# Date 2008-01-16 Time 05:19:52 PST -0800 (1200489592.57 s)
#phil __OFF__

Command line arguments: "../693.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 754
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 693

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.6339, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.9515
Completeness in resolution range: 0.92615
Completeness with d_max=infinity: 0.9234

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.9515
Completeness in resolution range: 0.92615
Completeness with d_max=infinity: 0.9234

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1764 [2225/2254]  2002   223  10.0%
  bin  2:  4.1764 -  3.3271 [2123/2146]  1911   212  10.0%
  bin  3:  3.3271 -  2.9101 [2099/2124]  1891   208   9.9%
  bin  4:  2.9101 -  2.6456 [2081/2098]  1874   207   9.9%
  bin  5:  2.6456 -  2.4569 [2084/2127]  1876   208  10.0%
  bin  6:  2.4569 -  2.3126 [2048/2076]  1848   200   9.8%
  bin  7:  2.3126 -  2.1972 [2042/2078]  1836   206  10.1%
  bin  8:  2.1972 -  2.1018 [2046/2088]  1836   210  10.3%
  bin  9:  2.1018 -  2.0211 [2014/2074]  1812   202  10.0%
  bin 10:  2.0211 -  1.9515 [ 827/2086]   744    83  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_693/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:
        1.47 -     2.15: 22
        2.15 -     2.84: 1065
        2.84 -     3.53: 4411
        3.53 -     4.21: 9349
        4.21 -     4.90: 13648
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.466 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.534 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.627 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.695 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 324 " - " O   HOH Z 396 "  1.773 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28490 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_693/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_693/model_refine_001.geo

CPU time processing inputs: 9.21


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.63395 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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4356   r_free= 0.4303   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.246637                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6584 0.99   1442  163 0.3443 0.3507      6.5017      6.5074|
|  2:  4.6584 -  3.7164 0.99   1380  148 0.3651 0.3638      6.7388      6.7023|
|  3:  3.7164 -  3.2522 0.99   1365  153 0.3903 0.3838      6.5938      6.6809|
|  4:  3.2522 -  2.9574 0.99   1351  149 0.4204 0.3954      6.4574      6.4334|
|  5:  2.9574 -  2.7469 0.99   1332  148 0.4414 0.4171       6.312      6.2731|
|  6:  2.7469 -  2.5858 0.99   1344  150 0.4644 0.4392      6.2353      6.1528|
|  7:  2.5858 -  2.4569 0.98   1340  147 0.4635 0.4294      6.2191      6.1623|
|  8:  2.4569 -  2.3504 0.98   1302  147 0.4886 0.5212      6.1307      6.1833|
|  9:  2.3504 -  2.2602 0.99   1339  147 0.5043 0.4978      6.1275      6.1271|
| 10:  2.2602 -  2.1825 0.98   1307  146 0.4917 0.5062      6.0694      6.1189|
| 11:  2.1825 -  2.1144 0.97   1313  143 0.5036 0.5460      6.0135      5.9992|
| 12:  2.1144 -  2.0541 0.98   1306  148 0.4993 0.5377      5.9317      5.9877|
| 13:  2.0541 -  2.0002 0.89   1173  134 0.5069 0.4550      5.8684      5.8267|
| 14:  2.0002 -  1.9515 0.25    336   36 0.5731 0.4860      5.8381        5.75|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6584  1442   163  0.72  32.32   0.84     0.75      63069.29|
|  2:  4.6584 -  3.7164  1380   148  0.74  31.59   0.93     0.83      86103.30|
|  3:  3.7164 -  3.2522  1365   153  0.66  38.62   0.94     0.84      90431.60|
|  4:  3.2522 -  2.9574  1351   149  0.59  44.70   0.94     0.81      80320.49|
|  5:  2.9574 -  2.7469  1332   148  0.55  47.91   0.90     0.76      63360.92|
|  6:  2.7469 -  2.5858  1344   150  0.51  51.00   0.93     0.72      55570.21|
|  7:  2.5858 -  2.4569  1340   147  0.50  52.10   0.94     0.67      51964.00|
|  8:  2.4569 -  2.3504  1302   147  0.41  58.91   0.90     0.60      53333.89|
|  9:  2.3504 -  2.2602  1339   147  0.38  61.36   0.94     0.55      50727.89|
| 10:  2.2602 -  2.1825  1307   146  0.33  65.45   0.98     0.49      51384.06|
| 11:  2.1825 -  2.1144  1313   143  0.28  68.90   0.95     0.44      49046.13|
| 12:  2.1144 -  2.0541  1306   148  0.24  72.49   0.95     0.39      47595.55|
| 13:  2.0541 -  2.0002  1173   134  0.25  71.32   0.96     0.41      39578.36|
| 14:  2.0002 -  1.9515   336    36  0.31  66.85   0.87     0.48      31711.79|
|alpha:            min =        0.39 max =            0.84 mean =         0.64|
|beta:             min =    31711.79 max =        90431.60 mean =     60045.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.38|
|phase err.(test): min =        0.00 max =           89.81 mean =        53.45|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.576001              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.819   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.281425              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.164   (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 |  1.466 -  1.810:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.810 -  2.153:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.153 -  2.497:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.497 -  2.840:     1035 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.840 -  3.183:     1974 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.183 -  3.527:     2437 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.527 -  3.870:     4666 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.870 -  4.213:     4683 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.213 -  4.557:     6179 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.557 -  4.900:     7469 |
|-----------------------------------------------------------------------------|
|-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 |        0.189 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.466 |       0.579 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.753)------------------------------------------|
|    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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4356   r_free= 0.4303   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.246637                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4241   r_free= 0.4169   ksol= 0.33   Bsol= 50.00   scale= 0.951   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,2.27,2.52,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.237465                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.956083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.664   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.984857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.912   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4241      final r-factor (work) = 0.3206          |
| start r-factor (free) = 0.4169      final r-factor (free) = 0.3485          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8774 = 6.96 * 0.50 * 6.2358 + 1.00 * 0.1888                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3032 = 6.96 * 0.50 * 6.0924 + 1.00 * 0.1135                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3206      final r-factor (work) = 0.2925          |
| start r-factor (free) = 0.3485      final r-factor (free) = 0.3600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0064 = 0.98 * 1.00 * 6.0924 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8892 = 0.98 * 1.00 * 5.9594 + 1.00 * 0.0200                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.753)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.97   18.77    None  None   None       |
|    all(noH): 2823   0      0.00    95.97   18.77    None  None   None       |
|    Sol.    : 438    0      2.81    93.76   40.16    None  None   None       |
|    Mac.    : 2385   0      0.00    95.97   14.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.597:  868   |   5:    47.985 -  57.581:   90        |
|      1:     9.597 -  19.194:  984   |   6:    57.581 -  67.178:   54        |
|      2:    19.194 -  28.791:  431   |   7:    67.178 -  76.775:   28        |
|      3:    28.791 -  38.388:  221   |   8:    76.775 -  86.372:   12        |
