# Date 2008-01-16 Time 05:19:27 PST -0800 (1200489567.59 s)
#phil __OFF__

Command line arguments: "../689.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14155
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 689

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.3993, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.0006
Completeness in resolution range: 0.968219
Completeness with d_max=infinity: 0.965166

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   2.0006

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.0006
Completeness in resolution range: 0.968219
Completeness with d_max=infinity: 0.965166

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.2801 [2130/2157]  1916   214  10.0%
  bin  2:  4.2801 -  3.4103 [2036/2052]  1833   203  10.0%
  bin  3:  3.4103 -  2.9830 [2027/2046]  1825   202  10.0%
  bin  4:  2.9830 -  2.7120 [1988/2018]  1785   203  10.2%
  bin  5:  2.7120 -  2.5186 [1987/2006]  1791   196   9.9%
  bin  6:  2.5186 -  2.3707 [1976/2001]  1781   195   9.9%
  bin  7:  2.3707 -  2.2524 [1969/2003]  1774   195   9.9%
  bin  8:  2.2524 -  2.1547 [1940/1970]  1742   198  10.2%
  bin  9:  2.1547 -  2.0719 [1943/1985]  1749   194  10.0%
  bin 10:  2.0719 -  2.0006 [1593/1994]  1434   159  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_689/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 12
        2.42 -     3.04: 2169
        3.04 -     3.66: 4616
        3.66 -     4.28: 8915
        4.28 -     4.90: 12310
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.043 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.125 3.040 -x+1/2,-y+1,z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.214 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28017 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_689/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_689/model_refine_001.geo

