# Date 2008-01-16 Time 05:47:41 PST -0800 (1200491261.30 s)
#phil __OFF__

Command line arguments: "../882.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28355
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 882

-------------------------------------------------------------------------------
  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: (70.9525, 46.4607, 85.0941, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97103
Completeness in resolution range: 0.9586
Completeness with d_max=infinity: 0.955701

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             d_min =   1.9710

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: (70.9525, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97103
Completeness in resolution range: 0.9586
Completeness with d_max=infinity: 0.955701

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.2182 [2143/2169]  1932   211   9.8%
  bin  2:  4.2182 -  3.3604 [2063/2082]  1855   208  10.1%
  bin  3:  3.3604 -  2.9392 [2032/2051]  1827   205  10.1%
  bin  4:  2.9392 -  2.6721 [2014/2044]  1813   201  10.0%
  bin  5:  2.6721 -  2.4815 [2017/2036]  1820   197   9.8%
  bin  6:  2.4815 -  2.3357 [1987/2012]  1781   206  10.4%
  bin  7:  2.3357 -  2.2192 [1990/2018]  1790   200  10.1%
  bin  8:  2.2192 -  2.1228 [1968/2004]  1778   190   9.7%
  bin  9:  2.1228 -  2.0413 [1974/2016]  1773   201  10.2%
  bin 10:  2.0413 -  1.9710 [1401/2003]  1261   140  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_882/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: 29
        2.42 -     3.04: 2207
        3.04 -     3.66: 4753
        3.66 -     4.28: 9098
        4.28 -     4.90: 12409
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.006 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.069 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  2.076 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.107 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28491 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_882/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_882/model_refine_001.geo

CPU time processing inputs: 8.84


============================ 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 = 70.9525 46.4607 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3738   r_free= 0.3727   ksol= 0.00   Bsol= 0.00   scale= 0.956    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.139405                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7050 0.99   1392  155 0.3082 0.3063      6.4013      6.3691|
|  2:  4.7050 -  3.7536 0.99   1343  146 0.2993 0.2809      6.5554      6.5136|
|  3:  3.7536 -  3.2848 0.99   1313  147 0.3294 0.3144      6.4442      6.5497|
|  4:  3.2848 -  2.9870 0.99   1315  153 0.3422 0.3794       6.342      6.3368|
|  5:  2.9870 -  2.7743 0.99   1297  139 0.3861 0.3840      6.2083      6.1933|
|  6:  2.7743 -  2.6117 0.99   1287  143 0.3987 0.4084      6.1418       6.141|
|  7:  2.6117 -  2.4815 0.99   1300  139 0.3989 0.3806      6.1166      6.0879|
|  8:  2.4815 -  2.3739 0.98   1261  151 0.4254 0.4036      6.0719      6.0493|
|  9:  2.3739 -  2.2828 0.98   1280  145 0.4083 0.3838      6.0096      5.9546|
| 10:  2.2828 -  2.2043 0.99   1280  138 0.4183 0.4621      5.9892      6.0529|
| 11:  2.2043 -  2.1356 0.98   1286  138 0.4415 0.4344      5.9625      5.9896|
| 12:  2.1356 -  2.0747 0.97   1241  139 0.4366 0.4700      5.9015      5.9623|
| 13:  2.0747 -  2.0202 1.00   1265  140 0.4343 0.4221      5.8003      5.7329|
| 14:  2.0202 -  1.9710 0.59    770   86 0.4739 0.4473      5.8053      5.7279|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7050  1392   155  0.78  27.09   0.86     0.80      46232.04|
|  2:  4.7050 -  3.7536  1343   146  0.81  25.28   0.96     0.90      58880.39|
|  3:  3.7536 -  3.2848  1313   147  0.75  31.01   0.99     0.93      62495.26|
|  4:  3.2848 -  2.9870  1315   153  0.70  35.57   0.99     0.89      58043.42|
|  5:  2.9870 -  2.7743  1297   139  0.63  41.05   0.95     0.84      48463.94|
|  6:  2.7743 -  2.6117  1287   143  0.62  42.00   0.97     0.83      42489.26|
|  7:  2.6117 -  2.4815  1300   139  0.64  40.99   0.98     0.84      37198.00|
|  8:  2.4815 -  2.3739  1261   151  0.62  42.29   0.95     0.86      33700.74|
|  9:  2.3739 -  2.2828  1280   145  0.63  41.72   1.01     0.85      31035.19|
| 10:  2.2828 -  2.2043  1280   138  0.59  44.68   1.02     0.83      31355.87|
| 11:  2.2043 -  2.1356  1286   138  0.55  48.08   1.02     0.81      31547.05|
| 12:  2.1356 -  2.0747  1241   139  0.55  48.55   1.01     0.80      29623.92|
| 13:  2.0747 -  2.0202  1265   140  0.52  50.62   1.01     0.78      25529.52|
| 14:  2.0202 -  1.9710   770    86  0.54  49.15   0.98     0.73      20767.49|
|alpha:            min =        0.73 max =            0.93 mean =         0.84|
|beta:             min =    20767.49 max =        62495.26 mean =     40594.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.95 mean =        40.14|
|phase err.(test): min =        0.00 max =           89.98 mean =        40.34|
|-----------------------------------------------------------------------------|