|      4:    38.388 -  47.985:  130   |   9:    86.372 -  95.969:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2925 r_free = 0.3600             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2921 r_free = 0.3608             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2921   r_free= 0.3608   ksol= 0.33   Bsol= 50.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,2.27,2.52,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.967532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2899   r_free= 0.3583   ksol= 0.33   Bsol= 57.17   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,0.40,0.25,0.00,0.00,0.00); trace/3= -0.59                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.965284                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.315981              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.248   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482294              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.616  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2899      final r-factor (work) = 0.2123          |
| start r-factor (free) = 0.3583      final r-factor (free) = 0.2684          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9505 = 5.32 * 0.50 * 5.9583 + 1.00 * 0.1135                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6387 = 5.32 * 0.50 * 5.8525 + 1.00 * 0.0828                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2123      final r-factor (work) = 0.1921          |
| start r-factor (free) = 0.2684      final r-factor (free) = 0.2464          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8417 = 0.48 * 1.00 * 5.8525 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7391 = 0.48 * 1.00 * 5.6568 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.753)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.74   18.14    None  None   None       |
|    all(noH): 2823   0      0.00    93.74   18.14    None  None   None       |
|    Sol.    : 438    0      5.58    87.48   41.69    None  None   None       |
|    Mac.    : 2385   0      0.00    93.74   13.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.374:  908   |   5:    46.869 -  56.243:  100        |
|      1:     9.374 -  18.748: 1091   |   6:    56.243 -  65.617:   56        |
|      2:    18.748 -  28.121:  313   |   7:    65.617 -  74.991:   33        |
|      3:    28.121 -  37.495:  164   |   8:    74.991 -  84.364:   14        |
|      4:    37.495 -  46.869:  140   |   9:    84.364 -  93.738:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1921 r_free = 0.2464             target_work(ml) = 5.615         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1919 r_free = 0.2465             target_work(ml) = 5.615         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1919   r_free= 0.2465   ksol= 0.33   Bsol= 57.17   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,0.40,0.25,0.00,0.00,0.00); trace/3= -0.59                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.614524                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1915   r_free= 0.2449   ksol= 0.32   Bsol= 49.06   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-0.78,-1.12,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.609730                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.336295              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.037   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.882846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.632  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1915      final r-factor (work) = 0.1535          |
| start r-factor (free) = 0.2449      final r-factor (free) = 0.2012          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6920 = 2.34 * 0.50 * 5.6578 + 1.00 * 0.0828                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4976 = 2.34 * 0.50 * 5.5182 + 1.00 * 0.0515                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1535      final r-factor (work) = 0.1436          |
| start r-factor (free) = 0.2012      final r-factor (free) = 0.1946          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4008 = 1.88 * 1.00 * 5.5182 + 1.00 * 0.0109                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1480 = 1.88 * 1.00 * 5.3830 + 1.00 * 0.0127                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.753)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.52  18.52    None  None   None       |
|    all(noH): 2823   0      0.00    113.52  18.52    None  None   None       |
|    Sol.    : 438    0      0.90    93.44   45.37    None  None   None       |
|    Mac.    : 2385   0      0.00    113.52  13.59    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 -  11.353: 1285   |   5:    56.762 -  68.115:   85        |
|      1:    11.353 -  22.705:  930   |   6:    68.115 -  79.467:   42        |
|      2:    22.705 -  34.058:  196   |   7:    79.467 -  90.820:   24        |
|      3:    34.058 -  45.410:  131   |   8:    90.820 - 102.172:    5        |
|      4:    45.410 -  56.762:  122   |   9:   102.172 - 113.525:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1436 r_free = 0.1946             target_work(ml) = 5.363         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1435 r_free = 0.1946             target_work(ml) = 5.363         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1946   ksol= 0.32   Bsol= 49.06   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-0.78,-1.12,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.362540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1438   r_free= 0.1948   ksol= 0.32   Bsol= 54.81   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.34,-1.63,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.364376                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.160871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.797  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.413647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.971  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1438      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1948      final r-factor (free) = 0.1737          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8701 = 2.16 * 0.50 * 5.3855 + 1.00 * 0.0515                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7896 = 2.16 * 0.50 * 5.3075 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1260      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1737      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2081 = 0.41 * 1.00 * 5.3075 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1771 = 0.41 * 1.00 * 5.2385 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.753)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    112.92  17.77    None  None   None       |
|    all(noH): 2823   0      1.43    112.92  17.77    None  None   None       |
|    Sol.    : 438    0      2.58    89.22   43.02    None  None   None       |
|    Mac.    : 2385   0      1.43    112.92  13.13    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:     1.434 -  12.582: 1564   |   5:    57.175 -  68.324:   64        |
|      1:    12.582 -  23.731:  719   |   6:    68.324 -  79.472:   33        |
|      2:    23.731 -  34.879:  176   |   7:    79.472 -  90.620:   17        |
|      3:    34.879 -  46.027:  121   |   8:    90.620 - 101.769:    3        |
|      4:    46.027 -  57.175:  123   |   9:   101.769 - 112.917:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1222 r_free = 0.1684             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1684             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1684   ksol= 0.32   Bsol= 54.81   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.34,-1.63,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.220467                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1220   r_free= 0.1683   ksol= 0.32   Bsol= 50.35   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.52,-1.75,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.220262                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.707478              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.940  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.132683              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.565  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5273 = 1.71 * 0.50 * 5.2382 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4951 = 1.71 * 0.50 * 5.2052 + 1.00 * 0.0512                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7008 = 0.13 * 1.00 * 5.2052 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6963 = 0.13 * 1.00 * 5.1902 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.753)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.36    104.46  16.98    None  None   None       |