CPU time processing inputs: 9.30


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.3993 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3102   r_free= 0.2998   ksol= 0.00   Bsol= 0.00   scale= 0.968    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.008779                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1383  153 0.2712 0.2751      6.3065      6.2625|
|  2:  4.7735 -  3.8091 0.99   1319  150 0.2369 0.2244      6.3653      6.3593|
|  3:  3.8091 -  3.3336 0.99   1313  144 0.2658 0.2626      6.3111      6.3101|
|  4:  3.3336 -  3.0316 0.99   1294  139 0.2935 0.2944      6.2066      6.1609|
|  5:  3.0316 -  2.8158 0.99   1281  143 0.3201 0.2470       6.075      5.9314|
|  6:  2.8158 -  2.6507 0.99   1279  145 0.3208 0.3339      5.9996      5.9762|
|  7:  2.6507 -  2.5186 0.99   1281  144 0.3237 0.3132      5.9481      5.9142|
|  8:  2.5186 -  2.4094 0.98   1278  139 0.3424 0.3258      5.9539      5.9275|
|  9:  2.4094 -  2.3170 0.98   1249  140 0.3403 0.3147      5.8651      5.8244|
| 10:  2.3170 -  2.2373 0.99   1267  139 0.3611 0.2999      5.9273      5.7354|
| 11:  2.2373 -  2.1676 0.99   1265  143 0.3565 0.3451      5.8395      5.8561|
| 12:  2.1676 -  2.1058 0.97   1245  134 0.3614 0.3720      5.7778      5.8595|
| 13:  2.1058 -  2.0505 0.99   1281  143 0.3728 0.3530      5.7329      5.7113|
| 14:  2.0505 -  2.0006 0.72    895  103 0.3570 0.4085      5.6487      5.6783|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7735  1383   153  0.80  25.40   0.86     0.81      40581.06|
|  2:  4.7735 -  3.8091  1319   150  0.85  20.85   0.97     0.91      40780.34|
|  3:  3.8091 -  3.3336  1313   144  0.83  23.11   0.98     0.94      37189.86|
|  4:  3.3336 -  3.0316  1294   139  0.81  25.57   0.98     0.93      32016.82|
|  5:  3.0316 -  2.8158  1281   143  0.76  30.08   1.00     0.90      26335.46|
|  6:  2.8158 -  2.6507  1279   145  0.75  31.32   0.99     0.89      24387.67|
|  7:  2.6507 -  2.5186  1281   144  0.74  32.27   1.02     0.90      22526.36|
|  8:  2.5186 -  2.4094  1278   139  0.74  31.88   1.00     0.92      21244.22|
|  9:  2.4094 -  2.3170  1249   140  0.74  31.93   1.02     0.95      18559.06|
| 10:  2.3170 -  2.2373  1267   139  0.74  32.09   1.04     0.95      17369.01|
| 11:  2.2373 -  2.1676  1265   143  0.73  33.49   1.02     0.95      17458.19|
| 12:  2.1676 -  2.1058  1245   134  0.70  36.18   1.03     0.94      18424.28|
| 13:  2.1058 -  2.0505  1281   143  0.66  39.06   1.02     0.90      18378.53|
| 14:  2.0505 -  2.0006   895   103  0.61  43.20   1.04     0.83      17602.72|
|alpha:            min =        0.81 max =            0.95 mean =         0.91|
|beta:             min =    17369.01 max =        40780.34 mean =     25559.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           90.00 mean =        30.82|
|phase err.(test): min =        0.00 max =           89.64 mean =        30.75|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.788582              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.052   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561014              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.599   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      181 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1988 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1831 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2785 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4587 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4328 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5620 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6690 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.146 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.125)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3102   r_free= 0.2998   ksol= 0.00   Bsol= 0.00   scale= 0.968    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.008779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2960   r_free= 0.2863   ksol= 0.32   Bsol= 54.23   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.46,0.55,0.43,0.00,0.00,0.00); trace/3= -0.83                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.982375                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.514207              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.967   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.322853              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.494   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2960      final r-factor (work) = 0.1732          |
| start r-factor (free) = 0.2863      final r-factor (free) = 0.1914          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6924 = 3.51 * 0.50 * 5.9933 + 1.00 * 0.1615                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0427 = 3.51 * 0.50 * 5.6787 + 1.00 * 0.0646                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1732      final r-factor (work) = 0.1602          |
| start r-factor (free) = 0.1914      final r-factor (free) = 0.1935          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8402 = 0.32 * 1.00 * 5.6787 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8540 = 0.32 * 1.00 * 5.4212 + 1.00 * 0.1037                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.125)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.02   16.47    None  None   None       |
|    all(noH): 2823   0      0.00    94.02   16.47    None  None   None       |
|    Sol.    : 438    0      7.69    63.61   37.44    None  None   None       |
|    Mac.    : 2385   0      0.00    94.02   12.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.402:  841   |   5:    47.011 -  56.414:   90        |
|      1:     9.402 -  18.805: 1297   |   6:    56.414 -  65.816:   29        |
|      2:    18.805 -  28.207:  263   |   7:    65.816 -  75.218:    0        |
|      3:    28.207 -  37.609:  158   |   8:    75.218 -  84.620:    0        |
|      4:    37.609 -  47.011:  144   |   9:    84.620 -  94.023:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1602 r_free = 0.1935             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1598 r_free = 0.1936             target_work(ml) = 5.425         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1598   r_free= 0.1936   ksol= 0.32   Bsol= 54.23   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.46,0.55,0.43,0.00,0.00,0.00); trace/3= -0.83                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.424684                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1588   r_free= 0.1916   ksol= 0.33   Bsol= 64.72   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.39,-1.43,-0.91,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.420482                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.610713              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.530  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581548              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.894   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1588      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1916      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1519 = 2.61 * 0.50 * 5.4294 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9937 = 2.61 * 0.50 * 5.3104 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1255      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1031 = 0.58 * 1.00 * 5.3104 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0214 = 0.58 * 1.00 * 5.1787 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.125)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    87.66   17.18    None  None   None       |
|    all(noH): 2823   0      1.03    87.66   17.18    None  None   None       |
|    Sol.    : 438    0      3.35    78.06   40.41    None  None   None       |
|    Mac.    : 2385   0      1.03    87.66   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.034 -   9.696:  972   |   5:    44.345 -  53.008:   99        |
|      1:     9.696 -  18.359: 1144   |   6:    53.008 -  61.670:   69        |
|      2:    18.359 -  27.021:  232   |   7:    61.670 -  70.332:   44        |
|      3:    27.021 -  35.683:  136   |   8:    70.332 -  78.995:   13        |
|      4:    35.683 -  44.345:  111   |   9:    78.995 -  87.657:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1574             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1573             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1573   ksol= 0.33   Bsol= 64.72   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.39,-1.43,-0.91,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.171603                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1572   ksol= 0.33   Bsol= 64.72   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.65,-0.79,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170620                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.492642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.536  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.166875              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.025  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5158 = 2.49 * 0.50 * 5.1785 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4788 = 2.49 * 0.50 * 5.1444 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8681 = 0.17 * 1.00 * 5.1444 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8659 = 0.17 * 1.00 * 5.1433 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.125)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.37    85.14   16.46    None  None   None       |
|    all(noH): 2823   0      1.37    85.14   16.46    None  None   None       |
|    Sol.    : 438    0      2.06    75.80   37.54    None  None   None       |
|    Mac.    : 2385   0      1.37    85.14   12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.369 -   9.746:  996   |   5:    43.252 -  51.629:   84        |
|      1:     9.746 -  18.122: 1134   |   6:    51.629 -  60.005:   69        |
|      2:    18.122 -  26.499:  242   |   7:    60.005 -  68.382:   22        |
|      3:    26.499 -  34.876:  128   |   8:    68.382 -  76.759:    7        |