============================== 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 = 5.462852              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.630   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.074332              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.901   (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:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      206 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2001 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2862 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4676 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4422 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5658 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6751 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.212 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3738   r_free= 0.3727   ksol= 0.00   Bsol= 0.00   scale= 0.956    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.139405                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3627   r_free= 0.3625   ksol= 0.33   Bsol= 39.44   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.51,0.72,-0.00,0.00,0.00); trace/3= -0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.127992                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.558455              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.735   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.511668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.728   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3627      final r-factor (work) = 0.2065          |
| start r-factor (free) = 0.3625      final r-factor (free) = 0.2327          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1295 = 4.56 * 0.50 * 6.1274 + 1.00 * 0.1639                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4434 = 4.56 * 0.50 * 5.8659 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2065      final r-factor (work) = 0.1909          |
| start r-factor (free) = 0.2327      final r-factor (free) = 0.2416          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0077 = 0.51 * 1.00 * 5.8659 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8892 = 0.51 * 1.00 * 5.5859 + 1.00 * 0.0311                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.92   16.94    None  None   None       |
|    all(noH): 2823   0      0.00    61.92   16.94    None  None   None       |
|    Sol.    : 438    0      5.79    61.92   38.55    None  None   None       |
|    Mac.    : 2385   0      0.00    61.21   12.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.192:  299   |   5:    30.961 -  37.154:  108        |
|      1:     6.192 -  12.385: 1080   |   6:    37.154 -  43.346:  113        |
|      2:    12.385 -  18.577:  661   |   7:    43.346 -  49.538:   83        |
|      3:    18.577 -  24.769:  255   |   8:    49.538 -  55.731:   63        |
|      4:    24.769 -  30.961:  122   |   9:    55.731 -  61.923:   39        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1909 r_free = 0.2416             target_work(ml) = 5.603         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1904 r_free = 0.2417             target_work(ml) = 5.602         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1904   r_free= 0.2417   ksol= 0.33   Bsol= 39.44   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.51,0.72,-0.00,0.00,0.00); trace/3= -0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.601773                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1892   r_free= 0.2395   ksol= 0.32   Bsol= 39.44   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.29,-1.24,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.598196                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.950038              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.651   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.352824              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.761   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1892      final r-factor (work) = 0.1379          |
| start r-factor (free) = 0.2395      final r-factor (free) = 0.1831          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3365 = 2.95 * 0.50 * 5.6019 + 1.00 * 0.0737                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1268 = 2.95 * 0.50 * 5.4735 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1379      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9488 = 0.35 * 1.00 * 5.4735 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8709 = 0.35 * 1.00 * 5.2793 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.20    74.54   17.10    None  None   None       |
|    all(noH): 2823   0      1.20    74.54   17.10    None  None   None       |
|    Sol.    : 438    0      5.69    73.52   39.72    None  None   None       |
|    Mac.    : 2385   0      1.20    74.54   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.204 -   8.537:  642   |   5:    37.871 -  45.204:  102        |
|      1:     8.537 -  15.871: 1279   |   6:    45.204 -  52.537:   97        |
|      2:    15.871 -  23.204:  371   |   7:    52.537 -  59.871:   71        |
|      3:    23.204 -  30.537:  115   |   8:    59.871 -  67.204:   28        |
|      4:    30.537 -  37.871:  108   |   9:    67.204 -  74.537:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1699             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1269 r_free = 0.1698             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1698   ksol= 0.32   Bsol= 39.44   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.29,-1.24,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.237559                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1699   ksol= 0.32   Bsol= 43.15   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.29,-1.24,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.237769                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.957555              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.925  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.344174              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.827  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2203 = 1.96 * 0.50 * 5.2791 + 1.00 * 0.0532                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1370 = 1.96 * 0.50 * 5.1943 + 1.00 * 0.0529                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7960 = 0.34 * 1.00 * 5.1943 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7799 = 0.34 * 1.00 * 5.1475 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    83.95   17.00    None  None   None       |
|    all(noH): 2823   0      1.03    83.95   17.00    None  None   None       |
|    Sol.    : 438    0      4.66    80.18   39.43    None  None   None       |
|    Mac.    : 2385   0      1.03    83.95   12.88    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:     1.026 -   9.318:  856   |   5:    42.487 -  50.780:  108        |
|      1:     9.318 -  17.610: 1205   |   6:    50.780 -  59.072:   70        |
|      2:    17.610 -  25.903:  279   |   7:    59.072 -  67.364:   33        |
|      3:    25.903 -  34.195:  134   |   8:    67.364 -  75.657:   16        |
|      4:    34.195 -  42.487:  118   |   9:    75.657 -  83.949:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1553             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1552             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1552   ksol= 0.32   Bsol= 43.15   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.29,-1.24,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1551   ksol= 0.32   Bsol= 43.15   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.50,-1.58,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139482                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.288553              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.765  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206621              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.648  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9434 = 2.29 * 0.50 * 5.1478 + 1.00 * 0.0529                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9192 = 2.29 * 0.50 * 5.1200 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0662 = 0.21 * 1.00 * 5.1200 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0637 = 0.21 * 1.00 * 5.1116 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.45    85.25   16.66    None  None   None       |
|    all(noH): 2823   0      1.45    85.25   16.66    None  None   None       |
|    Sol.    : 438    0      5.67    81.93   38.00    None  None   None       |
|    Mac.    : 2385   0      1.45    85.25   12.74    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:     1.452 -   9.832:  989   |   5:    43.349 -  51.728:   98        |
|      1:     9.832 -  18.211: 1125   |   6:    51.728 -  60.108:   57        |
