# Date 2008-01-16 Time 05:28:59 PST -0800 (1200490139.18 s)
#phil __OFF__

Command line arguments: "../751.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22417
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 751

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.2261, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, 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: (70.6012, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.97157
Completeness in resolution range: 0.9645
Completeness with d_max=infinity: 0.961565

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9716

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.97157
Completeness in resolution range: 0.9645
Completeness with d_max=infinity: 0.961565

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2191 [2126/2151]  1916   210   9.9%
  bin  2:  4.2191 -  3.3612 [2050/2070]  1844   206  10.0%
  bin  3:  3.3612 -  2.9400 [2031/2050]  1825   206  10.1%
  bin  4:  2.9400 -  2.6728 [2005/2035]  1810   195   9.7%
  bin  5:  2.6728 -  2.4821 [2000/2019]  1801   199   9.9%
  bin  6:  2.4821 -  2.3364 [1986/2011]  1781   205  10.3%
  bin  7:  2.3364 -  2.2198 [1948/1976]  1753   195  10.0%
  bin  8:  2.2198 -  2.1234 [1986/2022]  1786   200  10.1%
  bin  9:  2.1234 -  2.0419 [1955/1997]  1762   193   9.9%
  bin 10:  2.0419 -  1.9716 [1502/1979]  1352   150  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_751/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: 0.13 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: 31
        2.42 -     3.04: 2216
        3.04 -     3.66: 4758
        3.66 -     4.28: 9133
        4.28 -     4.90: 12421
  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 204 " - " O   HOH Z 296 "  1.975 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.137 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28554 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_751/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_751/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3735   r_free= 0.3698   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.152849                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7060 0.99   1390  155 0.3122 0.3110        6.42      6.3959|
|  2:  4.7060 -  3.7545 0.99   1333  147 0.3035 0.2866      6.5906      6.5149|
|  3:  3.7545 -  3.2856 0.99   1303  142 0.3250 0.2983       6.476      6.5725|
|  4:  3.2856 -  2.9878 0.99   1304  153 0.3429 0.3912      6.3656      6.3736|
|  5:  2.9878 -  2.7751 0.99   1293  142 0.3876 0.3600       6.232         6.2|
|  6:  2.7751 -  2.6124 0.99   1283  138 0.3935 0.3887      6.1534      6.1292|
|  7:  2.6124 -  2.4821 0.99   1290  139 0.4001 0.3826      6.1224      6.1054|
|  8:  2.4821 -  2.3745 0.98   1260  148 0.4161 0.4029      6.0754       6.067|
|  9:  2.3745 -  2.2835 0.98   1267  141 0.4107 0.3961      6.0307       5.992|
| 10:  2.2835 -  2.2049 1.00   1280  139 0.4173 0.4356      5.9919      6.0163|
| 11:  2.2049 -  2.1362 0.97   1256  140 0.4304 0.4394      5.9635      6.0046|
| 12:  2.1362 -  2.0753 0.98   1250  139 0.4396 0.4511      5.9194      5.9452|
| 13:  2.0753 -  2.0208 0.99   1291  143 0.4263 0.4426      5.8022      5.7461|
| 14:  2.0208 -  1.9716 0.66    830   93 0.4674 0.4290      5.8198      5.7576|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7060  1390   155  0.77  27.77   0.85     0.81      48815.56|
|  2:  4.7060 -  3.7545  1333   147  0.81  25.69   0.96     0.90      61689.71|
|  3:  3.7545 -  3.2856  1303   142  0.75  31.24   0.99     0.92      64961.22|
|  4:  3.2856 -  2.9878  1304   153  0.69  35.96   0.98     0.89      60117.89|
|  5:  2.9878 -  2.7751  1293   142  0.63  41.16   0.95     0.84      49598.78|
|  6:  2.7751 -  2.6124  1283   138  0.62  42.35   0.96     0.82      43435.88|
|  7:  2.6124 -  2.4821  1290   139  0.62  42.68   0.98     0.82      39234.39|
|  8:  2.4821 -  2.3745  1260   148  0.61  43.71   0.98     0.83      36000.13|
|  9:  2.3745 -  2.2835  1267   141  0.62  42.71   0.98     0.83      32438.08|
| 10:  2.2835 -  2.2049  1280   139  0.60  44.20   1.01     0.84      30432.96|
| 11:  2.2049 -  2.1362  1256   140  0.58  46.11   1.02     0.83      30370.61|
| 12:  2.1362 -  2.0753  1250   139  0.56  47.86   1.02     0.82      28778.64|
| 13:  2.0753 -  2.0208  1291   143  0.53  50.32   1.02     0.78      25484.94|
| 14:  2.0208 -  1.9716   830    93  0.55  48.64   1.00     0.74      20961.15|
|alpha:            min =        0.74 max =            0.92 mean =         0.84|
|beta:             min =    20961.15 max =        64961.22 mean =     41601.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.91 mean =        40.38|
|phase err.(test): min =        0.00 max =           89.94 mean =        40.40|
|-----------------------------------------------------------------------------|

============================== 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 = 8.673919              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.436   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.113995              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.773   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       28 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      209 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2007 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1888 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2870 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4682 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4451 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5649 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6772 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.228 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.681)------------------------------------------|
|    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: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3735   r_free= 0.3698   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.152849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3604   r_free= 0.3587   ksol= 0.33   Bsol= 36.55   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,2.09,-0.63,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.138272                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.380564              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.514   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553135              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.616   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3604      final r-factor (work) = 0.2003          |
| start r-factor (free) = 0.3587      final r-factor (free) = 0.2278          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8147 = 7.38 * 0.50 * 6.1377 + 1.00 * 0.1647                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7373 = 7.38 * 0.50 * 5.8662 + 1.00 * 0.0893                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2003      final r-factor (work) = 0.1829          |
| start r-factor (free) = 0.2278      final r-factor (free) = 0.2369          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2508 = 0.55 * 1.00 * 5.8662 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0822 = 0.55 * 1.00 * 5.5532 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.23   17.41    None  None   None       |
|    all(noH): 2823   0      0.00    82.23   17.41    None  None   None       |
|    Sol.    : 438    0      7.51    82.23   40.63    None  None   None       |
|    Mac.    : 2385   0      0.00    73.34   13.15    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 -   8.223:  625   |   5:    41.114 -  49.337:  119        |
|      1:     8.223 -  16.446: 1279   |   6:    49.337 -  57.559:   84        |
|      2:    16.446 -  24.668:  383   |   7:    57.559 -  65.782:   46        |
|      3:    24.668 -  32.891:  143   |   8:    65.782 -  74.005:   18        |