|      4:    34.876 -  43.252:  139   |   9:    76.759 -  85.135:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1545             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1544             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1544   ksol= 0.33   Bsol= 64.72   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.65,-0.79,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1545   ksol= 0.32   Bsol= 55.15   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.73,-0.73,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137614                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.561252              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.691  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.195675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.801  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6535 = 2.56 * 0.50 * 5.1430 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6400 = 2.56 * 0.50 * 5.1309 + 1.00 * 0.0693                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0115 = 0.20 * 1.00 * 5.1309 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0112 = 0.20 * 1.00 * 5.1302 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.125)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    81.96   16.18    None  None   None       |
|    all(noH): 2823   0      1.30    81.96   16.18    None  None   None       |
|    Sol.    : 438    0      3.35    72.46   36.83    None  None   None       |
|    Mac.    : 2385   0      1.30    81.96   12.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.300 -   9.366:  942   |   5:    41.628 -  49.694:   97        |
|      1:     9.366 -  17.431: 1155   |   6:    49.694 -  57.760:   74        |
|      2:    17.431 -  25.497:  260   |   7:    57.760 -  65.826:   18        |
|      3:    25.497 -  33.563:  127   |   8:    65.826 -  73.891:    8        |
|      4:    33.563 -  41.628:  140   |   9:    73.891 -  81.957:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1551             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1552             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1552   ksol= 0.32   Bsol= 55.15   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.73,-0.73,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1551   ksol= 0.32   Bsol= 55.15   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.66,-0.60,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.131873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.449905              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.284  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.078  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7887 = 1.45 * 0.50 * 5.1306 + 1.00 * 0.0693                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7854 = 1.45 * 0.50 * 5.1463 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9920 = 0.19 * 1.00 * 5.1463 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9933 = 0.19 * 1.00 * 5.1521 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.125)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.08    81.74   16.04    None  None   None       |
|    all(noH): 2823   0      1.08    81.74   16.04    None  None   None       |
|    Sol.    : 438    0      5.48    72.27   36.73    None  None   None       |
|    Mac.    : 2385   0      1.08    81.74   12.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.080 -   9.146:  940   |   5:    41.408 -  49.474:   99        |
|      1:     9.146 -  17.211: 1155   |   6:    49.474 -  57.539:   75        |
|      2:    17.211 -  25.277:  260   |   7:    57.539 -  65.605:   18        |
|      3:    25.277 -  33.343:  127   |   8:    65.605 -  73.671:    8        |
|      4:    33.343 -  41.408:  139   |   9:    73.671 -  81.736:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1571             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1571             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1571   ksol= 0.32   Bsol= 55.15   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.66,-0.60,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153497                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1383  153 0.1033 0.1314      5.4176      5.5241|
|  2:  4.7735 -  3.8091 0.99   1319  150 0.0883 0.1098      5.4584      5.6481|
|  3:  3.8091 -  3.3336 0.99   1313  144 0.1061 0.1505      5.4805        5.85|
|  4:  3.3336 -  3.0316 0.99   1294  139 0.1210 0.1498      5.4485      5.5724|
|  5:  3.0316 -  2.8158 0.99   1281  143 0.1353 0.1692      5.3445      5.5417|
|  6:  2.8158 -  2.6507 0.99   1279  145 0.1228 0.1972      5.2266      5.4833|
|  7:  2.6507 -  2.5186 0.99   1281  144 0.1268 0.1664       5.177      5.3736|
|  8:  2.5186 -  2.4094 0.98   1278  139 0.1176 0.1697      5.0868      5.3442|
|  9:  2.4094 -  2.3170 0.98   1249  140 0.1176 0.1826      5.0287      5.2999|
| 10:  2.3170 -  2.2373 0.99   1267  139 0.1159 0.1666      4.9882      5.1959|
| 11:  2.2373 -  2.1676 0.99   1265  143 0.1178 0.1775      4.9459      5.2364|
| 12:  2.1676 -  2.1058 0.97   1245  134 0.1145 0.1640      4.8827      5.2021|
| 13:  2.1058 -  2.0505 0.99   1281  143 0.1111 0.1693      4.7908      5.0474|
| 14:  2.0505 -  2.0006 0.72    895  103 0.1032 0.1825      4.6711      4.9784|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7735  1383   153  0.94   9.49   0.97     0.94       7588.47|
|  2:  4.7735 -  3.8091  1319   150  0.95   8.02   1.00     0.98       9092.73|
|  3:  3.8091 -  3.3336  1313   144  0.94  11.03   1.01     1.00      10272.50|
|  4:  3.3336 -  3.0316  1294   139  0.92  13.18   0.99     0.98      10002.12|
|  5:  3.0316 -  2.8158  1281   143  0.90  15.88   0.99     0.96       8367.20|
|  6:  2.8158 -  2.6507  1279   145  0.90  15.95   0.97     0.95       7131.93|
|  7:  2.6507 -  2.5186  1281   144  0.91  15.48   0.98     0.95       6223.59|
|  8:  2.5186 -  2.4094  1278   139  0.91  14.84   0.98     0.96       5351.40|
|  9:  2.4094 -  2.3170  1249   140  0.91  15.39   0.99     0.96       4989.34|
| 10:  2.3170 -  2.2373  1267   139  0.90  15.78   0.98     0.94       4491.63|
| 11:  2.2373 -  2.1676  1265   143  0.90  15.96   0.98     0.95       4308.42|
| 12:  2.1676 -  2.1058  1245   134  0.91  15.38   0.99     0.98       3921.56|
| 13:  2.1058 -  2.0505  1281   143  0.91  15.39   0.98     0.97       3300.93|
| 14:  2.0505 -  2.0006   895   103  0.92  14.38   0.95     0.91       2532.39|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2532.39 max =        10272.50 mean =      6370.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.95|
|phase err.(test): min =        0.00 max =           89.65 mean =        13.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1570   ksol= 0.32   Bsol= 55.12   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-1.53,-0.46,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1570   ksol= 0.32   Bsol= 55.12   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-1.53,-0.46,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153540                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1383  153 0.1033 0.1315       5.418      5.5248|
|  2:  4.7735 -  3.8091 0.99   1319  150 0.0883 0.1097      5.4586       5.648|
|  3:  3.8091 -  3.3336 0.99   1313  144 0.1061 0.1506      5.4805      5.8502|
|  4:  3.3336 -  3.0316 0.99   1294  139 0.1210 0.1498      5.4485      5.5725|
|  5:  3.0316 -  2.8158 0.99   1281  143 0.1353 0.1692      5.3444      5.5416|
|  6:  2.8158 -  2.6507 0.99   1279  145 0.1227 0.1971      5.2265      5.4831|
|  7:  2.6507 -  2.5186 0.99   1281  144 0.1268 0.1665       5.177      5.3737|
|  8:  2.5186 -  2.4094 0.98   1278  139 0.1176 0.1697      5.0869      5.3442|
|  9:  2.4094 -  2.3170 0.98   1249  140 0.1176 0.1826      5.0287      5.2998|
| 10:  2.3170 -  2.2373 0.99   1267  139 0.1159 0.1666      4.9883       5.196|
| 11:  2.2373 -  2.1676 0.99   1265  143 0.1178 0.1775      4.9459      5.2363|
| 12:  2.1676 -  2.1058 0.97   1245  134 0.1145 0.1639      4.8826      5.2019|
| 13:  2.1058 -  2.0505 0.99   1281  143 0.1111 0.1693      4.7907      5.0473|
| 14:  2.0505 -  2.0006 0.72    895  103 0.1032 0.1825       4.671      4.9783|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7735  1383   153  0.94   9.50   0.97     0.94       7597.92|
|  2:  4.7735 -  3.8091  1319   150  0.95   8.02   1.00     0.98       9098.18|
|  3:  3.8091 -  3.3336  1313   144  0.94  11.03   1.01     1.00      10274.08|
|  4:  3.3336 -  3.0316  1294   139  0.92  13.18   1.00     0.98      10001.88|
|  5:  3.0316 -  2.8158  1281   143  0.90  15.88   0.99     0.96       8365.40|
|  6:  2.8158 -  2.6507  1279   145  0.90  15.95   0.98     0.95       7130.40|
|  7:  2.6507 -  2.5186  1281   144  0.91  15.48   0.98     0.96       6223.49|
|  8:  2.5186 -  2.4094  1278   139  0.91  14.85   0.99     0.96       5351.44|
|  9:  2.4094 -  2.3170  1249   140  0.91  15.39   1.00     0.96       4990.41|
| 10:  2.3170 -  2.2373  1267   139  0.90  15.78   0.99     0.94       4491.54|
| 11:  2.2373 -  2.1676  1265   143  0.90  15.96   0.99     0.95       4308.29|
| 12:  2.1676 -  2.1058  1245   134  0.91  15.38   1.00     0.99       3921.02|
| 13:  2.1058 -  2.0505  1281   143  0.91  15.39   0.99     0.97       3300.07|
| 14:  2.0505 -  2.0006   895   103  0.92  14.37   0.96     0.92       2531.54|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2531.54 max =        10274.08 mean =      6371.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.95|
|phase err.(test): min =        0.00 max =           89.65 mean =        13.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.125)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    81.70   16.01    None  None   None       |
|    all(noH): 2823   0      1.04    81.70   16.01    None  None   None       |
|    Sol.    : 438    0      5.45    72.23   36.69    None  None   None       |
|    Mac.    : 2385   0      1.04    81.70   12.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.042 -   9.108:  940   |   5:    41.371 -  49.436:   99        |
|      1:     9.108 -  17.174: 1155   |   6:    49.436 -  57.502:   75        |
|      2:    17.174 -  25.239:  260   |   7:    57.502 -  65.567:   18        |
|      3:    25.239 -  33.305:  127   |   8:    65.567 -  73.633:    8        |
|      4:    33.305 -  41.371:  139   |   9:    73.633 -  81.699:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.468 - 4.855
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 300
   mapped sites are within: 0.712 - 4.855

