# Date 2008-01-16 Time 05:08:22 PST -0800 (1200488902.36 s)
#phil __OFF__

Command line arguments: "../613.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27017
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 613

-------------------------------------------------------------------------------
  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, 45.7567, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.95351
Completeness in resolution range: 0.929269
Completeness with d_max=infinity: 0.926588

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9535

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, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.95351
Completeness in resolution range: 0.929269
Completeness with d_max=infinity: 0.926588

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.1815 [2213/2239]  1990   223  10.1%
  bin  2:  4.1815 -  3.3308 [2135/2155]  1925   210   9.8%
  bin  3:  3.3308 -  2.9132 [2091/2110]  1882   209  10.0%
  bin  4:  2.9132 -  2.6484 [2087/2117]  1869   218  10.4%
  bin  5:  2.6484 -  2.4595 [2068/2087]  1868   200   9.7%
  bin  6:  2.4595 -  2.3150 [2069/2094]  1859   210  10.1%
  bin  7:  2.3150 -  2.1994 [2023/2051]  1819   204  10.1%
  bin  8:  2.1994 -  2.1040 [2053/2089]  1846   207  10.1%
  bin  9:  2.1040 -  2.0232 [2032/2083]  1840   192   9.4%
  bin 10:  2.0232 -  1.9535 [ 818/2055]   732    86  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_613/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: 0.15 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:
        1.68 -     2.32: 34
        2.32 -     2.97: 1778
        2.97 -     3.61: 4604
        3.61 -     4.26: 9215
        4.26 -     4.90: 12829
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.680 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.759 3.040 -x+1,y-1/2,-z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28455 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_613/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_613/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 45.75675 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4506   r_free= 0.4517   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.271163                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6645 0.99   1433  157 0.3745 0.3717      6.5831      6.5623|
|  2:  4.6645 -  3.7207 0.99   1384  158 0.3899 0.3794      6.8015      6.7459|
|  3:  3.7207 -  3.2558 0.99   1368  148 0.4192 0.4139      6.6574       6.657|
|  4:  3.2558 -  2.9606 0.99   1337  154 0.4503 0.4715      6.5253      6.5363|
|  5:  2.9606 -  2.7498 0.99   1348  148 0.4807 0.4515      6.3415      6.3714|
|  6:  2.7498 -  2.5885 0.99   1327  146 0.4763 0.5003      6.2471      6.1776|
|  7:  2.5885 -  2.4595 0.99   1337  149 0.4748 0.4622      6.2193      6.1636|
|  8:  2.4595 -  2.3528 0.98   1316  150 0.5015 0.5075      6.1567      6.1472|
|  9:  2.3528 -  2.2626 0.98   1305  143 0.4835 0.5442      6.1072      6.2007|
| 10:  2.2626 -  2.1847 1.00   1343  148 0.4979 0.5175      6.0624       6.068|
| 11:  2.1847 -  2.1166 0.98   1319  144 0.4925 0.4911       6.014      6.0126|
| 12:  2.1166 -  2.0563 0.98   1293  139 0.4866 0.4548      5.9244      5.9355|
| 13:  2.0563 -  2.0023 0.91   1205  136 0.4924 0.4810      5.8701      5.7979|
| 14:  2.0023 -  1.9535 0.24    315   39 0.5302 0.4974      5.8686      5.8445|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6645  1433   157  0.72  32.17   0.82     0.78      66606.02|
|  2:  4.6645 -  3.7207  1384   158  0.71  34.64   0.90     0.82     106544.11|
|  3:  3.7207 -  3.2558  1368   148  0.59  45.05   0.94     0.77     115320.20|
|  4:  3.2558 -  2.9606  1337   154  0.49  52.42   0.91     0.68     107374.82|
|  5:  2.9606 -  2.7498  1348   148  0.44  56.92   0.89     0.63      78700.93|
|  6:  2.7498 -  2.5885  1327   146  0.42  58.09   0.90     0.60      66882.43|
|  7:  2.5885 -  2.4595  1337   149  0.42  58.15   0.93     0.58      59100.13|
|  8:  2.4595 -  2.3528  1316   150  0.38  61.17   0.92     0.55      56022.77|
|  9:  2.3528 -  2.2626  1305   143  0.37  62.04   0.94     0.55      53838.70|
| 10:  2.2626 -  2.1847  1343   148  0.36  62.71   0.94     0.54      47854.06|
| 11:  2.1847 -  2.1166  1319   144  0.37  62.20   0.97     0.57      45988.80|
| 12:  2.1166 -  2.0563  1293   139  0.38  61.43   0.96     0.60      39789.04|
| 13:  2.0563 -  2.0023  1205   136  0.37  62.18   0.97     0.61      34697.78|
| 14:  2.0023 -  1.9535   315    39  0.43  57.75   1.00     0.61      26937.65|