|    all(noH): 2823   0      2.36    104.46  16.98    None  None   None       |
|    Sol.    : 438    0      5.12    85.47   39.44    None  None   None       |
|    Mac.    : 2385   0      2.36    104.46  12.86    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:     2.364 -  12.574: 1601   |   5:    53.413 -  63.623:   63        |
|      1:    12.574 -  22.784:  701   |   6:    63.623 -  73.833:   26        |
|      2:    22.784 -  32.993:  165   |   7:    73.833 -  84.043:   15        |
|      3:    32.993 -  43.203:  147   |   8:    84.043 -  94.253:    3        |
|      4:    43.203 -  53.413:   98   |   9:    94.253 - 104.463:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1610             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1610             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1610   ksol= 0.32   Bsol= 50.35   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.52,-1.75,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182507                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6584 0.99   1442  163 0.1009 0.1246      5.3805      5.5262|
|  2:  4.6584 -  3.7164 0.99   1380  148 0.0870 0.1084      5.4346      5.6307|
|  3:  3.7164 -  3.2522 0.99   1365  153 0.1076 0.1635      5.4794      5.8902|
|  4:  3.2522 -  2.9574 0.99   1351  149 0.1339 0.1538      5.5044       5.618|
|  5:  2.9574 -  2.7469 0.99   1332  148 0.1393 0.1850      5.3578      5.5085|
|  6:  2.7469 -  2.5858 0.99   1344  150 0.1337 0.2008      5.2572      5.4904|
|  7:  2.5858 -  2.4569 0.98   1340  147 0.1286 0.1730      5.1942      5.4002|
|  8:  2.4569 -  2.3504 0.98   1302  147 0.1289 0.1688      5.1103      5.2922|
|  9:  2.3504 -  2.2602 0.99   1339  147 0.1239 0.1922      5.0615       5.321|
| 10:  2.2602 -  2.1825 0.98   1307  146 0.1205 0.1750      4.9922      5.2516|
| 11:  2.1825 -  2.1144 0.97   1313  143 0.1187 0.1836      4.9391       5.217|
| 12:  2.1144 -  2.0541 0.98   1306  148 0.1187 0.1776      4.8706      5.1199|
| 13:  2.0541 -  2.0002 0.89   1173  134 0.1202 0.1777      4.8105      5.0016|
| 14:  2.0002 -  1.9515 0.25    336   36 0.1228 0.1656      4.7207      4.9814|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6584  1442   163  0.94   8.86   0.98     0.96       6794.78|
|  2:  4.6584 -  3.7164  1380   148  0.95   7.83   1.02     1.00       8637.22|
|  3:  3.7164 -  3.2522  1365   153  0.93  11.56   1.03     1.02      10370.94|
|  4:  3.2522 -  2.9574  1351   149  0.91  14.78   1.01     0.98      11011.28|
|  5:  2.9574 -  2.7469  1332   148  0.89  16.63   1.00     0.97       8676.80|
|  6:  2.7469 -  2.5858  1344   150  0.90  16.49   0.99     0.96       7404.85|
|  7:  2.5858 -  2.4569  1340   147  0.90  15.86   0.99     0.97       6437.97|
|  8:  2.4569 -  2.3504  1302   147  0.90  16.50   1.01     0.98       5787.03|
|  9:  2.3504 -  2.2602  1339   147  0.90  16.47   1.00     0.97       5235.25|
| 10:  2.2602 -  2.1825  1307   146  0.91  15.51   1.00     0.97       4560.29|
| 11:  2.1825 -  2.1144  1313   143  0.90  16.22   1.00     0.97       4263.26|
| 12:  2.1144 -  2.0541  1306   148  0.91  15.32   1.00     1.00       3764.35|
| 13:  2.0541 -  2.0002  1173   134  0.90  16.76   1.01     1.00       3411.12|
| 14:  2.0002 -  1.9515   336    36  0.89  16.93   0.99     0.96       2833.23|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2833.23 max =        11011.28 mean =      6628.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.48|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.02|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1612   ksol= 0.32   Bsol= 47.84   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.60,-1.79,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.184335                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1612   ksol= 0.32   Bsol= 47.84   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.60,-1.79,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.184335                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6584 0.99   1442  163 0.1007 0.1240      5.3841      5.5367|
|  2:  4.6584 -  3.7164 0.99   1380  148 0.0883 0.1106      5.4471      5.6482|
|  3:  3.7164 -  3.2522 0.99   1365  153 0.1080 0.1620      5.4873      5.8853|
|  4:  3.2522 -  2.9574 0.99   1351  149 0.1342 0.1525      5.5031      5.6122|
|  5:  2.9574 -  2.7469 0.99   1332  148 0.1397 0.1853      5.3586      5.5073|
|  6:  2.7469 -  2.5858 0.99   1344  150 0.1340 0.2012      5.2575      5.4909|
|  7:  2.5858 -  2.4569 0.98   1340  147 0.1285 0.1733      5.1941      5.4022|
|  8:  2.4569 -  2.3504 0.98   1302  147 0.1287 0.1688      5.1109      5.2923|
|  9:  2.3504 -  2.2602 0.99   1339  147 0.1235 0.1919      5.0601      5.3202|
| 10:  2.2602 -  2.1825 0.98   1307  146 0.1204 0.1750       4.992      5.2524|
| 11:  2.1825 -  2.1144 0.97   1313  143 0.1186 0.1835      4.9388      5.2174|
| 12:  2.1144 -  2.0541 0.98   1306  148 0.1186 0.1782      4.8712      5.1218|
| 13:  2.0541 -  2.0002 0.89   1173  134 0.1201 0.1778      4.8112      5.0018|
| 14:  2.0002 -  1.9515 0.25    336   36 0.1229 0.1651      4.7203      4.9794|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6584  1442   163  0.94   8.93   0.98     0.96       6856.70|
|  2:  4.6584 -  3.7164  1380   148  0.95   8.03   1.01     1.00       8891.07|
|  3:  3.7164 -  3.2522  1365   153  0.93  11.74   1.02     1.02      10653.01|
|  4:  3.2522 -  2.9574  1351   149  0.91  14.73   1.01     0.98      10924.20|
|  5:  2.9574 -  2.7469  1332   148  0.89  16.59   0.99     0.96       8635.51|
|  6:  2.7469 -  2.5858  1344   150  0.90  16.51   0.98     0.96       7414.99|
|  7:  2.5858 -  2.4569  1340   147  0.90  15.88   0.99     0.96       6450.71|
|  8:  2.4569 -  2.3504  1302   147  0.90  16.52   1.00     0.97       5801.83|
|  9:  2.3504 -  2.2602  1339   147  0.90  16.48   0.99     0.96       5238.46|
| 10:  2.2602 -  2.1825  1307   146  0.91  15.51   1.00     0.97       4561.50|
| 11:  2.1825 -  2.1144  1313   143  0.90  16.24   1.00     0.96       4266.26|
| 12:  2.1144 -  2.0541  1306   148  0.91  15.34   0.99     0.99       3773.04|
| 13:  2.0541 -  2.0002  1173   134  0.90  16.78   1.00     0.99       3418.68|
| 14:  2.0002 -  1.9515   336    36  0.89  16.92   0.98     0.95       2829.84|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2829.84 max =        10924.20 mean =      6669.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.52|
|phase err.(test): min =        0.00 max =           89.39 mean =        14.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.753)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.28    104.38  16.90    None  None   None       |
|    all(noH): 2823   0      2.28    104.38  16.90    None  None   None       |
|    Sol.    : 438    0      5.03    85.38   39.35    None  None   None       |
|    Mac.    : 2385   0      2.28    104.38  12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.278 -  12.488: 1601   |   5:    53.327 -  63.537:   63        |
|      1:    12.488 -  22.698:  701   |   6:    63.537 -  73.747:   26        |
|      2:    22.698 -  32.908:  165   |   7:    73.747 -  83.957:   15        |
|      3:    32.908 -  43.118:  147   |   8:    83.957 -  94.167:    3        |
|      4:    43.118 -  53.327:   98   |   9:    94.167 - 104.377:    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)= 335         
Filter by distance & map next to the model:
   mapped sites are within: 0.443 - 5.897
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 335
   mapped sites are within: 0.708 - 5.897

peak=    5.483 closest distance to " O   HOH Z 113 " =    2.230
peak=    5.473 closest distance to " CG  PRO A  54 " =    1.291
peak=    5.419 closest distance to " CB  GLN A 223 " =    1.425
peak=    5.333 closest distance to " O   HOH Z 124 " =    1.580
peak=    5.317 closest distance to " CB  SER A  63 " =    1.188
peak=    5.093 closest distance to " CG  PRO A 198 " =    1.291
peak=    4.961 closest distance to " O   HOH Z 132 " =    1.267
peak=    4.935 closest distance to " CG  PRO A  90 " =    1.174
peak=    4.887 closest distance to " CB  ARG A 275 " =    0.895
peak=    4.883 closest distance to " CG  PRO A 213 " =    1.276
peak=    4.775 closest distance to " O   HOH Z 234 " =    3.817
peak=    4.649 closest distance to " O   HOH Z 272 " =    1.919
peak=    4.635 closest distance to " O   HOH Z 142 " =    1.597
peak=    4.618 closest distance to " ND2 ASN A 249 " =    1.970
peak=    4.618 closest distance to " O   HOH Z 214 " =    1.197
peak=    4.614 closest distance to " CB  SER A   3 " =    1.358