|      2:    18.211 -  26.590:  247   |   7:    60.108 -  68.487:   19        |
|      3:    26.590 -  34.970:  139   |   8:    68.487 -  76.866:   12        |
|      4:    34.970 -  43.349:  133   |   9:    76.866 -  85.246:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1530             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1080 r_free = 0.1530             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1530   ksol= 0.32   Bsol= 43.15   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.50,-1.58,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.111328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1530   ksol= 0.32   Bsol= 43.15   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.42,-1.51,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.111345                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.286440              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.519  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.700974              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.897  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3485 = 1.29 * 0.50 * 5.1117 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3436 = 1.29 * 0.50 * 5.1233 + 1.00 * 0.0482                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5988 = 0.70 * 1.00 * 5.1233 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6007 = 0.70 * 1.00 * 5.1240 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.53    92.32   16.87    None  None   None       |
|    all(noH): 2823   0      0.53    92.32   16.87    None  None   None       |
|    Sol.    : 438    0      6.21    85.11   39.40    None  None   None       |
|    Mac.    : 2385   0      0.53    92.32   12.73    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:     0.527 -   9.706: 1004   |   5:    46.423 -  55.602:  103        |
|      1:     9.706 -  18.885: 1142   |   6:    55.602 -  64.782:   55        |
|      2:    18.885 -  28.065:  231   |   7:    64.782 -  73.961:   13        |
|      3:    28.065 -  37.244:  139   |   8:    73.961 -  83.140:   11        |
|      4:    37.244 -  46.423:  121   |   9:    83.140 -  92.319:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1554             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1098 r_free = 0.1554             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1554   ksol= 0.32   Bsol= 43.15   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.42,-1.51,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129621                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7050 0.99   1392  155 0.0985 0.1235      5.3668      5.4932|
|  2:  4.7050 -  3.7536 0.99   1343  146 0.0856 0.1107      5.4257      5.6123|
|  3:  3.7536 -  3.2848 0.99   1313  147 0.1052 0.1521      5.4689      5.8495|
|  4:  3.2848 -  2.9870 0.99   1315  153 0.1183 0.1534      5.4424      5.5763|
|  5:  2.9870 -  2.7743 0.99   1297  139 0.1311 0.1758      5.3124       5.529|
|  6:  2.7743 -  2.6117 0.99   1287  143 0.1180 0.1680      5.1821      5.4136|
|  7:  2.6117 -  2.4815 0.99   1300  139 0.1222 0.1557      5.1475      5.3279|
|  8:  2.4815 -  2.3739 0.98   1261  151 0.1139 0.1763      5.0206      5.3359|
|  9:  2.3739 -  2.2828 0.98   1280  145 0.1128 0.1714      5.0099      5.3154|
| 10:  2.2828 -  2.2043 0.99   1280  138 0.1081 0.1723      4.9308      5.1925|
| 11:  2.2043 -  2.1356 0.98   1286  138 0.1134 0.1751      4.9466      5.3054|
| 12:  2.1356 -  2.0747 0.97   1241  139 0.1087 0.1587      4.8761      5.0841|
| 13:  2.0747 -  2.0202 1.00   1265  140 0.1137 0.1793      4.7851      5.0827|
| 14:  2.0202 -  1.9710 0.59    770   86 0.0991 0.1653      4.6346      4.9107|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7050  1392   155  0.94   8.35   0.98     0.95       6309.02|
|  2:  4.7050 -  3.7536  1343   146  0.95   7.64   1.02     1.01       8531.97|
|  3:  3.7536 -  3.2848  1313   147  0.93  11.18   1.03     1.02      10178.60|
|  4:  3.2848 -  2.9870  1315   153  0.92  13.31   1.01     0.99      10036.70|
|  5:  2.9870 -  2.7743  1297   139  0.90  15.66   0.99     0.97       7995.53|
|  6:  2.7743 -  2.6117  1287   143  0.91  15.33   0.99     0.96       6692.00|
|  7:  2.6117 -  2.4815  1300   139  0.91  14.95   0.99     0.97       5970.93|
|  8:  2.4815 -  2.3739  1261   151  0.91  14.68   0.99     0.96       4750.15|
|  9:  2.3739 -  2.2828  1280   145  0.92  14.42   1.00     0.98       4700.30|
| 10:  2.2828 -  2.2043  1280   138  0.91  15.01   1.00     0.96       4096.98|
| 11:  2.2043 -  2.1356  1286   138  0.90  16.27   0.99     0.95       4395.14|
| 12:  2.1356 -  2.0747  1241   139  0.92  14.81   1.01     1.00       3984.09|
| 13:  2.0747 -  2.0202  1265   140  0.90  16.39   1.00     0.99       3358.35|
| 14:  2.0202 -  1.9710   770    86  0.92  14.08   0.98     0.94       2435.36|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2435.36 max =        10178.60 mean =      6098.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.65|
|phase err.(test): min =        0.00 max =           89.56 mean =        13.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1555   ksol= 0.32   Bsol= 43.14   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.26,-1.37,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129699                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1555   ksol= 0.32   Bsol= 43.14   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.26,-1.37,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129699                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7050 0.99   1392  155 0.0985 0.1236      5.3676      5.4944|
|  2:  4.7050 -  3.7536 0.99   1343  146 0.0856 0.1106      5.4261      5.6121|
|  3:  3.7536 -  3.2848 0.99   1313  147 0.1053 0.1522      5.4689      5.8497|
|  4:  3.2848 -  2.9870 0.99   1315  153 0.1183 0.1534      5.4424      5.5764|
|  5:  2.9870 -  2.7743 0.99   1297  139 0.1311 0.1758      5.3123      5.5286|
|  6:  2.7743 -  2.6117 0.99   1287  143 0.1180 0.1681      5.1821      5.4139|
|  7:  2.6117 -  2.4815 0.99   1300  139 0.1223 0.1557      5.1476      5.3281|
|  8:  2.4815 -  2.3739 0.98   1261  151 0.1139 0.1763      5.0207      5.3357|
|  9:  2.3739 -  2.2828 0.98   1280  145 0.1128 0.1713      5.0099      5.3156|
| 10:  2.2828 -  2.2043 0.99   1280  138 0.1080 0.1723      4.9309      5.1923|
| 11:  2.2043 -  2.1356 0.98   1286  138 0.1134 0.1750      4.9466      5.3055|
| 12:  2.1356 -  2.0747 0.97   1241  139 0.1087 0.1587      4.8758       5.084|
| 13:  2.0747 -  2.0202 1.00   1265  140 0.1137 0.1792      4.7849      5.0821|
| 14:  2.0202 -  1.9710 0.59    770   86 0.0991 0.1653      4.6345      4.9109|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7050  1392   155  0.94   8.36   0.98     0.95       6322.29|
|  2:  4.7050 -  3.7536  1343   146  0.95   7.65   1.02     1.01       8542.31|
|  3:  3.7536 -  3.2848  1313   147  0.93  11.18   1.03     1.03      10180.56|
|  4:  3.2848 -  2.9870  1315   153  0.92  13.31   1.01     0.99      10034.30|
|  5:  2.9870 -  2.7743  1297   139  0.90  15.66   1.00     0.97       7994.39|
|  6:  2.7743 -  2.6117  1287   143  0.91  15.33   0.99     0.96       6691.62|
|  7:  2.6117 -  2.4815  1300   139  0.91  14.95   1.00     0.98       5972.29|
|  8:  2.4815 -  2.3739  1261   151  0.91  14.68   0.99     0.97       4750.55|
|  9:  2.3739 -  2.2828  1280   145  0.92  14.43   1.01     0.99       4701.31|
| 10:  2.2828 -  2.2043  1280   138  0.91  15.01   1.00     0.96       4097.74|
| 11:  2.2043 -  2.1356  1286   138  0.90  16.27   1.00     0.96       4394.88|
| 12:  2.1356 -  2.0747  1241   139  0.92  14.81   1.01     1.00       3981.67|
| 13:  2.0747 -  2.0202  1265   140  0.90  16.38   1.01     1.00       3356.82|
| 14:  2.0202 -  1.9710   770    86  0.92  14.08   0.99     0.95       2434.91|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2434.91 max =        10180.56 mean =      6100.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.65|
|phase err.(test): min =        0.00 max =           89.56 mean =        13.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.51    92.30   16.85    None  None   None       |
|    all(noH): 2823   0      0.51    92.30   16.85    None  None   None       |
|    Sol.    : 438    0      6.19    85.09   39.38    None  None   None       |
|    Mac.    : 2385   0      0.51    92.30   12.71    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:     0.510 -   9.689: 1004   |   5:    46.406 -  55.586:  103        |
|      1:     9.689 -  18.869: 1142   |   6:    55.586 -  64.765:   55        |
|      2:    18.869 -  28.048:  231   |   7:    64.765 -  73.944:   13        |
|      3:    28.048 -  37.227:  139   |   8:    73.944 -  83.123:   11        |
|      4:    37.227 -  46.406:  121   |   9:    83.123 -  92.303:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.515 - 4.502
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 300
   mapped sites are within: 0.719 - 4.502

