82.241  0.030  2.323   4.7141e-02
   2_adp:   6.876  0.046  0.265 82.241  0.030  2.323   4.7141e-02
   2_occ:   6.876  0.046  0.265 82.241  0.030  2.323   4.7141e-02
   3_bss:   6.876  0.046  0.265 82.241  0.030  2.323   4.7141e-02
   3_xyz:   6.592  0.039  0.228 82.762  0.035  2.380   3.4540e-02
   3_adp:   6.592  0.039  0.228 82.762  0.035  2.380   3.4540e-02
   3_occ:   6.592  0.039  0.228 82.762  0.035  2.380   3.4540e-02
   4_bss:   6.592  0.039  0.228 82.762  0.035  2.380   3.4540e-02
   4_xyz:   6.926  0.050  0.272 83.048  0.035  2.300   4.7932e-02
   4_adp:   6.926  0.050  0.272 83.048  0.035  2.300   4.7932e-02
   4_occ:   6.926  0.050  0.272 83.048  0.035  2.300   4.7932e-02
   5_bss:   6.926  0.050  0.272 83.048  0.035  2.300   4.7932e-02
   5_xyz:   6.579  0.049  0.254 83.451  0.034  2.328   4.3498e-02
   5_adp:   6.579  0.049  0.254 83.451  0.034  2.328   4.3498e-02
   5_occ:   6.579  0.049  0.254 83.451  0.034  2.328   4.3498e-02
   5_bss:   6.579  0.049  0.254 83.451  0.034  2.328   4.3498e-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:  83.47   0.00  16.18  83.47   0.00  12.35  62.57   5.96  37.07
   1_occ:  83.47   0.00  16.18  83.47   0.00  12.35  62.57   5.96  37.07
   2_bss:  83.47   0.00  16.18  83.47   0.00  12.35  62.57   5.96  37.07
   2_xyz:  83.47   0.00  16.18  83.47   0.00  12.35  62.57   5.96  37.07
   2_adp:  78.10   0.76  17.18  77.43   0.76  12.91  78.10   2.95  40.45
   2_occ:  78.10   0.76  17.18  77.43   0.76  12.91  78.10   2.95  40.45
   3_bss:  78.10   0.76  17.18  77.43   0.76  12.91  78.10   2.95  40.45
   3_xyz:  78.10   0.76  17.18  77.43   0.76  12.91  78.10   2.95  40.45
   3_adp:  80.80   0.67  16.82  80.80   0.86  12.70  76.50   0.67  39.22
   3_occ:  80.80   0.67  16.82  80.80   0.86  12.70  76.50   0.67  39.22
   4_bss:  80.80   0.67  16.82  80.80   0.86  12.70  76.50   0.67  39.22
   4_xyz:  80.80   0.67  16.82  80.80   0.86  12.70  76.50   0.67  39.22
   4_adp:  79.86   0.67  16.39  79.86   1.23  12.49  73.79   0.67  37.63
   4_occ:  79.86   0.67  16.39  79.86   1.23  12.49  73.79   0.67  37.63
   5_bss:  79.86   0.67  16.39  79.86   1.23  12.49  73.79   0.67  37.63
   5_xyz:  79.86   0.67  16.39  79.86   1.23  12.49  73.79   0.67  37.63
   5_adp:  81.45   0.51  16.37  81.45   0.51  12.36  74.89   1.85  38.23
   5_occ:  81.45   0.51  16.37  81.45   0.51  12.36  74.89   1.85  38.23
   5_bss:  81.43   0.49  16.35  81.43   0.49  12.34  74.87   1.83  38.22
------------------------------------------------------------------------
 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:    1.002    0.014    0.275
   1_adp:    1.002    0.014    0.275
   1_occ:    1.002    0.014    0.275
   2_bss:    1.002    0.014    0.275
   2_xyz:    0.915    0.019    0.327
   2_adp:    0.915    0.019    0.327
   2_occ:    0.915    0.019    0.327
   3_bss:    0.915    0.019    0.327
   3_xyz:    0.931    0.017    0.331
   3_adp:    0.931    0.017    0.331
   3_occ:    0.931    0.017    0.331
   4_bss:    0.931    0.017    0.331
   4_xyz:    1.201    0.021    0.348
   4_adp:    1.201    0.021    0.348
   4_occ:    1.201    0.021    0.348
   5_bss:    1.201    0.021    0.348
   5_xyz:    1.371    0.013    0.355
   5_adp:    1.371    0.013    0.355
   5_occ:    1.371    0.013    0.355
   5_bss:    1.371    0.013    0.355
------------------------------------------------------------------------

CPU time actual refinement: 321.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_657/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_657/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_657/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_657/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_657/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.87 
  Macro-tasks:
    bulk solvent and scale       = 35.92  
    individual site refinement   = 136.31 
    weights calculation          = 28.97  
    collect and process          = 6.65   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 207.97 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 101.27 
    alpha_beta                      = 7.90   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 111.95 
    fmodel                         = 6.44   
    r_factors                      = 0.16   
    phase_errors                   = 11.39  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 241.68 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.510 micro seconds
Total CPU time: 5.57 minutes
from_scatterers_fft:    648 calls, 100.92 s
gradients_fft:          593 calls,  97.86 s

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

# Date 2008-01-16 Time 05:20:15 PST -0800 (1200489615.05 s)
Start R-work = 0.3018, R-free = 0.2962 (no bulk solvent and anisotropic scale)
Final R-work = 0.1316, R-free = 0.1742 (no bulk solvent and anisotropic scale)

Start R-work = 0.2849, R-free = 0.2815
Final R-work = 0.1090, R-free = 0.1558