# Date 2008-01-16 Time 05:52:36 PST -0800 (1200491556.45 s)
#phil __OFF__

Command line arguments: "../913.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1708
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 913

-------------------------------------------------------------------------------
  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, 47.1647, 84.2302, 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: 3.31, per 1000 atoms: 1.17


================================== 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, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95138
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923052

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9514

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, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95138
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923052

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1767 [2219/2248]  1999   220   9.9%
  bin  2:  4.1767 -  3.3271 [2129/2152]  1916   213  10.0%
  bin  3:  3.3271 -  2.9100 [2096/2121]  1881   215  10.3%
  bin  4:  2.9100 -  2.6455 [2099/2115]  1896   203   9.7%
  bin  5:  2.6455 -  2.4568 [2053/2092]  1846   207  10.1%
  bin  6:  2.4568 -  2.3125 [2080/2113]  1876   204   9.8%
  bin  7:  2.3125 -  2.1970 [2039/2075]  1827   212  10.4%
  bin  8:  2.1970 -  2.1017 [2022/2064]  1823   199   9.8%
  bin  9:  2.1017 -  2.0210 [2059/2097]  1856   203   9.9%
  bin 10:  2.0210 -  1.9514 [ 793/2082]   710    83  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_913/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:
        1.49 -     2.18: 20
        2.18 -     2.86: 1150
        2.86 -     3.54: 4448
        3.54 -     4.22: 9282
        4.22 -     4.90: 13576
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.494 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.511 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  17 " - " O   HOH Z 333 "  1.877 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28471 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_913/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_913/model_refine_001.geo

CPU time processing inputs: 9.18


============================ 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 47.16465 84.23025 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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3934   r_free= 0.3961   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.185812                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6590 0.99   1439  162 0.3151 0.3136      6.4394      6.4317|
|  2:  4.6590 -  3.7166 0.99   1384  149 0.3149 0.2997      6.6191       6.619|
|  3:  3.7166 -  3.2522 0.99   1364  155 0.3519 0.3703       6.516       6.614|
|  4:  3.2522 -  2.9574 0.99   1349  149 0.3763 0.3707      6.3846      6.3904|
|  5:  2.9574 -  2.7468 0.98   1332  147 0.4031 0.3806      6.2415      6.2378|
|  6:  2.7468 -  2.5857 0.99   1344  151 0.4268 0.4219      6.1776      6.1232|
|  7:  2.5857 -  2.4568 0.99   1326  145 0.4167 0.3806        6.15      6.0908|
|  8:  2.4568 -  2.3503 0.99   1329  148 0.4341 0.4552      6.0812       6.139|
|  9:  2.3503 -  2.2601 0.99   1314  151 0.4393 0.4355      6.0584      6.0209|
| 10:  2.2601 -  2.1823 0.98   1331  146 0.4600 0.4895      6.0323      6.0778|
| 11:  2.1823 -  2.1143 0.98   1313  138 0.4533 0.5491      5.9649      6.0516|
| 12:  2.1143 -  2.0540 1.00   1315  150 0.4560 0.4704      5.9023       5.948|
| 13:  2.0540 -  2.0001 0.87   1163  138 0.4725 0.4560      5.8356      5.8088|
| 14:  2.0001 -  1.9514 0.24    327   30 0.5671 0.5173      5.8253      5.8034|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6590  1439   162  0.76  28.59   0.85     0.78      50070.73|
|  2:  4.6590 -  3.7166  1384   149  0.78  27.94   0.96     0.87      68863.41|
|  3:  3.7166 -  3.2522  1364   155  0.71  34.49   0.96     0.88      74798.26|
|  4:  3.2522 -  2.9574  1349   149  0.64  40.68   0.97     0.84      68214.77|
|  5:  2.9574 -  2.7468  1332   147  0.58  45.49   0.94     0.79      55700.37|
|  6:  2.7468 -  2.5857  1344   151  0.57  46.08   0.95     0.77      46701.87|
|  7:  2.5857 -  2.4568  1326   145  0.58  45.58   0.97     0.76      42519.70|
|  8:  2.4568 -  2.3503  1329   148  0.55  47.99   0.95     0.77      40760.38|
|  9:  2.3503 -  2.2601  1314   151  0.53  49.96   0.99     0.75      39161.17|
| 10:  2.2601 -  2.1823  1331   146  0.48  53.82   1.00     0.69      40499.05|
| 11:  2.1823 -  2.1143  1313   138  0.44  57.11   0.99     0.65      38938.01|
| 12:  2.1143 -  2.0540  1315   150  0.41  59.60   0.99     0.65      38190.95|
| 13:  2.0540 -  2.0001  1163   138  0.40  60.15   0.97     0.62      32461.47|
| 14:  2.0001 -  1.9514   327    30  0.36  62.86   0.91     0.54      27981.73|
|alpha:            min =        0.54 max =            0.88 mean =         0.75|
|beta:             min =    27981.73 max =        74798.26 mean =     48923.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        45.92|
|phase err.(test): min =        0.00 max =           89.88 mean =        45.84|
|-----------------------------------------------------------------------------|