|alpha:            min =        0.54 max =            0.82 mean =         0.64|
|beta:             min =    26937.65 max =       115320.20 mean =     67426.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.98 mean =        54.32|
|phase err.(test): min =        0.00 max =           89.75 mean =        54.78|
|-----------------------------------------------------------------------------|

============================== 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 = 9.257941              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.570   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.459427              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.491   (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 |  1.680 -  2.002:       14 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.002 -  2.324:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.324 -  2.646:       79 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.646 -  2.968:     1699 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.968 -  3.290:     1925 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2679 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4770 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4445 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5842 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6987 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.680 |       0.558 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4506   r_free= 0.4517   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.271163                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4390   r_free= 0.4433   ksol= 0.34   Bsol= 41.15   scale= 0.929   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,2.54,1.23,0.00,0.00,0.00); trace/3= 0.12                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.264758                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.439657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.499   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.200918              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.248   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4390      final r-factor (work) = 0.3770          |
| start r-factor (free) = 0.4433      final r-factor (free) = 0.4129          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.4706 = 7.44 * 0.50 * 6.2592 + 1.00 * 0.1876                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0978 = 7.44 * 0.50 * 6.1815 + 1.00 * 0.1036                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3770      final r-factor (work) = 0.3471          |
| start r-factor (free) = 0.4129      final r-factor (free) = 0.4190          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4296 = 1.20 * 1.00 * 6.1815 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3668 = 1.20 * 1.00 * 6.1190 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.93  18.89    None  None   None       |
|    all(noH): 2823   0      0.00    100.93  18.89    None  None   None       |
|    Sol.    : 438    0      0.00    100.93  34.70    None  None   None       |
|    Mac.    : 2385   0      0.00    83.50   15.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.093:  835   |   5:    50.464 -  60.557:   63        |
|      1:    10.093 -  20.186:  965   |   6:    60.557 -  70.650:   36        |
|      2:    20.186 -  30.279:  544   |   7:    70.650 -  80.743:    9        |
|      3:    30.279 -  40.372:  249   |   8:    80.743 -  90.836:    5        |
|      4:    40.372 -  50.464:  115   |   9:    90.836 - 100.929:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3471 r_free = 0.4190             target_work(ml) = 6.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3469 r_free = 0.4195             target_work(ml) = 6.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3469   r_free= 0.4195   ksol= 0.34   Bsol= 41.15   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,2.54,1.23,0.00,0.00,0.00); trace/3= 0.12                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.122089                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3470   r_free= 0.4176   ksol= 0.35   Bsol= 67.24   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,1.00,0.61,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.125191                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.370757              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.180  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.542235              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.665  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3470      final r-factor (work) = 0.2899          |