peak=    4.599 closest distance to " O   HOH Z  15 " =    2.082
peak=    4.587 closest distance to " C   PRO A 198 " =    1.594
peak=    4.548 closest distance to " CB  PRO A  54 " =    0.823
peak=    4.540 closest distance to " O   HOH Z 247 " =    1.415
peak=    4.509 closest distance to " O   HOH Z 134 " =    1.678
peak=    4.500 closest distance to " CB  GLU A 128 " =    1.183
peak=    4.456 closest distance to " O   HOH Z 193 " =    1.854
peak=    4.454 closest distance to " O   HOH Z  40 " =    1.750
peak=    4.440 closest distance to " O   HOH Z  59 " =    2.363
peak=    4.402 closest distance to " CG  PRO A 280 " =    0.726
peak=    4.392 closest distance to " CA  TYR A  30 " =    1.025
peak=    4.373 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.365 closest distance to " O   HOH Z  44 " =    2.421
peak=    4.343 closest distance to " O   SER A  87 " =    2.101
peak=    4.339 closest distance to " O   HOH Z  97 " =    1.880
peak=    4.330 closest distance to " O   HOH Z  80 " =    1.744
peak=    4.318 closest distance to " NH2 ARG A 156 " =    1.238
peak=    4.304 closest distance to " O   HOH Z 403 " =    1.725
peak=    4.294 closest distance to " O   HOH Z 426 " =    1.479
peak=    4.294 closest distance to " O   HOH Z 126 " =    1.778
peak=    4.286 closest distance to " CB  GLU A 152 " =    1.130
peak=    4.286 closest distance to " O   HOH Z  11 " =    1.352
peak=    4.282 closest distance to " O   HOH Z 260 " =    1.345
peak=    4.267 closest distance to " O   HOH Z 368 " =    2.065
peak=    4.250 closest distance to " O   HOH Z 154 " =    1.495
peak=    4.217 closest distance to " CA  ALA A  21 " =    1.215
peak=    4.216 closest distance to " O   HOH Z 411 " =    3.490
peak=    4.201 closest distance to " O   HOH Z 316 " =    2.964
peak=    4.197 closest distance to " O   HOH Z 278 " =    1.032
peak=    4.187 closest distance to " CB  GLU A 277 " =    3.586
peak=    4.187 closest distance to " CG1 ILE A  33 " =    1.280
peak=    4.172 closest distance to " O   HOH Z 133 " =    1.599
peak=    4.160 closest distance to " O   HOH Z 189 " =    1.834
peak=    4.152 closest distance to " CA  ASP A 191 " =    0.883
peak=    4.115 closest distance to " CB  VAL A 202 " =    1.543
peak=    4.115 closest distance to " O   HOH Z 236 " =    1.953
peak=    4.114 closest distance to " CB  SER A 141 " =    1.019
peak=    4.094 closest distance to " CG  ARG A  66 " =    2.668
peak=    4.091 closest distance to " N   ASN A  39 " =    1.275
peak=    4.083 closest distance to " CB  ARG A 190 " =    1.702
peak=    4.068 closest distance to " CB  LEU A 228 " =    1.166
peak=    4.059 closest distance to " O   HOH Z 108 " =    1.354
peak=    4.044 closest distance to " CB  TYR A 169 " =    0.827
peak=    4.042 closest distance to " O   HOH Z 232 " =    2.249
peak=    4.037 closest distance to " O   HOH Z 344 " =    2.961
peak=    4.021 closest distance to " CG AARG A 275 " =    0.916
peak=    4.005 closest distance to " O   HOH Z 313 " =    1.867
peak=    3.989 closest distance to " O   HOH Z  54 " =    2.352
peak=    3.989 closest distance to " NZ  LYS A 117 " =    3.210
peak=    3.977 closest distance to " O   HOH Z 156 " =    3.304
peak=    3.973 closest distance to " O   HOH Z 207 " =    1.849
peak=    3.950 closest distance to " CB  PRO A 198 " =    1.084
peak=    3.946 closest distance to " CD  LYS A 119 " =    1.452
peak=    3.942 closest distance to " O   HOH Z 427 " =    2.761
peak=    3.940 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.923 closest distance to " O   HOH Z  61 " =    1.546
peak=    3.919 closest distance to " O   GLY A  23 " =    2.345
peak=    3.918 closest distance to " CG  PRO A 243 " =    1.197
peak=    3.915 closest distance to " CG1BVAL A  72 " =    1.604
peak=    3.902 closest distance to " ND2 ASN A 187 " =    1.671
peak=    3.898 closest distance to " O   HOH Z  44 " =    1.886
peak=    3.890 closest distance to " O   HOH Z  67 " =    1.878
peak=    3.889 closest distance to " O   HOH Z  88 " =    3.271
peak=    3.885 closest distance to " O   HOH Z  43 " =    1.475
peak=    3.884 closest distance to " O   HOH Z 402 " =    1.437
peak=    3.876 closest distance to " O   HOH Z  63 " =    2.010
peak=    3.876 closest distance to " OD2 ASP A 286 " =    2.832
peak=    3.861 closest distance to " O   HOH Z 298 " =    1.821
peak=    3.858 closest distance to " O   HOH Z 374 " =    2.474
peak=    3.853 closest distance to " OE1 GLN A  11 " =    1.853
peak=    3.849 closest distance to " O   HOH Z 326 " =    1.596
peak=    3.845 closest distance to " O   HOH Z 203 " =    1.778
peak=    3.840 closest distance to " CA  THR A 221 " =    0.907
peak=    3.838 closest distance to " O   HOH Z  59 " =    1.907
peak=    3.837 closest distance to " O   HOH Z 276 " =    1.388
peak=    3.830 closest distance to " O   HOH Z 369 " =    2.049
peak=    3.829 closest distance to " O   HOH Z 173 " =    2.088
peak=    3.828 closest distance to " CB  PRO A  54 " =    1.330
peak=    3.823 closest distance to " CA  ARG A  36 " =    1.064
peak=    3.819 closest distance to " NH2AARG A 190 " =    1.356
peak=    3.808 closest distance to " O   HOH Z 423 " =    1.939
peak=    3.802 closest distance to " O   HOH Z 126 " =    1.634
peak=    3.799 closest distance to " OD1 ASN A  69 " =    2.624
peak=    3.798 closest distance to " CD  ARG A 269 " =    0.974
peak=    3.796 closest distance to " NH2BARG A 145 " =    1.928
peak=    3.794 closest distance to " O   HOH Z 358 " =    2.141
peak=    3.792 closest distance to " O   HOH Z 416 " =    2.808
peak=    3.790 closest distance to " O   HOH Z 279 " =    2.138
peak=    3.785 closest distance to " O   HOH Z 132 " =    2.854
peak=    3.783 closest distance to " NZ  LYS A  76 " =    1.204
peak=    3.782 closest distance to " O   HOH Z  54 " =    1.656
peak=    3.781 closest distance to " CG2 THR A 221 " =    1.089
peak=    3.771 closest distance to " O   HOH Z 145 " =    2.172
peak=    3.762 closest distance to " NZ  LYS A 119 " =    1.830
peak=    3.760 closest distance to " O   HOH Z 434 " =    1.292
peak=    3.752 closest distance to " O   HOH Z 102 " =    1.283
peak=    3.751 closest distance to " O   HOH Z 144 " =    2.219
peak=    3.743 closest distance to " O   HOH Z 227 " =    1.757
peak=    3.743 closest distance to " O   HOH Z  66 " =    2.323
peak=    3.733 closest distance to " O   HOH Z 215 " =    1.476
peak=    3.725 closest distance to " O   HOH Z 133 " =    1.954
peak=    3.724 closest distance to " CB  ASN A 148 " =    1.621
peak=    3.719 closest distance to " CB  ARG A 139 " =    0.983
peak=    3.717 closest distance to " CA  ASP A 140 " =    1.167
peak=    3.700 closest distance to " O   HOH Z 108 " =    2.184
peak=    3.692 closest distance to " O   HOH Z  20 " =    1.585
peak=    3.692 closest distance to " CB  TRP A 179 " =    1.235
peak=    3.688 closest distance to " NE2 GLN A  11 " =    1.039
peak=    3.677 closest distance to " O   HOH Z  97 " =    2.497
peak=    3.672 closest distance to " CD2 LEU A 297 " =    0.932
peak=    3.660 closest distance to " NH1AARG A 145 " =    1.093
peak=    3.645 closest distance to " CB  ASN A 187 " =    1.418
peak=    3.639 closest distance to " NE AARG A 275 " =    1.299
peak=    3.638 closest distance to " CG2BVAL A  41 " =    0.903
peak=    3.633 closest distance to " O   HOH Z 215 " =    1.455
peak=    3.631 closest distance to " O   HOH Z 227 " =    1.748
peak=    3.625 closest distance to " NH2BARG A 102 " =    0.980
peak=    3.623 closest distance to " CD2 HIS A  81 " =    1.187
peak=    3.622 closest distance to " O   HOH Z 408 " =    1.500
peak=    3.617 closest distance to " O   HOH Z  10 " =    1.774
peak=    3.616 closest distance to " O   HOH Z 147 " =    1.729
peak=    3.606 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.606 closest distance to " CB  ALA A 291 " =    1.162
peak=    3.603 closest distance to " O   HOH Z 346 " =    1.562
peak=    3.598 closest distance to " CB  MET A  47 " =    1.079
peak=    3.597 closest distance to " O   HOH Z  21 " =    1.770
peak=    3.592 closest distance to " O   HOH Z 135 " =    1.864
peak=    3.590 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.589 closest distance to " O   HOH Z  48 " =    1.446
peak=    3.582 closest distance to " O   HOH Z  30 " =    1.382
peak=    3.581 closest distance to " O   HOH Z 303 " =    2.005
peak=    3.580 closest distance to " CG AARG A 275 " =    0.929
peak=    3.574 closest distance to " O   TRP A 274 " =    1.744
peak=    3.567 closest distance to " O   HOH Z 406 " =    1.661
peak=    3.563 closest distance to " O   HOH Z 394 " =    1.611