============================== 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 = 6.003085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.850   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.434739              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.200   (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 |  1.494 -  1.835:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.835 -  2.175:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.175 -  2.516:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.516 -  2.856:     1124 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.856 -  3.197:     1974 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.197 -  3.538:     2474 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.538 -  3.878:     4651 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.878 -  4.219:     4631 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.219 -  4.559:     6183 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7393 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.494 |       0.434 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3934   r_free= 0.3961   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.185812                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3815   r_free= 0.3852   ksol= 0.30   Bsol= 50.00   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.91,3.27,-0.00,0.00,0.00); trace/3= -0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.175658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.793455              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.934   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.668363              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.065   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3815      final r-factor (work) = 0.2716          |
| start r-factor (free) = 0.3852      final r-factor (free) = 0.3046          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9718 = 4.79 * 0.50 * 6.1721 + 1.00 * 0.1790                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4670 = 4.79 * 0.50 * 5.9978 + 1.00 * 0.0919                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2716      final r-factor (work) = 0.2487          |
| start r-factor (free) = 0.3046      final r-factor (free) = 0.3105          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0150 = 0.67 * 1.00 * 5.9978 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9195 = 0.67 * 1.00 * 5.8459 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.05   17.90    None  None   None       |
|    all(noH): 2823   0      0.00    85.05   17.90    None  None   None       |
|    Sol.    : 438    0      4.26    83.12   40.22    None  None   None       |
|    Mac.    : 2385   0      0.00    85.05   13.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.505:  726   |   5:    42.525 -  51.030:  104        |
|      1:     8.505 -  17.010: 1088   |   6:    51.030 -  59.535:   62        |
|      2:    17.010 -  25.515:  443   |   7:    59.535 -  68.040:   46        |
|      3:    25.515 -  34.020:  182   |   8:    68.040 -  76.545:   21        |
|      4:    34.020 -  42.525:  147   |   9:    76.545 -  85.050:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2487 r_free = 0.3105             target_work(ml) = 5.854         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2483 r_free = 0.3105             target_work(ml) = 5.853         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2483   r_free= 0.3105   ksol= 0.30   Bsol= 50.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.91,3.27,-0.00,0.00,0.00); trace/3= -0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.852883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2468   r_free= 0.3065   ksol= 0.32   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.02,0.36,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.848410                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.264200              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.456   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.437343              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.350  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2468      final r-factor (work) = 0.1760          |
| start r-factor (free) = 0.3065      final r-factor (free) = 0.2273          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5589 = 4.26 * 0.50 * 5.8473 + 1.00 * 0.0919                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2708 = 4.26 * 0.50 * 5.7209 + 1.00 * 0.0733                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1760      final r-factor (work) = 0.1586          |
| start r-factor (free) = 0.2273      final r-factor (free) = 0.2097          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5143 = 0.44 * 1.00 * 5.7209 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4099 = 0.44 * 1.00 * 5.4884 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    82.59   17.83    None  None   None       |
|    all(noH): 2823   0      0.98    82.59   17.83    None  None   None       |
|    Sol.    : 438    0      5.98    82.44   41.91    None  None   None       |
|    Mac.    : 2385   0      0.98    82.59   13.41    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:     0.984 -   9.145:  802   |   5:    41.788 -  49.949:  111        |
|      1:     9.145 -  17.305: 1164   |   6:    49.949 -  58.110:   91        |
|      2:    17.305 -  25.466:  325   |   7:    58.110 -  66.270:   39        |
|      3:    25.466 -  33.627:  138   |   8:    66.270 -  74.431:   26        |
|      4:    33.627 -  41.788:  111   |   9:    74.431 -  82.592:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1586 r_free = 0.2097             target_work(ml) = 5.448         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1584 r_free = 0.2096             target_work(ml) = 5.447         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1584   r_free= 0.2096   ksol= 0.32   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.02,0.36,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.446978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1578   r_free= 0.2081   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.31,-1.38,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.442342                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.633031              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.648   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216698              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.190  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1578      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.2081      final r-factor (free) = 0.1722          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0464 = 3.63 * 0.50 * 5.4903 + 1.00 * 0.0732                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7911 = 3.63 * 0.50 * 5.3556 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1214          |
| start r-factor (free) = 0.1722      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1701 = 0.22 * 1.00 * 5.3556 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1417 = 0.22 * 1.00 * 5.2318 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.46    84.57   17.37    None  None   None       |
|    all(noH): 2823   0      2.46    84.57   17.37    None  None   None       |
|    Sol.    : 438    0      4.90    79.06   40.35    None  None   None       |
|    Mac.    : 2385   0      2.46    84.57   13.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.464 -  10.674: 1129   |   5:    43.515 -  51.725:  111        |
|      1:    10.674 -  18.884:  997   |   6:    51.725 -  59.935:   51        |
|      2:    18.884 -  27.094:  227   |   7:    59.935 -  68.146:   35        |
|      3:    27.094 -  35.305:  120   |   8:    68.146 -  76.356:   23        |
|      4:    35.305 -  43.515:  124   |   9:    76.356 -  84.566:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1214 r_free = 0.1654             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1212 r_free = 0.1652             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1652   ksol= 0.33   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.31,-1.38,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.204905                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1646   ksol= 0.33   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.42,-2.02,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204907                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.394870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.405  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.507630              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.638  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1214      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9446 = 3.39 * 0.50 * 5.2327 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8466 = 3.39 * 0.50 * 5.1693 + 1.00 * 0.0720                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6320 = 0.51 * 1.00 * 5.1693 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6142 = 0.51 * 1.00 * 5.1328 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.99    92.79   17.32    None  None   None       |