peak=    5.833 closest distance to " NE2 GLN A  11 " =    1.190
peak=    5.788 closest distance to " CG  PRO A  54 " =    1.254
peak=    5.553 closest distance to " O   HOH Z 126 " =    2.017
peak=    5.404 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.245 closest distance to " CG  PRO A 213 " =    1.244
peak=    5.206 closest distance to " CB  ARG A 275 " =    0.907
peak=    5.100 closest distance to " NH2 ARG A  56 " =    2.108
peak=    5.071 closest distance to " CB  SER A  63 " =    1.259
peak=    4.973 closest distance to " O   HOH Z 232 " =    2.323
peak=    4.943 closest distance to " CG  PRO A  90 " =    1.103
peak=    4.848 closest distance to " CB  PRO A  54 " =    0.972
peak=    4.848 closest distance to " O   HOH Z 144 " =    1.693
peak=    4.848 closest distance to " CB  GLU A 128 " =    1.043
peak=    4.749 closest distance to " O   HOH Z  78 " =    1.828
peak=    4.729 closest distance to " C   PRO A 198 " =    1.546
peak=    4.671 closest distance to " CB  GLN A 183 " =    1.212
peak=    4.639 closest distance to " CG  PRO A 198 " =    1.271
peak=    4.546 closest distance to " O   HOH Z 427 " =    2.783
peak=    4.508 closest distance to " O   HOH Z 298 " =    1.927
peak=    4.506 closest distance to " CG2 VAL A 257 " =    0.988
peak=    4.483 closest distance to " CB  LEU A 228 " =    1.106
peak=    4.467 closest distance to " O   HOH Z 236 " =    2.140
peak=    4.454 closest distance to " O   HOH Z 193 " =    1.787
peak=    4.426 closest distance to " CA  TYR A  30 " =    0.965
peak=    4.419 closest distance to " CB  SER A 216 " =    0.836
peak=    4.364 closest distance to " O   HOH Z   9 " =    2.266
peak=    4.320 closest distance to " CB  ASN A 148 " =    1.319
peak=    4.284 closest distance to " CB  TYR A 169 " =    0.719
peak=    4.278 closest distance to " CB  GLU A 152 " =    1.292
peak=    4.265 closest distance to " CG  PRO A 243 " =    1.090
peak=    4.263 closest distance to " O   HOH Z 316 " =    3.028
peak=    4.233 closest distance to " CB  SER A   3 " =    1.411
peak=    4.226 closest distance to " OD1 ASN A  69 " =    2.630
peak=    4.215 closest distance to " ND2 ASN A 187 " =    1.473
peak=    4.193 closest distance to " CG  PRO A 280 " =    0.785
peak=    4.192 closest distance to " O   HOH Z 369 " =    2.126
peak=    4.147 closest distance to " CA  THR A 264 " =    0.836
peak=    4.141 closest distance to " O   HOH Z 132 " =    2.315
peak=    4.071 closest distance to " CB  TRP A 266 " =    0.997
peak=    4.058 closest distance to " CB  VAL A 265 " =    1.247
peak=    4.044 closest distance to " O   HOH Z 234 " =    3.731
peak=    4.013 closest distance to " CB  TRP A 179 " =    1.350
peak=    3.997 closest distance to " O   HOH Z 344 " =    3.162
peak=    3.988 closest distance to " O   HOH Z 423 " =    1.505
peak=    3.981 closest distance to " O   HOH Z 272 " =    1.803
peak=    3.974 closest distance to " CB  ARG A  79 " =    1.392
peak=    3.941 closest distance to " O   HOH Z  10 " =    1.860
peak=    3.933 closest distance to " CG1 ILE A  33 " =    1.275
peak=    3.932 closest distance to " O   HOH Z 217 " =    3.105
peak=    3.931 closest distance to " CA  ASN A 215 " =    1.210
peak=    3.919 closest distance to " CA  ALA A  21 " =    1.154
peak=    3.908 closest distance to " OD2 ASP A 286 " =    2.858
peak=    3.905 closest distance to " O   HOH Z 128 " =    2.143
peak=    3.904 closest distance to " O   HOH Z 368 " =    3.611
peak=    3.901 closest distance to " O   HOH Z   1 " =    1.776
peak=    3.897 closest distance to " O   HOH Z 303 " =    2.196
peak=    3.895 closest distance to " O   HOH Z 425 " =    1.277
peak=    3.894 closest distance to " O   HOH Z 214 " =    2.031
peak=    3.890 closest distance to " CD BLYS A 290 " =    1.152
peak=    3.890 closest distance to " O   HOH Z 368 " =    1.915
peak=    3.875 closest distance to " O   HOH Z   1 " =    1.894
peak=    3.861 closest distance to " O   HOH Z  59 " =    1.745
peak=    3.841 closest distance to " O   HOH Z 346 " =    1.696
peak=    3.830 closest distance to " CD  ARG A 159 " =    0.765
peak=    3.821 closest distance to " CD2 LEU A 255 " =    1.480
peak=    3.809 closest distance to " CD  ARG A  66 " =    2.336
peak=    3.804 closest distance to " O   HOH Z 108 " =    1.355
peak=    3.799 closest distance to " O   HOH Z   9 " =    1.986
peak=    3.792 closest distance to " O   HOH Z 144 " =    2.308
peak=    3.791 closest distance to " CD1 LEU A 300 " =    1.235
peak=    3.761 closest distance to " O   HOH Z  44 " =    1.801
peak=    3.747 closest distance to " O   HOH Z 389 " =    1.832
peak=    3.740 closest distance to " O   HOH Z 425 " =    2.090
peak=    3.733 closest distance to " O   HOH Z  21 " =    1.667
peak=    3.729 closest distance to " NH1AARG A 145 " =    1.100
peak=    3.729 closest distance to " O   HOH Z 219 " =    2.229
peak=    3.726 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.721 closest distance to " O   HOH Z  61 " =    1.558
peak=    3.714 closest distance to " O   HOH Z  64 " =    2.243
peak=    3.711 closest distance to " CA  GLY A 241 " =    3.796
peak=    3.706 closest distance to " O   HOH Z 180 " =    2.117
peak=    3.703 closest distance to " O   HOH Z 189 " =    2.125
peak=    3.702 closest distance to " O   HOH Z  61 " =    1.651
peak=    3.693 closest distance to " O   HOH Z 163 " =    1.784
peak=    3.682 closest distance to " O   HOH Z 403 " =    1.678
peak=    3.681 closest distance to " CB  ARG A 139 " =    0.974
peak=    3.680 closest distance to " O   HOH Z 158 " =    2.957
peak=    3.677 closest distance to " CG  LEU A 167 " =    1.179
peak=    3.676 closest distance to " CB  ARG A 190 " =    1.649
peak=    3.667 closest distance to " O   SER A  87 " =    2.251
peak=    3.661 closest distance to " O   MET A 105 " =    1.836
peak=    3.660 closest distance to " OD1BASN A 224 " =    2.258
peak=    3.659 closest distance to " O   HOH Z 207 " =    1.763
peak=    3.656 closest distance to " ND1 HIS A  86 " =    1.750
peak=    3.654 closest distance to " O   HOH Z 250 " =    1.395
peak=    3.648 closest distance to " CG2 THR A 221 " =    1.098
peak=    3.645 closest distance to " CA  THR A 221 " =    0.969
peak=    3.644 closest distance to " O   HOH Z 352 " =    1.855
peak=    3.634 closest distance to " O   HOH Z 407 " =    2.276
peak=    3.633 closest distance to " O   HOH Z 261 " =    1.804
peak=    3.632 closest distance to " N   PHE A 130 " =    1.248
peak=    3.630 closest distance to " O   HOH Z 108 " =    1.974
peak=    3.627 closest distance to " O   HOH Z 419 " =    2.017
peak=    3.620 closest distance to " O   HOH Z 371 " =    2.979
peak=    3.615 closest distance to " O   HOH Z  40 " =    2.060
peak=    3.610 closest distance to " O   HOH Z  66 " =    2.171
peak=    3.609 closest distance to " O   HOH Z 211 " =    2.577
peak=    3.608 closest distance to " CB  SER A 212 " =    1.070
peak=    3.597 closest distance to " CZ  PHE A 218 " =    1.005
peak=    3.580 closest distance to " OG BSER A 164 " =    2.353
peak=    3.569 closest distance to " O   HOH Z 327 " =    1.788
peak=    3.554 closest distance to " N   ASN A  39 " =    1.341
peak=    3.551 closest distance to " O   HOH Z 133 " =    1.585
peak=    3.550 closest distance to " O   HOH Z  88 " =    3.320
peak=    3.545 closest distance to " O   HOH Z  40 " =    1.919
peak=    3.534 closest distance to " O   HOH Z 227 " =    2.114
peak=    3.528 closest distance to " CB  ALA A  34 " =    1.044
peak=    3.524 closest distance to " CG1BVAL A  72 " =    1.478
peak=    3.523 closest distance to " CB  LEU A 143 " =    1.114
peak=    3.523 closest distance to " O   HOH Z 193 " =    1.676
peak=    3.523 closest distance to " CB  ALA A 291 " =    1.398
peak=    3.517 closest distance to " O   HOH Z 134 " =    1.304
peak=    3.512 closest distance to " O   HOH Z  97 " =    1.974
peak=    3.506 closest distance to " CA  MET A  40 " =    1.045
peak=    3.505 closest distance to " O   HOH Z 227 " =    1.640
peak=    3.502 closest distance to " O   HOH Z 295 " =    1.502
peak=    3.501 closest distance to " O   HOH Z 135 " =    1.685
peak=    3.499 closest distance to " O   HOH Z 437 " =    1.609
peak=    3.487 closest distance to " O   HOH Z 371 " =    1.683
peak=    3.487 closest distance to " N   GLN A 278 " =    1.067
peak=    3.485 closest distance to " O   HOH Z 353 " =    2.723
peak=    3.483 closest distance to " CA  ILE A 234 " =    1.017
peak=    3.477 closest distance to " O   HOH Z 426 " =    1.653
peak=    3.459 closest distance to " N   ARG A 156 " =    1.269
peak=    3.455 closest distance to " O   HOH Z 265 " =    2.388
peak=    3.453 closest distance to " CB  VAL A 202 " =    1.638
peak=    3.450 closest distance to " CG  ARG A 159 " =    0.851
peak=    3.447 closest distance to " CD  PRO A 243 " =    1.630
peak=    3.444 closest distance to " OG  SER A  97 " =    3.494
peak=    3.442 closest distance to " O   HOH Z 261 " =    2.061
peak=    3.441 closest distance to " O   HOH Z 423 " =    2.528
peak=    3.439 closest distance to " O   HOH Z 386 " =    3.145
peak=    3.427 closest distance to " O   HOH Z   3 " =    1.876
peak=    3.421 closest distance to " O   THR A 220 " =    1.393
peak=    3.419 closest distance to " CB  VAL A 268 " =    0.845
peak=    3.406 closest distance to " CB  SER A  62 " =    1.221
peak=    3.405 closest distance to " O   HOH Z 286 " =    2.369
peak=    3.404 closest distance to " O   HOH Z 402 " =    1.403