peak=    5.727 closest distance to " NH2 ARG A  56 " =    2.330
peak=    5.626 closest distance to " CB  GLN A 223 " =    1.396
peak=    5.370 closest distance to " CG  PRO A  54 " =    1.373
peak=    5.167 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.866 closest distance to " O   HOH Z 126 " =    1.831
peak=    4.852 closest distance to " O   HOH Z 232 " =    2.331
peak=    4.724 closest distance to " CB  SER A  63 " =    1.178
peak=    4.637 closest distance to " CB  ARG A 190 " =    1.678
peak=    4.628 closest distance to " CG  PRO A 198 " =    1.332
peak=    4.625 closest distance to " CG  PRO A  90 " =    1.266
peak=    4.613 closest distance to " CG  PRO A 213 " =    1.269
peak=    4.609 closest distance to " CB  GLU A 152 " =    1.146
peak=    4.607 closest distance to " CB  GLN A 183 " =    1.209
peak=    4.554 closest distance to " C   PRO A 198 " =    1.524
peak=    4.484 closest distance to " CZ  PHE A 218 " =    1.097
peak=    4.468 closest distance to " CA  TYR A  30 " =    0.921
peak=    4.440 closest distance to " CB  TYR A 169 " =    0.718
peak=    4.421 closest distance to " O   HOH Z 298 " =    1.873
peak=    4.406 closest distance to " CB  LEU A 228 " =    1.080
peak=    4.390 closest distance to " CB  ARG A  79 " =    1.362
peak=    4.389 closest distance to " CB  PRO A  54 " =    0.942
peak=    4.328 closest distance to " O   HOH Z 236 " =    2.057
peak=    4.320 closest distance to " O   HOH Z 303 " =    2.158
peak=    4.298 closest distance to " O   HOH Z 369 " =    2.182
peak=    4.275 closest distance to " CG  PRO A 243 " =    1.033
peak=    4.228 closest distance to " CB  ASN A 148 " =    1.459
peak=    4.183 closest distance to " O   HOH Z 234 " =    3.822
peak=    4.167 closest distance to " ND2 ASN A 187 " =    1.509
peak=    4.135 closest distance to " CA  ARG A  36 " =    1.089
peak=    4.127 closest distance to " CB  GLU A 128 " =    1.000
peak=    4.123 closest distance to " O   HOH Z 250 " =    1.482
peak=    4.113 closest distance to " O   HOH Z 189 " =    2.641
peak=    4.061 closest distance to " O   HOH Z  40 " =    1.865
peak=    4.041 closest distance to " O   HOH Z  78 " =    1.637
peak=    4.038 closest distance to " CB  TRP A 266 " =    0.970
peak=    4.035 closest distance to " O   HOH Z 158 " =    3.129
peak=    4.034 closest distance to " O   HOH Z 402 " =    1.454
peak=    4.024 closest distance to " O   SER A  87 " =    2.214
peak=    4.023 closest distance to " CD  ARG A 269 " =    0.951
peak=    4.022 closest distance to " CG2 VAL A 257 " =    0.888
peak=    4.006 closest distance to " CB  GLU A  46 " =    0.974
peak=    3.988 closest distance to " CB  GLU A 277 " =    3.667
peak=    3.984 closest distance to " O   HOH Z  19 " =    2.199
peak=    3.981 closest distance to " O   HOH Z  15 " =    2.103
peak=    3.977 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.977 closest distance to " O   HOH Z 209 " =    2.237
peak=    3.963 closest distance to " O   HOH Z 272 " =    1.897
peak=    3.955 closest distance to " O   HOH Z 346 " =    1.666
peak=    3.938 closest distance to " CB  VAL A 265 " =    1.239
peak=    3.933 closest distance to " CB  ASP A 124 " =    0.712
peak=    3.913 closest distance to " CG2 ILE A 120 " =    1.067
peak=    3.906 closest distance to " O   HOH Z 423 " =    1.964
peak=    3.903 closest distance to " CA  ASN A 215 " =    1.055
peak=    3.901 closest distance to " O   HOH Z 128 " =    2.050
peak=    3.897 closest distance to " CD1 LEU A 300 " =    1.200
peak=    3.888 closest distance to " O   HOH Z 197 " =    2.898
peak=    3.876 closest distance to " CE  LYS A  76 " =    0.892
peak=    3.874 closest distance to " O   HOH Z 142 " =    1.595
peak=    3.868 closest distance to " O   HOH Z 403 " =    1.599
peak=    3.868 closest distance to " O   HOH Z 265 " =    2.264
peak=    3.865 closest distance to " CB  VAL A 202 " =    1.501
peak=    3.861 closest distance to " CA  PRO A  54 " =    1.363
peak=    3.855 closest distance to " O   HOH Z  21 " =    1.867
peak=    3.853 closest distance to " O   HOH Z 147 " =    1.844
peak=    3.848 closest distance to " O   HOH Z 368 " =    2.107
peak=    3.845 closest distance to " NH2 ARG A 156 " =    1.156
peak=    3.838 closest distance to " O   HOH Z 427 " =    3.066
peak=    3.835 closest distance to " CD2 TRP A 179 " =    1.292
peak=    3.815 closest distance to " O   HOH Z 389 " =    1.916
peak=    3.812 closest distance to " CD  LYS A 166 " =    1.284
peak=    3.806 closest distance to " CB  ASN A 187 " =    1.085
peak=    3.805 closest distance to " CA  ARG A 195 " =    1.204
peak=    3.802 closest distance to " N   GLY A  98 " =    1.107
peak=    3.799 closest distance to " CB  SER A   3 " =    1.281
peak=    3.794 closest distance to " O   HOH Z 203 " =    1.744
peak=    3.788 closest distance to " O   HOH Z 291 " =    1.569
peak=    3.786 closest distance to " OD1 ASN A  69 " =    2.567
peak=    3.779 closest distance to " O   HOH Z  43 " =    1.943
peak=    3.772 closest distance to " CA  SER A  87 " =    1.040
peak=    3.769 closest distance to " NE2 GLN A  11 " =    1.060
peak=    3.768 closest distance to " CA  THR A 264 " =    0.885
peak=    3.752 closest distance to " CZ  PHE A  38 " =    1.304
peak=    3.736 closest distance to " CD1 LEU A  96 " =    0.753
peak=    3.732 closest distance to " CB  ALA A 291 " =    1.097
peak=    3.732 closest distance to " CB  ASP A 140 " =    0.957
peak=    3.719 closest distance to " O   HOH Z 214 " =    2.125
peak=    3.709 closest distance to " O   HOH Z  61 " =    1.608
peak=    3.708 closest distance to " CA  ALA A  51 " =    0.878
peak=    3.695 closest distance to " O   HOH Z 313 " =    1.948
peak=    3.693 closest distance to " NH1AARG A 145 " =    1.304
peak=    3.692 closest distance to " CG2AVAL A  72 " =    1.755
peak=    3.687 closest distance to " O   HOH Z  63 " =    2.091
peak=    3.659 closest distance to " CG  MET A 185 " =    1.088
peak=    3.649 closest distance to " CB  ILE A 120 " =    1.219
peak=    3.643 closest distance to " O   HOH Z 280 " =    2.940
peak=    3.641 closest distance to " CD2 LEU A 297 " =    0.826
peak=    3.624 closest distance to " CG1 VAL A 153 " =    0.932
peak=    3.623 closest distance to " O   HOH Z 193 " =    1.934
peak=    3.613 closest distance to " CB  ASN A 142 " =    1.049
peak=    3.606 closest distance to " CB  ALA A 114 " =    1.099
peak=    3.604 closest distance to " O   HOH Z 185 " =    1.800
peak=    3.602 closest distance to " O   HOH Z 383 " =    1.966
peak=    3.589 closest distance to " CG  GLN A  11 " =    1.478
peak=    3.589 closest distance to " O   HOH Z 421 " =    1.788
peak=    3.585 closest distance to " O   TRP A 274 " =    1.886
peak=    3.584 closest distance to " CG1 ILE A  33 " =    1.270
peak=    3.583 closest distance to " O   HOH Z 403 " =    1.451
peak=    3.582 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.580 closest distance to " O   HOH Z 180 " =    2.100
peak=    3.577 closest distance to " O   HOH Z 261 " =    1.927
peak=    3.576 closest distance to " NE2 GLN A  77 " =    3.342
peak=    3.571 closest distance to " O   HOH Z 316 " =    3.164
peak=    3.570 closest distance to " O   HOH Z  97 " =    1.972
peak=    3.568 closest distance to " O   HOH Z   1 " =    2.163
peak=    3.560 closest distance to " O   HOH Z 406 " =    1.595
peak=    3.557 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.556 closest distance to " O   MET A 105 " =    1.891
peak=    3.550 closest distance to " O   HOH Z 172 " =    3.844
peak=    3.550 closest distance to " NZ  LYS A 117 " =    3.259
peak=    3.544 closest distance to " CB  TRP A 179 " =    1.404
peak=    3.534 closest distance to " CB  ALA A 242 " =    0.890
peak=    3.529 closest distance to " N   ARG A 156 " =    1.452
peak=    3.529 closest distance to " CD1 ILE A 106 " =    0.883
peak=    3.529 closest distance to " CB  MET A  47 " =    0.962
peak=    3.527 closest distance to " CG  ARG A  66 " =    2.533
peak=    3.513 closest distance to " CA  ALA A  21 " =    1.165
peak=    3.510 closest distance to " CE1 TYR A 186 " =    1.375
peak=    3.508 closest distance to " CA  ASP A 162 " =    0.974
peak=    3.500 closest distance to " O   HOH Z 368 " =    3.682
peak=    3.497 closest distance to " O   HOH Z 261 " =    1.697
peak=    3.497 closest distance to " CB  PRO A 198 " =    1.083
peak=    3.492 closest distance to " CA  ASP A 124 " =    0.723
peak=    3.489 closest distance to " CZ2 TRP A 179 " =    1.757
peak=    3.485 closest distance to " O   HOH Z 371 " =    3.097
peak=    3.482 closest distance to " O   HOH Z 148 " =    3.325
peak=    3.480 closest distance to " O   ALA A 165 " =    1.528
peak=    3.479 closest distance to " O   HOH Z  66 " =    2.252
peak=    3.477 closest distance to " O   HOH Z 294 " =    1.522
peak=    3.475 closest distance to " O   HOH Z 234 " =    1.887
peak=    3.475 closest distance to " N   ASN A  39 " =    1.240
peak=    3.473 closest distance to " O  BHOH Z 338 " =    2.285
peak=    3.468 closest distance to " OG1 THR A 294 " =    2.456
peak=    3.465 closest distance to " O   ASN A  74 " =    1.558
peak=    3.465 closest distance to " CA  MET A 105 " =    1.005
peak=    3.443 closest distance to " O   HOH Z  97 " =    2.422
peak=    3.442 closest distance to " O   HOH Z 412 " =    3.841
peak=    3.440 closest distance to " CA  ASP A 191 " =    0.813
peak=    3.438 closest distance to " O   HOH Z  10 " =    1.762