|      4:    32.891 -  41.114:  124   |   9:    74.005 -  82.228:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1829 r_free = 0.2369             target_work(ml) = 5.568         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1826 r_free = 0.2362             target_work(ml) = 5.567         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1826   r_free= 0.2362   ksol= 0.33   Bsol= 36.55   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,2.09,-0.63,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.566738                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1798   r_free= 0.2328   ksol= 0.32   Bsol= 36.55   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.40,-1.42,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.552041                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.823231              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.564   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.139105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.350  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1798      final r-factor (work) = 0.1408          |
| start r-factor (free) = 0.2328      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1597 = 1.82 * 0.50 * 5.5621 + 1.00 * 0.0893                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0164 = 1.82 * 0.50 * 5.4510 + 1.00 * 0.0472                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1408      final r-factor (work) = 0.1356          |
| start r-factor (free) = 0.1875      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7688 = 0.14 * 1.00 * 5.4510 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7473 = 0.14 * 1.00 * 5.3218 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.01    77.59   16.92    None  None   None       |
|    all(noH): 2823   0      2.01    77.59   16.92    None  None   None       |
|    Sol.    : 438    0      7.01    77.59   38.42    None  None   None       |
|    Mac.    : 2385   0      2.01    74.25   12.97    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:     2.012 -   9.570:  850   |   5:    39.803 -  47.361:   96        |
|      1:     9.570 -  17.129: 1169   |   6:    47.361 -  54.919:   87        |
|      2:    17.129 -  24.687:  306   |   7:    54.919 -  62.478:   46        |
|      3:    24.687 -  32.245:  123   |   8:    62.478 -  70.036:   14        |
|      4:    32.245 -  39.803:  128   |   9:    70.036 -  77.594:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1356 r_free = 0.1767             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1355 r_free = 0.1768             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1768   ksol= 0.32   Bsol= 36.55   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.40,-1.42,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.292476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1765   ksol= 0.32   Bsol= 43.04   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.36,-1.56,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.290303                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.065526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.544  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.794485              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.656  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1356      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1765      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2034 = 3.07 * 0.50 * 5.3212 + 1.00 * 0.0472                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0562 = 3.07 * 0.50 * 5.2149 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1501 = 0.79 * 1.00 * 5.2149 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0858 = 0.79 * 1.00 * 5.1317 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.25    86.54   17.25    None  None   None       |
|    all(noH): 2823   0      0.25    86.54   17.25    None  None   None       |
|    Sol.    : 438    0      6.57    82.07   40.46    None  None   None       |
|    Mac.    : 2385   0      0.25    86.54   12.99    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:     0.252 -   8.881:  734   |   5:    43.398 -  52.027:  100        |
|      1:     8.881 -  17.510: 1320   |   6:    52.027 -  60.656:   71        |
|      2:    17.510 -  26.139:  288   |   7:    60.656 -  69.285:   38        |
|      3:    26.139 -  34.768:  130   |   8:    69.285 -  77.915:   19        |
|      4:    34.768 -  43.398:  119   |   9:    77.915 -  86.544:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1548             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1548             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1548   ksol= 0.32   Bsol= 43.04   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.36,-1.56,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.125599                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1548   ksol= 0.32   Bsol= 43.04   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.53,-1.57,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.125155                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.000918              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.092  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.007  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1964 = 2.00 * 0.50 * 5.1315 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1770 = 2.00 * 0.50 * 5.1207 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7290 = 0.34 * 1.00 * 5.1207 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7278 = 0.34 * 1.00 * 5.1176 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    87.45   17.06    None  None   None       |
|    all(noH): 2823   0      0.75    87.45   17.06    None  None   None       |
|    Sol.    : 438    0      6.44    81.83   39.87    None  None   None       |
|    Mac.    : 2385   0      0.75    87.45   12.87    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:     0.755 -   9.424:  895   |   5:    44.104 -  52.774:   97        |
|      1:     9.424 -  18.094: 1206   |   6:    52.774 -  61.443:   66        |
|      2:    18.094 -  26.764:  251   |   7:    61.443 -  70.113:   33        |
|      3:    26.764 -  35.434:  136   |   8:    70.113 -  78.783:   13        |
|      4:    35.434 -  44.104:  122   |   9:    78.783 -  87.453:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1533             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1533             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1533   ksol= 0.32   Bsol= 43.04   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.53,-1.57,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1538   ksol= 0.32   Bsol= 45.72   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.49,-1.45,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118000                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.424780              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.200  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.746345              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.624  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2593 = 2.42 * 0.50 * 5.1183 + 1.00 * 0.0539                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2513 = 2.42 * 0.50 * 5.1065 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1060          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8197 = 0.75 * 1.00 * 5.1065 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8159 = 0.75 * 1.00 * 5.1008 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.26    91.20   16.94    None  None   None       |
|    all(noH): 2823   0      0.26    91.20   16.94    None  None   None       |
|    Sol.    : 438    0      6.36    83.25   39.64    None  None   None       |
|    Mac.    : 2385   0      0.26    91.20   12.77    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:     0.262 -   9.357:  920   |   5:    45.733 -  54.828:   95        |
|      1:     9.357 -  18.451: 1204   |   6:    54.828 -  63.922:   54        |
|      2:    18.451 -  27.545:  237   |   7:    63.922 -  73.016:   27        |