peak=    3.401 closest distance to " CB  THR A 157 " =    1.063
peak=    3.399 closest distance to " NH2 ARG A 156 " =    1.195
peak=    3.392 closest distance to " CE AMET A  47 " =    1.390
peak=    3.389 closest distance to " O   HOH Z 409 " =    2.679
peak=    3.377 closest distance to " CB  GLU A 236 " =    1.193
peak=    3.376 closest distance to " O   HOH Z 213 " =    2.370
peak=    3.371 closest distance to " CB  VAL A 265 " =    1.937
peak=    3.370 closest distance to " OG  SER A  22 " =    2.763
peak=    3.368 closest distance to " CG1 ILE A 151 " =    0.971
peak=    3.365 closest distance to " O   HOH Z 193 " =    1.999
peak=    3.362 closest distance to " CD2 TRP A 179 " =    1.351
peak=    3.357 closest distance to " CB  LEU A 255 " =    0.796
peak=    3.356 closest distance to " O   HOH Z 147 " =    1.735
peak=    3.352 closest distance to " CE1 TYR A 186 " =    1.379
peak=    3.351 closest distance to " O   HOH Z  44 " =    3.239
peak=    3.350 closest distance to " CB  ASN A  39 " =    0.908
peak=    3.350 closest distance to " O   HOH Z 280 " =    3.069
peak=    3.348 closest distance to " O   HOH Z 245 " =    1.238
peak=    3.347 closest distance to " O   HOH Z 172 " =    3.320
peak=    3.341 closest distance to " NH2BARG A 145 " =    1.949
peak=    3.337 closest distance to " O   HOH Z 236 " =    1.520
peak=    3.336 closest distance to " CB  MET A  40 " =    0.775
peak=    3.335 closest distance to " CB  ASP A 132 " =    4.020
peak=    3.329 closest distance to " O   HOH Z 391 " =    2.978
peak=    3.329 closest distance to " O   HOH Z 153 " =    1.616
peak=    3.328 closest distance to " O   HOH Z 247 " =    1.219
peak=    3.326 closest distance to " O   HOH Z  49 " =    2.027
peak=    3.325 closest distance to " CD  ARG A 269 " =    0.961
peak=    3.325 closest distance to " CB  LYS A 117 " =    1.180
peak=    3.325 closest distance to " CD  LYS A 166 " =    1.253
peak=    3.323 closest distance to " CB  MET A  47 " =    1.032
peak=    3.323 closest distance to " CD  ARG A 219 " =    1.081
peak=    3.323 closest distance to " CB  ALA A 248 " =    0.935
peak=    3.322 closest distance to " CB  ARG A  79 " =    0.848
peak=    3.322 closest distance to " CB  ASN A 142 " =    0.931
peak=    3.316 closest distance to " CA  ALA A 233 " =    1.229
peak=    3.316 closest distance to " O   HOH Z 271 " =    2.345
peak=    3.314 closest distance to " OG  SER A 206 " =    1.241
peak=    3.314 closest distance to " CA  LYS A 290 " =    1.284
peak=    3.314 closest distance to " O   HOH Z  93 " =    2.453
peak=    3.314 closest distance to " CB  GLU A 277 " =    3.547
peak=    3.313 closest distance to " O   ALA A   1 " =    1.499
peak=    3.308 closest distance to " CA  SER A  87 " =    1.013
peak=    3.307 closest distance to " O   HOH Z 329 " =    3.607
peak=    3.307 closest distance to " O   HOH Z 366 " =    2.891
peak=    3.306 closest distance to " CB  TYR A 116 " =    0.823
peak=    3.304 closest distance to " CB  ASP A 171 " =    0.927
peak=    3.302 closest distance to " CG  GLN A  88 " =    1.010
peak=    3.300 closest distance to " O   HOH Z 305 " =    3.598
peak=    3.297 closest distance to " OE1 GLN A  11 " =    2.142
peak=    3.295 closest distance to " N   ASN A 127 " =    1.263
peak=    3.294 closest distance to " NH2AARG A 275 " =    3.731
peak=    3.293 closest distance to " CB  ALA A   1 " =    4.502
peak=    3.291 closest distance to " CA  ALA A  51 " =    0.969
peak=    3.291 closest distance to " CG  MET A 113 " =    1.203
peak=    3.286 closest distance to " CB  GLU A 152 " =    1.391
peak=    3.273 closest distance to " CD1 ILE A 106 " =    0.847
peak=    3.267 closest distance to " O   HOH Z 188 " =    1.941
peak=    3.263 closest distance to " CD1 LEU A  96 " =    0.807
peak=    3.261 closest distance to " CA  ALA A 154 " =    0.968
peak=    3.258 closest distance to " CB  PRO A 198 " =    0.992
peak=    3.256 closest distance to " CD  LYS A 119 " =    1.124
peak=    3.255 closest distance to " CG  MET A 185 " =    1.018
peak=    3.255 closest distance to " O   HOH Z 345 " =    3.515
peak=    3.254 closest distance to " O   HOH Z   2 " =    1.406
peak=    3.254 closest distance to " O   HOH Z 435 " =    2.007
peak=    3.254 closest distance to " CG2 ILE A 106 " =    1.047
peak=    3.252 closest distance to " CZ  PHE A 208 " =    1.113
peak=    3.251 closest distance to " O   HOH Z  63 " =    1.436
peak=    3.248 closest distance to " CA  ARG A 102 " =    1.175
peak=    3.248 closest distance to " O  BHOH Z  74 " =    1.346
peak=    3.241 closest distance to " N   TYR A  15 " =    0.759
peak=    3.240 closest distance to " CB  ASP A 140 " =    0.837
peak=    3.239 closest distance to " CG  GLU A 277 " =    2.164
peak=    3.238 closest distance to " CB  SER A 276 " =    1.176
peak=    3.235 closest distance to " NH2AARG A 190 " =    1.661
peak=    3.233 closest distance to " CA  ARG A  36 " =    1.096
peak=    3.228 closest distance to " O   HOH Z 273 " =    2.724
peak=    3.228 closest distance to " CG  MET A 185 " =    1.235
peak=    3.227 closest distance to " CA  ALA A 291 " =    0.972
peak=    3.227 closest distance to " O   HOH Z 291 " =    1.630
peak=    3.222 closest distance to " CA  ALA A 158 " =    1.154
peak=    3.220 closest distance to " OG  SER A  62 " =    3.040
peak=    3.217 closest distance to " O   HOH Z 340 " =    2.269
peak=    3.216 closest distance to " CA  ASP A 140 " =    1.160
peak=    3.215 closest distance to " O   HOH Z  43 " =    1.794
peak=    3.214 closest distance to " O   HOH Z 175 " =    2.081
peak=    3.210 closest distance to " CA  ASP A 162 " =    1.123
peak=    3.206 closest distance to " ND1 HIS A  81 " =    1.612
peak=    3.206 closest distance to " CG  LYS A  76 " =    1.050
peak=    3.203 closest distance to " CB  ILE A 120 " =    1.302
peak=    3.203 closest distance to " O   GLY A 229 " =    1.593
peak=    3.203 closest distance to " CA  TYR A 186 " =    1.539
peak=    3.194 closest distance to " O   HOH Z 433 " =    1.774
peak=    3.189 closest distance to " NH1BARG A 145 " =    1.210
peak=    3.186 closest distance to " O   GLY A  57 " =    2.603
peak=    3.186 closest distance to " CG2BVAL A  41 " =    0.868
peak=    3.184 closest distance to " O   HOH Z 374 " =    2.597
peak=    3.182 closest distance to " C   TYR A 214 " =    1.487
peak=    3.182 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.178 closest distance to " O   HOH Z 213 " =    1.805
peak=    3.178 closest distance to " CG  GLN A  89 " =    1.442
peak=    3.177 closest distance to " CD  GLN A 240 " =    1.641
peak=    3.171 closest distance to " O   HOH Z 411 " =    1.768
peak=    3.170 closest distance to " CB  ASN A 110 " =    1.115
peak=    3.169 closest distance to " O   HOH Z 163 " =    1.921
peak=    3.169 closest distance to " O   HOH Z 128 " =    2.115
peak=    3.164 closest distance to " OD1 ASP A 238 " =    1.074
peak=    3.164 closest distance to " NZ  LYS A 119 " =    1.305
peak=    3.163 closest distance to " O   HOH Z 291 " =    1.929
peak=    3.160 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.160 closest distance to " CD2 HIS A  81 " =    1.229
peak=    3.160 closest distance to " OG BSER A  99 " =    2.176
peak=    3.158 closest distance to " CA  ARG A 195 " =    1.226
peak=    3.151 closest distance to " O   HOH Z 403 " =    1.344
peak=    3.145 closest distance to " NZ  LYS A  76 " =    1.396
peak=    3.144 closest distance to " NE2 GLN A  73 " =    3.596
peak=    3.142 closest distance to " N   ALA A 154 " =    0.912
peak=    3.141 closest distance to " CA  ALA A  43 " =    1.223
peak=    3.138 closest distance to " CB  ARG A 138 " =    1.016
peak=    3.137 closest distance to " O   HOH Z 379 " =    1.899
peak=    3.130 closest distance to " CG2 VAL A  67 " =    1.041
peak=    3.130 closest distance to " O   HOH Z 218 " =    2.273
peak=    3.129 closest distance to " CA  GLY A 267 " =    1.280
peak=    3.121 closest distance to " CB  ALA A 161 " =    0.911
peak=    3.118 closest distance to " O   HOH Z 148 " =    3.281
peak=    3.107 closest distance to " CA  LEU A 282 " =    1.101
peak=    3.105 closest distance to " O   HOH Z 371 " =    3.281
peak=    3.105 closest distance to " O   HOH Z 216 " =    2.505
peak=    3.101 closest distance to " O   HOH Z 285 " =    1.601
peak=    3.098 closest distance to " O   THR A  31 " =    1.533
peak=    3.093 closest distance to " CD1AILE A 234 " =    0.954
peak=    3.091 closest distance to " O   HOH Z 298 " =    2.647
peak=    3.087 closest distance to " ND2 ASN A 249 " =    0.886
peak=    3.084 closest distance to " CA  THR A 221 " =    1.410
peak=    3.080 closest distance to " O   ALA A   1 " =    1.667
peak=    3.078 closest distance to " N   ASN A 252 " =    1.434
peak=    3.076 closest distance to " OD1 ASN A 217 " =    1.620
peak=    3.071 closest distance to " O   HOH Z 357 " =    1.835
peak=    3.070 closest distance to " CZ3 TRP A 123 " =    1.241
peak=    3.066 closest distance to " CB  VAL A 126 " =    1.034
peak=    3.065 closest distance to " O   HOH Z 217 " =    1.392
peak=    3.056 closest distance to " CB  ALA A  43 " =    0.877
peak=    3.052 closest distance to " N   SER A 134 " =    1.370
peak=    3.051 closest distance to " CB  ASN A 215 " =    1.089
peak=    3.048 closest distance to " O   ASN A 209 " =    1.362
peak=    3.031 closest distance to " CA  ALA A 299 " =    0.912
peak=    3.003 closest distance to " O   HOH Z 346 " =    1.398