peak=    3.436 closest distance to " CB  PHE A 204 " =    0.846
peak=    3.431 closest distance to " O   HOH Z 305 " =    3.727
peak=    3.430 closest distance to " CB  GLN A 103 " =    0.811
peak=    3.422 closest distance to " CG2 THR A 220 " =    0.838
peak=    3.420 closest distance to " CB  SER A 141 " =    0.990
peak=    3.416 closest distance to " CB  ASN A 215 " =    1.193
peak=    3.415 closest distance to " NH2BARG A 145 " =    2.170
peak=    3.414 closest distance to " O   HOH Z 353 " =    2.671
peak=    3.413 closest distance to " OD1 ASN A 217 " =    1.716
peak=    3.409 closest distance to " CB  SER A 212 " =    1.196
peak=    3.405 closest distance to " CA  ASN A 217 " =    1.298
peak=    3.405 closest distance to " O   HOH Z 245 " =    1.328
peak=    3.405 closest distance to " O   HOH Z 426 " =    1.615
peak=    3.404 closest distance to " CA  ASN A 176 " =    1.216
peak=    3.401 closest distance to " O   HOH Z  54 " =    1.668
peak=    3.400 closest distance to " CG2 ILE A  20 " =    1.258
peak=    3.389 closest distance to " CG AARG A 275 " =    1.160
peak=    3.387 closest distance to " CA  THR A 221 " =    0.942
peak=    3.382 closest distance to " CB  THR A  31 " =    1.601
peak=    3.381 closest distance to " CA  ALA A  84 " =    1.180
peak=    3.380 closest distance to " O   HOH Z 273 " =    2.885
peak=    3.376 closest distance to " CB  MET A  40 " =    0.795
peak=    3.376 closest distance to " O   THR A 220 " =    1.223
peak=    3.375 closest distance to " O   THR A 251 " =    1.118
peak=    3.369 closest distance to " O   HOH Z 411 " =    1.755
peak=    3.368 closest distance to " O   HOH Z  96 " =    2.135
peak=    3.367 closest distance to " O   HOH Z 419 " =    1.928
peak=    3.367 closest distance to " CG  GLU A  37 " =    0.897
peak=    3.363 closest distance to " O   HOH Z 126 " =    1.690
peak=    3.352 closest distance to " O   ASP A 124 " =    1.172
peak=    3.348 closest distance to " O   HOH Z 128 " =    2.254
peak=    3.345 closest distance to " CG  LYS A  76 " =    1.026
peak=    3.344 closest distance to " O   HOH Z 425 " =    1.892
peak=    3.336 closest distance to " NZ  LYS A  48 " =    1.282
peak=    3.334 closest distance to " CG2 VAL A 197 " =    1.128
peak=    3.332 closest distance to " CA  ALA A 154 " =    0.911
peak=    3.329 closest distance to " CB  GLN A  89 " =    1.279
peak=    3.327 closest distance to " CB  TYR A 116 " =    0.754
peak=    3.325 closest distance to " O   HOH Z  66 " =    2.170
peak=    3.323 closest distance to " OG BSER A 164 " =    2.381
peak=    3.319 closest distance to " CB  LEU A  83 " =    0.773
peak=    3.318 closest distance to " O   HOH Z 183 " =    1.480
peak=    3.317 closest distance to " O   HOH Z 344 " =    3.196
peak=    3.316 closest distance to " CA  ALA A 248 " =    1.129
peak=    3.313 closest distance to " C   TYR A 214 " =    1.479
peak=    3.312 closest distance to " O   HOH Z 213 " =    1.832
peak=    3.309 closest distance to " O   HOH Z 133 " =    2.595
peak=    3.306 closest distance to " CB  GLN A  88 " =    1.160
peak=    3.306 closest distance to " CB  TYR A 169 " =    1.210
peak=    3.304 closest distance to " OD2 ASP A 286 " =    2.930
peak=    3.301 closest distance to " O   HOH Z  48 " =    1.671
peak=    3.295 closest distance to " OG  SER A  28 " =    1.473
peak=    3.293 closest distance to " CA  ALA A 233 " =    1.470
peak=    3.288 closest distance to " O   HOH Z  62 " =    2.218
peak=    3.285 closest distance to " CB  ALA A 248 " =    1.292
peak=    3.283 closest distance to " CB  SER A  26 " =    1.735
peak=    3.277 closest distance to " CA  TYR A 116 " =    1.435
peak=    3.276 closest distance to " O   HOH Z 173 " =    2.038
peak=    3.274 closest distance to " CA  ALA A 160 " =    0.954
peak=    3.268 closest distance to " CD BLYS A 290 " =    1.002
peak=    3.266 closest distance to " CA  GLU A 152 " =    0.890
peak=    3.265 closest distance to " OE1 GLU A 236 " =    1.109
peak=    3.265 closest distance to " OH  TYR A  30 " =    1.067
peak=    3.262 closest distance to " CA  GLY A 241 " =    0.846
peak=    3.260 closest distance to " O   ASN A  74 " =    2.087
peak=    3.259 closest distance to " OG BSER A 134 " =    2.859
peak=    3.258 closest distance to " CB  ARG A 139 " =    0.925
peak=    3.254 closest distance to " CZ3 TRP A 266 " =    1.094
peak=    3.251 closest distance to " CG1 ILE A 151 " =    1.033
peak=    3.247 closest distance to " O   HOH Z 248 " =    1.684
peak=    3.237 closest distance to " CA  GLY A 211 " =    1.232
peak=    3.237 closest distance to " N   PHE A 130 " =    1.240
peak=    3.233 closest distance to " O   HOH Z 417 " =    3.292
peak=    3.233 closest distance to " N   ASN A 127 " =    1.236
peak=    3.233 closest distance to " O   HOH Z 246 " =    1.386
peak=    3.230 closest distance to " CB  ASN A 110 " =    1.071
peak=    3.229 closest distance to " CD1 ILE A 199 " =    0.981
peak=    3.227 closest distance to " CA  ASP A 140 " =    1.237
peak=    3.223 closest distance to " CB  PRO A 243 " =    1.563
peak=    3.220 closest distance to " CB  ALA A  34 " =    1.005
peak=    3.220 closest distance to " O   HOH Z 295 " =    1.497
peak=    3.219 closest distance to " CB  SER A  62 " =    0.913
peak=    3.216 closest distance to " O   HOH Z 329 " =    3.979
peak=    3.216 closest distance to " O   HOH Z  80 " =    1.648
peak=    3.214 closest distance to " O   HOH Z 108 " =    2.788
peak=    3.212 closest distance to " CG  PHE A 204 " =    0.869
peak=    3.212 closest distance to " CB  HIS A 108 " =    0.792
peak=    3.208 closest distance to " O   HOH Z 359 " =    1.498
peak=    3.208 closest distance to " CG  MET A 185 " =    0.996
peak=    3.207 closest distance to " CA  ASP A 191 " =    1.073
peak=    3.207 closest distance to " CG2 THR A 221 " =    1.045
peak=    3.205 closest distance to " CA  ILE A 106 " =    0.786
peak=    3.204 closest distance to " O   HOH Z  59 " =    2.308
peak=    3.202 closest distance to " O   HOH Z 365 " =    2.915
peak=    3.201 closest distance to " CB  GLN A 278 " =    0.836
peak=    3.199 closest distance to " CD1AILE A 234 " =    0.922
peak=    3.196 closest distance to " O   HOH Z  88 " =    1.783
peak=    3.195 closest distance to " O   HOH Z  88 " =    3.329
peak=    3.194 closest distance to " O   HOH Z 337 " =    3.588
peak=    3.191 closest distance to " CA  ALA A 295 " =    1.042
peak=    3.191 closest distance to " O   HOH Z 285 " =    1.614
peak=    3.178 closest distance to " CB  GLN A 205 " =    1.073
peak=    3.178 closest distance to " O   HOH Z 336 " =    1.660
peak=    3.177 closest distance to " OG  SER A  22 " =    2.651
peak=    3.174 closest distance to " CB  ASP A 298 " =    1.171
peak=    3.171 closest distance to " N   CYS A 260 " =    0.793
peak=    3.169 closest distance to " NE2 HIS A 207 " =    1.180
peak=    3.167 closest distance to " CG1 ILE A  49 " =    1.573
peak=    3.163 closest distance to " O   HOH Z 299 " =    4.498
peak=    3.162 closest distance to " CA  ALA A 291 " =    0.804
peak=    3.160 closest distance to " N   TYR A 116 " =    1.545
peak=    3.160 closest distance to " O   HOH Z 285 " =    2.761
peak=    3.156 closest distance to " CA  LYS A 117 " =    1.273
peak=    3.155 closest distance to " O   HOH Z 387 " =    2.978
peak=    3.154 closest distance to " CB  PRO A  90 " =    1.100
peak=    3.152 closest distance to " O   HOH Z 422 " =    2.712
peak=    3.149 closest distance to " CE  MET A 113 " =    1.643
peak=    3.147 closest distance to " CE1 HIS A 108 " =    1.143
peak=    3.145 closest distance to " CG  ARG A 138 " =    1.136
peak=    3.140 closest distance to " O   HOH Z 188 " =    2.102
peak=    3.132 closest distance to " CB  ALA A   1 " =    4.855
peak=    3.131 closest distance to " CB  ALA A 248 " =    0.983
peak=    3.118 closest distance to " O   HOH Z 171 " =    3.995
peak=    3.118 closest distance to " O   HOH Z  44 " =    1.712
peak=    3.114 closest distance to " CA  LEU A 282 " =    1.022
peak=    3.109 closest distance to " N   SER A 135 " =    1.328
peak=    3.109 closest distance to " ND2 ASN A 110 " =    1.578
peak=    3.108 closest distance to " O   ALA A   1 " =    1.674
peak=    3.106 closest distance to " ND1 HIS A  81 " =    1.696
peak=    3.105 closest distance to " CG BARG A 275 " =    1.423
peak=    3.105 closest distance to " O   HOH Z 193 " =    1.657
peak=    3.102 closest distance to " O   HOH Z  88 " =    2.574
peak=    3.100 closest distance to " O   SER A 164 " =    1.257
peak=    3.093 closest distance to " O   HOH Z 298 " =    2.466
peak=    3.091 closest distance to " O   HOH Z 343 " =    2.172
peak=    3.078 closest distance to " O   HOH Z 163 " =    1.580
peak=    3.075 closest distance to " CZ  PHE A 192 " =    1.009
peak=    3.075 closest distance to " O   HOH Z 156 " =    3.451
peak=    3.073 closest distance to " CA  VAL A 125 " =    1.057
peak=    3.072 closest distance to " O   HOH Z  85 " =    1.992
peak=    3.071 closest distance to " CB  PHE A 204 " =    1.019
peak=    3.069 closest distance to " CB  ALA A 227 " =    1.073
peak=    3.068 closest distance to " CB  SER A 216 " =    0.778
peak=    3.065 closest distance to " CA  ALA A 292 " =    1.023
peak=    3.059 closest distance to " CD  ARG A  66 " =    2.424
peak=    3.036 closest distance to " CD  LYS A 119 " =    1.466
peak=    3.017 closest distance to " CZ3 TRP A  85 " =    0.985