|    all(noH): 2823   0      1.99    92.79   17.32    None  None   None       |
|    Sol.    : 438    0      5.51    81.00   40.39    None  None   None       |
|    Mac.    : 2385   0      1.99    92.79   13.08    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:     1.991 -  11.071: 1243   |   5:    47.390 -  56.470:  106        |
|      1:    11.071 -  20.151:  940   |   6:    56.470 -  65.550:   43        |
|      2:    20.151 -  29.231:  213   |   7:    65.550 -  74.630:   25        |
|      3:    29.231 -  38.310:  119   |   8:    74.630 -  83.710:   10        |
|      4:    38.310 -  47.390:  120   |   9:    83.710 -  92.789:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1568             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1567             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1567   ksol= 0.33   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.42,-2.02,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133001                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1567   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.29,-2.06,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132905                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.299323              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.229  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.180541              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.876  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5392 = 3.30 * 0.50 * 5.1327 + 1.00 * 0.0720                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5272 = 3.30 * 0.50 * 5.1254 + 1.00 * 0.0721                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9340 = 0.18 * 1.00 * 5.1254 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9336 = 0.18 * 1.00 * 5.1309 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.39    90.25   16.69    None  None   None       |
|    all(noH): 2823   0      2.39    90.25   16.69    None  None   None       |
|    Sol.    : 438    0      6.21    72.52   37.82    None  None   None       |
|    Mac.    : 2385   0      2.39    90.25   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.387 -  11.173: 1287   |   5:    46.317 -  55.103:   94        |
|      1:    11.173 -  19.959:  918   |   6:    55.103 -  63.889:   34        |
|      2:    19.959 -  28.745:  193   |   7:    63.889 -  72.675:   20        |
|      3:    28.745 -  37.531:  149   |   8:    72.675 -  81.461:    2        |
|      4:    37.531 -  46.317:  122   |   9:    81.461 -  90.247:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1567             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1566             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1566   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.29,-2.06,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130497                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6590 0.99   1439  162 0.0957 0.1295      5.3673      5.5648|
|  2:  4.6590 -  3.7166 0.99   1384  149 0.0820 0.1053      5.4047      5.6314|
|  3:  3.7166 -  3.2522 0.99   1364  155 0.1013 0.1630      5.4371      5.8562|
|  4:  3.2522 -  2.9574 0.99   1349  149 0.1201 0.1505      5.4385      5.5689|
|  5:  2.9574 -  2.7468 0.98   1332  147 0.1245 0.1783      5.2919      5.5176|
|  6:  2.7468 -  2.5857 0.99   1344  151 0.1196 0.1813      5.1906      5.4073|
|  7:  2.5857 -  2.4568 0.99   1326  145 0.1176 0.1671      5.1295      5.3638|
|  8:  2.4568 -  2.3503 0.99   1329  148 0.1101 0.1677      5.0258      5.2583|
|  9:  2.3503 -  2.2601 0.99   1314  151 0.1126 0.1864      4.9909       5.299|
| 10:  2.2601 -  2.1823 0.98   1331  146 0.1081 0.1605      4.9428      5.1941|
| 11:  2.1823 -  2.1143 0.98   1313  138 0.1101 0.1902      4.9155      5.2868|
| 12:  2.1143 -  2.0540 1.00   1315  150 0.1066 0.1611      4.8419      5.0556|
| 13:  2.0540 -  2.0001 0.87   1163  138 0.1090 0.1702       4.747      4.9803|
| 14:  2.0001 -  1.9514 0.24    327   30 0.1059 0.1505      4.6166       4.895|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6590  1439   162  0.94   8.78   0.98     0.95       6988.90|
|  2:  4.6590 -  3.7166  1384   149  0.95   7.98   1.01     1.00       8751.74|
|  3:  3.7166 -  3.2522  1364   155  0.94  11.11   1.02     1.02      10007.50|
|  4:  3.2522 -  2.9574  1349   149  0.92  14.14   1.00     0.98      10385.32|
|  5:  2.9574 -  2.7468  1332   147  0.90  16.09   0.99     0.96       8117.03|
|  6:  2.7468 -  2.5857  1344   151  0.90  15.93   0.98     0.95       6885.06|
|  7:  2.5857 -  2.4568  1326   145  0.91  14.91   0.99     0.96       5907.05|
|  8:  2.4568 -  2.3503  1329   148  0.91  15.38   0.99     0.96       5118.41|
|  9:  2.3503 -  2.2601  1314   151  0.90  15.70   1.00     0.97       4729.95|
| 10:  2.2601 -  2.1823  1331   146  0.91  15.03   0.99     0.96       4367.82|
| 11:  2.1823 -  2.1143  1313   138  0.90  16.41   1.00     0.96       4337.55|
| 12:  2.1143 -  2.0540  1315   150  0.91  15.77   1.00     0.99       3881.31|
| 13:  2.0540 -  2.0001  1163   138  0.91  15.65   0.99     0.98       3115.92|
| 14:  2.0001 -  1.9514   327    30  0.90  15.47   0.99     0.96       2375.57|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2375.57 max =        10385.32 mean =      6339.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1566   ksol= 0.33   Bsol= 49.91   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.09,-1.89,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130550                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1566   ksol= 0.33   Bsol= 49.91   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.09,-1.89,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130550                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6590 0.99   1439  162 0.0957 0.1296      5.3679      5.5656|
|  2:  4.6590 -  3.7166 0.99   1384  149 0.0820 0.1053      5.4049      5.6313|
|  3:  3.7166 -  3.2522 0.99   1364  155 0.1013 0.1630      5.4369      5.8561|
|  4:  3.2522 -  2.9574 0.99   1349  149 0.1201 0.1505      5.4385      5.5689|
|  5:  2.9574 -  2.7468 0.98   1332  147 0.1245 0.1783      5.2919      5.5176|
|  6:  2.7468 -  2.5857 0.99   1344  151 0.1196 0.1813      5.1907      5.4074|
|  7:  2.5857 -  2.4568 0.99   1326  145 0.1176 0.1671      5.1296      5.3639|
|  8:  2.4568 -  2.3503 0.99   1329  148 0.1101 0.1677      5.0258      5.2583|
|  9:  2.3503 -  2.2601 0.99   1314  151 0.1126 0.1863      4.9909      5.2987|
| 10:  2.2601 -  2.1823 0.98   1331  146 0.1081 0.1605      4.9428      5.1939|
| 11:  2.1823 -  2.1143 0.98   1313  138 0.1101 0.1901      4.9156      5.2869|
| 12:  2.1143 -  2.0540 1.00   1315  150 0.1066 0.1610      4.8416      5.0554|
| 13:  2.0540 -  2.0001 0.87   1163  138 0.1090 0.1702      4.7469      4.9802|
| 14:  2.0001 -  1.9514 0.24    327   30 0.1059 0.1505      4.6167      4.8955|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6590  1439   162  0.94   8.79   0.98     0.95       6996.33|
|  2:  4.6590 -  3.7166  1384   149  0.95   7.99   1.01     1.00       8754.51|
|  3:  3.7166 -  3.2522  1364   155  0.94  11.11   1.02     1.02      10004.39|
|  4:  3.2522 -  2.9574  1349   149  0.92  14.14   1.01     0.98      10384.12|
|  5:  2.9574 -  2.7468  1332   147  0.90  16.10   0.99     0.96       8117.51|
|  6:  2.7468 -  2.5857  1344   151  0.90  15.93   0.99     0.96       6886.39|
|  7:  2.5857 -  2.4568  1326   145  0.91  14.91   0.99     0.96       5908.11|
|  8:  2.4568 -  2.3503  1329   148  0.91  15.39   1.00     0.97       5118.33|
|  9:  2.3503 -  2.2601  1314   151  0.90  15.70   1.00     0.97       4728.97|
| 10:  2.2601 -  2.1823  1331   146  0.91  15.03   1.00     0.97       4367.02|
| 11:  2.1823 -  2.1143  1313   138  0.90  16.42   1.00     0.97       4336.73|
| 12:  2.1143 -  2.0540  1315   150  0.91  15.76   1.01     1.00       3879.67|
| 13:  2.0540 -  2.0001  1163   138  0.91  15.66   1.00     0.99       3115.80|
| 14:  2.0001 -  1.9514   327    30  0.90  15.47   0.99     0.96       2376.71|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2376.71 max =        10384.12 mean =      6339.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.30    90.16   16.61    None  None   None       |
|    all(noH): 2823   0      2.30    90.16   16.61    None  None   None       |
|    Sol.    : 438    0      6.13    72.43   37.74    None  None   None       |
|    Mac.    : 2385   0      2.30    90.16   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:     2.300 -  11.086: 1287   |   5:    46.230 -  55.016:   94        |
|      1:    11.086 -  19.872:  918   |   6:    55.016 -  63.802:   34        |
|      2:    19.872 -  28.658:  193   |   7:    63.802 -  72.588:   20        |
|      3:    28.658 -  37.444:  149   |   8:    72.588 -  81.374:    2        |
|      4:    37.444 -  46.230:  122   |   9:    81.374 -  90.160:    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)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.522 - 4.294
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 308
   mapped sites are within: 0.708 - 4.294