|      3:    27.545 -  36.639:  145   |   8:    73.016 -  82.110:    9        |
|      4:    36.639 -  45.733:  128   |   9:    82.110 -  91.204:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1060 r_free = 0.1540             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1060 r_free = 0.1540             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1540   ksol= 0.32   Bsol= 45.72   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.49,-1.45,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104306                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7060 0.99   1390  155 0.0946 0.1213      5.3446      5.4918|
|  2:  4.7060 -  3.7545 0.99   1333  147 0.0823 0.1124      5.4096       5.609|
|  3:  3.7545 -  3.2856 0.99   1303  142 0.1028 0.1510      5.4507      5.8521|
|  4:  3.2856 -  2.9878 0.99   1304  153 0.1161 0.1533      5.4253      5.5545|
|  5:  2.9878 -  2.7751 0.99   1293  142 0.1261 0.1803       5.292      5.5537|
|  6:  2.7751 -  2.6124 0.99   1283  138 0.1126 0.1659      5.1666      5.4015|
|  7:  2.6124 -  2.4821 0.99   1290  139 0.1202 0.1521      5.1273      5.3266|
|  8:  2.4821 -  2.3745 0.98   1260  148 0.1089 0.1695      5.0049       5.327|
|  9:  2.3745 -  2.2835 0.98   1267  141 0.1083 0.1701      4.9849      5.2485|
| 10:  2.2835 -  2.2049 1.00   1280  139 0.1039 0.1749      4.9093      5.2564|
| 11:  2.2049 -  2.1362 0.97   1256  140 0.1073 0.1671      4.9175      5.2424|
| 12:  2.1362 -  2.0753 0.98   1250  139 0.1054 0.1639      4.8472      5.1416|
| 13:  2.0753 -  2.0208 0.99   1291  143 0.1048 0.1749       4.744      5.0506|
| 14:  2.0208 -  1.9716 0.66    830   93 0.0963 0.1541      4.6033      4.8385|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7060  1390   155  0.94   8.61   0.98     0.95       6524.70|
|  2:  4.7060 -  3.7545  1333   147  0.95   7.67   1.02     1.01       8685.75|
|  3:  3.7545 -  3.2856  1303   142  0.94  10.93   1.03     1.02       9901.97|
|  4:  3.2856 -  2.9878  1304   153  0.92  13.30   1.01     0.99       9961.14|
|  5:  2.9878 -  2.7751  1293   142  0.90  15.40   1.00     0.97       7851.09|
|  6:  2.7751 -  2.6124  1283   138  0.90  15.44   0.99     0.97       6728.85|
|  7:  2.6124 -  2.4821  1290   139  0.91  14.92   0.99     0.96       5773.66|
|  8:  2.4821 -  2.3745  1260   148  0.91  14.37   0.99     0.97       4720.38|
|  9:  2.3745 -  2.2835  1267   141  0.92  14.40   1.00     0.98       4601.60|
| 10:  2.2835 -  2.2049  1280   139  0.91  14.59   1.00     0.97       4039.63|
| 11:  2.2049 -  2.1362  1256   140  0.90  15.82   0.99     0.95       4200.19|
| 12:  2.1362 -  2.0753  1250   139  0.92  14.61   1.01     1.00       3810.78|
| 13:  2.0753 -  2.0208  1291   143  0.91  15.58   1.00     0.99       3135.82|
| 14:  2.0208 -  1.9716   830    93  0.93  13.31   0.98     0.95       2283.07|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2283.07 max =         9961.14 mean =      5995.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.08 mean =        13.05|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1540   ksol= 0.32   Bsol= 45.71   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.35,-1.28,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104388                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1540   ksol= 0.32   Bsol= 45.71   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.35,-1.28,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104388                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7060 0.99   1390  155 0.0947 0.1215      5.3456      5.4932|
|  2:  4.7060 -  3.7545 0.99   1333  147 0.0823 0.1124        5.41      5.6088|
|  3:  3.7545 -  3.2856 0.99   1303  142 0.1028 0.1511      5.4507      5.8524|
|  4:  3.2856 -  2.9878 0.99   1304  153 0.1161 0.1533      5.4253      5.5545|
|  5:  2.9878 -  2.7751 0.99   1293  142 0.1261 0.1802      5.2919      5.5533|
|  6:  2.7751 -  2.6124 0.99   1283  138 0.1126 0.1659      5.1664      5.4012|
|  7:  2.6124 -  2.4821 0.99   1290  139 0.1202 0.1522      5.1274      5.3271|
|  8:  2.4821 -  2.3745 0.98   1260  148 0.1089 0.1695      5.0049      5.3267|
|  9:  2.3745 -  2.2835 0.98   1267  141 0.1083 0.1701      4.9849      5.2484|
| 10:  2.2835 -  2.2049 1.00   1280  139 0.1039 0.1750      4.9095      5.2569|
| 11:  2.2049 -  2.1362 0.97   1256  140 0.1073 0.1671      4.9177      5.2425|
| 12:  2.1362 -  2.0753 0.98   1250  139 0.1053 0.1639      4.8471      5.1416|
| 13:  2.0753 -  2.0208 0.99   1291  143 0.1048 0.1748      4.7437        5.05|
| 14:  2.0208 -  1.9716 0.66    830   93 0.0963 0.1539       4.603      4.8378|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7060  1390   155  0.94   8.62   0.98     0.95       6540.26|
|  2:  4.7060 -  3.7545  1333   147  0.95   7.68   1.02     1.02       8697.68|
|  3:  3.7545 -  3.2856  1303   142  0.94  10.93   1.03     1.03       9904.39|
|  4:  3.2856 -  2.9878  1304   153  0.92  13.30   1.02     1.00       9960.08|
|  5:  2.9878 -  2.7751  1293   142  0.90  15.39   1.00     0.97       7847.82|
|  6:  2.7751 -  2.6124  1283   138  0.90  15.44   1.00     0.97       6726.92|
|  7:  2.6124 -  2.4821  1290   139  0.91  14.92   1.00     0.96       5773.49|
|  8:  2.4821 -  2.3745  1260   148  0.91  14.37   1.00     0.98       4719.76|
|  9:  2.3745 -  2.2835  1267   141  0.92  14.41   1.01     0.98       4601.95|
| 10:  2.2835 -  2.2049  1280   139  0.91  14.60   1.01     0.98       4041.68|
| 11:  2.2049 -  2.1362  1256   140  0.90  15.82   1.00     0.96       4201.95|
| 12:  2.1362 -  2.0753  1250   139  0.92  14.61   1.02     1.01       3810.97|
| 13:  2.0753 -  2.0208  1291   143  0.91  15.57   1.01     1.00       3133.62|
| 14:  2.0208 -  1.9716   830    93  0.93  13.30   0.99     0.96       2280.44|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2280.44 max =         9960.08 mean =      5997.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.08 mean =        13.05|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.26    91.20   16.93    None  None   None       |
|    all(noH): 2823   0      0.26    91.20   16.93    None  None   None       |
|    Sol.    : 438    0      6.35    83.25   39.63    None  None   None       |
|    Mac.    : 2385   0      0.26    91.20   12.76    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:     0.256 -   9.350:  920   |   5:    45.727 -  54.821:   95        |
|      1:     9.350 -  18.444: 1204   |   6:    54.821 -  63.915:   54        |
|      2:    18.444 -  27.538:  237   |   7:    63.915 -  73.009:   27        |
|      3:    27.538 -  36.632:  145   |   8:    73.009 -  82.103:    9        |
|      4:    36.632 -  45.727:  128   |   9:    82.103 -  91.197:    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)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.533 - 4.575
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 291
   mapped sites are within: 0.737 - 4.575

peak=    6.226 closest distance to " NE2 GLN A  11 " =    1.206
peak=    5.791 closest distance to " NH2 ARG A  56 " =    2.143
peak=    5.754 closest distance to " O   HOH Z 126 " =    1.978
peak=    5.496 closest distance to " CG  PRO A  54 " =    1.204
peak=    5.188 closest distance to " O   HOH Z 144 " =    1.711
peak=    5.003 closest distance to " CB  GLN A 223 " =    1.468
peak=    4.898 closest distance to " CB  SER A  63 " =    1.194
peak=    4.819 closest distance to " CG  PRO A 213 " =    1.230
peak=    4.768 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.755 closest distance to " CB  ARG A 275 " =    0.899
peak=    4.720 closest distance to " O   HOH Z 369 " =    2.146
peak=    4.717 closest distance to " O   HOH Z  78 " =    1.765
peak=    4.711 closest distance to " C   PRO A 198 " =    1.451
peak=    4.684 closest distance to " O   HOH Z 232 " =    2.394
peak=    4.648 closest distance to " CB  PRO A  54 " =    0.936
peak=    4.609 closest distance to " O   HOH Z 427 " =    2.667
peak=    4.581 closest distance to " O   HOH Z 287 " =    2.194
peak=    4.498 closest distance to " O   HOH Z  63 " =    1.497