| start r-factor (free) = 0.4176      final r-factor (free) = 0.3737          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.7851 = 9.37 * 0.50 * 6.1215 + 1.00 * 0.1036                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.4754 = 9.37 * 0.50 * 6.0562 + 1.00 * 0.0997                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2899      final r-factor (work) = 0.2767          |
| start r-factor (free) = 0.3737      final r-factor (free) = 0.3628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3022 = 0.54 * 1.00 * 6.0562 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2752 = 0.54 * 1.00 * 5.9731 + 1.00 * 0.0364                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.36  18.39    None  None   None       |
|    all(noH): 2823   0      0.00    101.36  18.39    None  None   None       |
|    Sol.    : 438    0      1.24    101.36  35.41    None  None   None       |
|    Mac.    : 2385   0      0.00    84.08   15.26    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 -  10.136:  881   |   5:    50.681 -  60.817:   61        |
|      1:    10.136 -  20.272: 1009   |   6:    60.817 -  70.953:   31        |
|      2:    20.272 -  30.408:  500   |   7:    70.953 -  81.089:    3        |
|      3:    30.408 -  40.545:  228   |   8:    81.089 -  91.225:    3        |
|      4:    40.545 -  50.681:  105   |   9:    91.225 - 101.361:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2767 r_free = 0.3628             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2764 r_free = 0.3626             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2764   r_free= 0.3626   ksol= 0.35   Bsol= 67.24   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,1.00,0.61,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.958534                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2767   r_free= 0.3614   ksol= 0.33   Bsol= 54.95   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.32,0.40,-0.00,0.00,0.00); trace/3= -0.44                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.957134                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.778416              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.829   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.181637              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.145   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2767      final r-factor (work) = 0.2222          |
| start r-factor (free) = 0.3614      final r-factor (free) = 0.2863          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3441 = 6.78 * 0.50 * 5.9732 + 1.00 * 0.0997                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9926 = 6.78 * 0.50 * 5.8755 + 1.00 * 0.0795                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2222      final r-factor (work) = 0.1975          |
| start r-factor (free) = 0.2863      final r-factor (free) = 0.2714          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.6419 = 4.18 * 1.00 * 5.8755 + 1.00 * 0.0729                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.8136 = 4.18 * 1.00 * 5.6904 + 1.00 * 0.0182                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.76  19.55    None  None   None       |
|    all(noH): 2823   0      0.00    108.76  19.55    None  None   None       |
|    Sol.    : 438    0      2.92    108.76  46.70    None  None   None       |
|    Mac.    : 2385   0      0.00    103.04  14.56    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 -  10.876: 1140   |   5:    54.381 -  65.257:  102        |
|      1:    10.876 -  21.753:  879   |   6:    65.257 -  76.134:   59        |
|      2:    21.753 -  32.629:  305   |   7:    76.134 -  87.010:   27        |
|      3:    32.629 -  43.505:  171   |   8:    87.010 -  97.886:    3        |