peak=    5.806 closest distance to " NH2 ARG A  56 " =    2.204
peak=    5.441 closest distance to " CB  SER A  63 " =    1.213
peak=    5.400 closest distance to " CB  GLN A 223 " =    1.468
peak=    5.160 closest distance to " O   HOH Z 126 " =    1.820
peak=    5.142 closest distance to " CG  PRO A  54 " =    1.162
peak=    4.988 closest distance to " O   HOH Z 193 " =    1.940
peak=    4.847 closest distance to " O   HOH Z 232 " =    2.279
peak=    4.833 closest distance to " CB  GLN A 183 " =    1.246
peak=    4.764 closest distance to " O   HOH Z 236 " =    1.920
peak=    4.700 closest distance to " CB  GLU A 152 " =    1.177
peak=    4.589 closest distance to " CB  PRO A  54 " =    0.862
peak=    4.588 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.562 closest distance to " CB  SER A   3 " =    1.389
peak=    4.554 closest distance to " OD2 ASP A 286 " =    2.826
peak=    4.537 closest distance to " OD1 ASN A  69 " =    2.563
peak=    4.520 closest distance to " O   HOH Z 108 " =    1.593
peak=    4.501 closest distance to " NE2 GLN A  11 " =    1.092
peak=    4.468 closest distance to " C   PRO A 198 " =    1.514
peak=    4.444 closest distance to " O   HOH Z  15 " =    2.090
peak=    4.395 closest distance to " CB  ASN A 148 " =    1.805
peak=    4.343 closest distance to " CB  TYR A 169 " =    0.737
peak=    4.334 closest distance to " O   HOH Z 144 " =    1.615
peak=    4.331 closest distance to " CG  PRO A 213 " =    1.160
peak=    4.328 closest distance to " O   HOH Z 368 " =    1.976
peak=    4.319 closest distance to " CA  ALA A  21 " =    1.187
peak=    4.316 closest distance to " O   HOH Z 298 " =    1.858
peak=    4.308 closest distance to " O   HOH Z 207 " =    1.918
peak=    4.300 closest distance to " CA  TYR A  30 " =    0.945
peak=    4.266 closest distance to " ND2 ASN A 187 " =    1.654
peak=    4.265 closest distance to " O   HOH Z 369 " =    1.933
peak=    4.228 closest distance to " CB  LEU A 228 " =    1.066
peak=    4.216 closest distance to " CA  THR A 221 " =    0.969
peak=    4.203 closest distance to " O   HOH Z  78 " =    1.739
peak=    4.200 closest distance to " CB  GLU A 128 " =    1.114
peak=    4.185 closest distance to " CB  ARG A  79 " =    1.431
peak=    4.180 closest distance to " O   HOH Z 344 " =    3.033
peak=    4.167 closest distance to " O   HOH Z 234 " =    3.733
peak=    4.155 closest distance to " O   HOH Z 180 " =    2.161
peak=    4.139 closest distance to " O   HOH Z  21 " =    1.671
peak=    4.123 closest distance to " NH2BARG A 145 " =    2.057
peak=    4.078 closest distance to " CB  VAL A 202 " =    1.640
peak=    4.075 closest distance to " O   HOH Z 389 " =    1.949
peak=    4.046 closest distance to " O   HOH Z  61 " =    1.618
peak=    4.039 closest distance to " O   SER A  87 " =    2.207
peak=    4.011 closest distance to " O   HOH Z 203 " =    1.877
peak=    4.005 closest distance to " O   HOH Z  54 " =    1.704
peak=    4.003 closest distance to " CB  GLU A 277 " =    3.550
peak=    3.980 closest distance to " CB  TRP A 179 " =    1.372
peak=    3.965 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.954 closest distance to " O   HOH Z 426 " =    1.534
peak=    3.936 closest distance to " CG  PRO A  90 " =    1.107
peak=    3.935 closest distance to " O   HOH Z 261 " =    2.128
peak=    3.931 closest distance to " CA  ALA A  51 " =    0.914
peak=    3.916 closest distance to " O   MET A 105 " =    1.750
peak=    3.906 closest distance to " O   HOH Z  93 " =    2.488
peak=    3.905 closest distance to " O   HOH Z 371 " =    3.264
peak=    3.902 closest distance to " O   HOH Z 193 " =    2.080
peak=    3.892 closest distance to " O   HOH Z 197 " =    2.707
peak=    3.888 closest distance to " O   HOH Z 134 " =    1.489
peak=    3.887 closest distance to " NH1AARG A 145 " =    1.086
peak=    3.875 closest distance to " CG  PRO A 243 " =    1.172
peak=    3.864 closest distance to " CA  ASN A 215 " =    1.241
peak=    3.860 closest distance to " O   HOH Z 272 " =    1.851
peak=    3.846 closest distance to " O   HOH Z 303 " =    1.995
peak=    3.843 closest distance to " O   HOH Z  10 " =    1.877
peak=    3.835 closest distance to " O   HOH Z 403 " =    1.610
peak=    3.829 closest distance to " O   HOH Z 316 " =    2.991
peak=    3.814 closest distance to " O   HOH Z  68 " =    1.689
peak=    3.800 closest distance to " O   HOH Z 284 " =    3.061
peak=    3.788 closest distance to " CB  TYR A 169 " =    0.836
peak=    3.788 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.787 closest distance to " O   HOH Z  20 " =    1.706
peak=    3.783 closest distance to " O   HOH Z 128 " =    2.279
peak=    3.780 closest distance to " O   HOH Z  49 " =    2.228
peak=    3.776 closest distance to " O   HOH Z 427 " =    2.843
peak=    3.771 closest distance to " O   HOH Z  88 " =    3.426
peak=    3.769 closest distance to " O   HOH Z 133 " =    1.650
peak=    3.766 closest distance to " CB  ASN A 148 " =    1.011
peak=    3.764 closest distance to " O   HOH Z 133 " =    2.264
peak=    3.752 closest distance to " O   ALA A 165 " =    1.376
peak=    3.750 closest distance to " O   HOH Z 411 " =    1.765
peak=    3.734 closest distance to " O   HOH Z   6 " =    2.173
peak=    3.728 closest distance to " CA  MET A  40 " =    1.054
peak=    3.726 closest distance to " O   HOH Z 135 " =    1.661
peak=    3.724 closest distance to " O   HOH Z  97 " =    1.887
peak=    3.721 closest distance to " CG1 ILE A  33 " =    1.249
peak=    3.719 closest distance to " O   HOH Z 346 " =    1.652
peak=    3.711 closest distance to " O   HOH Z 108 " =    1.823
peak=    3.709 closest distance to " O   HOH Z 313 " =    1.662
peak=    3.708 closest distance to " O   HOH Z 132 " =    2.506
peak=    3.707 closest distance to " O   HOH Z 411 " =    3.806
peak=    3.707 closest distance to " O   HOH Z 128 " =    2.206
peak=    3.704 closest distance to " O   HOH Z 158 " =    2.994
peak=    3.700 closest distance to " CB  ARG A 139 " =    0.931
peak=    3.690 closest distance to " O   HOH Z 374 " =    2.587
peak=    3.670 closest distance to " CG2 THR A 221 " =    1.065
peak=    3.663 closest distance to " CD  LYS A 166 " =    1.292
peak=    3.645 closest distance to " CD BLYS A 290 " =    1.137
peak=    3.637 closest distance to " O   HOH Z 406 " =    1.694
peak=    3.633 closest distance to " O   HOH Z   1 " =    2.001
peak=    3.630 closest distance to " O   HOH Z 214 " =    1.963
peak=    3.630 closest distance to " CA  THR A 264 " =    0.903
peak=    3.627 closest distance to " OG BSER A 164 " =    2.431
peak=    3.623 closest distance to " CG  PRO A 198 " =    1.338
peak=    3.622 closest distance to " CB  SER A 141 " =    1.010
peak=    3.622 closest distance to " CB  ARG A 190 " =    1.654
peak=    3.620 closest distance to " O   HOH Z 423 " =    1.962
peak=    3.612 closest distance to " CB  VAL A 265 " =    1.274
peak=    3.611 closest distance to " O   HOH Z 295 " =    1.466
peak=    3.610 closest distance to " CG1BVAL A  72 " =    1.611
peak=    3.594 closest distance to " O   HOH Z 279 " =    2.218
peak=    3.594 closest distance to " N   ARG A 156 " =    1.355
peak=    3.589 closest distance to " O   HOH Z 250 " =    1.479
peak=    3.585 closest distance to " CG  MET A 185 " =    1.069
peak=    3.576 closest distance to " CB  ASP A 140 " =    0.891
peak=    3.576 closest distance to " O   HOH Z 209 " =    2.374
peak=    3.575 closest distance to " OG  SER A  22 " =    2.764
peak=    3.568 closest distance to " O   HOH Z 261 " =    2.096
peak=    3.567 closest distance to " O   HOH Z 273 " =    2.697
peak=    3.551 closest distance to " OD1 ASN A 217 " =    1.759
peak=    3.547 closest distance to " CB  GLN A  88 " =    1.222
peak=    3.545 closest distance to " O   ALA A   1 " =    1.519
peak=    3.545 closest distance to " O   HOH Z 126 " =    1.620
peak=    3.544 closest distance to " CA  ASN A 176 " =    1.194
peak=    3.539 closest distance to " O   HOH Z 183 " =    1.547
peak=    3.536 closest distance to " NH2AARG A 190 " =    1.388
peak=    3.529 closest distance to " O   HOH Z 327 " =    1.714
peak=    3.527 closest distance to " CB  MET A  40 " =    0.898
peak=    3.520 closest distance to " CG  GLN A  77 " =    1.735
peak=    3.519 closest distance to " O   HOH Z 147 " =    1.728
peak=    3.519 closest distance to " OE1 GLU A 277 " =    1.911
peak=    3.513 closest distance to " CG2 ILE A 120 " =    1.180
peak=    3.507 closest distance to " O   HOH Z 214 " =    2.426
peak=    3.506 closest distance to " O   HOH Z 281 " =    4.272
peak=    3.500 closest distance to " CA  ILE A  33 " =    1.598
peak=    3.500 closest distance to " O   HOH Z  44 " =    1.782
peak=    3.498 closest distance to " O   HOH Z 427 " =    3.132
peak=    3.495 closest distance to " O   HOH Z 425 " =    1.328
peak=    3.485 closest distance to " O   HOH Z 172 " =    3.775
peak=    3.479 closest distance to " CA  LYS A 117 " =    1.230
peak=    3.476 closest distance to " CA  ASP A 140 " =    1.174
peak=    3.468 closest distance to " CD1 ILE A 106 " =    0.954
peak=    3.464 closest distance to " O   HOH Z 163 " =    1.871
peak=    3.463 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.461 closest distance to " CG1 ILE A 151 " =    0.937
peak=    3.461 closest distance to " CA  SER A  87 " =    0.947
peak=    3.455 closest distance to " O   HOH Z 106 " =    2.374
peak=    3.453 closest distance to " CD2 LEU A 255 " =    1.271
peak=    3.447 closest distance to " NZ  LYS A 117 " =    3.339
peak=    3.446 closest distance to " O   HOH Z 326 " =    1.502
peak=    3.446 closest distance to " CG1 VAL A 202 " =    1.914