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 187         
Filter by distance & map next to the model:
   mapped sites are within: 0.532 - 5.283
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 187
   mapped sites are within: 0.782 - 5.283

peak=   -4.984 closest distance to " CD  GLN A  58 " =    0.913
peak=   -4.595 closest distance to " CB  PRO A 243 " =    2.684
peak=   -4.569 closest distance to " O   HOH Z 266 " =    5.283
peak=   -4.399 closest distance to " O   HOH Z 290 " =    1.069
peak=   -4.342 closest distance to " C   HIS A 108 " =    1.090
peak=   -4.336 closest distance to " CD  ARG A 156 " =    2.085
peak=   -4.221 closest distance to " O   VAL A  67 " =    2.647
peak=   -4.134 closest distance to " CD  ARG A  14 " =    3.448
peak=   -4.133 closest distance to " O   HOH Z 231 " =    2.286
peak=   -4.124 closest distance to " OG  SER A  97 " =    2.295
peak=   -4.116 closest distance to " CB  ALA A 161 " =    2.566
peak=   -4.108 closest distance to " CZ3 TRP A 179 " =    1.192
peak=   -4.078 closest distance to " O   HOH Z  73 " =    2.330
peak=   -4.017 closest distance to " CD2 PHE A  61 " =    2.578
peak=   -4.003 closest distance to " O   HOH Z 196 " =    1.977
peak=   -3.988 closest distance to " O   PRO A 198 " =    1.241
peak=   -3.988 closest distance to " CG1 VAL A 112 " =    2.628
peak=   -3.950 closest distance to " N   ALA A  43 " =    2.615
peak=   -3.942 closest distance to " CG  GLN A 223 " =    1.980
peak=   -3.934 closest distance to " CG1 VAL A 112 " =    2.824
peak=   -3.867 closest distance to " CA  VAL A  67 " =    2.915
peak=   -3.858 closest distance to " CD2 PHE A 192 " =    2.076
peak=   -3.854 closest distance to " O   HOH Z  10 " =    1.534
peak=   -3.844 closest distance to " OD1 ASN A 148 " =    1.447
peak=   -3.841 closest distance to " ND2 ASN A  45 " =    1.572
peak=   -3.841 closest distance to " OXT GLY A 302 " =    2.851
peak=   -3.830 closest distance to " CE2 TYR A  30 " =    2.763
peak=   -3.830 closest distance to " O   HOH Z 372 " =    2.306
peak=   -3.811 closest distance to " CD2 TYR A 293 " =    2.074
peak=   -3.770 closest distance to " O   HOH Z 198 " =    2.096
peak=   -3.760 closest distance to " O   HOH Z 394 " =    1.500
peak=   -3.725 closest distance to " CG  ASP A 132 " =    2.310
peak=   -3.725 closest distance to " CG1 VAL A 265 " =    2.366
peak=   -3.722 closest distance to " CD1 LEU A 101 " =    2.446
peak=   -3.711 closest distance to " ND2 ASN A  45 " =    1.083
peak=   -3.696 closest distance to " CG  ARG A 269 " =    2.396
peak=   -3.694 closest distance to " O   HOH Z 114 " =    3.210
peak=   -3.693 closest distance to " OG BSER A 134 " =    1.315
peak=   -3.685 closest distance to " O   HOH Z 377 " =    2.017
peak=   -3.660 closest distance to " CA  ASP A 298 " =    1.119
peak=   -3.657 closest distance to " N   SER A 212 " =    1.972
peak=   -3.641 closest distance to " CZ  PHE A 155 " =    1.119
peak=   -3.637 closest distance to " O   HOH Z 351 " =    1.484
peak=   -3.617 closest distance to " CG1 VAL A 250 " =    2.728
peak=   -3.615 closest distance to " NH2 ARG A  79 " =    1.567
peak=   -3.611 closest distance to " CB  ASN A  39 " =    2.342
peak=   -3.608 closest distance to " NH2AARG A 275 " =    5.265
peak=   -3.597 closest distance to " CB  ALA A 248 " =    2.354
peak=   -3.595 closest distance to " O   HOH Z  52 " =    1.451
peak=   -3.584 closest distance to " O   HOH Z 185 " =    2.422
peak=   -3.570 closest distance to " N   THR A  52 " =    1.681
peak=   -3.568 closest distance to " O   HOH Z 407 " =    3.182
peak=   -3.557 closest distance to " CG  GLU A 277 " =    1.160
peak=   -3.553 closest distance to " O   HOH Z 353 " =    2.181
peak=   -3.552 closest distance to " CB  ALA A 291 " =    2.354
peak=   -3.550 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.550 closest distance to " CD1 PHE A  59 " =    2.035
peak=   -3.547 closest distance to " O   HOH Z 211 " =    1.583
peak=   -3.536 closest distance to " CA  GLY A 241 " =    2.405
peak=   -3.530 closest distance to " CA  GLY A 241 " =    3.278
peak=   -3.520 closest distance to " O   HOH Z 389 " =    1.807
peak=   -3.513 closest distance to " NE2 GLN A 194 " =    1.892
peak=   -3.500 closest distance to " CB  ALA A  43 " =    2.639
peak=   -3.483 closest distance to " CG  ARG A  66 " =    2.498
peak=   -3.478 closest distance to " O   ALA A  10 " =    1.729
peak=   -3.477 closest distance to " C   SER A 206 " =    1.512
peak=   -3.474 closest distance to " ND2 ASN A 249 " =    2.422
peak=   -3.466 closest distance to " NE2 GLN A 103 " =    1.796
peak=   -3.462 closest distance to " CZ  TYR A 169 " =    1.797
peak=   -3.461 closest distance to " O   HOH Z 311 " =    3.696
peak=   -3.460 closest distance to " CD  GLN A 223 " =    1.310
peak=   -3.457 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.453 closest distance to " NH2 ARG A 159 " =    2.316
peak=   -3.446 closest distance to " CB  ALA A 248 " =    2.243
peak=   -3.438 closest distance to " N   MET A 105 " =    2.645
peak=   -3.435 closest distance to " O   HOH Z 166 " =    1.862
peak=   -3.434 closest distance to " NE2 GLN A  88 " =    0.940
peak=   -3.422 closest distance to " CE3 TRP A 150 " =    2.203
peak=   -3.412 closest distance to " CD  ARG A 139 " =    1.604
peak=   -3.412 closest distance to " CE  MET A 105 " =    2.348
peak=   -3.404 closest distance to " CD1 LEU A   5 " =    2.495
peak=   -3.399 closest distance to " O   HOH Z 177 " =    1.763
peak=   -3.397 closest distance to " CD  ARG A  79 " =    1.147
peak=   -3.397 closest distance to " O   PRO A 163 " =    2.104
peak=   -3.393 closest distance to " CG  LYS A 193 " =    2.661
peak=   -3.391 closest distance to " CG  PHE A 283 " =    2.698
peak=   -3.391 closest distance to " CG1 VAL A  67 " =    3.085
peak=   -3.389 closest distance to " O   HOH Z 292 " =    4.611
peak=   -3.387 closest distance to " CG  GLN A  11 " =    1.582
peak=   -3.386 closest distance to " CD  ARG A 195 " =    5.142