|      4:    43.505 -  54.381:  134   |   9:    97.886 - 108.762:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1975 r_free = 0.2714             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1975 r_free = 0.2711             target_work(ml) = 5.663         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1975   r_free= 0.2711   ksol= 0.33   Bsol= 54.95   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.32,0.40,-0.00,0.00,0.00); trace/3= -0.44                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.663292                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1972   r_free= 0.2708   ksol= 0.33   Bsol= 65.84   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.46,-0.03,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.661295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.110401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.715   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.829016              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.687  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1972      final r-factor (work) = 0.1589          |
| start r-factor (free) = 0.2708      final r-factor (free) = 0.2228          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6243 = 5.11 * 0.50 * 5.6922 + 1.00 * 0.0795                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3184 = 5.11 * 0.50 * 5.5783 + 1.00 * 0.0648                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1589      final r-factor (work) = 0.1452          |
| start r-factor (free) = 0.2228      final r-factor (free) = 0.2038          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2210 = 1.83 * 1.00 * 5.5783 + 1.00 * 0.0183                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9542 = 1.83 * 1.00 * 5.4343 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.35  18.84    None  None   None       |
|    all(noH): 2823   0      0.00    112.35  18.84    None  None   None       |
|    Sol.    : 438    0      5.21    112.35  48.48    None  None   None       |
|    Mac.    : 2385   0      0.00    105.42  13.39    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 -  11.235: 1309   |   5:    56.174 -  67.409:   90        |
|      1:    11.235 -  22.470:  882   |   6:    67.409 -  78.643:   70        |
|      2:    22.470 -  33.704:  206   |   7:    78.643 -  89.878:   23        |
|      3:    33.704 -  44.939:  118   |   8:    89.878 - 101.113:   11        |
|      4:    44.939 -  56.174:  111   |   9:   101.113 - 112.348:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1452 r_free = 0.2038             target_work(ml) = 5.385         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1452 r_free = 0.2035             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1452   r_free= 0.2035   ksol= 0.33   Bsol= 65.84   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.46,-0.03,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.384417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1455   r_free= 0.2032   ksol= 0.32   Bsol= 63.47   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.93,-0.09,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.383114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.932945              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.155  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.722058              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.733  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1455      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.2032      final r-factor (free) = 0.1886          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3179 = 1.93 * 0.50 * 5.4354 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2267 = 1.93 * 0.50 * 5.3599 + 1.00 * 0.0465                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1358      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1886      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2447 = 1.72 * 1.00 * 5.3599 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1487 = 1.72 * 1.00 * 5.3048 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.09  18.35    None  None   None       |
|    all(noH): 2823   0      0.00    115.09  18.35    None  None   None       |
|    Sol.    : 438    0      5.36    115.09  48.30    None  None   None       |
|    Mac.    : 2385   0      0.00    107.14  12.85    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 -  11.509: 1437   |   5:    57.545 -  69.054:   86        |
|      1:    11.509 -  23.018:  810   |   6:    69.054 -  80.563:   63        |
|      2:    23.018 -  34.527:  188   |   7:    80.563 -  92.072:   25        |
|      3:    34.527 -  46.036:  108   |   8:    92.072 - 103.581:   11        |