peak=    3.445 closest distance to " O   HOH Z 337 " =    3.586
peak=    3.435 closest distance to " CB  TRP A 266 " =    0.911
peak=    3.432 closest distance to " O   HOH Z  40 " =    1.666
peak=    3.429 closest distance to " CZ2 TRP A 179 " =    1.678
peak=    3.424 closest distance to " O   HOH Z 334 " =    1.484
peak=    3.418 closest distance to " O   HOH Z 173 " =    1.957
peak=    3.418 closest distance to " O   HOH Z 425 " =    1.909
peak=    3.415 closest distance to " N   ASN A  39 " =    1.243
peak=    3.412 closest distance to " CG  ARG A  66 " =    2.433
peak=    3.412 closest distance to " SD AMET A  47 " =    1.142
peak=    3.410 closest distance to " ND1 HIS A  81 " =    1.545
peak=    3.408 closest distance to " NZ  LYS A 166 " =    3.008
peak=    3.408 closest distance to " CB  MET A  47 " =    1.007
peak=    3.401 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.399 closest distance to " CB  ALA A 248 " =    0.933
peak=    3.394 closest distance to " CA  ASP A 191 " =    0.786
peak=    3.392 closest distance to " O   HOH Z  35 " =    2.626
peak=    3.388 closest distance to " CB  SER A 216 " =    0.708
peak=    3.387 closest distance to " O   HOH Z 227 " =    1.667
peak=    3.382 closest distance to " O   HOH Z 368 " =    3.659
peak=    3.382 closest distance to " CB  ARG A 259 " =    1.866
peak=    3.372 closest distance to " CD2 LEU A 297 " =    0.835
peak=    3.371 closest distance to " O   HOH Z  59 " =    2.257
peak=    3.369 closest distance to " CD  ARG A 269 " =    0.905
peak=    3.363 closest distance to " O   HOH Z 292 " =    1.662
peak=    3.363 closest distance to " CB  LEU A 143 " =    1.098
peak=    3.362 closest distance to " O   HOH Z  89 " =    2.162
peak=    3.360 closest distance to " CB  GLU A  46 " =    1.026
peak=    3.359 closest distance to " O   HOH Z 407 " =    2.631
peak=    3.355 closest distance to " O   TRP A 274 " =    1.884
peak=    3.354 closest distance to " O   HOH Z 409 " =    3.120
peak=    3.348 closest distance to " O   HOH Z  53 " =    2.462
peak=    3.345 closest distance to " N   ASN A 127 " =    1.262
peak=    3.344 closest distance to " O   HOH Z 267 " =    2.161
peak=    3.343 closest distance to " O   HOH Z 124 " =    1.423
peak=    3.339 closest distance to " CB  SER A 212 " =    1.147
peak=    3.339 closest distance to " CG  MET A 113 " =    1.389
peak=    3.335 closest distance to " O   HOH Z 366 " =    3.064
peak=    3.332 closest distance to " O   HOH Z  48 " =    1.369
peak=    3.332 closest distance to " O   HOH Z 157 " =    1.580
peak=    3.326 closest distance to " O   HOH Z 329 " =    3.511
peak=    3.325 closest distance to " O   ALA A 158 " =    1.270
peak=    3.325 closest distance to " CA  ALA A 233 " =    1.260
peak=    3.325 closest distance to " CG  GLN A  58 " =    2.606
peak=    3.323 closest distance to " O   HOH Z 286 " =    2.160
peak=    3.323 closest distance to " O   HOH Z 263 " =    2.293
peak=    3.319 closest distance to " NZ  LYS A  76 " =    1.125
peak=    3.318 closest distance to " O   HOH Z 245 " =    1.351
peak=    3.311 closest distance to " O   HOH Z 353 " =    2.604
peak=    3.310 closest distance to " O   HOH Z  63 " =    1.942
peak=    3.310 closest distance to " O   HOH Z  40 " =    1.854
peak=    3.304 closest distance to " CG  LYS A  76 " =    1.029
peak=    3.303 closest distance to " O   HOH Z 163 " =    1.724
peak=    3.303 closest distance to " O   HOH Z 276 " =    1.259
peak=    3.303 closest distance to " O   HOH Z 278 " =    1.066
peak=    3.302 closest distance to " O   HOH Z 185 " =    1.744
peak=    3.301 closest distance to " CA  ASN A  74 " =    1.112
peak=    3.300 closest distance to " ND1 HIS A  86 " =    1.654
peak=    3.299 closest distance to " O   HOH Z 189 " =    2.092
peak=    3.295 closest distance to " CA  ALA A 248 " =    1.185
peak=    3.291 closest distance to " O   HOH Z 388 " =    1.887
peak=    3.288 closest distance to " CZ  PHE A 218 " =    1.007
peak=    3.285 closest distance to " CG  LEU A 167 " =    1.214
peak=    3.278 closest distance to " CD  LYS A 119 " =    1.446
peak=    3.273 closest distance to " O   HOH Z 291 " =    1.585
peak=    3.266 closest distance to " CG  GLU A 277 " =    2.251
peak=    3.266 closest distance to " O   HOH Z 175 " =    2.149
peak=    3.265 closest distance to " O   HOH Z 345 " =    3.334
peak=    3.264 closest distance to " O   HOH Z  43 " =    1.948
peak=    3.261 closest distance to " O   HOH Z 403 " =    1.398
peak=    3.260 closest distance to " O   GLY A  57 " =    2.535
peak=    3.257 closest distance to " CB  ALA A 291 " =    1.374
peak=    3.255 closest distance to " CG2 VAL A 174 " =    1.350
peak=    3.254 closest distance to " CG  MET A 185 " =    1.177
peak=    3.249 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.242 closest distance to " O   HOH Z 271 " =    2.177
peak=    3.237 closest distance to " O   HOH Z  66 " =    2.092
peak=    3.234 closest distance to " O   HOH Z 188 " =    2.148
peak=    3.232 closest distance to " O   HOH Z 402 " =    1.481
peak=    3.232 closest distance to " CA  ARG A 195 " =    1.318
peak=    3.226 closest distance to " CD2 TRP A 179 " =    1.344
peak=    3.219 closest distance to " CB  GLN A 103 " =    0.953
peak=    3.217 closest distance to " CB  TRP A 150 " =    1.539
peak=    3.214 closest distance to " O   HOH Z 171 " =    3.841
peak=    3.208 closest distance to " OG  SER A  97 " =    3.542
peak=    3.208 closest distance to " O   HOH Z 266 " =    2.785
peak=    3.205 closest distance to " CA  GLY A 267 " =    1.067
peak=    3.204 closest distance to " CB  SER A  62 " =    1.341
peak=    3.204 closest distance to " O   HOH Z  54 " =    2.401
peak=    3.203 closest distance to " O   HOH Z 422 " =    2.675
peak=    3.203 closest distance to " NE2 GLN A  58 " =    4.294
peak=    3.202 closest distance to " O   HOH Z 287 " =    2.207
peak=    3.200 closest distance to " CB  ALA A  71 " =    1.315
peak=    3.197 closest distance to " O   HOH Z  80 " =    1.610
peak=    3.196 closest distance to " O   HOH Z 116 " =    1.863
peak=    3.195 closest distance to " O   HOH Z 234 " =    1.726
peak=    3.194 closest distance to " CA  ALA A 154 " =    0.923
peak=    3.193 closest distance to " CE1 TYR A 186 " =    1.243
peak=    3.193 closest distance to " O   HOH Z 106 " =    2.349
peak=    3.188 closest distance to " ND2 ASN A 301 " =    1.529
peak=    3.186 closest distance to " O   HOH Z 329 " =    2.634
peak=    3.186 closest distance to " O   HOH Z 250 " =    1.641
peak=    3.184 closest distance to " O   THR A 220 " =    1.505
peak=    3.182 closest distance to " NH1BARG A 145 " =    1.186
peak=    3.178 closest distance to " CG BARG A 102 " =    1.891
peak=    3.175 closest distance to " CB  ASN A 224 " =    1.126
peak=    3.171 closest distance to " O   HOH Z 392 " =    1.651
peak=    3.169 closest distance to " O   HOH Z  71 " =    1.982
peak=    3.168 closest distance to " OH  TYR A  30 " =    1.185
peak=    3.165 closest distance to " O   HOH Z 258 " =    1.742
peak=    3.158 closest distance to " O   HOH Z 211 " =    2.405
peak=    3.158 closest distance to " NH2 ARG A 219 " =    1.892
peak=    3.150 closest distance to " CB  TYR A 116 " =    0.979
peak=    3.148 closest distance to " CB  PHE A  16 " =    1.034
peak=    3.145 closest distance to " O   ALA A 233 " =    1.721
peak=    3.142 closest distance to " CB  GLU A 152 " =    1.516
peak=    3.141 closest distance to " O   HOH Z 151 " =    2.059
peak=    3.139 closest distance to " CD  ARG A 219 " =    0.960
peak=    3.139 closest distance to " OG BSER A  99 " =    2.139
peak=    3.136 closest distance to " O   HOH Z 341 " =    1.740
peak=    3.136 closest distance to " CA  ARG A  36 " =    1.133
peak=    3.133 closest distance to " CD  PRO A 243 " =    1.556
peak=    3.131 closest distance to " CG  GLN A  55 " =    2.083
peak=    3.131 closest distance to " O   HOH Z 336 " =    1.766
peak=    3.130 closest distance to " O   HOH Z  63 " =    2.301
peak=    3.129 closest distance to " CH2 TRP A  92 " =    2.127
peak=    3.128 closest distance to " CG  MET A  93 " =    0.919
peak=    3.128 closest distance to " NE AARG A 275 " =    1.520
peak=    3.128 closest distance to " CG BARG A 275 " =    1.441
peak=    3.127 closest distance to " CA  GLN A 223 " =    0.906
peak=    3.121 closest distance to " O   HOH Z 193 " =    1.575
peak=    3.118 closest distance to " O   HOH Z 301 " =    1.890
peak=    3.117 closest distance to " CA  ALA A 291 " =    0.955
peak=    3.116 closest distance to " CG  GLN A  11 " =    1.553
peak=    3.115 closest distance to " CG2 THR A 220 " =    0.983
peak=    3.100 closest distance to " O   HOH Z  78 " =    1.907
peak=    3.099 closest distance to " CB  ASN A 215 " =    1.080
peak=    3.089 closest distance to " O   HOH Z 189 " =    1.411
peak=    3.086 closest distance to " OE1 GLN A  11 " =    2.015
peak=    3.086 closest distance to " OD1 ASP A 286 " =    1.529
peak=    3.081 closest distance to " CE  LYS A 193 " =    1.944
peak=    3.079 closest distance to " O   HOH Z 368 " =    2.564
peak=    3.077 closest distance to " O   HOH Z 175 " =    3.596
peak=    3.068 closest distance to " O   HOH Z 365 " =    2.768
peak=    3.059 closest distance to " O   HOH Z 213 " =    2.266
peak=    3.053 closest distance to " OD2 ASP A 286 " =    3.211
peak=    3.035 closest distance to " O   HOH Z 154 " =    2.251
peak=    3.021 closest distance to " O   HOH Z  66 " =    2.214
peak=    3.019 closest distance to " O   HOH Z  64 " =    2.208
peak=    3.015 closest distance to " O   HOH Z  20 " =    1.891
peak=    3.010 closest distance to " O   HOH Z  40 " =    2.756