peak=    4.472 closest distance to " O   HOH Z 298 " =    1.902
peak=    4.464 closest distance to " O   HOH Z 303 " =    2.240
peak=    4.450 closest distance to " CB  GLU A 152 " =    1.301
peak=    4.426 closest distance to " O   HOH Z 423 " =    1.576
peak=    4.413 closest distance to " O   HOH Z 193 " =    1.836
peak=    4.404 closest distance to " O   HOH Z   9 " =    2.301
peak=    4.368 closest distance to " CB  ASN A 148 " =    1.381
peak=    4.364 closest distance to " CA  TYR A  30 " =    0.941
peak=    4.355 closest distance to " CB  GLU A 128 " =    1.017
peak=    4.347 closest distance to " O   HOH Z   1 " =    1.950
peak=    4.315 closest distance to " ND2 ASN A 187 " =    1.460
peak=    4.312 closest distance to " O   HOH Z 209 " =    2.249
peak=    4.304 closest distance to " CB  ARG A  79 " =    1.403
peak=    4.259 closest distance to " O   HOH Z 419 " =    2.140
peak=    4.233 closest distance to " O   HOH Z 217 " =    2.991
peak=    4.195 closest distance to " O   HOH Z 203 " =    1.829
peak=    4.174 closest distance to " O   HOH Z 316 " =    3.048
peak=    4.165 closest distance to " O   HOH Z 234 " =    3.696
peak=    4.164 closest distance to " CB  LEU A 228 " =    1.079
peak=    4.157 closest distance to " O   HOH Z 261 " =    2.288
peak=    4.156 closest distance to " O   HOH Z  78 " =    2.113
peak=    4.141 closest distance to " CG2 VAL A 257 " =    0.904
peak=    4.084 closest distance to " CD  ARG A  66 " =    2.338
peak=    4.053 closest distance to " CB  SER A   3 " =    1.337
peak=    4.034 closest distance to " O   HOH Z 158 " =    3.084
peak=    4.033 closest distance to " CB  VAL A 265 " =    1.334
peak=    4.026 closest distance to " O   HOH Z 132 " =    2.344
peak=    4.003 closest distance to " O   HOH Z 371 " =    1.841
peak=    4.003 closest distance to " O   HOH Z 425 " =    2.035
peak=    3.995 closest distance to " OD1 ASN A  69 " =    2.664
peak=    3.992 closest distance to " CB  ARG A 139 " =    1.012
peak=    3.986 closest distance to " O   HOH Z  61 " =    1.497
peak=    3.970 closest distance to " CB  SER A 216 " =    0.807
peak=    3.957 closest distance to " O   HOH Z 272 " =    1.786
peak=    3.945 closest distance to " CA  ASN A 215 " =    1.230
peak=    3.934 closest distance to " O   SER A  87 " =    2.185
peak=    3.930 closest distance to " O   HOH Z 368 " =    3.635
peak=    3.930 closest distance to " O   HOH Z  61 " =    1.607
peak=    3.928 closest distance to " O   HOH Z 368 " =    1.987
peak=    3.922 closest distance to " CG1 ILE A  33 " =    1.254
peak=    3.918 closest distance to " CG  PRO A 198 " =    1.232
peak=    3.911 closest distance to " CB  ARG A 190 " =    1.614
peak=    3.866 closest distance to " O   HOH Z 180 " =    2.148
peak=    3.863 closest distance to " O   HOH Z  44 " =    1.692
peak=    3.859 closest distance to " O   HOH Z 128 " =    2.160
peak=    3.856 closest distance to " CE  LYS A  76 " =    0.891
peak=    3.838 closest distance to " CG  PRO A  90 " =    1.094
peak=    3.826 closest distance to " OG BSER A 164 " =    2.258
peak=    3.809 closest distance to " O   HOH Z 344 " =    3.087
peak=    3.808 closest distance to " ND1 HIS A  86 " =    1.792
peak=    3.800 closest distance to " CB  TRP A 179 " =    1.438
peak=    3.788 closest distance to " O   HOH Z   9 " =    1.970
peak=    3.787 closest distance to " O   HOH Z 437 " =    1.729
peak=    3.786 closest distance to " CB  SER A 212 " =    1.030
peak=    3.785 closest distance to " O   HOH Z  64 " =    2.329
peak=    3.782 closest distance to " OD2 ASP A 286 " =    2.794
peak=    3.778 closest distance to " O   HOH Z 425 " =    1.264
peak=    3.776 closest distance to " CB  TYR A 169 " =    0.737
peak=    3.763 closest distance to " CD  ARG A 159 " =    0.754
peak=    3.761 closest distance to " O   HOH Z  40 " =    2.065
peak=    3.755 closest distance to " CD2 TRP A 179 " =    1.336
peak=    3.749 closest distance to " CB  TRP A 266 " =    1.039
peak=    3.744 closest distance to " CD BLYS A 290 " =    1.200
peak=    3.739 closest distance to " O   HOH Z 175 " =    2.112
peak=    3.716 closest distance to " O   HOH Z 189 " =    2.116
peak=    3.704 closest distance to " CA  THR A 264 " =    0.832
peak=    3.703 closest distance to " O   HOH Z  66 " =    2.164
peak=    3.692 closest distance to " O   HOH Z 403 " =    1.644
peak=    3.686 closest distance to " O   HOH Z 214 " =    2.080
peak=    3.686 closest distance to " O   HOH Z 405 " =    1.203
peak=    3.681 closest distance to " O   HOH Z 327 " =    1.649
peak=    3.681 closest distance to " O   HOH Z   1 " =    1.694
peak=    3.679 closest distance to " O   HOH Z  10 " =    1.773
peak=    3.678 closest distance to " O   HOH Z 250 " =    1.494
peak=    3.674 closest distance to " NH2BARG A 145 " =    2.016
peak=    3.674 closest distance to " OD1BASN A 224 " =    2.279
peak=    3.672 closest distance to " O   HOH Z 219 " =    2.250
peak=    3.670 closest distance to " O   HOH Z   3 " =    1.930
peak=    3.670 closest distance to " O   HOH Z 236 " =    1.451
peak=    3.667 closest distance to " O   HOH Z 407 " =    2.265
peak=    3.666 closest distance to " CB  ALA A  34 " =    1.028
peak=    3.663 closest distance to " O   HOH Z 386 " =    3.197
peak=    3.663 closest distance to " CG  LEU A 167 " =    1.223
peak=    3.662 closest distance to " CA  ALA A 233 " =    1.074
peak=    3.657 closest distance to " O   HOH Z 207 " =    1.706
peak=    3.651 closest distance to " CG  PRO A 243 " =    1.136
peak=    3.649 closest distance to " N   PHE A 130 " =    1.242
peak=    3.648 closest distance to " CA  MET A  40 " =    1.095
peak=    3.648 closest distance to " CA  GLY A 241 " =    3.814
peak=    3.642 closest distance to " O   HOH Z 389 " =    1.846
peak=    3.639 closest distance to " O   HOH Z 371 " =    2.878
peak=    3.634 closest distance to " O   HOH Z 346 " =    1.679
peak=    3.633 closest distance to " O   HOH Z 193 " =    1.682
peak=    3.617 closest distance to " O   HOH Z  21 " =    1.716
peak=    3.616 closest distance to " CB  THR A 157 " =    1.138
peak=    3.611 closest distance to " O   HOH Z  93 " =    2.267
peak=    3.609 closest distance to " CG2 THR A 221 " =    1.061
peak=    3.597 closest distance to " O   HOH Z 362 " =    2.532
peak=    3.587 closest distance to " CA  ALA A  21 " =    1.123
peak=    3.582 closest distance to " CD2 LEU A 255 " =    1.486
peak=    3.580 closest distance to " O   HOH Z 133 " =    2.343
peak=    3.565 closest distance to " O   HOH Z 133 " =    1.560
peak=    3.554 closest distance to " O   HOH Z  88 " =    3.180
peak=    3.553 closest distance to " CB  GLU A 277 " =    3.517
peak=    3.524 closest distance to " CB  TYR A 169 " =    0.801
peak=    3.524 closest distance to " CD  PRO A 243 " =    1.636
peak=    3.509 closest distance to " O   HOH Z 391 " =    2.909
peak=    3.506 closest distance to " O   HOH Z 128 " =    2.051
peak=    3.505 closest distance to " O   HOH Z 409 " =    2.437
peak=    3.504 closest distance to " O   HOH Z 217 " =    1.568
peak=    3.497 closest distance to " O   HOH Z  97 " =    1.962
peak=    3.492 closest distance to " O   HOH Z 147 " =    1.760
peak=    3.487 closest distance to " O   HOH Z 325 " =    3.743
peak=    3.481 closest distance to " CB  ALA A   1 " =    4.575
peak=    3.481 closest distance to " N   ALA A   1 " =    2.177
peak=    3.468 closest distance to " O   HOH Z 213 " =    2.310
peak=    3.467 closest distance to " OG  SER A  62 " =    2.959
peak=    3.466 closest distance to " O   HOH Z 172 " =    3.064
peak=    3.462 closest distance to " CB  ASP A 140 " =    0.904
peak=    3.461 closest distance to " O   HOH Z 305 " =    3.588
peak=    3.459 closest distance to " O   HOH Z 245 " =    1.283
peak=    3.456 closest distance to " O   HOH Z 366 " =    2.765
peak=    3.453 closest distance to " CZ  PHE A 218 " =    1.015
peak=    3.448 closest distance to " CA  ALA A 291 " =    0.912
peak=    3.444 closest distance to " CB  VAL A 202 " =    1.648
peak=    3.442 closest distance to " O   HOH Z 108 " =    2.128