|      4:    46.036 -  57.545:   91   |   9:   103.581 - 115.090:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1312 r_free = 0.1829             target_work(ml) = 5.287         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1828             target_work(ml) = 5.287         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1828   ksol= 0.32   Bsol= 63.47   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.93,-0.09,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.287224                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6645 0.99   1433  157 0.1016 0.1359      5.4167      5.6358|
|  2:  4.6645 -  3.7207 0.99   1384  158 0.0900 0.1210      5.4935      5.7329|
|  3:  3.7207 -  3.2558 0.99   1368  148 0.1196 0.1617      5.5704      5.8339|
|  4:  3.2558 -  2.9606 0.99   1337  154 0.1489 0.2030      5.6053      5.7894|
|  5:  2.9606 -  2.7498 0.99   1348  148 0.1602 0.2084      5.4873      5.7371|
|  6:  2.7498 -  2.5885 0.99   1327  146 0.1473 0.2251       5.352      5.5792|
|  7:  2.5885 -  2.4595 0.99   1337  149 0.1463 0.1911      5.3062      5.4872|
|  8:  2.4595 -  2.3528 0.98   1316  150 0.1474 0.2032      5.2353      5.4855|
|  9:  2.3528 -  2.2626 0.98   1305  143 0.1415 0.2061      5.1829      5.4584|
| 10:  2.2626 -  2.1847 1.00   1343  148 0.1350 0.1860       5.073       5.298|
| 11:  2.1847 -  2.1166 0.98   1319  144 0.1341 0.2216      5.0813      5.4484|
| 12:  2.1166 -  2.0563 0.98   1293  139 0.1435 0.2155      5.0289      5.2922|
| 13:  2.0563 -  2.0023 0.91   1205  136 0.1327 0.1769      4.9366      5.0935|
| 14:  2.0023 -  1.9535 0.24    315   39 0.1230 0.2134      4.8281       5.145|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6645  1433   157  0.93   9.94   0.97     0.94       7957.07|
|  2:  4.6645 -  3.7207  1384   158  0.95   8.55   1.03     1.01      10133.65|
|  3:  3.7207 -  3.2558  1368   148  0.92  13.28   1.05     1.05      12786.61|
|  4:  3.2558 -  2.9606  1337   154  0.89  17.09   1.03     0.99      13936.49|
|  5:  2.9606 -  2.7498  1348   148  0.87  19.22   1.01     0.99      11650.47|
|  6:  2.7498 -  2.5885  1327   146  0.87  19.54   0.99     0.95       9433.60|
|  7:  2.5885 -  2.4595  1337   149  0.88  18.75   1.01     0.97       8564.58|
|  8:  2.4595 -  2.3528  1316   150  0.87  19.34   1.01     0.98       7498.26|
|  9:  2.3528 -  2.2626  1305   143  0.88  18.94   1.00     0.95       6778.38|
| 10:  2.2626 -  2.1847  1343   148  0.88  18.41   1.01     0.97       5567.83|
| 11:  2.1847 -  2.1166  1319   144  0.88  18.96   0.99     0.93       5722.72|
| 12:  2.1166 -  2.0563  1293   139  0.87  19.39   1.01     1.00       5370.80|
| 13:  2.0563 -  2.0023  1205   136  0.86  20.48   0.99     0.97       4732.11|
| 14:  2.0023 -  1.9535   315    39  0.91  15.67   0.99     0.95       3470.91|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     3470.91 max =        13936.49 mean =      8434.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.94|
|phase err.(test): min =        0.00 max =           88.09 mean =        16.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1828   ksol= 0.32   Bsol= 63.48   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.93,-0.09,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.287224                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1828   ksol= 0.32   Bsol= 63.48   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.93,-0.09,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.287224                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6645 0.99   1433  157 0.1016 0.1359      5.4167      5.6358|
|  2:  4.6645 -  3.7207 0.99   1384  158 0.0900 0.1210      5.4935      5.7329|
|  3:  3.7207 -  3.2558 0.99   1368  148 0.1196 0.1617      5.5704      5.8339|
|  4:  3.2558 -  2.9606 0.99   1337  154 0.1489 0.2030      5.6053      5.7894|
|  5:  2.9606 -  2.7498 0.99   1348  148 0.1602 0.2084      5.4873      5.7371|
|  6:  2.7498 -  2.5885 0.99   1327  146 0.1473 0.2251       5.352      5.5792|
|  7:  2.5885 -  2.4595 0.99   1337  149 0.1463 0.1911      5.3062      5.4872|
|  8:  2.4595 -  2.3528 0.98   1316  150 0.1474 0.2032      5.2353      5.4855|
|  9:  2.3528 -  2.2626 0.98   1305  143 0.1415 0.2061      5.1829      5.4584|
| 10:  2.2626 -  2.1847 1.00   1343  148 0.1350 0.1860       5.073       5.298|
| 11:  2.1847 -  2.1166 0.98   1319  144 0.1341 0.2216      5.0813      5.4484|
| 12:  2.1166 -  2.0563 0.98   1293  139 0.1435 0.2155      5.0289      5.2922|
| 13:  2.0563 -  2.0023 0.91   1205  136 0.1327 0.1769      4.9366      5.0935|
| 14:  2.0023 -  1.9535 0.24    315   39 0.1230 0.2134      4.8281       5.145|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6645  1433   157  0.93   9.94   0.97     0.94       7957.07|