peak=   -3.385 closest distance to " C   MET A 188 " =    1.423
peak=   -3.383 closest distance to " CD  GLU A 236 " =    1.045
peak=   -3.376 closest distance to " CB  ASP A 286 " =    1.874
peak=   -3.374 closest distance to " CD1 ILE A 239 " =    2.082
peak=   -3.372 closest distance to " OG BSER A 210 " =    2.175
peak=   -3.369 closest distance to " C   LEU A 143 " =    1.022
peak=   -3.366 closest distance to " O   HOH Z 377 " =    1.657
peak=   -3.355 closest distance to " N   GLN A  58 " =    1.830
peak=   -3.353 closest distance to " O   HOH Z 357 " =    2.018
peak=   -3.349 closest distance to " CA  GLY A 203 " =    2.395
peak=   -3.331 closest distance to " O   ALA A  34 " =    2.539
peak=   -3.328 closest distance to " CB  PHE A 208 " =    2.288
peak=   -3.328 closest distance to " O   HOH Z 435 " =    2.805
peak=   -3.327 closest distance to " NE2 GLN A  88 " =    1.826
peak=   -3.326 closest distance to " N   ALA A 226 " =    2.096
peak=   -3.321 closest distance to " O   HOH Z  13 " =    1.571
peak=   -3.320 closest distance to " C   ALA A 158 " =    1.364
peak=   -3.318 closest distance to " O   HOH Z 232 " =    1.621
peak=   -3.318 closest distance to " O   HOH Z  38 " =    1.472
peak=   -3.317 closest distance to " ND2 ASN A 187 " =    1.556
peak=   -3.310 closest distance to " CD2 LEU A 300 " =    2.874
peak=   -3.309 closest distance to " CE BMET A  47 " =    1.780
peak=   -3.308 closest distance to " N   ALA A 248 " =    1.738
peak=   -3.306 closest distance to " O   SER A  95 " =    1.720
peak=   -3.299 closest distance to " OD1 ASP A 171 " =    1.557
peak=   -3.292 closest distance to " OD2 ASP A 171 " =    2.489
peak=   -3.291 closest distance to " O   HOH Z 243 " =    1.971
peak=   -3.287 closest distance to " O   HOH Z  71 " =    1.991
peak=   -3.285 closest distance to " CB  PRO A 163 " =    2.504
peak=   -3.284 closest distance to " O   GLY A 196 " =    1.087
peak=   -3.280 closest distance to " CB  PHE A  16 " =    2.586
peak=   -3.278 closest distance to " OD2 ASP A  50 " =    2.136
peak=   -3.278 closest distance to " CD  PRO A 243 " =    2.110
peak=   -3.277 closest distance to " CG1 VAL A 125 " =    1.957
peak=   -3.272 closest distance to " O   HOH Z 128 " =    2.650
peak=   -3.272 closest distance to " CG1 VAL A  78 " =    2.910
peak=   -3.264 closest distance to " O   HOH Z  60 " =    2.218
peak=   -3.259 closest distance to " O   HOH Z 393 " =    1.345
peak=   -3.256 closest distance to " NE2 GLN A 278 " =    1.776
peak=   -3.252 closest distance to " OE1 GLN A  88 " =    1.154
peak=   -3.251 closest distance to " O   HOH Z 322 " =    1.676
peak=   -3.250 closest distance to " CG  HIS A  86 " =    1.158
peak=   -3.245 closest distance to " O   HOH Z 253 " =    4.006
peak=   -3.242 closest distance to " CB  TRP A  85 " =    2.506
peak=   -3.242 closest distance to " C   GLY A 262 " =    1.803
peak=   -3.238 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.231 closest distance to " O   HOH Z 126 " =    1.964
peak=   -3.225 closest distance to " O   HOH Z 134 " =    2.822
peak=   -3.223 closest distance to " O   HOH Z 166 " =    1.642
peak=   -3.222 closest distance to " O   GLY A 211 " =    1.344
peak=   -3.219 closest distance to " O   HOH Z  76 " =    1.996
peak=   -3.216 closest distance to " OD2 ASP A 171 " =    1.911
peak=   -3.215 closest distance to " O   HOH Z 171 " =    1.942
peak=   -3.215 closest distance to " O   HOH Z  19 " =    0.927
peak=   -3.214 closest distance to " O   HOH Z  37 " =    1.817
peak=   -3.208 closest distance to " CD2 LEU A 237 " =    2.870
peak=   -3.207 closest distance to " O   HOH Z  44 " =    2.226
peak=   -3.201 closest distance to " O   HOH Z 421 " =    3.316
peak=   -3.200 closest distance to " CD2 TYR A 293 " =    2.134
peak=   -3.195 closest distance to " O   HOH Z   6 " =    1.453
peak=   -3.194 closest distance to " CG1AVAL A  41 " =    2.799
peak=   -3.193 closest distance to " O   HOH Z 165 " =    1.873
peak=   -3.187 closest distance to " O   PHE A 218 " =    1.563
peak=   -3.187 closest distance to " CA  ILE A 263 " =    1.203
peak=   -3.187 closest distance to " O   HOH Z 313 " =    1.979
peak=   -3.184 closest distance to " CG  GLU A 152 " =    0.890
peak=   -3.183 closest distance to " CG  LEU A  83 " =    1.920
peak=   -3.173 closest distance to " CG  GLU A  53 " =    1.460
peak=   -3.171 closest distance to " O   GLY A  17 " =    1.205
peak=   -3.164 closest distance to " CE3 TRP A 274 " =    2.582
peak=   -3.157 closest distance to " O   HOH Z 234 " =    4.275
peak=   -3.156 closest distance to " CG2BVAL A  41 " =    1.994
peak=   -3.145 closest distance to " NH2 ARG A  79 " =    2.070
peak=   -3.143 closest distance to " O   HOH Z 351 " =    1.457
peak=   -3.142 closest distance to " C   ASN A 285 " =    2.331
peak=   -3.141 closest distance to " CG  TRP A 266 " =    1.975
peak=   -3.136 closest distance to " O   HOH Z  43 " =    1.592
peak=   -3.133 closest distance to " SG ACYS A 201 " =    2.057
peak=   -3.131 closest distance to " O   HOH Z 298 " =    2.539
peak=   -3.129 closest distance to " O   HOH Z 174 " =    4.094
peak=   -3.128 closest distance to " CG2 VAL A 189 " =    2.197
peak=   -3.123 closest distance to " ND2 ASN A  60 " =    1.283
peak=   -3.122 closest distance to " CD2 TYR A 247 " =    2.430
peak=   -3.117 closest distance to " O   HOH Z 123 " =    2.482
peak=   -3.110 closest distance to " CD1 LEU A 228 " =    2.293
peak=   -3.092 closest distance to " CG  ARG A 219 " =    2.775
peak=   -3.092 closest distance to " O   HOH Z 313 " =    1.031
peak=   -3.092 closest distance to " CB  LEU A  83 " =    2.391
peak=   -3.083 closest distance to " O   SER A 135 " =    1.464
peak=   -3.071 closest distance to " O   HOH Z  41 " =    2.438
peak=   -3.065 closest distance to " OG BSER A 134 " =    1.914
peak=   -3.053 closest distance to " CZ  PHE A  38 " =    1.992
peak=   -3.048 closest distance to " N   ASP A 171 " =    2.362
peak=   -3.028 closest distance to " O   HOH Z 317 " =    2.296