peak=    3.440 closest distance to " O   HOH Z  43 " =    1.995
peak=    3.438 closest distance to " O   HOH Z   2 " =    1.376
peak=    3.437 closest distance to " O   MET A 105 " =    1.801
peak=    3.430 closest distance to " CB  ASN A 142 " =    0.929
peak=    3.429 closest distance to " NH1BARG A 145 " =    1.260
peak=    3.418 closest distance to " CD2 LEU A 297 " =    0.958
peak=    3.416 closest distance to " O   HOH Z 271 " =    2.494
peak=    3.416 closest distance to " O   HOH Z 284 " =    3.052
peak=    3.414 closest distance to " O   HOH Z 426 " =    1.825
peak=    3.412 closest distance to " O   HOH Z 188 " =    1.965
peak=    3.412 closest distance to " CB  LYS A 117 " =    1.196
peak=    3.406 closest distance to " CB  SER A  62 " =    1.245
peak=    3.404 closest distance to " CB  ASP A 132 " =    4.006
peak=    3.399 closest distance to " O   HOH Z 380 " =    1.589
peak=    3.398 closest distance to " NH1AARG A 145 " =    1.131
peak=    3.395 closest distance to " O   HOH Z 286 " =    2.352
peak=    3.388 closest distance to " O   HOH Z 298 " =    2.580
peak=    3.386 closest distance to " CG1BVAL A  72 " =    1.470
peak=    3.385 closest distance to " CB  TYR A 116 " =    0.817
peak=    3.381 closest distance to " O   HOH Z 146 " =    1.697
peak=    3.374 closest distance to " CD  LYS A 166 " =    1.274
peak=    3.374 closest distance to " CA  LYS A 290 " =    1.372
peak=    3.373 closest distance to " O   HOH Z 266 " =    3.214
peak=    3.371 closest distance to " OG  SER A  22 " =    2.770
peak=    3.366 closest distance to " O   HOH Z 402 " =    1.433
peak=    3.362 closest distance to " O   HOH Z 193 " =    2.006
peak=    3.356 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.353 closest distance to " CB  LEU A 143 " =    1.130
peak=    3.352 closest distance to " CB  ILE A 120 " =    1.396
peak=    3.348 closest distance to " O   HOH Z  59 " =    1.634
peak=    3.347 closest distance to " O   HOH Z 261 " =    2.247
peak=    3.347 closest distance to " O   HOH Z 258 " =    2.239
peak=    3.345 closest distance to " O   HOH Z 211 " =    2.779
peak=    3.342 closest distance to " O   HOH Z 435 " =    1.919
peak=    3.335 closest distance to " O   HOH Z 343 " =    3.440
peak=    3.333 closest distance to " O   HOH Z 313 " =    1.945
peak=    3.332 closest distance to " CG  GLN A  89 " =    1.468
peak=    3.329 closest distance to " NE2 GLN A  73 " =    3.656
peak=    3.327 closest distance to " CD1 ILE A 106 " =    0.846
peak=    3.326 closest distance to " O   HOH Z 213 " =    1.870
peak=    3.314 closest distance to " O   HOH Z 116 " =    2.945
peak=    3.312 closest distance to " CA  ASP A 162 " =    1.069
peak=    3.298 closest distance to " NH2AARG A 275 " =    3.613
peak=    3.294 closest distance to " CD1 LEU A 300 " =    1.254
peak=    3.293 closest distance to " NH2 ARG A 219 " =    1.856
peak=    3.292 closest distance to " O   HOH Z 423 " =    2.365
peak=    3.289 closest distance to " O   HOH Z 227 " =    1.728
peak=    3.288 closest distance to " O   HOH Z 329 " =    3.712
peak=    3.286 closest distance to " CA  TYR A 116 " =    1.273
peak=    3.284 closest distance to " CA  ILE A 234 " =    0.992
peak=    3.279 closest distance to " CB  ALA A 291 " =    1.432
peak=    3.278 closest distance to " CB  ASN A 110 " =    1.125
peak=    3.276 closest distance to " O   HOH Z 292 " =    1.724
peak=    3.275 closest distance to " CA  THR A 221 " =    0.991
peak=    3.274 closest distance to " O   HOH Z  88 " =    2.603
peak=    3.273 closest distance to " CE1 TYR A 186 " =    1.329
peak=    3.272 closest distance to " CA  ALA A  84 " =    1.456
peak=    3.272 closest distance to " CH2 TRP A  92 " =    2.135
peak=    3.271 closest distance to " CG1 VAL A 153 " =    0.851
peak=    3.269 closest distance to " CA  ALA A 299 " =    0.892
peak=    3.267 closest distance to " CD1 ILE A 263 " =    1.357
peak=    3.262 closest distance to " O   HOH Z  59 " =    1.888
peak=    3.262 closest distance to " CA  ALA A 158 " =    1.097
peak=    3.260 closest distance to " CG  MET A 113 " =    1.211
peak=    3.259 closest distance to " CB  GLN A  89 " =    1.436
peak=    3.258 closest distance to " NE AARG A 275 " =    1.339
peak=    3.258 closest distance to " ND1 HIS A  81 " =    1.615
peak=    3.253 closest distance to " O   HOH Z  49 " =    1.956
peak=    3.252 closest distance to " N   SER A 134 " =    1.356
peak=    3.248 closest distance to " CG  LYS A  76 " =    1.019
peak=    3.248 closest distance to " O   HOH Z  85 " =    2.114
peak=    3.247 closest distance to " OG  SER A  62 " =    3.059
peak=    3.245 closest distance to " O   HOH Z 359 " =    1.396
peak=    3.245 closest distance to " CB  THR A  31 " =    1.732
peak=    3.244 closest distance to " CE BLYS A 290 " =    1.274
peak=    3.243 closest distance to " O   HOH Z 154 " =    2.029
peak=    3.243 closest distance to " CB  GLN A  88 " =    1.312
peak=    3.238 closest distance to " O   ASN A 209 " =    1.361
peak=    3.235 closest distance to " O   HOH Z  44 " =    3.015
peak=    3.234 closest distance to " O   HOH Z  53 " =    2.524
peak=    3.233 closest distance to " N   ASN A 127 " =    1.340
peak=    3.232 closest distance to " CA  LEU A 101 " =    1.607
peak=    3.227 closest distance to " CG  LYS A 119 " =    1.179
peak=    3.225 closest distance to " O   HOH Z 422 " =    2.628
peak=    3.224 closest distance to " O   HOH Z  64 " =    2.050
peak=    3.220 closest distance to " O  BHOH Z 338 " =    2.348
peak=    3.220 closest distance to " O   HOH Z 128 " =    1.994
peak=    3.217 closest distance to " O   HOH Z 135 " =    1.666
peak=    3.215 closest distance to " N   TYR A  15 " =    0.787
peak=    3.213 closest distance to " O   HOH Z 291 " =    1.638
peak=    3.212 closest distance to " O   HOH Z 227 " =    2.056
peak=    3.204 closest distance to " CD  ARG A  79 " =    2.342
peak=    3.203 closest distance to " O   HOH Z 357 " =    1.823
peak=    3.202 closest distance to " CG  GLN A  77 " =    2.364
peak=    3.200 closest distance to " NZ  LYS A  76 " =    1.426
peak=    3.200 closest distance to " CB  SER A 276 " =    1.188
peak=    3.196 closest distance to " O   HOH Z 130 " =    3.817
peak=    3.194 closest distance to " NH2BARG A 190 " =    1.551
peak=    3.193 closest distance to " CG2 VAL A 197 " =    1.099
peak=    3.193 closest distance to " CB  ALA A 114 " =    1.443
peak=    3.190 closest distance to " O   HOH Z 153 " =    1.641
peak=    3.187 closest distance to " CA  SER A  87 " =    1.012
peak=    3.186 closest distance to " CB  SER A  26 " =    1.594
peak=    3.185 closest distance to " O   HOH Z 144 " =    1.890
peak=    3.184 closest distance to " O   HOH Z 108 " =    1.243
peak=    3.182 closest distance to " CA  GLY A 267 " =    1.259
peak=    3.168 closest distance to " CA  ASN A  74 " =    1.289
peak=    3.168 closest distance to " CG  GLN A  88 " =    1.048
peak=    3.163 closest distance to " N   CYS A 260 " =    0.888
peak=    3.163 closest distance to " O   HOH Z 132 " =    3.487
peak=    3.161 closest distance to " O  BHOH Z  74 " =    1.385
peak=    3.159 closest distance to " OG BSER A  99 " =    2.155
peak=    3.158 closest distance to " CG BARG A 102 " =    1.815
peak=    3.155 closest distance to " O   ARG A 145 " =    1.753
peak=    3.154 closest distance to " N   GLN A 278 " =    1.141
peak=    3.152 closest distance to " O   HOH Z 406 " =    1.648
peak=    3.151 closest distance to " O   HOH Z 303 " =    1.719
peak=    3.150 closest distance to " O   ALA A 165 " =    1.349
peak=    3.150 closest distance to " O   HOH Z 374 " =    2.638
peak=    3.148 closest distance to " CB  ARG A 138 " =    0.956
peak=    3.147 closest distance to " O   HOH Z 433 " =    1.753
peak=    3.136 closest distance to " N   ARG A 156 " =    1.290
peak=    3.133 closest distance to " CB  ALA A  71 " =    1.387
peak=    3.132 closest distance to " CB  GLU A 236 " =    1.177
peak=    3.117 closest distance to " CG1 VAL A 189 " =    1.910
peak=    3.113 closest distance to " O   HOH Z 371 " =    3.355