peak=    3.562 closest distance to " O   HOH Z 291 " =    1.578
peak=    3.557 closest distance to " CB  ASN A 148 " =    1.205
peak=    3.556 closest distance to " CB  ARG A  79 " =    1.346
peak=    3.555 closest distance to " O   HOH Z 180 " =    2.224
peak=    3.548 closest distance to " O   HOH Z 421 " =    1.574
peak=    3.544 closest distance to " NE1 TRP A 274 " =    0.912
peak=    3.537 closest distance to " CA  ASP A 124 " =    0.708
peak=    3.537 closest distance to " CG  GLN A  11 " =    1.179
peak=    3.534 closest distance to " NZ  LYS A 117 " =    1.124
peak=    3.532 closest distance to " O   HOH Z 221 " =    1.547
peak=    3.527 closest distance to " C   GLY A  80 " =    1.171
peak=    3.524 closest distance to " O   HOH Z 118 " =    1.297
peak=    3.523 closest distance to " O   HOH Z  78 " =    1.702
peak=    3.521 closest distance to " CA  GLY A 211 " =    1.143
peak=    3.521 closest distance to " O   HOH Z 284 " =    2.907
peak=    3.519 closest distance to " O   HOH Z   6 " =    2.163
peak=    3.516 closest distance to " O   HOH Z 345 " =    1.738
peak=    3.511 closest distance to " CG  ARG A  66 " =    1.096
peak=    3.507 closest distance to " OD1 ASP A 231 " =    1.909
peak=    3.507 closest distance to " CB  PHE A  16 " =    1.035
peak=    3.503 closest distance to " O   HOH Z  19 " =    1.772
peak=    3.500 closest distance to " O   HOH Z 295 " =    1.489
peak=    3.496 closest distance to " CB  ARG A 102 " =    0.716
peak=    3.490 closest distance to " OE1 GLN A  58 " =    5.897
peak=    3.488 closest distance to " CD BLYS A 290 " =    1.121
peak=    3.485 closest distance to " CA  ASN A 176 " =    1.786
peak=    3.484 closest distance to " O   HOH Z 387 " =    2.513
peak=    3.478 closest distance to " O   HOH Z 234 " =    1.864
peak=    3.477 closest distance to " OD1 ASP A 238 " =    0.863
peak=    3.463 closest distance to " CA  GLN A 223 " =    0.839
peak=    3.458 closest distance to " O   HOH Z 199 " =    1.038
peak=    3.456 closest distance to " CA  VAL A  41 " =    0.812
peak=    3.456 closest distance to " CA  ARG A 195 " =    1.248
peak=    3.452 closest distance to " CD  ARG A 139 " =    1.396
peak=    3.443 closest distance to " CG2 VAL A 257 " =    0.831
peak=    3.442 closest distance to " O   HOH Z 368 " =    2.441
peak=    3.442 closest distance to " O   HOH Z 427 " =    2.996
peak=    3.432 closest distance to " CB  GLN A  58 " =    0.748
peak=    3.427 closest distance to " OG BSER A 258 " =    3.447
peak=    3.424 closest distance to " OH  TYR A  30 " =    1.153
peak=    3.423 closest distance to " O   HOH Z  71 " =    1.151
peak=    3.420 closest distance to " OG BSER A 164 " =    2.508
peak=    3.418 closest distance to " CB  SER A  62 " =    0.762
peak=    3.412 closest distance to " CB  ASN A 285 " =    0.930
peak=    3.411 closest distance to " O   HOH Z 163 " =    1.504
peak=    3.405 closest distance to " O   HOH Z 106 " =    1.465
peak=    3.403 closest distance to " CB  ALA A 256 " =    1.047
peak=    3.399 closest distance to " CG1 VAL A 153 " =    1.068
peak=    3.393 closest distance to " O   HOH Z 250 " =    1.803
peak=    3.387 closest distance to " O   HOH Z 214 " =    2.264
peak=    3.385 closest distance to " O   HOH Z 171 " =    2.679
peak=    3.385 closest distance to " CB  ALA A 100 " =    1.314
peak=    3.382 closest distance to " O   HOH Z 362 " =    3.564
peak=    3.381 closest distance to " O   MET A 105 " =    1.873
peak=    3.380 closest distance to " CA  ARG A  66 " =    1.113
peak=    3.378 closest distance to " O   HOH Z 211 " =    1.112
peak=    3.372 closest distance to " O   HOH Z 357 " =    1.975
peak=    3.371 closest distance to " O   HOH Z 313 " =    2.278
peak=    3.366 closest distance to " O   HOH Z 404 " =    1.525
peak=    3.355 closest distance to " CB  SER A 273 " =    0.782
peak=    3.355 closest distance to " O   ALA A 158 " =    1.209
peak=    3.352 closest distance to " O   ALA A 165 " =    1.313
peak=    3.349 closest distance to " CA  ASP A 162 " =    1.180
peak=    3.346 closest distance to " CZ  PHE A 218 " =    1.028
peak=    3.345 closest distance to " O   HOH Z 361 " =    2.390
peak=    3.343 closest distance to " CB  GLN A 278 " =    0.836
peak=    3.341 closest distance to " CA  LEU A 282 " =    1.153
peak=    3.340 closest distance to " O   HOH Z 166 " =    1.347
peak=    3.339 closest distance to " CD  PRO A  54 " =    1.139
peak=    3.338 closest distance to " CB  GLN A 194 " =    0.857
peak=    3.334 closest distance to " CG  GLN A  77 " =    0.839
peak=    3.333 closest distance to " O   HOH Z 419 " =    1.554
peak=    3.333 closest distance to " CG2 VAL A 197 " =    1.177
peak=    3.330 closest distance to " CB  ARG A 269 " =    0.983
peak=    3.324 closest distance to " CB  ASN A  39 " =    0.926
peak=    3.321 closest distance to " CG2 ILE A 120 " =    1.203
peak=    3.321 closest distance to " O  BHOH Z  74 " =    1.426
peak=    3.321 closest distance to " O   HOH Z  20 " =    2.029
peak=    3.320 closest distance to " O   HOH Z 292 " =    1.660
peak=    3.320 closest distance to " O   HOH Z 287 " =    1.750
peak=    3.319 closest distance to " O   THR A 251 " =    1.277
peak=    3.315 closest distance to " O   HOH Z 334 " =    1.557
peak=    3.313 closest distance to " O   HOH Z 207 " =    2.040
peak=    3.312 closest distance to " CG2 THR A 220 " =    0.762
peak=    3.309 closest distance to " O   HOH Z 281 " =    4.180
peak=    3.304 closest distance to " CB  ILE A 199 " =    1.111
peak=    3.304 closest distance to " CA  ALA A 248 " =    1.190
peak=    3.304 closest distance to " NE2 GLN A  58 " =    4.397
peak=    3.302 closest distance to " O   HOH Z 210 " =    1.168
peak=    3.300 closest distance to " CG2 VAL A  78 " =    0.989
peak=    3.300 closest distance to " OG  SER A  62 " =    3.004
peak=    3.300 closest distance to " O   HOH Z 273 " =    2.734
peak=    3.299 closest distance to " O   HOH Z 427 " =    3.407
peak=    3.296 closest distance to " O   HOH Z  35 " =    2.442
peak=    3.294 closest distance to " CA  LYS A 117 " =    1.231
peak=    3.292 closest distance to " O   HOH Z 128 " =    1.717
peak=    3.291 closest distance to " O   HOH Z 261 " =    2.039
peak=    3.289 closest distance to " O   HOH Z   4 " =    1.929
peak=    3.283 closest distance to " CE  LYS A 119 " =    1.039
peak=    3.282 closest distance to " OG1 THR A 294 " =    2.447
peak=    3.282 closest distance to " C   SER A  32 " =    1.023
peak=    3.280 closest distance to " CD1 LEU A 300 " =    1.237
peak=    3.279 closest distance to " O   HOH Z 250 " =    1.398
peak=    3.277 closest distance to " O   HOH Z 193 " =    2.238
peak=    3.274 closest distance to " O   HOH Z 183 " =    1.467
peak=    3.274 closest distance to " O   HOH Z 345 " =    2.916
peak=    3.272 closest distance to " O   HOH Z 245 " =    1.392
peak=    3.272 closest distance to " O   HOH Z 352 " =    1.249
peak=    3.269 closest distance to " O   HOH Z 166 " =    3.276
peak=    3.264 closest distance to " CA  ILE A 263 " =    0.962
peak=    3.261 closest distance to " O   HOH Z 285 " =    1.972
peak=    3.259 closest distance to " O   GLY A  91 " =    1.288
peak=    3.257 closest distance to " O   HOH Z 197 " =    2.385
peak=    3.256 closest distance to " CA  VAL A 126 " =    0.911
peak=    3.251 closest distance to " O   HOH Z 194 " =    2.014
peak=    3.250 closest distance to " O   HOH Z 112 " =    1.542
peak=    3.248 closest distance to " O   HOH Z 106 " =    2.209
peak=    3.242 closest distance to " CG  MET A  93 " =    1.085
peak=    3.241 closest distance to " O   SER A  26 " =    1.739
peak=    3.236 closest distance to " O   HOH Z 280 " =    2.250
peak=    3.234 closest distance to " O   THR A  31 " =    1.588
peak=    3.228 closest distance to " O   HOH Z 112 " =    3.091
peak=    3.228 closest distance to " O   HOH Z  44 " =    3.458
peak=    3.223 closest distance to " O   HOH Z 255 " =    1.687
peak=    3.222 closest distance to " CG2AVAL A 121 " =    2.134
peak=    3.220 closest distance to " CD2 TRP A 179 " =    1.288
peak=    3.214 closest distance to " O   HOH Z 104 " =    2.988
peak=    3.210 closest distance to " O   HOH Z  98 " =    2.125
peak=    3.209 closest distance to " O   HOH Z 261 " =    1.538
peak=    3.206 closest distance to " O   HOH Z 366 " =    2.899
peak=    3.206 closest distance to " O   HOH Z 155 " =    3.011
peak=    3.204 closest distance to " CD  ARG A 195 " =    0.892
peak=    3.197 closest distance to " CD  ARG A 159 " =    0.771
peak=    3.196 closest distance to " CA  MET A  40 " =    1.069
peak=    3.196 closest distance to " CG  MET A 113 " =    1.381