|  2:  4.6645 -  3.7207  1384   158  0.95   8.55   1.03     1.01      10133.65|
|  3:  3.7207 -  3.2558  1368   148  0.92  13.28   1.05     1.05      12786.61|
|  4:  3.2558 -  2.9606  1337   154  0.89  17.09   1.03     0.99      13936.49|
|  5:  2.9606 -  2.7498  1348   148  0.87  19.22   1.01     0.99      11650.47|
|  6:  2.7498 -  2.5885  1327   146  0.87  19.54   0.99     0.95       9433.60|
|  7:  2.5885 -  2.4595  1337   149  0.88  18.75   1.01     0.97       8564.58|
|  8:  2.4595 -  2.3528  1316   150  0.87  19.34   1.01     0.98       7498.26|
|  9:  2.3528 -  2.2626  1305   143  0.88  18.94   1.00     0.95       6778.38|
| 10:  2.2626 -  2.1847  1343   148  0.88  18.41   1.01     0.97       5567.83|
| 11:  2.1847 -  2.1166  1319   144  0.88  18.96   0.99     0.93       5722.72|
| 12:  2.1166 -  2.0563  1293   139  0.87  19.39   1.01     1.00       5370.80|
| 13:  2.0563 -  2.0023  1205   136  0.86  20.48   0.99     0.97       4732.11|
| 14:  2.0023 -  1.9535   315    39  0.91  15.67   0.99     0.95       3470.91|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     3470.91 max =        13936.49 mean =      8434.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.94|
|phase err.(test): min =        0.00 max =           88.09 mean =        16.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.09  18.35    None  None   None       |
|    all(noH): 2823   0      0.00    115.09  18.35    None  None   None       |
|    Sol.    : 438    0      5.36    115.09  48.30    None  None   None       |
|    Mac.    : 2385   0      0.00    107.14  12.85    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:     0.003 -  11.512: 1437   |   5:    57.548 -  69.057:   86        |
|      1:    11.512 -  23.021:  810   |   6:    69.057 -  80.566:   63        |
|      2:    23.021 -  34.530:  188   |   7:    80.566 -  92.075:   25        |
|      3:    34.530 -  46.039:  108   |   8:    92.075 - 103.584:   11        |
|      4:    46.039 -  57.548:   91   |   9:   103.584 - 115.093:    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)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.649 - 4.309
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 334
   mapped sites are within: 0.704 - 4.309

peak=    9.067 closest distance to " O   HOH Z 390 " =    1.467
peak=    7.274 closest distance to " O   HOH Z 385 " =    1.853
peak=    6.693 closest distance to " O   HOH Z 245 " =    1.270
peak=    6.237 closest distance to " O   HOH Z  77 " =    1.211
peak=    5.654 closest distance to " O   HOH Z 422 " =    1.212
peak=    5.647 closest distance to " O   HOH Z 431 " =    1.809
peak=    5.510 closest distance to " O   HOH Z  65 " =    1.595
peak=    5.430 closest distance to " O   HOH Z 287 " =    2.190
peak=    5.428 closest distance to " O   HOH Z 417 " =    2.710
peak=    5.397 closest distance to " O   HOH Z 222 " =    1.430
peak=    5.338 closest distance to " NE2 GLN A  11 " =    1.376
peak=    5.138 closest distance to " O   HOH Z  66 " =    1.203
peak=    5.074 closest distance to " O   HOH Z 105 " =    1.308
peak=    5.006 closest distance to " O   HOH Z 403 " =    1.814
peak=    4.965 closest distance to " CG  PRO A  90 " =    1.299
peak=    4.961 closest distance to " CB  SER A 216 " =    1.057
peak=    4.943 closest distance to " O   HOH Z 293 " =    1.509
peak=    4.933 closest distance to " O   HOH Z  63 " =    2.092
peak=    4.912 closest distance to " O   HOH Z 130 " =    0.960
peak=    4.911 closest distance to " O   HOH Z  29 " =    1.424
peak=    4.889 closest distance to " O   HOH Z  46 " =    1.156
peak=    4.833 closest distance to " O   HOH Z  69 " =    1.621
peak=    4.832 closest distance to " O   HOH Z   7 " =    1.912
peak=    4.817 closest distance to " O   ASP A 286 " =    2.537
peak=    4.814 closest distance to " CG  PRO A  54 " =    1.456
peak=    4.787 closest distance to " O   HOH Z   9 " =    1.749
peak=    4.785 closest distance to " O   HOH Z 418 " =    1.157
peak=    4.768 closest distance to " O   HOH Z 142 " =    1.905
peak=    4.733 closest distance to " CG2 ILE A 120 " =    1.081
peak=    4.731 closest distance to " O   HOH Z 232 " =    2.175
peak=    4.725 closest distance to " CG  PRO A 280 " =    1.038
peak=    4.665 closest distance to " O   HOH Z 278 " =    1.033
peak=    4.608 closest distance to " O   HOH Z  63 " =    1.795
peak=    4.579 closest distance to " O   HOH Z 145 " =    1.804
peak=    4.579 closest distance to " O   PRO A 198 " =    1.265
peak=    4.538 closest distance to " O   HOH Z 139 " =    1.318
peak=    4.532 closest distance to " O   HOH Z 427 " =    1.986