peak=    3.113 closest distance to " O   PRO A  90 " =    1.428
peak=    3.109 closest distance to " O   HOH Z 173 " =    1.775
peak=    3.107 closest distance to " N   ALA A 154 " =    0.930
peak=    3.100 closest distance to " O   HOH Z 302 " =    1.666
peak=    3.100 closest distance to " O   HOH Z 116 " =    1.685
peak=    3.096 closest distance to " NH1 ARG A 138 " =    1.049
peak=    3.096 closest distance to " CA  GLY A 136 " =    1.082
peak=    3.089 closest distance to " O   HOH Z  88 " =    2.337
peak=    3.082 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.077 closest distance to " O   HOH Z 183 " =    1.354
peak=    3.070 closest distance to " O   HOH Z 285 " =    1.679
peak=    3.068 closest distance to " O   HOH Z 411 " =    1.705
peak=    3.057 closest distance to " CB  TRP A 150 " =    1.349
peak=    3.055 closest distance to " CA  MET A 105 " =    0.952
peak=    3.049 closest distance to " O   HOH Z  40 " =    2.803
peak=    3.046 closest distance to " O   HOH Z 188 " =    2.501
peak=    3.027 closest distance to " CB  ASP A 132 " =    4.104
peak=    3.016 closest distance to " CB  VAL A 126 " =    1.156

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.679 - 5.898
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.742 - 5.898

peak=   -4.669 closest distance to " O   HOH Z 377 " =    2.107
peak=   -4.597 closest distance to " CB  PRO A 243 " =    2.556
peak=   -4.539 closest distance to " CD  ARG A 156 " =    1.988
peak=   -4.453 closest distance to " O   HOH Z 266 " =    4.613
peak=   -4.371 closest distance to " C   HIS A 108 " =    1.114
peak=   -4.219 closest distance to " OG BSER A 134 " =    1.270
peak=   -4.180 closest distance to " CG  GLN A 223 " =    1.922
peak=   -4.177 closest distance to " O   HOH Z 435 " =    2.885
peak=   -4.108 closest distance to " SG  CYS A 254 " =    3.411
peak=   -4.083 closest distance to " CG1 VAL A 112 " =    2.816
peak=   -4.049 closest distance to " O   VAL A  67 " =    2.653
peak=   -4.035 closest distance to " CG  LYS A 193 " =    2.505
peak=   -4.010 closest distance to " O   HOH Z 313 " =    1.946
peak=   -3.998 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.993 closest distance to " O   HOH Z 231 " =    2.151
peak=   -3.985 closest distance to " O   HOH Z 389 " =    1.820
peak=   -3.939 closest distance to " O   HOH Z 290 " =    1.232
peak=   -3.923 closest distance to " CZ  PHE A  59 " =    1.495
peak=   -3.912 closest distance to " CA  GLY A  98 " =    1.866
peak=   -3.900 closest distance to " N   ALA A  43 " =    2.491
peak=   -3.885 closest distance to " CE2 PHE A 218 " =    2.458
peak=   -3.884 closest distance to " O   ARG A 145 " =    1.520
peak=   -3.877 closest distance to " O   SER A 135 " =    1.451
peak=   -3.850 closest distance to " O   VAL A  67 " =    2.711
peak=   -3.837 closest distance to " CZ3 TRP A 179 " =    1.174
peak=   -3.837 closest distance to " ND2 ASN A  45 " =    1.588
peak=   -3.822 closest distance to " O   HOH Z 152 " =    5.057
peak=   -3.813 closest distance to " CG  ASP A 231 " =    0.742
peak=   -3.791 closest distance to " N   GLN A  58 " =    1.616
peak=   -3.789 closest distance to " O   HOH Z 185 " =    2.073
peak=   -3.789 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.780 closest distance to " O   HOH Z 198 " =    2.034
peak=   -3.765 closest distance to " CG  PHE A 283 " =    2.648
peak=   -3.764 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.749 closest distance to " ND2 ASN A  45 " =    1.102
peak=   -3.744 closest distance to " CB  ALA A 291 " =    2.134
peak=   -3.738 closest distance to " O   HOH Z 351 " =    1.570
peak=   -3.735 closest distance to " O   HOH Z  43 " =    1.759
peak=   -3.719 closest distance to " O   HOH Z  60 " =    2.393
peak=   -3.711 closest distance to " CB  ALA A 161 " =    2.537
peak=   -3.710 closest distance to " O   PRO A 243 " =    2.470
peak=   -3.700 closest distance to " O   PRO A 198 " =    1.276
peak=   -3.691 closest distance to " CD1 PHE A  59 " =    1.877
peak=   -3.686 closest distance to " CE  MET A 105 " =    2.268
peak=   -3.683 closest distance to " O   HOH Z  52 " =    1.241
peak=   -3.679 closest distance to " O   HOH Z 407 " =    3.127
peak=   -3.657 closest distance to " OD1 ASP A 171 " =    1.597
peak=   -3.655 closest distance to " O   HOH Z 198 " =    1.523
peak=   -3.654 closest distance to " CA  GLY A 203 " =    2.197
peak=   -3.648 closest distance to " CB  CYS A 254 " =    2.205
peak=   -3.632 closest distance to " CD  ARG A 139 " =    1.492
peak=   -3.630 closest distance to " N   ASP A 286 " =    2.488
peak=   -3.624 closest distance to " CZ  TYR A 169 " =    1.518
peak=   -3.614 closest distance to " O   HOH Z 102 " =    1.602
peak=   -3.613 closest distance to " O   VAL A 189 " =    2.478
peak=   -3.605 closest distance to " OD1 ASN A 187 " =    1.535
peak=   -3.602 closest distance to " O   HOH Z  13 " =    1.540
peak=   -3.601 closest distance to " CD1 LEU A 228 " =    2.192
peak=   -3.586 closest distance to " NH2AARG A 275 " =    5.318
peak=   -3.585 closest distance to " NH2BARG A 275 " =    1.706
peak=   -3.580 closest distance to " O   PRO A 163 " =    1.973
peak=   -3.568 closest distance to " O   HOH Z 385 " =    1.986
peak=   -3.558 closest distance to " O   HOH Z 114 " =    2.904
peak=   -3.540 closest distance to " CB  PRO A 163 " =    2.497
peak=   -3.535 closest distance to " OD1 ASP A 191 " =    1.487
peak=   -3.530 closest distance to " C   ALA A 158 " =    1.388
peak=   -3.524 closest distance to " OD1 ASP A 191 " =    1.876
peak=   -3.523 closest distance to " O   HOH Z 131 " =    4.131
peak=   -3.513 closest distance to " CD  GLN A  58 " =    1.117
peak=   -3.509 closest distance to " CB  ASN A  39 " =    2.223
peak=   -3.503 closest distance to " CB  TYR A  15 " =    2.153
peak=   -3.500 closest distance to " CB  ASP A  27 " =    2.459
peak=   -3.498 closest distance to " O   HOH Z 298 " =    1.263
peak=   -3.496 closest distance to " OXT GLY A 302 " =    2.886
peak=   -3.490 closest distance to " O   HOH Z 409 " =    5.898
peak=   -3.489 closest distance to " O   HOH Z  38 " =    1.635
peak=   -3.482 closest distance to " O   SER A  95 " =    1.445
peak=   -3.482 closest distance to " O   HOH Z 345 " =    2.047
peak=   -3.481 closest distance to " O   HOH Z 126 " =    1.881
peak=   -3.480 closest distance to " OG  SER A  97 " =    2.152
peak=   -3.480 closest distance to " O   HOH Z  11 " =    1.860
peak=   -3.479 closest distance to " OD1 ASN A 148 " =    1.612
peak=   -3.475 closest distance to " O   HOH Z 140 " =    1.813
peak=   -3.470 closest distance to " OD2 ASP A 191 " =    1.461
peak=   -3.467 closest distance to " O   HOH Z 359 " =    3.289
peak=   -3.467 closest distance to " O   PHE A 218 " =    1.544
peak=   -3.460 closest distance to " CB  PHE A 192 " =    1.951
peak=   -3.457 closest distance to " CD2 PHE A 225 " =    1.103
peak=   -3.456 closest distance to " CB  TRP A  85 " =    2.460
peak=   -3.446 closest distance to " NH1 ARG A 195 " =    2.643
peak=   -3.446 closest distance to " NH2 ARG A  79 " =    1.910
peak=   -3.442 closest distance to " OG  SER A  87 " =    1.301
peak=   -3.433 closest distance to " CD1 LEU A 101 " =    2.294
peak=   -3.432 closest distance to " N   ALA A 248 " =    1.504
peak=   -3.430 closest distance to " O   HOH Z 263 " =    2.847
peak=   -3.423 closest distance to " CA  GLY A 133 " =    1.959
peak=   -3.407 closest distance to " O   HOH Z 211 " =    1.568
peak=   -3.403 closest distance to " NE  ARG A  36 " =    1.899
peak=   -3.403 closest distance to " N   THR A 157 " =    1.467
peak=   -3.400 closest distance to " CB  ALA A 248 " =    1.985
peak=   -3.398 closest distance to " C   LEU A 143 " =    1.196
peak=   -3.396 closest distance to " O   HOH Z  24 " =    1.279
peak=   -3.396 closest distance to " CD2 LEU A 237 " =    2.799
peak=   -3.393 closest distance to " O   SER A  22 " =    2.489
peak=   -3.389 closest distance to " O   HOH Z 348 " =    1.846
peak=   -3.385 closest distance to " OXT GLY A 302 " =    3.458
peak=   -3.383 closest distance to " O   HOH Z 193 " =    1.878