peak=    3.195 closest distance to " CA  GLU A 152 " =    0.816
peak=    3.193 closest distance to " CG  GLN A  89 " =    1.427
peak=    3.192 closest distance to " CB  GLN A  73 " =    1.058
peak=    3.192 closest distance to " CD1 TRP A 266 " =    1.230
peak=    3.185 closest distance to " NH1 ARG A 138 " =    1.144
peak=    3.185 closest distance to " CA  ALA A  84 " =    1.287
peak=    3.183 closest distance to " O   HOH Z 438 " =    2.331
peak=    3.178 closest distance to " CG1 ILE A 120 " =    1.079
peak=    3.176 closest distance to " CG  GLU A 277 " =    2.186
peak=    3.173 closest distance to " N   ARG A 156 " =    1.415
peak=    3.173 closest distance to " O   HOH Z 127 " =    1.207
peak=    3.171 closest distance to " O   HOH Z  20 " =    2.155
peak=    3.165 closest distance to " N   SER A 135 " =    1.247
peak=    3.163 closest distance to " CH2 TRP A 274 " =    1.983
peak=    3.162 closest distance to " CG  GLN A  58 " =    2.381
peak=    3.158 closest distance to " CG  MET A 185 " =    1.174
peak=    3.158 closest distance to " O   HOH Z 217 " =    1.166
peak=    3.155 closest distance to " CZ  PHE A 192 " =    1.109
peak=    3.155 closest distance to " N   ARG A 190 " =    1.028
peak=    3.155 closest distance to " CE1 PHE A 155 " =    1.340
peak=    3.154 closest distance to " O   HOH Z  50 " =    1.454
peak=    3.154 closest distance to " CG  GLN A  88 " =    1.032
peak=    3.151 closest distance to " CB  ALA A 244 " =    0.961
peak=    3.148 closest distance to " CB  THR A  31 " =    1.717
peak=    3.146 closest distance to " OG BSER A 210 " =    1.159
peak=    3.143 closest distance to " O   HOH Z 422 " =    2.494
peak=    3.142 closest distance to " CA  ILE A  33 " =    1.508
peak=    3.142 closest distance to " O   HOH Z  63 " =    2.078
peak=    3.136 closest distance to " CB  TRP A 266 " =    0.926
peak=    3.130 closest distance to " O   HOH Z 359 " =    1.982
peak=    3.128 closest distance to " O   HOH Z 403 " =    1.306
peak=    3.128 closest distance to " CA  ALA A 158 " =    1.069
peak=    3.124 closest distance to " O   HOH Z 409 " =    3.493
peak=    3.122 closest distance to " NH1 ARG A  14 " =    1.145
peak=    3.112 closest distance to " O   SER A 164 " =    1.384
peak=    3.104 closest distance to " CA  THR A 264 " =    0.818
peak=    3.095 closest distance to " NH1BARG A 145 " =    1.166
peak=    3.092 closest distance to " CD1 LEU A  96 " =    0.754
peak=    3.089 closest distance to " OD2 ASP A 298 " =    4.038
peak=    3.089 closest distance to " O   HOH Z 392 " =    1.984
peak=    3.087 closest distance to " O   HOH Z 125 " =    2.317
peak=    3.067 closest distance to " O   HOH Z  39 " =    1.088
peak=    3.055 closest distance to " CZ2 TRP A 274 " =    1.624
peak=    3.045 closest distance to " CA  GLU A  46 " =    0.806
peak=    3.035 closest distance to " O   HOH Z 273 " =    3.381
peak=    3.010 closest distance to " O   HOH Z 329 " =    3.271

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.397 - 5.150
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 193
   mapped sites are within: 0.773 - 5.150

peak=   -4.379 closest distance to " O   HOH Z 290 " =    0.914
peak=   -4.355 closest distance to " O   HOH Z 377 " =    0.959
peak=   -4.223 closest distance to " OXT GLY A 302 " =    2.930
peak=   -4.203 closest distance to " O   HOH Z 221 " =    1.093
peak=   -4.197 closest distance to " O   HOH Z  13 " =    1.384
peak=   -4.192 closest distance to " O   HOH Z 266 " =    4.091
peak=   -4.171 closest distance to " OG ASER A 134 " =    1.356
peak=   -4.063 closest distance to " CG  LYS A 193 " =    2.501
peak=   -4.058 closest distance to " CD  ARG A 156 " =    1.962
peak=   -4.038 closest distance to " O   HOH Z  92 " =    1.467
peak=   -3.982 closest distance to " CG  ASP A  50 " =    2.413
peak=   -3.962 closest distance to " ND2 ASN A  45 " =    0.935
peak=   -3.958 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.935 closest distance to " N   GLN A  58 " =    1.746
peak=   -3.931 closest distance to " C   ALA A 158 " =    1.227
peak=   -3.926 closest distance to " CA  SER A 164 " =    1.989
peak=   -3.900 closest distance to " O   HOH Z  43 " =    1.568
peak=   -3.899 closest distance to " O   HOH Z 166 " =    2.012
peak=   -3.891 closest distance to " O   HOH Z 234 " =    4.286
peak=   -3.884 closest distance to " O   HOH Z  11 " =    1.570
peak=   -3.877 closest distance to " NE2 GLN A  58 " =    0.964
peak=   -3.848 closest distance to " O   HOH Z 423 " =    2.341
peak=   -3.847 closest distance to " O   HOH Z  71 " =    1.126
peak=   -3.844 closest distance to " CA  TYR A  68 " =    2.749
peak=   -3.833 closest distance to " CD2 LEU A 300 " =    2.825
peak=   -3.823 closest distance to " O   HOH Z 418 " =    1.229
peak=   -3.813 closest distance to " C   HIS A 108 " =    1.079
peak=   -3.810 closest distance to " O   HOH Z  93 " =    1.293
peak=   -3.787 closest distance to " CD1 LEU A 101 " =    2.562
peak=   -3.787 closest distance to " NH2 ARG A  66 " =    1.579
peak=   -3.783 closest distance to " CE  MET A  93 " =    1.266
peak=   -3.769 closest distance to " O   TRP A  92 " =    1.892
peak=   -3.768 closest distance to " CE2 TYR A  30 " =    2.809
peak=   -3.763 closest distance to " CB  CYS A 254 " =    2.559
peak=   -3.755 closest distance to " O   HOH Z  10 " =    1.581
peak=   -3.749 closest distance to " N   SER A 276 " =    1.435
peak=   -3.747 closest distance to " C   ASN A 285 " =    2.359
peak=   -3.739 closest distance to " NH2 ARG A  79 " =    1.899
peak=   -3.739 closest distance to " CE  MET A 105 " =    1.865
peak=   -3.738 closest distance to " CZ  TYR A 169 " =    1.832
peak=   -3.734 closest distance to " CG  GLU A  53 " =    1.386
peak=   -3.730 closest distance to " O   VAL A  67 " =    2.767
peak=   -3.703 closest distance to " OE2 GLU A   2 " =    1.508
peak=   -3.681 closest distance to " ND2 ASN A 187 " =    1.626
peak=   -3.667 closest distance to " NH2 ARG A  66 " =    4.959
peak=   -3.665 closest distance to " O   HOH Z 313 " =    1.025
peak=   -3.661 closest distance to " CD  GLN A  88 " =    0.878
peak=   -3.651 closest distance to " N   ALA A  43 " =    2.524
peak=   -3.640 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.634 closest distance to " CB  ALA A 161 " =    2.581
peak=   -3.627 closest distance to " O   HOH Z 292 " =    4.412
peak=   -3.625 closest distance to " CG2 THR A   4 " =    1.869
peak=   -3.625 closest distance to " O   GLY A 196 " =    1.040
peak=   -3.618 closest distance to " O   HOH Z  17 " =    1.197
peak=   -3.615 closest distance to " O   HOH Z  52 " =    1.775
peak=   -3.604 closest distance to " CB  PRO A 243 " =    2.600
peak=   -3.604 closest distance to " O   HOH Z 407 " =    3.366
peak=   -3.602 closest distance to " CH2 TRP A 179 " =    1.232
peak=   -3.596 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.596 closest distance to " NH1 ARG A 195 " =    2.544
peak=   -3.583 closest distance to " O   HOH Z  98 " =    1.739
peak=   -3.582 closest distance to " O   HOH Z 388 " =    2.099
peak=   -3.582 closest distance to " O   HOH Z 377 " =    1.881
peak=   -3.581 closest distance to " OG  SER A  62 " =    1.430
peak=   -3.574 closest distance to " CG  GLN A  58 " =    1.346
peak=   -3.573 closest distance to " OG  SER A  97 " =    2.115
peak=   -3.560 closest distance to " O   HOH Z 150 " =    1.364
peak=   -3.558 closest distance to " CB  ALA A 291 " =    2.320
peak=   -3.554 closest distance to " O   ALA A 161 " =    1.498
peak=   -3.547 closest distance to " CD2 LEU A 237 " =    2.342
peak=   -3.529 closest distance to " CA  TRP A 274 " =    1.659
peak=   -3.519 closest distance to " O   ALA A 256 " =    1.466
peak=   -3.514 closest distance to " CD1 LEU A 228 " =    2.336
peak=   -3.510 closest distance to " N   MET A 188 " =    1.984
peak=   -3.504 closest distance to " OG  SER A 245 " =    0.928
peak=   -3.497 closest distance to " O   HOH Z 435 " =    2.501
peak=   -3.496 closest distance to " O   HOH Z  19 " =    2.044
peak=   -3.488 closest distance to " CD1 TYR A 247 " =    2.444
peak=   -3.482 closest distance to " O   ASN A 187 " =    1.463
peak=   -3.479 closest distance to " CD  PRO A 198 " =    1.289
peak=   -3.474 closest distance to " O   HOH Z 412 " =    4.637
peak=   -3.467 closest distance to " O   HOH Z  63 " =    1.120
peak=   -3.463 closest distance to " O   HOH Z 396 " =    1.786
peak=   -3.460 closest distance to " OG BSER A 134 " =    1.758
peak=   -3.455 closest distance to " O   HOH Z 165 " =    2.094
peak=   -3.453 closest distance to " O   HOH Z  38 " =    1.452
peak=   -3.446 closest distance to " O   HOH Z 265 " =    1.947