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.754 - 5.550
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.754 - 5.550

peak=   -4.488 closest distance to " O   HOH Z 266 " =    4.585
peak=   -4.433 closest distance to " O   HOH Z 377 " =    1.970
peak=   -4.433 closest distance to " CD  ARG A 156 " =    1.946
peak=   -4.315 closest distance to " CB  PRO A 243 " =    2.579
peak=   -4.276 closest distance to " O   PRO A 198 " =    1.275
peak=   -4.221 closest distance to " O   HOH Z 372 " =    2.440
peak=   -4.180 closest distance to " CG  GLN A 223 " =    1.888
peak=   -4.172 closest distance to " O   HOH Z 435 " =    2.782
peak=   -4.110 closest distance to " O   HOH Z 290 " =    1.168
peak=   -4.072 closest distance to " O   HOH Z 198 " =    1.997
peak=   -4.072 closest distance to " O   HOH Z 407 " =    3.219
peak=   -4.032 closest distance to " CZ3 TRP A 179 " =    1.166
peak=   -4.019 closest distance to " CZ  PHE A  59 " =    1.536
peak=   -3.999 closest distance to " O   HOH Z 389 " =    1.865
peak=   -3.998 closest distance to " SG  CYS A 254 " =    3.244
peak=   -3.991 closest distance to " C   HIS A 108 " =    1.039
peak=   -3.964 closest distance to " OG BSER A 134 " =    1.188
peak=   -3.923 closest distance to " CE  MET A 105 " =    2.246
peak=   -3.906 closest distance to " O   HOH Z 351 " =    1.454
peak=   -3.905 closest distance to " O   HOH Z 231 " =    2.049
peak=   -3.904 closest distance to " ND2 ASN A  45 " =    1.117
peak=   -3.900 closest distance to " O   VAL A  67 " =    2.670
peak=   -3.894 closest distance to " O   HOH Z 185 " =    2.133
peak=   -3.893 closest distance to " OD1 ASN A 187 " =    1.549
peak=   -3.862 closest distance to " O   HOH Z  52 " =    1.355
peak=   -3.859 closest distance to " N   ALA A  43 " =    2.460
peak=   -3.852 closest distance to " O   HOH Z  43 " =    1.646
peak=   -3.852 closest distance to " CA  GLY A  98 " =    1.927
peak=   -3.850 closest distance to " O   HOH Z 353 " =    2.154
peak=   -3.847 closest distance to " CE2 TYR A  30 " =    2.841
peak=   -3.842 closest distance to " CG  MET A 105 " =    0.950
peak=   -3.839 closest distance to " CA  GLY A 203 " =    2.295
peak=   -3.834 closest distance to " O   HOH Z 126 " =    1.825
peak=   -3.832 closest distance to " CB  ALA A 291 " =    2.177
peak=   -3.812 closest distance to " CB  ASN A  39 " =    2.227
peak=   -3.806 closest distance to " O   ARG A 145 " =    1.544
peak=   -3.799 closest distance to " CG1 VAL A 112 " =    2.891
peak=   -3.795 closest distance to " O   HOH Z 313 " =    2.016
peak=   -3.790 closest distance to " CE2 PHE A 218 " =    2.506
peak=   -3.768 closest distance to " O   PRO A 163 " =    1.916
peak=   -3.766 closest distance to " CD1 PHE A  59 " =    1.835
peak=   -3.719 closest distance to " O   ILE A 109 " =    2.614
peak=   -3.717 closest distance to " N   SER A 212 " =    1.765
peak=   -3.713 closest distance to " O   ALA A 161 " =    1.512
peak=   -3.707 closest distance to " ND2 ASN A  45 " =    1.592
peak=   -3.698 closest distance to " O   HOH Z 388 " =    2.002
peak=   -3.695 closest distance to " OD1 ASP A 191 " =    1.818
peak=   -3.692 closest distance to " O   HOH Z 152 " =    5.166
peak=   -3.684 closest distance to " CG  ASP A 231 " =    0.778
peak=   -3.673 closest distance to " O   VAL A  67 " =    2.695
peak=   -3.656 closest distance to " OD1 ASN A 148 " =    1.634
peak=   -3.640 closest distance to " CG  PHE A 283 " =    2.771
peak=   -3.639 closest distance to " CZ  TYR A 169 " =    1.586
peak=   -3.636 closest distance to " C   ALA A 158 " =    1.313
peak=   -3.629 closest distance to " O   VAL A 153 " =    2.270
peak=   -3.619 closest distance to " O   SER A 135 " =    1.456
peak=   -3.615 closest distance to " N   GLN A  58 " =    1.720
peak=   -3.610 closest distance to " CB  TYR A  15 " =    2.141
peak=   -3.607 closest distance to " CD  ARG A 139 " =    1.485
peak=   -3.595 closest distance to " O   HOH Z 118 " =    2.983
peak=   -3.587 closest distance to " N   ASP A 286 " =    2.450
peak=   -3.583 closest distance to " O   TYR A 247 " =    2.823
peak=   -3.579 closest distance to " CB  CYS A 254 " =    2.164
peak=   -3.574 closest distance to " O   HOH Z  13 " =    1.437
peak=   -3.567 closest distance to " O   HOH Z 102 " =    1.654
peak=   -3.559 closest distance to " O   HOH Z 168 " =    1.933
peak=   -3.559 closest distance to " O   HOH Z 298 " =    1.206
peak=   -3.553 closest distance to " CZ BARG A 275 " =    1.869
peak=   -3.537 closest distance to " CG  ARG A 269 " =    2.526
peak=   -3.526 closest distance to " O   HOH Z  98 " =    2.321
peak=   -3.514 closest distance to " O   HOH Z 385 " =    2.004
peak=   -3.510 closest distance to " CD1 LEU A 228 " =    2.243
peak=   -3.501 closest distance to " O   GLY A 211 " =    1.400
peak=   -3.496 closest distance to " O   HOH Z  24 " =    1.388
peak=   -3.496 closest distance to " CD1 LEU A 101 " =    2.414
peak=   -3.487 closest distance to " OXT GLY A 302 " =    2.805
peak=   -3.480 closest distance to " C   LEU A 143 " =    1.246
peak=   -3.480 closest distance to " CB  ALA A 291 " =    2.357
peak=   -3.471 closest distance to " CB  ASP A 132 " =    2.286
peak=   -3.466 closest distance to " O   ALA A 180 " =    1.243
peak=   -3.465 closest distance to " O   HOH Z 198 " =    1.512
peak=   -3.456 closest distance to " NH1 ARG A 195 " =    2.606
peak=   -3.452 closest distance to " NH2AARG A 275 " =    5.387
peak=   -3.451 closest distance to " C   LEU A 222 " =    0.754
peak=   -3.450 closest distance to " O   HOH Z  93 " =    2.236
peak=   -3.445 closest distance to " OE1 GLN A  88 " =    1.133
peak=   -3.431 closest distance to " NH1AARG A 275 " =    1.768
peak=   -3.430 closest distance to " O   HOH Z  38 " =    1.611
peak=   -3.430 closest distance to " O   HOH Z 191 " =    5.550
peak=   -3.428 closest distance to " OD1 ASP A 191 " =    1.436
peak=   -3.425 closest distance to " O   HOH Z 211 " =    1.577
peak=   -3.422 closest distance to " CB  PRO A 163 " =    2.548
peak=   -3.419 closest distance to " O   HOH Z  11 " =    1.868
peak=   -3.419 closest distance to " CE3 TRP A 274 " =    2.397
peak=   -3.411 closest distance to " OG  SER A  97 " =    2.087
peak=   -3.405 closest distance to " O   ALA A  34 " =    2.597
peak=   -3.404 closest distance to " CD2 PHE A 192 " =    2.016
peak=   -3.398 closest distance to " CB  TRP A  85 " =    2.401
peak=   -3.394 closest distance to " O   TRP A  70 " =    1.437
peak=   -3.391 closest distance to " O   GLY A 196 " =    1.034
peak=   -3.378 closest distance to " CA  ASP A  27 " =    2.450
peak=   -3.373 closest distance to " CB  ALA A 248 " =    1.976
peak=   -3.353 closest distance to " CB  ALA A  43 " =    2.474