peak=    4.529 closest distance to " O   HOH Z 316 " =    3.073
peak=    4.514 closest distance to " O   HOH Z 276 " =    1.375
peak=    4.514 closest distance to " O   HOH Z 380 " =    2.183
peak=    4.508 closest distance to " O   HOH Z 427 " =    1.288
peak=    4.505 closest distance to " O   HOH Z  39 " =    1.357
peak=    4.482 closest distance to " O   HOH Z  49 " =    1.392
peak=    4.441 closest distance to " CB  PRO A  54 " =    1.185
peak=    4.388 closest distance to " O   HOH Z 127 " =    1.031
peak=    4.329 closest distance to " CB  ALA A 114 " =    0.951
peak=    4.293 closest distance to " CB  GLN A 223 " =    1.530
peak=    4.263 closest distance to " O   HOH Z  78 " =    1.760
peak=    4.257 closest distance to " O   HOH Z 375 " =    1.046
peak=    4.255 closest distance to " O   HOH Z 423 " =    2.093
peak=    4.240 closest distance to " O   HOH Z 425 " =    1.343
peak=    4.231 closest distance to " O   HOH Z 298 " =    1.865
peak=    4.228 closest distance to " CG  PRO A 213 " =    1.310
peak=    4.223 closest distance to " CG  PRO A 198 " =    1.271
peak=    4.216 closest distance to " O   HOH Z 225 " =    1.905
peak=    4.204 closest distance to " N   GLN A 278 " =    1.071
peak=    4.179 closest distance to " O   HOH Z 368 " =    3.526
peak=    4.169 closest distance to " O   HOH Z 392 " =    1.279
peak=    4.149 closest distance to " O   HOH Z 295 " =    1.083
peak=    4.144 closest distance to " CB  ASN A 148 " =    1.441
peak=    4.134 closest distance to " CD  ARG A  66 " =    2.460
peak=    4.111 closest distance to " NH1AARG A 145 " =    1.194
peak=    4.104 closest distance to " O   HOH Z 146 " =    1.654
peak=    4.103 closest distance to " CB  GLU A 128 " =    1.054
peak=    4.083 closest distance to " CA  TYR A  30 " =    1.057
peak=    4.069 closest distance to " O   HOH Z 424 " =    1.259
peak=    4.069 closest distance to " CE3 TRP A 274 " =    1.450
peak=    4.056 closest distance to " O   HOH Z 359 " =    1.510
peak=    4.046 closest distance to " O   HOH Z  57 " =    2.205
peak=    4.041 closest distance to " O   HOH Z 358 " =    1.302
peak=    4.028 closest distance to " CG2 VAL A 257 " =    0.854
peak=    4.020 closest distance to " CB  ARG A 275 " =    1.159
peak=    4.005 closest distance to " O   HOH Z  11 " =    1.105
peak=    3.995 closest distance to " CB  TRP A 266 " =    1.057
peak=    3.993 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.985 closest distance to " O   HOH Z 272 " =    1.883
peak=    3.984 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    3.982 closest distance to " NZ  LYS A 117 " =    3.134
peak=    3.979 closest distance to " NH2 ARG A  56 " =    2.077
peak=    3.966 closest distance to " O   HOH Z 437 " =    2.097
peak=    3.955 closest distance to " O   HOH Z 369 " =    1.912
peak=    3.950 closest distance to " O   HOH Z 303 " =    2.124
peak=    3.935 closest distance to " O   HOH Z  92 " =    1.234
peak=    3.924 closest distance to " O   HOH Z 361 " =    1.444
peak=    3.922 closest distance to " CB  SER A  63 " =    1.436
peak=    3.921 closest distance to " N   GLU A   2 " =    1.413
peak=    3.905 closest distance to " O   HOH Z 112 " =    1.279
peak=    3.902 closest distance to " ND2 ASN A  60 " =    2.912
peak=    3.898 closest distance to " CA  ARG A 102 " =    1.095
peak=    3.896 closest distance to " CB  VAL A 202 " =    1.649
peak=    3.895 closest distance to " O   HOH Z 158 " =    1.196
peak=    3.888 closest distance to " O   HOH Z 133 " =    1.041
peak=    3.879 closest distance to " O   HOH Z 211 " =    1.224
peak=    3.879 closest distance to " O   HOH Z  61 " =    1.687
peak=    3.876 closest distance to " O   HOH Z 124 " =    1.440
peak=    3.875 closest distance to " CB  ASP A 124 " =    0.915
peak=    3.867 closest distance to " CG2 THR A 221 " =    1.241
peak=    3.864 closest distance to " O   HOH Z 414 " =    1.450
peak=    3.843 closest distance to " O   HOH Z 258 " =    1.995
peak=    3.841 closest distance to " O   HOH Z 426 " =    1.061
peak=    3.841 closest distance to " N   TYR A  15 " =    1.162
peak=    3.831 closest distance to " O   HOH Z  88 " =    3.670
peak=    3.825 closest distance to " O   HOH Z 193 " =    1.762
peak=    3.810 closest distance to " NZ BLYS A 290 " =    0.932
peak=    3.795 closest distance to " O   HOH Z 201 " =    1.705
peak=    3.791 closest distance to " O   HOH Z 244 " =    1.519
peak=    3.786 closest distance to " CB  TRP A 179 " =    1.442
peak=    3.782 closest distance to " NZ  LYS A 119 " =    2.398