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.568 - 5.312
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 221
   mapped sites are within: 0.758 - 5.312

peak=   -4.671 closest distance to " O   HOH Z 290 " =    0.980
peak=   -4.656 closest distance to " O   HOH Z 266 " =    4.184
peak=   -4.600 closest distance to " CB  PRO A 243 " =    2.599
peak=   -4.349 closest distance to " CB  ALA A 161 " =    2.598
peak=   -4.238 closest distance to " CD  ARG A 156 " =    1.953
peak=   -4.143 closest distance to " O   HOH Z 372 " =    2.456
peak=   -4.107 closest distance to " CD1 LEU A 228 " =    2.314
peak=   -4.064 closest distance to " N   ALA A  43 " =    2.385
peak=   -4.047 closest distance to " O   HOH Z  52 " =    1.299
peak=   -4.027 closest distance to " CD  ARG A 139 " =    1.623
peak=   -3.993 closest distance to " SG  CYS A 254 " =    3.319
peak=   -3.990 closest distance to " O   HOH Z 198 " =    2.420
peak=   -3.990 closest distance to " O   HOH Z 377 " =    2.034
peak=   -3.984 closest distance to " N   MET A 188 " =    1.884
peak=   -3.895 closest distance to " OE1 GLN A 223 " =    2.027
peak=   -3.875 closest distance to " CG  ASP A 231 " =    0.813
peak=   -3.868 closest distance to " O   HOH Z  10 " =    1.487
peak=   -3.860 closest distance to " O   VAL A  67 " =    2.742
peak=   -3.859 closest distance to " CD2 LEU A 300 " =    2.895
peak=   -3.835 closest distance to " C   ALA A 158 " =    1.274
peak=   -3.826 closest distance to " C   HIS A 108 " =    1.129
peak=   -3.816 closest distance to " O   PRO A 198 " =    1.354
peak=   -3.793 closest distance to " O   SER A 210 " =    2.003
peak=   -3.788 closest distance to " N   GLN A  58 " =    1.719
peak=   -3.787 closest distance to " O   HOH Z 353 " =    2.203
peak=   -3.780 closest distance to " OG  SER A  97 " =    2.129
peak=   -3.755 closest distance to " O   HOH Z 407 " =    3.251
peak=   -3.739 closest distance to " O   HOH Z 388 " =    2.028
peak=   -3.718 closest distance to " CD1 PHE A  59 " =    1.834
peak=   -3.716 closest distance to " O   HOH Z 231 " =    2.182
peak=   -3.709 closest distance to " CZ3 TRP A 179 " =    1.239
peak=   -3.699 closest distance to " OG  SER A  62 " =    1.464
peak=   -3.695 closest distance to " CD2 LEU A 237 " =    2.634
peak=   -3.691 closest distance to " OXT GLY A 302 " =    2.794
peak=   -3.688 closest distance to " O   PRO A 163 " =    2.067
peak=   -3.687 closest distance to " O   HOH Z  93 " =    1.598
peak=   -3.684 closest distance to " O   HOH Z  13 " =    1.440
peak=   -3.681 closest distance to " O   HOH Z 292 " =    4.531
peak=   -3.671 closest distance to " OG BSER A 134 " =    1.701
peak=   -3.667 closest distance to " O   VAL A 153 " =    2.356
peak=   -3.664 closest distance to " CD1 LEU A 101 " =    2.541
peak=   -3.663 closest distance to " O   HOH Z  43 " =    1.583
peak=   -3.662 closest distance to " O   HOH Z 283 " =    1.805
peak=   -3.656 closest distance to " O   HOH Z 166 " =    1.743
peak=   -3.646 closest distance to " O   HOH Z 185 " =    2.234
peak=   -3.627 closest distance to " C   ASN A 285 " =    2.459
peak=   -3.626 closest distance to " CE2 TYR A  30 " =    2.759
peak=   -3.619 closest distance to " O   HOH Z  76 " =    1.999
peak=   -3.614 closest distance to " CB  ALA A 291 " =    2.350
peak=   -3.612 closest distance to " N   THR A 157 " =    1.676
peak=   -3.609 closest distance to " NH1 ARG A 195 " =    2.543
peak=   -3.607 closest distance to " NE2 GLN A  88 " =    1.914
peak=   -3.605 closest distance to " O   VAL A  67 " =    2.694
peak=   -3.603 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.602 closest distance to " O   HOH Z 118 " =    2.900
peak=   -3.592 closest distance to " CD  LYS A 289 " =    2.524
peak=   -3.592 closest distance to " O   HOH Z 385 " =    2.073
peak=   -3.577 closest distance to " O   HOH Z  38 " =    1.466
peak=   -3.575 closest distance to " CZ  PHE A  59 " =    1.633
peak=   -3.560 closest distance to " O   HOH Z  97 " =    2.036
peak=   -3.560 closest distance to " CZ  TYR A 169 " =    1.759
peak=   -3.532 closest distance to " OG ASER A 134 " =    1.305
peak=   -3.530 closest distance to " O   ASP A 231 " =    2.544
peak=   -3.527 closest distance to " O   HOH Z  11 " =    1.936
peak=   -3.526 closest distance to " O   HOH Z  98 " =    1.918
peak=   -3.513 closest distance to " NH2 ARG A  79 " =    1.804
peak=   -3.509 closest distance to " ND2 ASN A 187 " =    1.374
peak=   -3.509 closest distance to " O   HOH Z  19 " =    2.399
peak=   -3.498 closest distance to " NE2 GLN A  58 " =    1.064
peak=   -3.497 closest distance to " O   GLY A 196 " =    1.117
peak=   -3.495 closest distance to " OG BSER A 134 " =    1.235
peak=   -3.493 closest distance to " OG  SER A  87 " =    1.394
peak=   -3.492 closest distance to " O   HOH Z 395 " =    5.201
peak=   -3.484 closest distance to " O   HOH Z 435 " =    2.684
peak=   -3.481 closest distance to " CG  PHE A 283 " =    2.704
peak=   -3.475 closest distance to " CG1 VAL A 197 " =    2.227
peak=   -3.467 closest distance to " CG  PRO A 163 " =    2.502
peak=   -3.465 closest distance to " OD1 ASN A 148 " =    1.684
peak=   -3.463 closest distance to " ND2 ASN A  45 " =    0.999
peak=   -3.453 closest distance to " O   HOH Z 234 " =    4.199
peak=   -3.452 closest distance to " O   HOH Z  11 " =    1.868
peak=   -3.451 closest distance to " O   VAL A 174 " =    2.059
peak=   -3.447 closest distance to " CE  MET A  93 " =    1.239
peak=   -3.443 closest distance to " NH2 ARG A  66 " =    2.068
peak=   -3.436 closest distance to " C   LEU A 143 " =    1.228
peak=   -3.428 closest distance to " OE1 GLN A  77 " =    1.791
peak=   -3.428 closest distance to " O   HOH Z 311 " =    3.573
peak=   -3.415 closest distance to " CE2 TYR A 186 " =    2.061
peak=   -3.413 closest distance to " NH2AARG A 275 " =    5.312
peak=   -3.411 closest distance to " O   HOH Z 102 " =    1.728
peak=   -3.410 closest distance to " CB  ASN A  39 " =    2.223
peak=   -3.409 closest distance to " NH2 ARG A  66 " =    4.977
peak=   -3.408 closest distance to " CB  ILE A 239 " =    2.051
peak=   -3.404 closest distance to " CG  LEU A  83 " =    1.907
peak=   -3.401 closest distance to " O   SER A 135 " =    1.572
peak=   -3.400 closest distance to " SG ACYS A 201 " =    2.098
peak=   -3.396 closest distance to " O   HOH Z  47 " =    1.444
peak=   -3.394 closest distance to " N   ALA A 248 " =    1.642
peak=   -3.374 closest distance to " O   HOH Z 436 " =    1.557
peak=   -3.371 closest distance to " CB  ASP A 132 " =    2.296
peak=   -3.371 closest distance to " CB  CYS A 254 " =    2.435
peak=   -3.370 closest distance to " O   HOH Z 275 " =    1.500
peak=   -3.368 closest distance to " OD1 ASP A 191 " =    1.722
peak=   -3.366 closest distance to " O   HOH Z  15 " =    1.649
peak=   -3.366 closest distance to " O   HOH Z  98 " =    2.270
peak=   -3.363 closest distance to " C   MET A 188 " =    1.620
peak=   -3.349 closest distance to " CE  LYS A  76 " =    2.753