peak=   -3.350 closest distance to " CD  ARG A  36 " =    1.962
peak=   -3.346 closest distance to " ND2 ASN A 249 " =    2.110
peak=   -3.332 closest distance to " O   HOH Z 417 " =    2.469
peak=   -3.331 closest distance to " CB  CYS A 201 " =    2.550
peak=   -3.329 closest distance to " CA  TRP A  70 " =    2.436
peak=   -3.326 closest distance to " OXT GLY A 302 " =    3.447
peak=   -3.321 closest distance to " OG BSER A 134 " =    1.615
peak=   -3.320 closest distance to " CG2 VAL A 189 " =    1.998
peak=   -3.317 closest distance to " OG  SER A  87 " =    1.385
peak=   -3.316 closest distance to " O   HOH Z 250 " =    1.462
peak=   -3.316 closest distance to " O   HOH Z 281 " =    2.759
peak=   -3.316 closest distance to " O   HOH Z 309 " =    2.449
peak=   -3.310 closest distance to " O   HOH Z 324 " =    2.092
peak=   -3.308 closest distance to " CE3 TRP A 123 " =    1.263
peak=   -3.303 closest distance to " CA  ARG A 139 " =    1.061
peak=   -3.302 closest distance to " CB  ALA A 131 " =    1.941
peak=   -3.299 closest distance to " CG  GLN A  88 " =    0.826
peak=   -3.298 closest distance to " O   HOH Z  10 " =    1.458
peak=   -3.296 closest distance to " CG  TRP A 266 " =    1.798
peak=   -3.293 closest distance to " N   SER A 276 " =    1.183
peak=   -3.288 closest distance to " CB  ILE A  33 " =    2.941
peak=   -3.287 closest distance to " O   HOH Z 266 " =    5.020
peak=   -3.286 closest distance to " O   PRO A 243 " =    2.503
peak=   -3.273 closest distance to " CG1 VAL A 197 " =    2.237
peak=   -3.271 closest distance to " O   VAL A 189 " =    2.482
peak=   -3.271 closest distance to " O   HOH Z  65 " =    1.307
peak=   -3.268 closest distance to " CB  ASP A 132 " =    2.195
peak=   -3.266 closest distance to " CA  TRP A 274 " =    1.517
peak=   -3.266 closest distance to " O   HOH Z  90 " =    2.746
peak=   -3.261 closest distance to " O   ASP A 162 " =    2.260
peak=   -3.254 closest distance to " N   ALA A 248 " =    1.558
peak=   -3.253 closest distance to " CE  LYS A  76 " =    2.735
peak=   -3.252 closest distance to " N   GLN A 122 " =    1.444
peak=   -3.251 closest distance to " O   VAL A 197 " =    1.404
peak=   -3.246 closest distance to " N   THR A 235 " =    1.303
peak=   -3.242 closest distance to " NE2 GLN A  88 " =    1.954
peak=   -3.242 closest distance to " O   GLN A 240 " =    2.031
peak=   -3.240 closest distance to " CE  MET A  93 " =    1.189
peak=   -3.237 closest distance to " O   HOH Z 168 " =    1.818
peak=   -3.235 closest distance to " OD2 ASP A 171 " =    1.738
peak=   -3.234 closest distance to " O   HOH Z 385 " =    1.964
peak=   -3.234 closest distance to " OD2 ASP A 191 " =    1.495
peak=   -3.233 closest distance to " CD2 LEU A 143 " =    2.570
peak=   -3.233 closest distance to " CB  ASP A 286 " =    2.211
peak=   -3.232 closest distance to " O   ASN A 249 " =    1.449
peak=   -3.226 closest distance to " CG2 ILE A 263 " =    2.303
peak=   -3.223 closest distance to " CA  GLY A 241 " =    2.222
peak=   -3.220 closest distance to " O   HOH Z 359 " =    3.204
peak=   -3.219 closest distance to " O   HOH Z 166 " =    1.492
peak=   -3.219 closest distance to " O   HOH Z 351 " =    1.685
peak=   -3.216 closest distance to " CB  ALA A   7 " =    2.086
peak=   -3.213 closest distance to " O   HOH Z 322 " =    1.573
peak=   -3.213 closest distance to " CE3 TRP A 150 " =    2.019
peak=   -3.210 closest distance to " CG1 VAL A 250 " =    2.600
peak=   -3.209 closest distance to " OH  TYR A 169 " =    1.016
peak=   -3.208 closest distance to " NH2 ARG A  79 " =    1.886
peak=   -3.207 closest distance to " SG ACYS A 201 " =    2.029
peak=   -3.205 closest distance to " O   HOH Z 417 " =    2.753
peak=   -3.204 closest distance to " OG  SER A  62 " =    1.635
peak=   -3.201 closest distance to " O   HOH Z 390 " =    2.432
peak=   -3.199 closest distance to " O   SER A  62 " =    1.977
peak=   -3.198 closest distance to " O   HOH Z 210 " =    1.055
peak=   -3.195 closest distance to " N   THR A 157 " =    1.464
peak=   -3.192 closest distance to " OD2 ASP A 171 " =    2.303
peak=   -3.186 closest distance to " O   HOH Z 266 " =    4.357
peak=   -3.186 closest distance to " CA  GLY A 133 " =    1.969
peak=   -3.186 closest distance to " OH  TYR A 214 " =    1.204
peak=   -3.179 closest distance to " O   HOH Z 298 " =    2.507
peak=   -3.178 closest distance to " CD  GLN A  58 " =    1.123
peak=   -3.176 closest distance to " O   HOH Z 350 " =    1.729
peak=   -3.173 closest distance to " CG  PRO A 163 " =    2.506
peak=   -3.173 closest distance to " CD2 TYR A 293 " =    2.003
peak=   -3.168 closest distance to " CZ2 TRP A 179 " =    2.291
peak=   -3.165 closest distance to " O   VAL A 174 " =    2.080
peak=   -3.160 closest distance to " O   HOH Z 137 " =    1.541
peak=   -3.158 closest distance to " O   HOH Z  97 " =    1.722
peak=   -3.155 closest distance to " CB  ALA A 248 " =    2.396
peak=   -3.154 closest distance to " O   GLY A 203 " =    2.466
peak=   -3.150 closest distance to " OD1 ASP A 171 " =    1.565
peak=   -3.149 closest distance to " O   HOH Z 244 " =    2.041
peak=   -3.146 closest distance to " CD  GLU A 236 " =    1.061
peak=   -3.146 closest distance to " OD1 ASP A 200 " =    1.408
peak=   -3.134 closest distance to " O   HOH Z  63 " =    1.483
peak=   -3.125 closest distance to " O   PRO A 198 " =    1.274
peak=   -3.121 closest distance to " ND2 ASN A 252 " =    1.583
peak=   -3.115 closest distance to " CD2 LEU A 300 " =    2.819
peak=   -3.102 closest distance to " CG  GLU A 277 " =    1.195
peak=   -3.102 closest distance to " O   SER A  22 " =    2.366
peak=   -3.093 closest distance to " CA  GLY A 241 " =    3.143
peak=   -3.091 closest distance to " O   HOH Z 423 " =    1.173
peak=   -3.091 closest distance to " O   HOH Z 222 " =    1.175
peak=   -3.088 closest distance to " CG  GLU A 152 " =    1.198
peak=   -3.082 closest distance to " CD1 ILE A 199 " =    2.592
peak=   -3.080 closest distance to " O   HOH Z 361 " =    3.388
peak=   -3.072 closest distance to " C   MET A 188 " =    1.518
peak=   -3.068 closest distance to " O   HOH Z  28 " =    2.057
peak=   -3.066 closest distance to " O   HOH Z 128 " =    2.459
peak=   -3.060 closest distance to " CD1 TYR A 247 " =    2.546
peak=   -3.058 closest distance to " O   HOH Z 111 " =    2.377
peak=   -3.054 closest distance to " O   HOH Z 348 " =    1.730
peak=   -3.052 closest distance to " CZ2 TRP A 150 " =    2.221
peak=   -3.048 closest distance to " CG  ARG A 269 " =    2.032
peak=   -3.045 closest distance to " O   ASN A 209 " =    1.783
peak=   -3.044 closest distance to " O   HOH Z 170 " =    1.889
peak=   -3.003 closest distance to " CD  GLN A 223 " =    1.361