peak=   -3.382 closest distance to " OG BSER A 134 " =    1.580
peak=   -3.381 closest distance to " CA  GLY A 241 " =    2.213
peak=   -3.379 closest distance to " O   HOH Z 353 " =    2.192
peak=   -3.371 closest distance to " CG  MET A 105 " =    0.958
peak=   -3.370 closest distance to " O   HOH Z  93 " =    2.174
peak=   -3.369 closest distance to " O   ALA A 161 " =    1.525
peak=   -3.367 closest distance to " O   HOH Z 266 " =    4.482
peak=   -3.360 closest distance to " O   HOH Z 191 " =    5.497
peak=   -3.352 closest distance to " O   TYR A  30 " =    2.842
peak=   -3.346 closest distance to " OD2 ASP A 171 " =    2.086
peak=   -3.345 closest distance to " O   HOH Z 137 " =    1.477
peak=   -3.343 closest distance to " O   MET A  40 " =    2.796
peak=   -3.325 closest distance to " O   HOH Z 388 " =    2.070
peak=   -3.323 closest distance to " NH1AARG A 275 " =    1.766
peak=   -3.317 closest distance to " N   SER A 212 " =    1.802
peak=   -3.317 closest distance to " O   HOH Z 426 " =    1.640
peak=   -3.316 closest distance to " O   GLY A  80 " =    2.361
peak=   -3.315 closest distance to " O   HOH Z  51 " =    1.189
peak=   -3.313 closest distance to " CG2 THR A 178 " =    2.178
peak=   -3.312 closest distance to " O   HOH Z  90 " =    2.559
peak=   -3.308 closest distance to " CG1 VAL A 197 " =    2.121
peak=   -3.305 closest distance to " N   THR A 235 " =    1.401
peak=   -3.304 closest distance to " O   VAL A 174 " =    2.233
peak=   -3.303 closest distance to " O   HOH Z 281 " =    2.743
peak=   -3.300 closest distance to " O   HOH Z 417 " =    3.061
peak=   -3.299 closest distance to " CB  ALA A 248 " =    2.360
peak=   -3.292 closest distance to " O   HOH Z 281 " =    3.065
peak=   -3.287 closest distance to " CA  ASP A 298 " =    1.033
peak=   -3.283 closest distance to " ND2 ASN A 187 " =    1.508
peak=   -3.281 closest distance to " O   HOH Z 351 " =    1.691
peak=   -3.278 closest distance to " CG  PRO A 163 " =    2.553
peak=   -3.275 closest distance to " CB  ASP A 132 " =    2.332
peak=   -3.273 closest distance to " O   HOH Z 111 " =    2.200
peak=   -3.271 closest distance to " CG  TRP A 266 " =    1.774
peak=   -3.261 closest distance to " CE3 TRP A 123 " =    1.308
peak=   -3.260 closest distance to " O   HOH Z 168 " =    1.822
peak=   -3.253 closest distance to " CG1 VAL A 268 " =    2.416
peak=   -3.246 closest distance to " CE3 TRP A 274 " =    2.363
peak=   -3.240 closest distance to " OD1 ASN A 176 " =    1.229
peak=   -3.236 closest distance to " CA  SER A 146 " =    2.320
peak=   -3.234 closest distance to " O   HOH Z 250 " =    1.424
peak=   -3.230 closest distance to " O   HOH Z 385 " =    1.912
peak=   -3.229 closest distance to " O   HOH Z 282 " =    1.251
peak=   -3.229 closest distance to " OE1 GLN A 223 " =    1.989
peak=   -3.228 closest distance to " ND2 ASN A 249 " =    2.257
peak=   -3.227 closest distance to " O   HOH Z  63 " =    1.950
peak=   -3.225 closest distance to " CG1 VAL A 230 " =    1.940
peak=   -3.223 closest distance to " O   TRP A  70 " =    1.455
peak=   -3.221 closest distance to " CB  ALA A   7 " =    2.060
peak=   -3.211 closest distance to " O   HOH Z 253 " =    3.810
peak=   -3.206 closest distance to " CG  GLN A  88 " =    0.821
peak=   -3.202 closest distance to " OG  SER A 245 " =    1.241
peak=   -3.200 closest distance to " O   ASN A 249 " =    1.397
peak=   -3.199 closest distance to " CE1 TYR A 169 " =    2.501
peak=   -3.192 closest distance to " O   HOH Z 414 " =    2.382
peak=   -3.186 closest distance to " CB  ASP A 132 " =    2.224
peak=   -3.184 closest distance to " CE  MET A  93 " =    1.195
peak=   -3.181 closest distance to " CB  PHE A 208 " =    2.204
peak=   -3.180 closest distance to " O   HOH Z 134 " =    2.985
peak=   -3.180 closest distance to " C   LYS A  76 " =    1.615
peak=   -3.175 closest distance to " CB  ASP A 286 " =    2.203
peak=   -3.175 closest distance to " O   HOH Z  10 " =    1.410
peak=   -3.172 closest distance to " O   HOH Z 174 " =    2.535
peak=   -3.167 closest distance to " CE  LYS A  76 " =    2.858
peak=   -3.160 closest distance to " N   ARG A  14 " =    1.048
peak=   -3.156 closest distance to " OH  TYR A 214 " =    1.238
peak=   -3.153 closest distance to " O   HOH Z 298 " =    2.417
peak=   -3.152 closest distance to " CD  LYS A 289 " =    2.333
peak=   -3.151 closest distance to " CA  TRP A 274 " =    1.513
peak=   -3.151 closest distance to " O   HOH Z 352 " =    2.133
peak=   -3.149 closest distance to " CB  ALA A 131 " =    1.942
peak=   -3.143 closest distance to " OD2 ASP A  50 " =    1.532
peak=   -3.141 closest distance to " O   HOH Z 414 " =    1.939
peak=   -3.135 closest distance to " OE1 GLN A  77 " =    1.806
peak=   -3.128 closest distance to " N   PHE A  59 " =    1.888
peak=   -3.122 closest distance to " ND2BASN A 224 " =    1.783
peak=   -3.122 closest distance to " CG2 VAL A 189 " =    1.932
peak=   -3.114 closest distance to " O   HOH Z 234 " =    3.976
peak=   -3.105 closest distance to " O   HOH Z 324 " =    2.102
peak=   -3.093 closest distance to " CG  GLU A 152 " =    1.419
peak=   -3.091 closest distance to " O   SER A   3 " =    1.171
peak=   -3.089 closest distance to " O   HOH Z 166 " =    1.338
peak=   -3.085 closest distance to " O   HOH Z 137 " =    1.424
peak=   -3.075 closest distance to " O   HOH Z 292 " =    1.510
peak=   -3.074 closest distance to " O   HOH Z 244 " =    2.033
peak=   -2.981 closest distance to " O   HOH Z 417 " =    2.679

================= 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    :  0.3735 0.3698   6.152849e+00   6.143744e+00
   1_bss:  0.3604 0.3587   6.138272e+00   6.121402e+00
   1_xyz:  0.2003 0.2278   5.618357e+00   5.722324e+00
   1_adp:  0.1829 0.2369   5.568387e+00   5.762854e+00
   1_occ:  0.1826 0.2362   5.566738e+00   5.761151e+00
   2_bss:  0.1798 0.2328   5.552041e+00   5.745827e+00
   2_xyz:  0.1408 0.1875   5.335717e+00   5.557809e+00
   2_adp:  0.1356 0.1767   5.292816e+00   5.499342e+00
   2_occ:  0.1355 0.1768   5.292476e+00   5.499587e+00
   3_bss:  0.1356 0.1765   5.290303e+00   5.497193e+00
   3_xyz:  0.1151 0.1577   5.150393e+00   5.382655e+00
   3_adp:  0.1107 0.1548   5.125472e+00   5.368411e+00
   3_occ:  0.1107 0.1548   5.125599e+00   5.368844e+00
   4_bss:  0.1107 0.1548   5.125155e+00   5.368489e+00
   4_xyz:  0.1093 0.1540   5.119329e+00   5.366682e+00
   4_adp:  0.1090 0.1533   5.116598e+00   5.364338e+00
   4_occ:  0.1089 0.1533   5.116700e+00   5.364734e+00
   5_bss:  0.1091 0.1538   5.118000e+00   5.365227e+00
   5_xyz:  0.1064 0.1533   5.103114e+00   5.360568e+00
   5_adp:  0.1060 0.1540   5.104403e+00   5.365522e+00
   5_occ:  0.1060 0.1540   5.104306e+00   5.365449e+00
   5_bss:  0.1059 0.1540   5.104388e+00   5.365488e+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:  0.334  36.546  -2.609   2.093  -0.632   0.000  -0.000  -0.000
   1_xyz:  0.334  36.546  -2.609   2.093  -0.632   0.000  -0.000  -0.000
   1_adp:  0.334  36.546  -2.609   2.093  -0.632   0.000  -0.000  -0.000
   1_occ:  0.334  36.546  -2.609   2.093  -0.632   0.000  -0.000  -0.000
   2_bss:  0.317  36.546  -2.556  -1.400  -1.416  -0.000  -0.000  -0.000
   2_xyz:  0.317  36.546  -2.556  -1.400  -1.416  -0.000  -0.000  -0.000
   2_adp:  0.317  36.546  -2.556  -1.400  -1.416  -0.000  -0.000  -0.000
   2_occ:  0.317  36.546  -2.556  -1.400  -1.416  -0.000  -0.000  -0.000
   3_bss:  0.323  43.043  -2.596  -2.364  -1.564  -0.000  -0.000  -0.000
   3_xyz:  0.323  43.043  -2.596  -2.364  -1.564  -0.000  -0.000  -0.000
   3_adp:  0.323  43.043  -2.596  -2.364  -1.564  -0.000  -0.000  -0.000
   3_occ:  0.323  43.043  -2.596  -2.364  -1.564  -0.000  -0.000  -0.000
   4_bss:  0.323  43.043  -2.504  -2.532  -1.570  -0.000  -0.000  -0.000
   4_xyz:  0.323  43.043  -2.504  -2.532  -1.570  -0.000  -0.000  -0.000
   4_adp:  0.323  43.043  -2.504  -2.532  -1.570  -0.000  -0.000  -0.000
   4_occ:  0.323  43.043  -2.504  -2.532  -1.570  -0.000  -0.000  -0.000
   5_bss:  0.321  45.717  -2.354  -2.495  -1.453  -0.000  -0.000  -0.000