peak=   -3.445 closest distance to " O   HOH Z 151 " =    1.361
peak=   -3.444 closest distance to " CG  ARG A 269 " =    2.284
peak=   -3.438 closest distance to " O   HOH Z 417 " =    2.647
peak=   -3.427 closest distance to " C   SER A 206 " =    1.679
peak=   -3.422 closest distance to " N   ALA A 226 " =    2.089
peak=   -3.412 closest distance to " CB  ASN A  39 " =    2.220
peak=   -3.410 closest distance to " O   ALA A   7 " =    1.552
peak=   -3.403 closest distance to " O   HOH Z 196 " =    2.211
peak=   -3.395 closest distance to " O   HOH Z 353 " =    2.306
peak=   -3.389 closest distance to " O   HOH Z 118 " =    2.914
peak=   -3.386 closest distance to " CD2 PHE A  59 " =    2.482
peak=   -3.382 closest distance to " CD  ARG A 195 " =    5.110
peak=   -3.382 closest distance to " C   THR A 279 " =    1.221
peak=   -3.381 closest distance to " CD1 PHE A  59 " =    1.881
peak=   -3.376 closest distance to " O   GLY A 118 " =    2.113
peak=   -3.375 closest distance to " CD  ARG A 139 " =    1.647
peak=   -3.362 closest distance to " CB  ALA A 248 " =    1.882
peak=   -3.358 closest distance to " O   HOH Z 185 " =    2.308
peak=   -3.352 closest distance to " O   GLY A 211 " =    1.430
peak=   -3.347 closest distance to " CG  LEU A  83 " =    1.939
peak=   -3.340 closest distance to " CD1 LEU A 101 " =    2.816
peak=   -3.333 closest distance to " NH2AARG A 275 " =    5.135
peak=   -3.329 closest distance to " SG ACYS A 201 " =    2.464
peak=   -3.328 closest distance to " O   HOH Z 311 " =    3.479
peak=   -3.322 closest distance to " CG  TRP A 266 " =    1.690
peak=   -3.319 closest distance to " CB  PHE A 208 " =    2.278
peak=   -3.319 closest distance to " CE3 TRP A 150 " =    1.922
peak=   -3.319 closest distance to " O   ASP A 191 " =    1.345
peak=   -3.311 closest distance to " OD1 ASP A 200 " =    1.228
peak=   -3.304 closest distance to " O   HOH Z 100 " =    0.844
peak=   -3.300 closest distance to " OD1 ASP A 191 " =    1.570
peak=   -3.297 closest distance to " CG1 VAL A 112 " =    2.565
peak=   -3.293 closest distance to " OXT GLY A 302 " =    2.908
peak=   -3.290 closest distance to " O   HOH Z 231 " =    2.248
peak=   -3.280 closest distance to " C   LEU A 143 " =    1.377
peak=   -3.278 closest distance to " ND2 ASN A  60 " =    1.491
peak=   -3.275 closest distance to " O   HOH Z  97 " =    1.579
peak=   -3.273 closest distance to " O   HOH Z 236 " =    1.456
peak=   -3.268 closest distance to " O   GLY A 262 " =    2.045
peak=   -3.268 closest distance to " N   LEU A 281 " =    1.814
peak=   -3.267 closest distance to " O   HOH Z 266 " =    4.639
peak=   -3.267 closest distance to " O   HOH Z 222 " =    1.264
peak=   -3.265 closest distance to " O   HOH Z 351 " =    1.449
peak=   -3.265 closest distance to " CD  GLN A  58 " =    1.278
peak=   -3.263 closest distance to " SG  CYS A 254 " =    3.220
peak=   -3.261 closest distance to " O   ALA A 160 " =    1.528
peak=   -3.252 closest distance to " ND2 ASN A 249 " =    1.979
peak=   -3.250 closest distance to " CA  ASP A 298 " =    1.100
peak=   -3.248 closest distance to " OD1 ASN A 187 " =    1.752
peak=   -3.247 closest distance to " O   HOH Z 298 " =    2.675
peak=   -3.240 closest distance to " N   GLN A  77 " =    1.351
peak=   -3.240 closest distance to " CA  GLY A 203 " =    2.179
peak=   -3.234 closest distance to " O  BHOH Z 338 " =    1.547
peak=   -3.232 closest distance to " CA  ASN A 148 " =    1.764
peak=   -3.231 closest distance to " O   HOH Z 148 " =    3.492
peak=   -3.227 closest distance to " O   LEU A 228 " =    2.410
peak=   -3.226 closest distance to " O   SER A 210 " =    1.875
peak=   -3.224 closest distance to " O   LEU A 167 " =    1.548
peak=   -3.219 closest distance to " O   HOH Z 424 " =    2.976
peak=   -3.219 closest distance to " OD2 ASP A  50 " =    1.534
peak=   -3.219 closest distance to " CA  VAL A 197 " =    0.999
peak=   -3.218 closest distance to " CA  GLY A 133 " =    1.734
peak=   -3.217 closest distance to " OG BSER A 134 " =    1.285
peak=   -3.212 closest distance to " O   PRO A 198 " =    1.271
peak=   -3.211 closest distance to " CD2 LEU A 237 " =    2.420
peak=   -3.207 closest distance to " O   SER A 146 " =    0.823
peak=   -3.205 closest distance to " O   GLN A  11 " =    1.250
peak=   -3.197 closest distance to " O   ALA A  34 " =    2.524
peak=   -3.195 closest distance to " O   HOH Z  78 " =    1.972
peak=   -3.188 closest distance to " CG  GLU A 152 " =    0.897
peak=   -3.187 closest distance to " O   HOH Z  20 " =    1.246
peak=   -3.186 closest distance to " O   GLY A  23 " =    1.748
peak=   -3.185 closest distance to " O   HOH Z 283 " =    1.709
peak=   -3.180 closest distance to " CD  GLN A 223 " =    0.904
peak=   -3.178 closest distance to " CD  LYS A 289 " =    2.551
peak=   -3.175 closest distance to " O   HOH Z 414 " =    1.455
peak=   -3.173 closest distance to " CD1 TRP A 179 " =    1.101
peak=   -3.173 closest distance to " O   HOH Z 166 " =    1.432
peak=   -3.173 closest distance to " OD2 ASP A 171 " =    2.183
peak=   -3.169 closest distance to " O   HOH Z 166 " =    1.738
peak=   -3.161 closest distance to " O   VAL A 174 " =    1.931
peak=   -3.154 closest distance to " NH1BARG A 190 " =    2.316
peak=   -3.151 closest distance to " O   VAL A 125 " =    2.069
peak=   -3.151 closest distance to " CB  SER A 146 " =    2.180
peak=   -3.145 closest distance to " CB  PHE A 283 " =    2.800
peak=   -3.143 closest distance to " OG  SER A 273 " =    2.176
peak=   -3.140 closest distance to " CG  ASP A 132 " =    2.225
peak=   -3.139 closest distance to " CB  LEU A 167 " =    2.104
peak=   -3.138 closest distance to " O   HOH Z  76 " =    2.078
peak=   -3.133 closest distance to " CB  PHE A 192 " =    1.903
peak=   -3.133 closest distance to " O   HOH Z 189 " =    1.403
peak=   -3.127 closest distance to " O   HOH Z 281 " =    2.798
peak=   -3.111 closest distance to " OE1 GLN A  88 " =    1.205
peak=   -3.101 closest distance to " CA  GLY A 241 " =    2.265
peak=   -3.097 closest distance to " CG2 VAL A 189 " =    2.236
peak=   -3.095 closest distance to " CB  ASP A 286 " =    2.267
peak=   -3.086 closest distance to " CB  TRP A  85 " =    2.502
peak=   -3.079 closest distance to " CG  ASN A 110 " =    1.155
peak=   -3.078 closest distance to " NZ  LYS A 117 " =    1.530
peak=   -3.068 closest distance to " O   THR A  52 " =    1.650
peak=   -3.064 closest distance to " O   HOH Z 197 " =    5.150
peak=   -3.047 closest distance to " N   ALA A 248 " =    1.744
peak=   -3.028 closest distance to " O   HOH Z 264 " =    1.844

================= 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    :  0.4356 0.4303   6.246637e+00   6.240643e+00
   1_bss:  0.4241 0.4169   6.237465e+00   6.222111e+00
   1_xyz:  0.3206 0.3485   6.018851e+00   6.084386e+00
   1_adp:  0.2925 0.3600   5.968305e+00   6.105736e+00
   1_occ:  0.2921 0.3608   5.967532e+00   6.105256e+00
   2_bss:  0.2899 0.3583   5.965284e+00   6.104187e+00
   2_xyz:  0.2123 0.2684   5.699970e+00   5.883490e+00
   2_adp:  0.1921 0.2464   5.614646e+00   5.808830e+00
   2_occ:  0.1919 0.2465   5.614524e+00   5.808700e+00
   3_bss:  0.1915 0.2449   5.609730e+00   5.803163e+00
   3_xyz:  0.1535 0.2012   5.411819e+00   5.626848e+00
   3_adp:  0.1436 0.1946   5.362729e+00   5.582418e+00
   3_occ:  0.1435 0.1946   5.362540e+00   5.582393e+00
   4_bss:  0.1438 0.1948   5.364376e+00   5.584313e+00
   4_xyz:  0.1260 0.1737   5.248798e+00   5.481693e+00
   4_adp:  0.1222 0.1684   5.220603e+00   5.448411e+00
   4_occ:  0.1221 0.1684   5.220467e+00   5.448846e+00
   5_bss:  0.1220 0.1683   5.220262e+00   5.448424e+00
   5_xyz:  0.1169 0.1630   5.185485e+00   5.414250e+00
   5_adp:  0.1177 0.1610   5.182615e+00   5.402690e+00
   5_occ:  0.1176 0.1610   5.182507e+00   5.403384e+00
   5_bss:  0.1178 0.1612   5.184335e+00   5.405021e+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:  0.331  50.000  -3.297   2.269   2.520   0.000   0.000   0.000
   1_xyz:  0.331  50.000  -3.297   2.269   2.520   0.000   0.000   0.000
   1_adp:  0.331  50.000  -3.297   2.269   2.520   0.000   0.000   0.000
   1_occ:  0.331  50.000  -3.297   2.269   2.520   0.000   0.000   0.000
   2_bss:  0.327  57.170  -2.428   0.398   0.248   0.000   0.000   0.000
   2_xyz:  0.327  57.170  -2.428   0.398   0.248   0.000   0.000   0.000
   2_adp:  0.327  57.170  -2.428   0.398   0.248   0.000   0.000   0.000
   2_occ:  0.327  57.170  -2.428   0.398   0.248   0.000   0.000   0.000
   3_bss:  0.320  49.060  -2.334  -0.776  -1.120  -0.000  -0.000  -0.000
   3_xyz:  0.320  49.060  -2.334  -0.776  -1.120  -0.000  -0.000  -0.000