================= 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    :  0.3738 0.3727   6.139405e+00   6.135005e+00
   1_bss:  0.3627 0.3625   6.127992e+00   6.112784e+00
   1_xyz:  0.2065 0.2327   5.641615e+00   5.746951e+00
   1_adp:  0.1909 0.2416   5.603276e+00   5.785078e+00
   1_occ:  0.1904 0.2417   5.601773e+00   5.784177e+00
   2_bss:  0.1892 0.2395   5.598196e+00   5.778399e+00
   2_xyz:  0.1379 0.1831   5.314621e+00   5.531772e+00
   2_adp:  0.1271 0.1699   5.238038e+00   5.458328e+00
   2_occ:  0.1269 0.1698   5.237559e+00   5.458135e+00
   3_bss:  0.1270 0.1699   5.237769e+00   5.457963e+00
   3_xyz:  0.1152 0.1574   5.155451e+00   5.388866e+00
   3_adp:  0.1132 0.1553   5.140030e+00   5.375324e+00
   3_occ:  0.1131 0.1552   5.139857e+00   5.375417e+00
   4_bss:  0.1130 0.1551   5.139482e+00   5.375267e+00
   4_xyz:  0.1081 0.1532   5.111278e+00   5.360776e+00
   4_adp:  0.1081 0.1530   5.111345e+00   5.359966e+00
   4_occ:  0.1080 0.1530   5.111328e+00   5.360235e+00
   5_bss:  0.1080 0.1530   5.111345e+00   5.360260e+00
   5_xyz:  0.1107 0.1541   5.128574e+00   5.369069e+00
   5_adp:  0.1098 0.1554   5.129665e+00   5.376699e+00
   5_occ:  0.1098 0.1554   5.129621e+00   5.376675e+00
   5_bss:  0.1098 0.1555   5.129699e+00   5.376727e+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:  0.330  39.443  -1.640  -0.507   0.721  -0.000   0.000   0.000
   1_xyz:  0.330  39.443  -1.640  -0.507   0.721  -0.000   0.000   0.000
   1_adp:  0.330  39.443  -1.640  -0.507   0.721  -0.000   0.000   0.000
   1_occ:  0.330  39.443  -1.640  -0.507   0.721  -0.000   0.000   0.000
   2_bss:  0.324  39.443  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   2_xyz:  0.324  39.443  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   2_adp:  0.324  39.443  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   2_occ:  0.324  39.443  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   3_bss:  0.323  43.155  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   3_xyz:  0.323  43.155  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   3_adp:  0.323  43.155  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   3_occ:  0.323  43.155  -2.236  -2.286  -1.235  -0.000  -0.000  -0.000
   4_bss:  0.323  43.155  -2.308  -2.496  -1.584  -0.000  -0.000  -0.000
   4_xyz:  0.323  43.155  -2.308  -2.496  -1.584  -0.000  -0.000  -0.000
   4_adp:  0.323  43.155  -2.308  -2.496  -1.584  -0.000  -0.000  -0.000
   4_occ:  0.323  43.155  -2.308  -2.496  -1.584  -0.000  -0.000  -0.000
   5_bss:  0.323  43.155  -2.182  -2.422  -1.515  -0.000  -0.000  -0.000
   5_xyz:  0.323  43.155  -2.182  -2.422  -1.515  -0.000  -0.000  -0.000
   5_adp:  0.323  43.155  -2.182  -2.422  -1.515  -0.000  -0.000  -0.000
   5_occ:  0.323  43.155  -2.182  -2.422  -1.515  -0.000  -0.000  -0.000
   5_bss:  0.323  43.138  -1.996  -2.262  -1.366  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.157 0.6432  0.8374    40596.746
   1_bss:  38.898 0.6559  0.8421    37142.977
   1_xyz:  22.302 0.8410  1.0043    14052.408
   1_adp:  23.712 0.8259  0.9919    15280.072
   1_occ:  23.696 0.8259  0.9913    15232.373
   2_bss:  23.490 0.8277  0.9430    14941.782
   2_xyz:  17.237 0.8870  0.9842     8499.592
   2_adp:  15.401 0.9034  0.9899     7364.687
   2_occ:  15.393 0.9034  0.9898     7355.532
   3_bss:  15.380 0.9035  0.9896     7351.530
   3_xyz:  13.965 0.9150  0.9931     6275.188
   3_adp:  13.642 0.9178  0.9897     6116.884
   3_occ:  13.644 0.9178  0.9896     6115.371
   4_bss:  13.637 0.9179  0.9820     6114.078
   4_xyz:  13.333 0.9202  0.9828     5918.502
   4_adp:  13.287 0.9207  0.9793     5916.505
   4_occ:  13.293 0.9206  0.9792     5919.493
   5_bss:  13.293 0.9206  0.9824     5920.731
   5_xyz:  13.436 0.9197  0.9814     6019.903
   5_adp:  13.603 0.9184  0.9757     6098.804
   5_occ:  13.604 0.9184  0.9756     6099.169
   5_bss:  13.606 0.9184  0.9809     6100.797
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6386e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6386e-01
   1_xyz:   1.134  0.008  0.074 15.061  0.005  4.107   7.3670e-02
   1_adp:   1.134  0.008  0.074 15.061  0.005  4.107   7.3670e-02
   1_occ:   1.134  0.008  0.074 15.061  0.005  4.107   7.3670e-02
   2_bss:   1.134  0.008  0.074 15.061  0.005  4.107   7.3670e-02
   2_xyz:   0.964  0.006  0.069 14.233  0.004  4.113   5.3248e-02
   2_adp:   0.964  0.006  0.069 14.233  0.004  4.113   5.3248e-02
   2_occ:   0.964  0.006  0.069 14.233  0.004  4.113   5.3248e-02
   3_bss:   0.964  0.006  0.069 14.233  0.004  4.113   5.3248e-02
   3_xyz:   0.935  0.006  0.070 14.390  0.004  4.114   5.2891e-02
   3_adp:   0.935  0.006  0.070 14.390  0.004  4.114   5.2891e-02
   3_occ:   0.935  0.006  0.070 14.390  0.004  4.114   5.2891e-02
   4_bss:   0.935  0.006  0.070 14.390  0.004  4.114   5.2891e-02
   4_xyz:   1.013  0.007  0.074 14.619  0.004  4.115   6.0548e-02
   4_adp:   1.013  0.007  0.074 14.619  0.004  4.115   6.0548e-02
   4_occ:   1.013  0.007  0.074 14.619  0.004  4.115   6.0548e-02
   5_bss:   1.013  0.007  0.074 14.619  0.004  4.115   6.0548e-02
   5_xyz:   0.878  0.005  0.066 14.268  0.003  4.115   4.8158e-02
   5_adp:   0.878  0.005  0.066 14.268  0.003  4.115   4.8158e-02
   5_occ:   0.878  0.005  0.066 14.268  0.003  4.115   4.8158e-02
   5_bss:   0.878  0.005  0.066 14.268  0.003  4.115   4.8158e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3962e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3962e-01
   1_xyz:   8.107  0.039  0.365 85.866  0.049  2.295   1.0097e-01
   1_adp:   8.107  0.039  0.365 85.866  0.049  2.295   1.0097e-01
   1_occ:   8.107  0.039  0.365 85.866  0.049  2.295   1.0097e-01
   2_bss:   8.107  0.039  0.365 85.866  0.049  2.295   1.0097e-01
   2_xyz:   8.280  0.045  0.231 83.414  0.039  2.345   4.6090e-02
   2_adp:   8.280  0.045  0.231 83.414  0.039  2.345   4.6090e-02
   2_occ:   8.280  0.045  0.231 83.414  0.039  2.345   4.6090e-02
   3_bss:   8.280  0.045  0.231 83.414  0.039  2.345   4.6090e-02
   3_xyz:   7.880  0.041  0.214 84.409  0.033  2.330   3.7429e-02
   3_adp:   7.880  0.041  0.214 84.409  0.033  2.330   3.7429e-02
   3_occ:   7.880  0.041  0.214 84.409  0.033  2.330   3.7429e-02
   4_bss:   7.880  0.041  0.214 84.409  0.033  2.330   3.7429e-02
   4_xyz:   7.298  0.039  0.229 83.716  0.040  2.284   4.5540e-02
   4_adp:   7.298  0.039  0.229 83.716  0.040  2.284   4.5540e-02
   4_occ:   7.298  0.039  0.229 83.716  0.040  2.284   4.5540e-02
   5_bss:   7.298  0.039  0.229 83.716  0.040  2.284   4.5540e-02
   5_xyz:   7.180  0.041  0.205 84.110  0.035  2.356   2.8318e-02
   5_adp:   7.180  0.041  0.205 84.110  0.035  2.356   2.8318e-02
   5_occ:   7.180  0.041  0.205 84.110  0.035  2.356   2.8318e-02
   5_bss:   7.180  0.041  0.205 84.110  0.035  2.356   2.8318e-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:  61.92   0.00  16.94  61.21   0.00  12.97  61.92   5.79  38.55
   1_occ:  61.92   0.00  16.94  61.21   0.00  12.97  61.92   5.79  38.55
   2_bss:  61.92   0.00  16.94  61.21   0.00  12.97  61.92   5.79  38.55
   2_xyz:  61.92   0.00  16.94  61.21   0.00  12.97  61.92   5.79  38.55
   2_adp:  74.54   1.20  17.10  74.54   1.20  12.95  73.52   5.69  39.72
   2_occ:  74.54   1.20  17.10  74.54   1.20  12.95  73.52   5.69  39.72
   3_bss:  74.54   1.20  17.10  74.54   1.20  12.95  73.52   5.69  39.72
   3_xyz:  74.54   1.20  17.10  74.54   1.20  12.95  73.52   5.69  39.72
   3_adp:  83.95   1.03  17.00  83.95   1.03  12.88  80.18   4.66  39.43
   3_occ:  83.95   1.03  17.00  83.95   1.03  12.88  80.18   4.66  39.43
   4_bss:  83.95   1.03  17.00  83.95   1.03  12.88  80.18   4.66  39.43
   4_xyz:  83.95   1.03  17.00  83.95   1.03  12.88  80.18   4.66  39.43
   4_adp:  85.25   1.45  16.66  85.25   1.45  12.74  81.93   5.67  38.00
   4_occ:  85.25   1.45  16.66  85.25   1.45  12.74  81.93   5.67  38.00
   5_bss:  85.25   1.45  16.66  85.25   1.45  12.74  81.93   5.67  38.00
   5_xyz:  85.25   1.45  16.66  85.25   1.45  12.74  81.93   5.67  38.00
   5_adp:  92.32   0.53  16.87  92.32   0.53  12.73  85.11   6.21  39.40
   5_occ:  92.32   0.53  16.87  92.32   0.53  12.73  85.11   6.21  39.40
   5_bss:  92.30   0.51  16.85  92.30   0.51  12.71  85.09   6.19  39.38
------------------------------------------------------------------------
 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:    1.514    0.012    0.349
   1_adp:    1.514    0.012    0.349
   1_occ:    1.514    0.012    0.349
   2_bss:    1.514    0.012    0.349
   2_xyz:    0.989    0.022    0.431
   2_adp:    0.989    0.022    0.431
   2_occ:    0.989    0.022    0.431
   3_bss:    0.989    0.022    0.431
   3_xyz:    0.891    0.040    0.466
   3_adp:    0.891    0.040    0.466
   3_occ:    0.891    0.040    0.466
   4_bss:    0.891    0.040    0.466
   4_xyz:    0.976    0.047    0.484
   4_adp:    0.976    0.047    0.484
   4_occ:    0.976    0.047    0.484
   5_bss:    0.976    0.047    0.484
   5_xyz:    1.024    0.047    0.487
   5_adp:    1.024    0.047    0.487
   5_occ:    1.024    0.047    0.487
   5_bss:    1.024    0.047    0.487
------------------------------------------------------------------------

CPU time actual refinement: 326.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_882/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_882/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_882/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_882/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_882/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.29 
  Macro-tasks:
    bulk solvent and scale       = 40.20  
    individual site refinement   = 132.99 
    weights calculation          = 29.94  
    collect and process          = 6.78   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 210.00 
  Micro-tasks:
    mask                            = 1.13   
    f_calc                          = 104.11 
    alpha_beta                      = 8.40   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 108.42 
    fmodel                         = 6.76   
    r_factors                      = 0.20   
    phase_errors                   = 12.03  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 242.54 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.625 micro seconds
Total CPU time: 5.66 minutes
from_scatterers_fft:    640 calls, 103.54 s
gradients_fft:          585 calls,  96.89 s

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

# Date 2008-01-16 Time 05:53:21 PST -0800 (1200491601.10 s)
Start R-work = 0.3738, R-free = 0.3727 (no bulk solvent and anisotropic scale)
Final R-work = 0.1341, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.3627, R-free = 0.3625
Final R-work = 0.1098, R-free = 0.1555