peak=   -3.348 closest distance to " O   HOH Z  88 " =    1.960
peak=   -3.348 closest distance to " O   HOH Z 200 " =    4.815
peak=   -3.343 closest distance to " N   SER A 276 " =    1.311
peak=   -3.342 closest distance to " O   HOH Z 351 " =    1.470
peak=   -3.339 closest distance to " CD2 LEU A 237 " =    2.540
peak=   -3.337 closest distance to " O   HOH Z 211 " =    1.791
peak=   -3.336 closest distance to " O   HOH Z 417 " =    2.549
peak=   -3.334 closest distance to " CB  SER A 245 " =    2.390
peak=   -3.332 closest distance to " NH2 ARG A 159 " =    2.390
peak=   -3.329 closest distance to " N   ALA A 226 " =    2.072
peak=   -3.328 closest distance to " CG  ARG A  66 " =    2.365
peak=   -3.326 closest distance to " CB  PRO A 163 " =    2.597
peak=   -3.326 closest distance to " CB  ASP A 132 " =    2.300
peak=   -3.321 closest distance to " O   HOH Z 166 " =    1.443
peak=   -3.319 closest distance to " CG  GLU A  53 " =    1.498
peak=   -3.319 closest distance to " CD1 LEU A 101 " =    2.902
peak=   -3.318 closest distance to " O   HOH Z  60 " =    2.395
peak=   -3.315 closest distance to " OE2 GLU A   2 " =    1.796
peak=   -3.315 closest distance to " O   HOH Z 361 " =    3.490
peak=   -3.312 closest distance to " CD  GLN A  88 " =    0.758
peak=   -3.309 closest distance to " CA  GLY A 133 " =    1.950
peak=   -3.309 closest distance to " CD2 TYR A 293 " =    2.064
peak=   -3.309 closest distance to " O   HOH Z 241 " =    1.357
peak=   -3.305 closest distance to " N   GLN A 122 " =    1.553
peak=   -3.299 closest distance to " CB  CYS A 201 " =    2.601
peak=   -3.298 closest distance to " CG  ASP A  50 " =    2.504
peak=   -3.297 closest distance to " CE3 TRP A 274 " =    2.476
peak=   -3.295 closest distance to " O   HOH Z  15 " =    2.094
peak=   -3.295 closest distance to " O   HOH Z 176 " =    0.833
peak=   -3.287 closest distance to " O   HOH Z 389 " =    1.758
peak=   -3.286 closest distance to " O   ASN A 249 " =    1.646
peak=   -3.281 closest distance to " OG1 THR A 178 " =    1.179
peak=   -3.278 closest distance to " CB  PHE A 192 " =    1.902
peak=   -3.275 closest distance to " O   VAL A 125 " =    2.232
peak=   -3.274 closest distance to " O   HOH Z 196 " =    1.968
peak=   -3.272 closest distance to " O   GLY A 211 " =    1.494
peak=   -3.269 closest distance to " CE  MET A 105 " =    1.904
peak=   -3.266 closest distance to " O   HOH Z 281 " =    2.685
peak=   -3.265 closest distance to " CG1 VAL A 112 " =    2.762
peak=   -3.256 closest distance to " CD1 LEU A 297 " =    2.266
peak=   -3.250 closest distance to " CB  SER A 258 " =    2.043
peak=   -3.248 closest distance to " O   HOH Z 282 " =    1.196
peak=   -3.241 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.238 closest distance to " O   HOH Z 266 " =    4.517
peak=   -3.238 closest distance to " O   HOH Z 317 " =    2.629
peak=   -3.235 closest distance to " O   HOH Z 409 " =    4.628
peak=   -3.232 closest distance to " OD2 ASP A 270 " =    1.476
peak=   -3.223 closest distance to " O   HOH Z 148 " =    3.391
peak=   -3.218 closest distance to " CG2 ILE A 263 " =    2.258
peak=   -3.216 closest distance to " CZ  ARG A 259 " =    0.851
peak=   -3.215 closest distance to " OE1 GLN A  88 " =    1.296
peak=   -3.214 closest distance to " O   HOH Z 222 " =    1.288
peak=   -3.202 closest distance to " CG2 VAL A 189 " =    2.086
peak=   -3.198 closest distance to " CZ  PHE A  38 " =    2.397
peak=   -3.196 closest distance to " O   HOH Z 359 " =    2.954
peak=   -3.195 closest distance to " CA  GLY A 241 " =    2.289
peak=   -3.194 closest distance to " N   HIS A 115 " =    1.989
peak=   -3.193 closest distance to " CE2 PHE A 218 " =    2.436
peak=   -3.193 closest distance to " OD2 ASP A 171 " =    2.250
peak=   -3.192 closest distance to " CE  MET A 105 " =    2.053
peak=   -3.187 closest distance to " O   HOH Z 263 " =    3.116
peak=   -3.187 closest distance to " CB  ALA A  43 " =    2.270
peak=   -3.186 closest distance to " CB  ALA A 248 " =    1.986
peak=   -3.185 closest distance to " CA  SER A 135 " =    1.323
peak=   -3.179 closest distance to " O   HOH Z  71 " =    1.200
peak=   -3.175 closest distance to " O   HOH Z  90 " =    3.016
peak=   -3.175 closest distance to " O   PRO A 198 " =    2.321
peak=   -3.174 closest distance to " CG  GLN A 278 " =    2.235
peak=   -3.173 closest distance to " O   HOH Z 141 " =    1.377
peak=   -3.172 closest distance to " NE  ARG A 259 " =    1.251
peak=   -3.171 closest distance to " C   SER A 206 " =    1.441
peak=   -3.171 closest distance to " O   HOH Z 278 " =    2.302
peak=   -3.165 closest distance to " CD  GLN A 223 " =    0.895
peak=   -3.165 closest distance to " ND2 ASN A 249 " =    2.221
peak=   -3.161 closest distance to " O   HOH Z 393 " =    1.473
peak=   -3.161 closest distance to " O   HOH Z 323 " =    1.283
peak=   -3.159 closest distance to " CB  LEU A 167 " =    2.137
peak=   -3.158 closest distance to " CZ3 TRP A 274 " =    1.123
peak=   -3.157 closest distance to " CB  ALA A 291 " =    2.211
peak=   -3.157 closest distance to " O   HOH Z 396 " =    1.642
peak=   -3.155 closest distance to " O   HOH Z 252 " =    4.279
peak=   -3.153 closest distance to " O   HOH Z 244 " =    1.917
peak=   -3.143 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.142 closest distance to " O   HOH Z 394 " =    1.533
peak=   -3.139 closest distance to " O   HOH Z  68 " =    2.637
peak=   -3.138 closest distance to " CD  PRO A  90 " =    1.802
peak=   -3.137 closest distance to " O   HOH Z 310 " =    3.368
peak=   -3.134 closest distance to " O   HOH Z 137 " =    1.494
peak=   -3.133 closest distance to " OD2 ASP A 171 " =    1.687
peak=   -3.129 closest distance to " O   HOH Z 371 " =    1.869
peak=   -3.126 closest distance to " O   HOH Z 148 " =    1.759
peak=   -3.116 closest distance to " O   HOH Z 377 " =    1.167
peak=   -3.115 closest distance to " O   HOH Z 265 " =    1.919
peak=   -3.112 closest distance to " OD2 ASP A 270 " =    1.298
peak=   -3.107 closest distance to " CA  GLY A 241 " =    3.105
peak=   -3.105 closest distance to " CE3 TRP A  70 " =    1.773
peak=   -3.099 closest distance to " O   HOH Z 111 " =    1.407
peak=   -3.099 closest distance to " O   ARG A  56 " =    1.518
peak=   -3.097 closest distance to " CB  PRO A  54 " =    2.335
peak=   -3.095 closest distance to " O   ASN A 301 " =    1.489
peak=   -3.094 closest distance to " CG2AVAL A  41 " =    2.809
peak=   -3.093 closest distance to " CG  GLN A  58 " =    1.345
peak=   -3.087 closest distance to " CD1 PHE A  16 " =    2.649
peak=   -3.077 closest distance to " O   HOH Z 377 " =    0.943
peak=   -3.061 closest distance to " CG  ARG A 269 " =    2.332
peak=   -3.054 closest distance to " O   HOH Z 119 " =    4.141
peak=   -3.041 closest distance to " O   HOH Z  60 " =    1.263
peak=   -3.029 closest distance to " N   ALA A 248 " =    2.216
peak=   -3.019 closest distance to " CB  ALA A  10 " =    2.105