================= 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    :  0.3102 0.2998   6.008779e+00   5.974581e+00
   1_bss:  0.2960 0.2863   5.982375e+00   5.942960e+00
   1_xyz:  0.1732 0.1914   5.477457e+00   5.569121e+00
   1_adp:  0.1602 0.1935   5.425915e+00   5.583700e+00
   1_occ:  0.1598 0.1936   5.424684e+00   5.583523e+00
   2_bss:  0.1588 0.1916   5.420482e+00   5.576107e+00
   2_xyz:  0.1255 0.1594   5.212530e+00   5.403858e+00
   2_adp:  0.1183 0.1574   5.171893e+00   5.386723e+00
   2_occ:  0.1182 0.1573   5.171603e+00   5.386680e+00
   3_bss:  0.1179 0.1572   5.170620e+00   5.385392e+00
   3_xyz:  0.1112 0.1566   5.140841e+00   5.380404e+00
   3_adp:  0.1116 0.1545   5.138145e+00   5.373071e+00
   3_occ:  0.1115 0.1544   5.137920e+00   5.373251e+00
   4_bss:  0.1114 0.1545   5.137614e+00   5.373346e+00
   4_xyz:  0.1099 0.1549   5.131074e+00   5.374576e+00
   4_adp:  0.1100 0.1551   5.131776e+00   5.376081e+00
   4_occ:  0.1100 0.1552   5.131880e+00   5.376458e+00
   5_bss:  0.1099 0.1551   5.131873e+00   5.376491e+00
   5_xyz:  0.1132 0.1568   5.153548e+00   5.388928e+00
   5_adp:  0.1132 0.1571   5.153431e+00   5.389437e+00
   5_occ:  0.1132 0.1571   5.153497e+00   5.389588e+00
   5_bss:  0.1132 0.1570   5.153540e+00   5.389621e+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:  0.315  54.229  -3.458   0.548   0.433   0.000   0.000   0.000
   1_xyz:  0.315  54.229  -3.458   0.548   0.433   0.000   0.000   0.000
   1_adp:  0.315  54.229  -3.458   0.548   0.433   0.000   0.000   0.000
   1_occ:  0.315  54.229  -3.458   0.548   0.433   0.000   0.000   0.000
   2_bss:  0.331  64.718  -3.394  -1.429  -0.907  -0.000  -0.000  -0.000
   2_xyz:  0.331  64.718  -3.394  -1.429  -0.907  -0.000  -0.000  -0.000
   2_adp:  0.331  64.718  -3.394  -1.429  -0.907  -0.000  -0.000  -0.000
   2_occ:  0.331  64.718  -3.394  -1.429  -0.907  -0.000  -0.000  -0.000
   3_bss:  0.331  64.718  -2.769  -1.650  -0.795  -0.000  -0.000  -0.000
   3_xyz:  0.331  64.718  -2.769  -1.650  -0.795  -0.000  -0.000  -0.000
   3_adp:  0.331  64.718  -2.769  -1.650  -0.795  -0.000  -0.000  -0.000
   3_occ:  0.331  64.718  -2.769  -1.650  -0.795  -0.000  -0.000  -0.000
   4_bss:  0.321  55.153  -2.541  -1.727  -0.727  -0.000  -0.000  -0.000
   4_xyz:  0.321  55.153  -2.541  -1.727  -0.727  -0.000  -0.000  -0.000
   4_adp:  0.321  55.153  -2.541  -1.727  -0.727  -0.000  -0.000  -0.000
   4_occ:  0.321  55.153  -2.541  -1.727  -0.727  -0.000  -0.000  -0.000
   5_bss:  0.321  55.153  -2.360  -1.664  -0.605  -0.000  -0.000  -0.000
   5_xyz:  0.321  55.153  -2.360  -1.664  -0.605  -0.000  -0.000  -0.000
   5_adp:  0.321  55.153  -2.360  -1.664  -0.605  -0.000  -0.000  -0.000
   5_occ:  0.321  55.153  -2.360  -1.664  -0.605  -0.000  -0.000  -0.000
   5_bss:  0.321  55.116  -2.198  -1.535  -0.457  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.814 0.7521  0.9093    25558.404
   1_bss:  29.659 0.7630  0.8968    22618.782
   1_xyz:  18.100 0.8803  0.9917     9336.156
   1_adp:  18.508 0.8761  0.9858     9574.083
   1_occ:  18.513 0.8760  0.9854     9558.382
   2_bss:  18.282 0.8783  0.9517     9406.445
   2_xyz:  14.475 0.9108  0.9683     6476.981
   2_adp:  14.059 0.9144  0.9625     6253.001
   2_occ:  14.059 0.9144  0.9623     6251.683
   3_bss:  14.040 0.9146  0.9687     6257.703
   3_xyz:  13.862 0.9162  0.9706     6231.201
   3_adp:  13.656 0.9180  0.9658     6170.553
   3_occ:  13.657 0.9180  0.9657     6170.620
   4_bss:  13.657 0.9180  0.9684     6167.550
   4_xyz:  13.658 0.9180  0.9684     6185.843
   4_adp:  13.665 0.9181  0.9624     6204.991
   4_occ:  13.671 0.9180  0.9622     6208.888
   5_bss:  13.671 0.9180  0.9665     6210.179
   5_xyz:  13.878 0.9165  0.9654     6359.175
   5_adp:  13.896 0.9163  0.9599     6367.214
   5_occ:  13.900 0.9163  0.9598     6370.046
   5_bss:  13.901 0.9163  0.9636     6370.966
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6152e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6152e-01
   1_xyz:   1.066  0.008  0.070 15.030  0.004  4.113   6.4622e-02
   1_adp:   1.066  0.008  0.070 15.030  0.004  4.113   6.4622e-02
   1_occ:   1.066  0.008  0.070 15.030  0.004  4.113   6.4622e-02
   2_bss:   1.066  0.008  0.070 15.030  0.004  4.113   6.4622e-02
   2_xyz:   1.031  0.008  0.076 14.667  0.004  4.127   6.1771e-02
   2_adp:   1.031  0.008  0.076 14.667  0.004  4.127   6.1771e-02
   2_occ:   1.031  0.008  0.076 14.667  0.004  4.127   6.1771e-02
   3_bss:   1.031  0.008  0.076 14.667  0.004  4.127   6.1771e-02
   3_xyz:   1.051  0.009  0.081 14.731  0.004  4.115   6.7268e-02
   3_adp:   1.051  0.009  0.081 14.731  0.004  4.115   6.7268e-02
   3_occ:   1.051  0.009  0.081 14.731  0.004  4.115   6.7268e-02
   4_bss:   1.051  0.009  0.081 14.731  0.004  4.115   6.7268e-02
   4_xyz:   1.061  0.010  0.083 14.671  0.004  4.117   6.9280e-02
   4_adp:   1.061  0.010  0.083 14.671  0.004  4.117   6.9280e-02
   4_occ:   1.061  0.010  0.083 14.671  0.004  4.117   6.9280e-02
   5_bss:   1.061  0.010  0.083 14.671  0.004  4.117   6.9280e-02
   5_xyz:   0.942  0.007  0.074 14.435  0.004  4.116   5.4541e-02
   5_adp:   0.942  0.007  0.074 14.435  0.004  4.116   5.4541e-02
   5_occ:   0.942  0.007  0.074 14.435  0.004  4.116   5.4541e-02
   5_bss:   0.942  0.007  0.074 14.435  0.004  4.116   5.4541e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4274e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4274e-01
   1_xyz:   7.711  0.044  0.269 83.604  0.024  2.305   6.5613e-02
   1_adp:   7.711  0.044  0.269 83.604  0.024  2.305   6.5613e-02
   1_occ:   7.711  0.044  0.269 83.604  0.024  2.305   6.5613e-02
   2_bss:   7.711  0.044  0.269 83.604  0.024  2.305   6.5613e-02
   2_xyz:   7.376  0.047  0.240 82.419  0.044  2.352   3.9653e-02
   2_adp:   7.376  0.047  0.240 82.419  0.044  2.352   3.9653e-02
   2_occ:   7.376  0.047  0.240 82.419  0.044  2.352   3.9653e-02
   3_bss:   7.376  0.047  0.240 82.419  0.044  2.352   3.9653e-02
   3_xyz:   7.747  0.049  0.287 82.469  0.039  2.360   4.9611e-02
   3_adp:   7.747  0.049  0.287 82.469  0.039  2.360   4.9611e-02
   3_occ:   7.747  0.049  0.287 82.469  0.039  2.360   4.9611e-02
   4_bss:   7.747  0.049  0.287 82.469  0.039  2.360   4.9611e-02
   4_xyz:   7.688  0.052  0.275 82.403  0.038  2.294   5.0818e-02
   4_adp:   7.688  0.052  0.275 82.403  0.038  2.294   5.0818e-02
   4_occ:   7.688  0.052  0.275 82.403  0.038  2.294   5.0818e-02
   5_bss:   7.688  0.052  0.275 82.403  0.038  2.294   5.0818e-02
   5_xyz:   6.826  0.043  0.232 82.352  0.034  2.390   3.2463e-02
   5_adp:   6.826  0.043  0.232 82.352  0.034  2.390   3.2463e-02
   5_occ:   6.826  0.043  0.232 82.352  0.034  2.390   3.2463e-02
   5_bss:   6.826  0.043  0.232 82.352  0.034  2.390   3.2463e-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:  94.02   0.00  16.47  94.02   0.00  12.63  63.61   7.69  37.44
   1_occ:  94.02   0.00  16.47  94.02   0.00  12.63  63.61   7.69  37.44
   2_bss:  94.02   0.00  16.47  94.02   0.00  12.63  63.61   7.69  37.44
   2_xyz:  94.02   0.00  16.47  94.02   0.00  12.63  63.61   7.69  37.44
   2_adp:  87.66   1.03  17.18  87.66   1.03  12.91  78.06   3.35  40.41
   2_occ:  87.66   1.03  17.18  87.66   1.03  12.91  78.06   3.35  40.41
   3_bss:  87.66   1.03  17.18  87.66   1.03  12.91  78.06   3.35  40.41
   3_xyz:  87.66   1.03  17.18  87.66   1.03  12.91  78.06   3.35  40.41
   3_adp:  85.14   1.37  16.46  85.14   1.37  12.58  75.80   2.06  37.54
   3_occ:  85.14   1.37  16.46  85.14   1.37  12.58  75.80   2.06  37.54
   4_bss:  85.14   1.37  16.46  85.14   1.37  12.58  75.80   2.06  37.54
   4_xyz:  85.14   1.37  16.46  85.14   1.37  12.58  75.80   2.06  37.54
   4_adp:  81.96   1.30  16.18  81.96   1.30  12.38  72.46   3.35  36.83
   4_occ:  81.96   1.30  16.18  81.96   1.30  12.38  72.46   3.35  36.83
   5_bss:  81.96   1.30  16.18  81.96   1.30  12.38  72.46   3.35  36.83
   5_xyz:  81.96   1.30  16.18  81.96   1.30  12.38  72.46   3.35  36.83
   5_adp:  81.74   1.08  16.04  81.74   1.08  12.24  72.27   5.48  36.73
   5_occ:  81.74   1.08  16.04  81.74   1.08  12.24  72.27   5.48  36.73
   5_bss:  81.70   1.04  16.01  81.70   1.04  12.21  72.23   5.45  36.69
------------------------------------------------------------------------
 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:    1.042    0.015    0.293
   1_adp:    1.042    0.015    0.293
   1_occ:    1.042    0.015    0.293
   2_bss:    1.042    0.015    0.293
   2_xyz:    0.794    0.044    0.352
   2_adp:    0.794    0.044    0.352
   2_occ:    0.794    0.044    0.352
   3_bss:    0.794    0.044    0.352
   3_xyz:    0.966    0.041    0.377
   3_adp:    0.966    0.041    0.377
   3_occ:    0.966    0.041    0.377
   4_bss:    0.966    0.041    0.377
   4_xyz:    1.060    0.027    0.386
   4_adp:    1.060    0.027    0.386
   4_occ:    1.060    0.027    0.386
   5_bss:    1.060    0.027    0.386
   5_xyz:    1.101    0.033    0.387
   5_adp:    1.101    0.033    0.387
   5_occ:    1.101    0.033    0.387
   5_bss:    1.101    0.033    0.387
------------------------------------------------------------------------

CPU time actual refinement: 319.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_689/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_689/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_689/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_689/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_689/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.76 
  Macro-tasks:
    bulk solvent and scale       = 38.76  
    individual site refinement   = 131.40 
    weights calculation          = 28.82  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 205.62 
  Micro-tasks:
    mask                            = 1.22   
    f_calc                          = 100.72 
    alpha_beta                      = 8.59   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 109.71 
    fmodel                         = 6.29   
    r_factors                      = 0.17   
    phase_errors                   = 10.87  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 239.03 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.546 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    637 calls, 100.43 s
gradients_fft:          582 calls,  96.27 s

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

# Date 2008-01-16 Time 05:24:59 PST -0800 (1200489899.43 s)
Start R-work = 0.3102, R-free = 0.2998 (no bulk solvent and anisotropic scale)
Final R-work = 0.1349, R-free = 0.1745 (no bulk solvent and anisotropic scale)

Start R-work = 0.2960, R-free = 0.2863
Final R-work = 0.1132, R-free = 0.1570