   5_xyz:  0.321  45.717  -2.354  -2.495  -1.453  -0.000  -0.000  -0.000
   5_adp:  0.321  45.717  -2.354  -2.495  -1.453  -0.000  -0.000  -0.000
   5_occ:  0.321  45.717  -2.354  -2.495  -1.453  -0.000  -0.000  -0.000
   5_bss:  0.321  45.711  -2.165  -2.353  -1.278  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.381 0.6408  0.8364    41602.580
   1_bss:  39.201 0.6527  0.8397    38070.080
   1_xyz:  21.736 0.8465  1.0105    13279.374
   1_adp:  22.900 0.8341  1.0006    14295.510
   1_occ:  22.873 0.8343  1.0003    14219.430
   2_bss:  22.331 0.8395  0.9573    13620.221
   2_xyz:  17.574 0.8841  0.9877     8856.725
   2_adp:  16.165 0.8973  0.9945     7997.257
   2_occ:  16.173 0.8972  0.9942     7995.501
   3_bss:  16.096 0.8978  0.9813     7961.117
   3_xyz:  13.845 0.9158  0.9890     6204.457
   3_adp:  13.557 0.9183  0.9854     6041.389
   3_occ:  13.562 0.9183  0.9853     6044.786
   4_bss:  13.552 0.9184  0.9845     6042.301
   4_xyz:  13.438 0.9196  0.9839     6003.131
   4_adp:  13.368 0.9202  0.9792     5976.078
   4_occ:  13.374 0.9201  0.9792     5979.479
   5_bss:  13.399 0.9199  0.9830     6000.797
   5_xyz:  13.318 0.9204  0.9837     5952.980
   5_adp:  13.409 0.9198  0.9782     5996.787
   5_occ:  13.407 0.9198  0.9781     5995.923
   5_bss:  13.409 0.9197  0.9839     5997.743
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6469e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6469e-01
   1_xyz:   1.279  0.010  0.086 15.130  0.006  4.108   8.9261e-02
   1_adp:   1.279  0.010  0.086 15.130  0.006  4.108   8.9261e-02
   1_occ:   1.279  0.010  0.086 15.130  0.006  4.108   8.9261e-02
   2_bss:   1.279  0.010  0.086 15.130  0.006  4.108   8.9261e-02
   2_xyz:   0.875  0.005  0.065 14.161  0.004  4.112   4.7180e-02
   2_adp:   0.875  0.005  0.065 14.161  0.004  4.112   4.7180e-02
   2_occ:   0.875  0.005  0.065 14.161  0.004  4.112   4.7180e-02
   3_bss:   0.875  0.005  0.065 14.161  0.004  4.112   4.7180e-02
   3_xyz:   1.027  0.007  0.076 14.750  0.004  4.112   6.2952e-02
   3_adp:   1.027  0.007  0.076 14.750  0.004  4.112   6.2952e-02
   3_occ:   1.027  0.007  0.076 14.750  0.004  4.112   6.2952e-02
   4_bss:   1.027  0.007  0.076 14.750  0.004  4.112   6.2952e-02
   4_xyz:   0.942  0.006  0.071 14.463  0.004  4.115   5.3936e-02
   4_adp:   0.942  0.006  0.071 14.463  0.004  4.115   5.3936e-02
   4_occ:   0.942  0.006  0.071 14.463  0.004  4.115   5.3936e-02
   5_bss:   0.942  0.006  0.071 14.463  0.004  4.115   5.3936e-02
   5_xyz:   1.003  0.007  0.075 14.622  0.004  4.115   6.0221e-02
   5_adp:   1.003  0.007  0.075 14.622  0.004  4.115   6.0221e-02
   5_occ:   1.003  0.007  0.075 14.622  0.004  4.115   6.0221e-02
   5_bss:   1.003  0.007  0.075 14.622  0.004  4.115   6.0221e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3919e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3919e-01
   1_xyz:   7.606  0.073  0.445 85.791  0.056  2.160   9.6329e-02
   1_adp:   7.606  0.073  0.445 85.791  0.056  2.160   9.6329e-02
   1_occ:   7.606  0.073  0.445 85.791  0.056  2.160   9.6329e-02
   2_bss:   7.606  0.073  0.445 85.791  0.056  2.160   9.6329e-02
   2_xyz:   7.291  0.044  0.199 82.537  0.042  2.388   5.4124e-02
   2_adp:   7.291  0.044  0.199 82.537  0.042  2.388   5.4124e-02
   2_occ:   7.291  0.044  0.199 82.537  0.042  2.388   5.4124e-02
   3_bss:   7.291  0.044  0.199 82.537  0.042  2.388   5.4124e-02
   3_xyz:   7.473  0.044  0.239 85.555  0.034  2.270   5.7826e-02
   3_adp:   7.473  0.044  0.239 85.555  0.034  2.270   5.7826e-02
   3_occ:   7.473  0.044  0.239 85.555  0.034  2.270   5.7826e-02
   4_bss:   7.473  0.044  0.239 85.555  0.034  2.270   5.7826e-02
   4_xyz:   7.038  0.040  0.215 84.339  0.043  2.315   3.9019e-02
   4_adp:   7.038  0.040  0.215 84.339  0.043  2.315   3.9019e-02
   4_occ:   7.038  0.040  0.215 84.339  0.043  2.315   3.9019e-02
   5_bss:   7.038  0.040  0.215 84.339  0.043  2.315   3.9019e-02
   5_xyz:   6.897  0.036  0.246 84.465  0.035  2.265   4.7566e-02
   5_adp:   6.897  0.036  0.246 84.465  0.035  2.265   4.7566e-02
   5_occ:   6.897  0.036  0.246 84.465  0.035  2.265   4.7566e-02
   5_bss:   6.897  0.036  0.246 84.465  0.035  2.265   4.7566e-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:  82.23   0.00  17.41  73.34   0.00  13.15  82.23   7.51  40.63
   1_occ:  82.23   0.00  17.41  73.34   0.00  13.15  82.23   7.51  40.63
   2_bss:  82.23   0.00  17.41  73.34   0.00  13.15  82.23   7.51  40.63
   2_xyz:  82.23   0.00  17.41  73.34   0.00  13.15  82.23   7.51  40.63
   2_adp:  77.59   2.01  16.92  74.25   2.01  12.97  77.59   7.01  38.42
   2_occ:  77.59   2.01  16.92  74.25   2.01  12.97  77.59   7.01  38.42
   3_bss:  77.59   2.01  16.92  74.25   2.01  12.97  77.59   7.01  38.42
   3_xyz:  77.59   2.01  16.92  74.25   2.01  12.97  77.59   7.01  38.42
   3_adp:  86.54   0.25  17.25  86.54   0.25  12.99  82.07   6.57  40.46
   3_occ:  86.54   0.25  17.25  86.54   0.25  12.99  82.07   6.57  40.46
   4_bss:  86.54   0.25  17.25  86.54   0.25  12.99  82.07   6.57  40.46
   4_xyz:  86.54   0.25  17.25  86.54   0.25  12.99  82.07   6.57  40.46
   4_adp:  87.45   0.75  17.06  87.45   0.75  12.87  81.83   6.44  39.87
   4_occ:  87.45   0.75  17.06  87.45   0.75  12.87  81.83   6.44  39.87
   5_bss:  87.45   0.75  17.06  87.45   0.75  12.87  81.83   6.44  39.87
   5_xyz:  87.45   0.75  17.06  87.45   0.75  12.87  81.83   6.44  39.87
   5_adp:  91.20   0.26  16.94  91.20   0.26  12.77  83.25   6.36  39.64
   5_occ:  91.20   0.26  16.94  91.20   0.26  12.77  83.25   6.36  39.64
   5_bss:  91.20   0.26  16.93  91.20   0.26  12.76  83.25   6.35  39.63
------------------------------------------------------------------------
 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:    1.172    0.014    0.417
   1_adp:    1.172    0.014    0.417
   1_occ:    1.172    0.014    0.417
   2_bss:    1.172    0.014    0.417
   2_xyz:    0.951    0.019    0.446
   2_adp:    0.951    0.019    0.446
   2_occ:    0.951    0.019    0.446
   3_bss:    0.951    0.019    0.446
   3_xyz:    0.947    0.041    0.504
   3_adp:    0.947    0.041    0.504
   3_occ:    0.947    0.041    0.504
   4_bss:    0.947    0.041    0.504
   4_xyz:    1.063    0.030    0.514
   4_adp:    1.063    0.030    0.514
   4_occ:    1.063    0.030    0.514
   5_bss:    1.063    0.030    0.514
   5_xyz:    1.220    0.010    0.526
   5_adp:    1.220    0.010    0.526
   5_occ:    1.220    0.010    0.526
   5_bss:    1.220    0.010    0.526
------------------------------------------------------------------------

CPU time actual refinement: 330.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_751/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_751/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_751/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_751/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_751/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.21 
  Macro-tasks:
    bulk solvent and scale       = 37.14  
    individual site refinement   = 141.13 
    weights calculation          = 29.62  
    collect and process          = 6.64   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 214.62 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 105.14 
    alpha_beta                      = 8.36   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 115.09 
    fmodel                         = 6.78   
    r_factors                      = 0.25   
    phase_errors                   = 11.15  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 249.94 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.612 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    653 calls, 104.82 s
gradients_fft:          598 calls, 101.02 s

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

# Date 2008-01-16 Time 05:34:42 PST -0800 (1200490482.28 s)
Start R-work = 0.3735, R-free = 0.3698 (no bulk solvent and anisotropic scale)
Final R-work = 0.1307, R-free = 0.1736 (no bulk solvent and anisotropic scale)

Start R-work = 0.3604, R-free = 0.3587
Final R-work = 0.1059, R-free = 0.1540