================= 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    :  0.3934 0.3961   6.185812e+00   6.196188e+00
   1_bss:  0.3815 0.3852   6.175658e+00   6.176927e+00
   1_xyz:  0.2716 0.3046   5.901667e+00   5.991694e+00
   1_adp:  0.2487 0.3105   5.854037e+00   6.008013e+00
   1_occ:  0.2483 0.3105   5.852883e+00   6.007125e+00
   2_bss:  0.2468 0.3065   5.848410e+00   6.000566e+00
   2_xyz:  0.1760 0.2273   5.537098e+00   5.730754e+00
   2_adp:  0.1586 0.2097   5.447644e+00   5.655703e+00
   2_occ:  0.1584 0.2096   5.446978e+00   5.655179e+00
   3_bss:  0.1578 0.2081   5.442342e+00   5.649491e+00
   3_xyz:  0.1274 0.1722   5.250394e+00   5.476625e+00
   3_adp:  0.1214 0.1654   5.205892e+00   5.430162e+00
   3_occ:  0.1212 0.1652   5.204905e+00   5.429394e+00
   4_bss:  0.1214 0.1646   5.204907e+00   5.429339e+00
   4_xyz:  0.1111 0.1565   5.141390e+00   5.380039e+00
   4_adp:  0.1088 0.1568   5.133366e+00   5.378779e+00
   4_occ:  0.1088 0.1567   5.133001e+00   5.378641e+00
   5_bss:  0.1087 0.1567   5.132905e+00   5.378514e+00
   5_xyz:  0.1066 0.1570   5.127889e+00   5.381257e+00
   5_adp:  0.1073 0.1567   5.130596e+00   5.381179e+00
   5_occ:  0.1072 0.1566   5.130497e+00   5.381383e+00
   5_bss:  0.1072 0.1566   5.130550e+00   5.381406e+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:  0.300  50.000  -1.615  -1.906   3.269  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -1.615  -1.906   3.269  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -1.615  -1.906   3.269  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -1.615  -1.906   3.269  -0.000   0.000   0.000
   2_bss:  0.321  50.000  -2.142  -2.022   0.358  -0.000   0.000   0.000
   2_xyz:  0.321  50.000  -2.142  -2.022   0.358  -0.000   0.000   0.000
   2_adp:  0.321  50.000  -2.142  -2.022   0.358  -0.000   0.000   0.000
   2_occ:  0.321  50.000  -2.142  -2.022   0.358  -0.000   0.000   0.000
   3_bss:  0.326  50.000  -2.355  -2.310  -1.381  -0.000  -0.000  -0.000
   3_xyz:  0.326  50.000  -2.355  -2.310  -1.381  -0.000  -0.000  -0.000
   3_adp:  0.326  50.000  -2.355  -2.310  -1.381  -0.000  -0.000  -0.000
   3_occ:  0.326  50.000  -2.355  -2.310  -1.381  -0.000  -0.000  -0.000
   4_bss:  0.326  50.000  -2.536  -2.421  -2.019  -0.000  -0.000  -0.000
   4_xyz:  0.326  50.000  -2.536  -2.421  -2.019  -0.000  -0.000  -0.000
   4_adp:  0.326  50.000  -2.536  -2.421  -2.019  -0.000  -0.000  -0.000
   4_occ:  0.326  50.000  -2.536  -2.421  -2.019  -0.000  -0.000  -0.000
   5_bss:  0.326  50.000  -2.412  -2.291  -2.062  -0.000  -0.000  -0.000
   5_xyz:  0.326  50.000  -2.412  -2.291  -2.062  -0.000  -0.000  -0.000
   5_adp:  0.326  50.000  -2.412  -2.291  -2.062  -0.000  -0.000  -0.000
   5_occ:  0.326  50.000  -2.412  -2.291  -2.062  -0.000  -0.000  -0.000
   5_bss:  0.326  49.913  -2.225  -2.091  -1.888  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.916 0.5718  0.7537    48922.543
   1_bss:  44.314 0.5893  0.7780    44921.842
   1_xyz:  32.040 0.7356  0.9356    25795.725
   1_adp:  33.310 0.7200  0.9237    27177.775
   1_occ:  33.290 0.7202  0.9239    27126.055
   2_bss:  32.816 0.7255  0.8927    26540.704
   2_xyz:  22.590 0.8353  0.9851    13391.087
   2_adp:  20.308 0.8586  0.9969    11396.645
   2_occ:  20.294 0.8587  0.9966    11380.788
   3_bss:  20.088 0.8607  0.9710    11219.267
   3_xyz:  16.162 0.8962  0.9877     7677.437
   3_adp:  15.032 0.9064  0.9889     7039.315
   3_occ:  15.005 0.9066  0.9888     7024.824
   4_bss:  15.000 0.9067  0.9776     7039.257
   4_xyz:  14.021 0.9146  0.9807     6294.765
   4_adp:  13.969 0.9152  0.9764     6267.670
   4_occ:  13.960 0.9153  0.9763     6266.759
   5_bss:  13.958 0.9153  0.9787     6267.574
   5_xyz:  14.009 0.9151  0.9771     6328.360
   5_adp:  13.972 0.9154  0.9731     6335.952
   5_occ:  13.973 0.9155  0.9730     6338.971
   5_bss:  13.974 0.9155  0.9765     6339.368
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7903e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7903e-01
   1_xyz:   1.274  0.010  0.079 15.531  0.005  4.111   9.1898e-02
   1_adp:   1.274  0.010  0.079 15.531  0.005  4.111   9.1898e-02
   1_occ:   1.274  0.010  0.079 15.531  0.005  4.111   9.1898e-02
   2_bss:   1.274  0.010  0.079 15.531  0.005  4.111   9.1898e-02
   2_xyz:   1.163  0.008  0.077 13.992  0.004  4.125   7.3324e-02
   2_adp:   1.163  0.008  0.077 13.992  0.004  4.125   7.3324e-02
   2_occ:   1.163  0.008  0.077 13.992  0.004  4.125   7.3324e-02
   3_bss:   1.163  0.008  0.077 13.992  0.004  4.125   7.3324e-02
   3_xyz:   1.044  0.008  0.073 14.498  0.004  4.119   6.2552e-02
   3_adp:   1.044  0.008  0.073 14.498  0.004  4.119   6.2552e-02
   3_occ:   1.044  0.008  0.073 14.498  0.004  4.119   6.2552e-02
   4_bss:   1.044  0.008  0.073 14.498  0.004  4.119   6.2552e-02
   4_xyz:   1.140  0.009  0.081 14.755  0.004  4.122   7.2000e-02
   4_adp:   1.140  0.009  0.081 14.755  0.004  4.122   7.2000e-02
   4_occ:   1.140  0.009  0.081 14.755  0.004  4.122   7.2000e-02
   5_bss:   1.140  0.009  0.081 14.755  0.004  4.122   7.2000e-02
   5_xyz:   1.126  0.009  0.080 14.766  0.005  4.109   7.2096e-02
   5_adp:   1.126  0.009  0.080 14.766  0.005  4.109   7.2096e-02
   5_occ:   1.126  0.009  0.080 14.766  0.005  4.109   7.2096e-02
   5_bss:   1.126  0.009  0.080 14.766  0.005  4.109   7.2096e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.494   2.4061e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.494   2.4061e-01
   1_xyz:   7.833  0.053  0.268 89.758  0.030  2.155   8.8781e-02
   1_adp:   7.833  0.053  0.268 89.758  0.030  2.155   8.8781e-02
   1_occ:   7.833  0.053  0.268 89.758  0.030  2.155   8.8781e-02
   2_bss:   7.833  0.053  0.268 89.758  0.030  2.155   8.8781e-02
   2_xyz:   7.685  0.051  0.251 82.374  0.021  2.363   1.5511e-01
   2_adp:   7.685  0.051  0.251 82.374  0.021  2.363   1.5511e-01
   2_occ:   7.685  0.051  0.251 82.374  0.021  2.363   1.5511e-01
   3_bss:   7.685  0.051  0.251 82.374  0.021  2.363   1.5511e-01
   3_xyz:   7.118  0.038  0.292 83.585  0.033  2.294   5.3728e-02
   3_adp:   7.118  0.038  0.292 83.585  0.033  2.294   5.3728e-02
   3_occ:   7.118  0.038  0.292 83.585  0.033  2.294   5.3728e-02
   4_bss:   7.118  0.038  0.292 83.585  0.033  2.294   5.3728e-02
   4_xyz:   7.016  0.050  0.259 82.823  0.038  2.300   6.0265e-02
   4_adp:   7.016  0.050  0.259 82.823  0.038  2.300   6.0265e-02
   4_occ:   7.016  0.050  0.259 82.823  0.038  2.300   6.0265e-02
   5_bss:   7.016  0.050  0.259 82.823  0.038  2.300   6.0265e-02
   5_xyz:   7.175  0.048  0.254 82.604  0.037  2.285   5.7380e-02
   5_adp:   7.175  0.048  0.254 82.604  0.037  2.285   5.7380e-02
   5_occ:   7.175  0.048  0.254 82.604  0.037  2.285   5.7380e-02
   5_bss:   7.175  0.048  0.254 82.604  0.037  2.285   5.7380e-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:  85.05   0.00  17.90  85.05   0.00  13.80  83.12   4.26  40.22
   1_occ:  85.05   0.00  17.90  85.05   0.00  13.80  83.12   4.26  40.22
   2_bss:  85.05   0.00  17.90  85.05   0.00  13.80  83.12   4.26  40.22
   2_xyz:  85.05   0.00  17.90  85.05   0.00  13.80  83.12   4.26  40.22
   2_adp:  82.59   0.98  17.83  82.59   0.98  13.41  82.44   5.98  41.91
   2_occ:  82.59   0.98  17.83  82.59   0.98  13.41  82.44   5.98  41.91
   3_bss:  82.59   0.98  17.83  82.59   0.98  13.41  82.44   5.98  41.91
   3_xyz:  82.59   0.98  17.83  82.59   0.98  13.41  82.44   5.98  41.91
   3_adp:  84.57   2.46  17.37  84.57   2.46  13.15  79.06   4.90  40.35
   3_occ:  84.57   2.46  17.37  84.57   2.46  13.15  79.06   4.90  40.35
   4_bss:  84.57   2.46  17.37  84.57   2.46  13.15  79.06   4.90  40.35
   4_xyz:  84.57   2.46  17.37  84.57   2.46  13.15  79.06   4.90  40.35
   4_adp:  92.79   1.99  17.32  92.79   1.99  13.08  81.00   5.51  40.39
   4_occ:  92.79   1.99  17.32  92.79   1.99  13.08  81.00   5.51  40.39
   5_bss:  92.79   1.99  17.32  92.79   1.99  13.08  81.00   5.51  40.39
   5_xyz:  92.79   1.99  17.32  92.79   1.99  13.08  81.00   5.51  40.39
   5_adp:  90.25   2.39  16.69  90.25   2.39  12.81  72.52   6.21  37.82
   5_occ:  90.25   2.39  16.69  90.25   2.39  12.81  72.52   6.21  37.82
   5_bss:  90.16   2.30  16.61  90.16   2.30  12.73  72.43   6.13  37.74
------------------------------------------------------------------------
 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:    1.885    0.019    0.305
   1_adp:    1.885    0.019    0.305
   1_occ:    1.885    0.019    0.305
   2_bss:    1.885    0.019    0.305
   2_xyz:    1.481    0.040    0.470
   2_adp:    1.481    0.040    0.470
   2_occ:    1.481    0.040    0.470
   3_bss:    1.481    0.040    0.470
   3_xyz:    1.537    0.041    0.527
   3_adp:    1.537    0.041    0.527
   3_occ:    1.537    0.041    0.527
   4_bss:    1.537    0.041    0.527
   4_xyz:    1.631    0.025    0.553
   4_adp:    1.631    0.025    0.553
   4_occ:    1.631    0.025    0.553
   5_bss:    1.631    0.025    0.553
   5_xyz:    1.811    0.077    0.565
   5_adp:    1.811    0.077    0.565
   5_occ:    1.811    0.077    0.565
   5_bss:    1.811    0.077    0.565
------------------------------------------------------------------------

CPU time actual refinement: 336.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_913/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_913/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_913/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_913/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_913/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.68 
  Macro-tasks:
    bulk solvent and scale       = 36.91  
    individual site refinement   = 138.02 
    weights calculation          = 29.45  
    collect and process          = 6.07   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 210.55 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 111.71 
    alpha_beta                      = 7.94   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 118.47 
    fmodel                         = 6.35   
    r_factors                      = 0.16   
    phase_errors                   = 10.96  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 258.90 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.843 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    623 calls, 111.40 s
gradients_fft:          568 calls, 105.68 s

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

# Date 2008-01-16 Time 05:58:27 PST -0800 (1200491907.32 s)
Start R-work = 0.3934, R-free = 0.3961 (no bulk solvent and anisotropic scale)
Final R-work = 0.1325, R-free = 0.1772 (no bulk solvent and anisotropic scale)

Start R-work = 0.3815, R-free = 0.3852
Final R-work = 0.1072, R-free = 0.1566