   3_adp:  0.320  49.060  -2.334  -0.776  -1.120  -0.000  -0.000  -0.000
   3_occ:  0.320  49.060  -2.334  -0.776  -1.120  -0.000  -0.000  -0.000
   4_bss:  0.322  54.812  -2.421  -1.337  -1.626  -0.000  -0.000  -0.000
   4_xyz:  0.322  54.812  -2.421  -1.337  -1.626  -0.000  -0.000  -0.000
   4_adp:  0.322  54.812  -2.421  -1.337  -1.626  -0.000  -0.000  -0.000
   4_occ:  0.322  54.812  -2.421  -1.337  -1.626  -0.000  -0.000  -0.000
   5_bss:  0.321  50.346  -2.375  -1.523  -1.748  -0.000  -0.000  -0.000
   5_xyz:  0.321  50.346  -2.375  -1.523  -1.748  -0.000  -0.000  -0.000
   5_adp:  0.321  50.346  -2.375  -1.523  -1.748  -0.000  -0.000  -0.000
   5_occ:  0.321  50.346  -2.375  -1.523  -1.748  -0.000  -0.000  -0.000
   5_bss:  0.318  47.844  -2.404  -1.605  -1.789  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.390 0.4771  0.6360    60037.713
   1_bss:  51.341 0.5013  0.6812    55350.616
   1_xyz:  37.459 0.6724  0.8892    33346.910
   1_adp:  39.084 0.6522  0.8739    35589.108
   1_occ:  39.084 0.6522  0.8734    35601.612
   2_bss:  38.733 0.6564  0.8487    35230.899
   2_xyz:  27.892 0.7794  0.9685    19255.141
   2_adp:  24.752 0.8138  0.9811    16017.118
   2_occ:  24.777 0.8136  0.9806    16032.841
   3_bss:  24.516 0.8160  0.9547    15705.604
   3_xyz:  19.540 0.8652  0.9878    10410.086
   3_adp:  18.393 0.8765  0.9875     9589.293
   3_occ:  18.394 0.8765  0.9873     9587.677
   4_bss:  18.401 0.8765  0.9741     9632.882
   4_xyz:  16.258 0.8956  0.9837     7778.965
   4_adp:  15.496 0.9024  0.9829     7305.794
   4_occ:  15.502 0.9024  0.9827     7313.178
   5_bss:  15.494 0.9024  0.9798     7303.746
   5_xyz:  14.732 0.9089  0.9817     6750.492
   5_adp:  14.427 0.9117  0.9805     6618.931
   5_occ:  14.438 0.9116  0.9803     6627.451
   5_bss:  14.474 0.9114  0.9751     6668.872
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8884e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8884e-01
   1_xyz:   1.434  0.011  0.085 15.771  0.006  4.112   1.1351e-01
   1_adp:   1.434  0.011  0.085 15.771  0.006  4.112   1.1351e-01
   1_occ:   1.434  0.011  0.085 15.771  0.006  4.112   1.1351e-01
   2_bss:   1.434  0.011  0.085 15.771  0.006  4.112   1.1351e-01
   2_xyz:   1.254  0.009  0.081 14.272  0.005  4.111   8.2790e-02
   2_adp:   1.254  0.009  0.081 14.272  0.005  4.111   8.2790e-02
   2_occ:   1.254  0.009  0.081 14.272  0.005  4.111   8.2790e-02
   3_bss:   1.254  0.009  0.081 14.272  0.005  4.111   8.2790e-02
   3_xyz:   0.927  0.006  0.061 14.056  0.004  4.116   5.1455e-02
   3_adp:   0.927  0.006  0.061 14.056  0.004  4.116   5.1455e-02
   3_occ:   0.927  0.006  0.061 14.056  0.004  4.116   5.1455e-02
   4_bss:   0.927  0.006  0.061 14.056  0.004  4.116   5.1455e-02
   4_xyz:   0.969  0.006  0.070 14.268  0.004  4.121   5.5251e-02
   4_adp:   0.969  0.006  0.070 14.268  0.004  4.121   5.5251e-02
   4_occ:   0.969  0.006  0.070 14.268  0.004  4.121   5.5251e-02
   5_bss:   0.969  0.006  0.070 14.268  0.004  4.121   5.5251e-02
   5_xyz:   0.931  0.006  0.067 14.229  0.003  4.112   5.1217e-02
   5_adp:   0.931  0.006  0.067 14.229  0.003  4.112   5.1217e-02
   5_occ:   0.931  0.006  0.067 14.229  0.003  4.112   5.1217e-02
   5_bss:   0.931  0.006  0.067 14.229  0.003  4.112   5.1217e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.466   2.4108e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.466   2.4108e-01
   1_xyz:   9.927  0.072  0.419 87.479  0.025  2.047   1.0477e-01
   1_adp:   9.927  0.072  0.419 87.479  0.025  2.047   1.0477e-01
   1_occ:   9.927  0.072  0.419 87.479  0.025  2.047   1.0477e-01
   2_bss:   9.927  0.072  0.419 87.479  0.025  2.047   1.0477e-01
   2_xyz:   8.082  0.048  0.262 82.353  0.040  2.259   1.3801e-01
   2_adp:   8.082  0.048  0.262 82.353  0.040  2.259   1.3801e-01
   2_occ:   8.082  0.048  0.262 82.353  0.040  2.259   1.3801e-01
   3_bss:   8.082  0.048  0.262 82.353  0.040  2.259   1.3801e-01
   3_xyz:   7.194  0.044  0.225 78.307  0.035  2.369   4.5250e-02
   3_adp:   7.194  0.044  0.225 78.307  0.035  2.369   4.5250e-02
   3_occ:   7.194  0.044  0.225 78.307  0.035  2.369   4.5250e-02
   4_bss:   7.194  0.044  0.225 78.307  0.035  2.369   4.5250e-02
   4_xyz:   6.496  0.042  0.220 81.988  0.027  2.348   4.6912e-02
   4_adp:   6.496  0.042  0.220 81.988  0.027  2.348   4.6912e-02
   4_occ:   6.496  0.042  0.220 81.988  0.027  2.348   4.6912e-02
   5_bss:   6.496  0.042  0.220 81.988  0.027  2.348   4.6912e-02
   5_xyz:   6.720  0.041  0.223 81.117  0.029  2.348   3.8699e-02
   5_adp:   6.720  0.041  0.223 81.117  0.029  2.348   3.8699e-02
   5_occ:   6.720  0.041  0.223 81.117  0.029  2.348   3.8699e-02
   5_bss:   6.720  0.041  0.223 81.117  0.029  2.348   3.8699e-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:  95.97   0.00  18.77  95.97   0.00  14.85  93.76   2.81  40.16
   1_occ:  95.97   0.00  18.77  95.97   0.00  14.85  93.76   2.81  40.16
   2_bss:  95.97   0.00  18.77  95.97   0.00  14.85  93.76   2.81  40.16
   2_xyz:  95.97   0.00  18.77  95.97   0.00  14.85  93.76   2.81  40.16
   2_adp:  93.74   0.00  18.14  93.74   0.00  13.82  87.48   5.58  41.69
   2_occ:  93.74   0.00  18.14  93.74   0.00  13.82  87.48   5.58  41.69
   3_bss:  93.74   0.00  18.14  93.74   0.00  13.82  87.48   5.58  41.69
   3_xyz:  93.74   0.00  18.14  93.74   0.00  13.82  87.48   5.58  41.69
   3_adp: 113.52   0.00  18.52 113.52   0.00  13.59  93.44   0.90  45.37
   3_occ: 113.52   0.00  18.52 113.52   0.00  13.59  93.44   0.90  45.37
   4_bss: 113.52   0.00  18.52 113.52   0.00  13.59  93.44   0.90  45.37
   4_xyz: 113.52   0.00  18.52 113.52   0.00  13.59  93.44   0.90  45.37
   4_adp: 112.92   1.43  17.77 112.92   1.43  13.13  89.22   2.58  43.02
   4_occ: 112.92   1.43  17.77 112.92   1.43  13.13  89.22   2.58  43.02
   5_bss: 112.92   1.43  17.77 112.92   1.43  13.13  89.22   2.58  43.02
   5_xyz: 112.92   1.43  17.77 112.92   1.43  13.13  89.22   2.58  43.02
   5_adp: 104.46   2.36  16.98 104.46   2.36  12.86  85.47   5.12  39.44
   5_occ: 104.46   2.36  16.98 104.46   2.36  12.86  85.47   5.12  39.44
   5_bss: 104.38   2.28  16.90 104.38   2.28  12.77  85.38   5.03  39.35
------------------------------------------------------------------------
 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:    1.984    0.019    0.346
   1_adp:    1.984    0.019    0.346
   1_occ:    1.984    0.019    0.346
   2_bss:    1.984    0.019    0.346
   2_xyz:    1.526    0.037    0.541
   2_adp:    1.526    0.037    0.541
   2_occ:    1.526    0.037    0.541
   3_bss:    1.526    0.037    0.541
   3_xyz:    1.584    0.009    0.618
   3_adp:    1.584    0.009    0.618
   3_occ:    1.584    0.009    0.618
   4_bss:    1.584    0.009    0.618
   4_xyz:    1.677    0.078    0.669
   4_adp:    1.677    0.078    0.669
   4_occ:    1.677    0.078    0.669
   5_bss:    1.677    0.078    0.669
   5_xyz:    1.782    0.074    0.687
   5_adp:    1.782    0.074    0.687
   5_occ:    1.782    0.074    0.687
   5_bss:    1.782    0.074    0.687
------------------------------------------------------------------------

CPU time actual refinement: 332.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_693/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_693/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_693/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_693/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_693/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.97 
  Macro-tasks:
    bulk solvent and scale       = 38.03  
    individual site refinement   = 132.73 
    weights calculation          = 29.67  
    collect and process          = 6.58   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 207.13 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 106.64 
    alpha_beta                      = 8.36   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 114.10 
    fmodel                         = 6.46   
    r_factors                      = 0.20   
    phase_errors                   = 10.70  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 250.43 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.775 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    639 calls, 106.28 s
gradients_fft:          584 calls, 101.30 s

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

# Date 2008-01-16 Time 05:25:37 PST -0800 (1200489937.42 s)
Start R-work = 0.4356, R-free = 0.4303 (no bulk solvent and anisotropic scale)
Final R-work = 0.1409, R-free = 0.1831 (no bulk solvent and anisotropic scale)

Start R-work = 0.4241, R-free = 0.4169
Final R-work = 0.1178, R-free = 0.1612