peak=    3.773 closest distance to " CE  LYS A 119 " =    1.262
peak=    3.769 closest distance to " O   HOH Z  59 " =    1.695
peak=    3.767 closest distance to " CE3 TRP A 150 " =    1.138
peak=    3.736 closest distance to " O   HOH Z  44 " =    1.931
peak=    3.736 closest distance to " CA  PHE A 283 " =    1.298
peak=    3.733 closest distance to " O   HOH Z 143 " =    1.232
peak=    3.732 closest distance to " CB  GLU A 277 " =    3.645
peak=    3.726 closest distance to " CB  SER A   3 " =    1.352
peak=    3.708 closest distance to " CB  THR A  31 " =    1.606
peak=    3.705 closest distance to " O   HOH Z 378 " =    1.039
peak=    3.693 closest distance to " CE AMET A  47 " =    1.410
peak=    3.686 closest distance to " O   HOH Z 434 " =    1.553
peak=    3.682 closest distance to " CG  LEU A 167 " =    1.293
peak=    3.673 closest distance to " O   HOH Z  68 " =    1.947
peak=    3.672 closest distance to " O   HOH Z 119 " =    1.462
peak=    3.672 closest distance to " ND2 ASN A 249 " =    0.790
peak=    3.666 closest distance to " CB  SER A  99 " =    0.847
peak=    3.663 closest distance to " O   HOH Z 236 " =    1.388
peak=    3.663 closest distance to " CB  SER A 276 " =    1.236
peak=    3.656 closest distance to " OE1 GLN A  77 " =    1.254
peak=    3.647 closest distance to " O   HOH Z  78 " =    1.869
peak=    3.647 closest distance to " ND2BASN A 224 " =    0.911
peak=    3.643 closest distance to " O   HOH Z 365 " =    1.496
peak=    3.635 closest distance to " O   TYR A 116 " =    1.292
peak=    3.635 closest distance to " O   HOH Z 368 " =    1.730
peak=    3.633 closest distance to " O   HOH Z  30 " =    2.002
peak=    3.632 closest distance to " CA  ARG A  36 " =    1.133
peak=    3.624 closest distance to " CB  SER A 273 " =    1.070
peak=    3.624 closest distance to " O   HOH Z 393 " =    1.279
peak=    3.619 closest distance to " NZ  LYS A 117 " =    1.192
peak=    3.614 closest distance to " CA  VAL A 125 " =    1.078
peak=    3.612 closest distance to " O   HOH Z  43 " =    1.155
peak=    3.606 closest distance to " CB  LYS A 117 " =    1.262
peak=    3.600 closest distance to " CG  LYS A  76 " =    1.867
peak=    3.599 closest distance to " CB  ARG A 219 " =    0.828
peak=    3.599 closest distance to " O   HOH Z 218 " =    1.649
peak=    3.599 closest distance to " CG  GLN A  89 " =    1.563
peak=    3.598 closest distance to " O   HOH Z 425 " =    2.168
peak=    3.583 closest distance to " N   CYS A 260 " =    0.890
peak=    3.580 closest distance to " OG BSER A 164 " =    2.213
peak=    3.577 closest distance to " O   HOH Z  91 " =    2.469
peak=    3.566 closest distance to " O   HOH Z 214 " =    2.197
peak=    3.552 closest distance to " O   HOH Z 106 " =    4.016
peak=    3.549 closest distance to " CD  LYS A 166 " =    1.512
peak=    3.545 closest distance to " O   HOH Z  27 " =    0.960
peak=    3.531 closest distance to " CA  ALA A  51 " =    1.013
peak=    3.530 closest distance to " O   HOH Z   2 " =    1.839
peak=    3.528 closest distance to " O   HOH Z 365 " =    2.518
peak=    3.527 closest distance to " CB  SER A 212 " =    1.410
peak=    3.521 closest distance to " O   HOH Z 153 " =    3.611
peak=    3.518 closest distance to " O   HOH Z   7 " =    3.096
peak=    3.516 closest distance to " CA  ARG A 195 " =    1.402
peak=    3.515 closest distance to " CE  LYS A  76 " =    0.860
peak=    3.512 closest distance to " O   HOH Z  11 " =    1.541
peak=    3.511 closest distance to " O   HOH Z 290 " =    1.116
peak=    3.508 closest distance to " O   HOH Z 130 " =    2.065
peak=    3.507 closest distance to " OE1 GLU A   2 " =    1.395
peak=    3.506 closest distance to " CA  LEU A 282 " =    1.133
peak=    3.504 closest distance to " O   HOH Z 405 " =    1.631
peak=    3.504 closest distance to " CG2BVAL A  41 " =    1.075
peak=    3.503 closest distance to " O   HOH Z 126 " =    1.389
peak=    3.502 closest distance to " CG  GLN A  58 " =    0.952
peak=    3.497 closest distance to " N   ALA A 292 " =    1.170
peak=    3.496 closest distance to " O   HOH Z 415 " =    1.005
peak=    3.491 closest distance to " CB  SER A  26 " =    1.399
peak=    3.490 closest distance to " O   HOH Z 352 " =    1.619
peak=    3.486 closest distance to " CA  ALA A 160 " =    0.941
peak=    3.485 closest distance to " NH2AARG A 190 " =    1.896
peak=    3.484 closest distance to " O  BHOH Z  74 " =    1.253
peak=    3.477 closest distance to " OD1 ASP A 238 " =    0.962
peak=    3.476 closest distance to " O   HOH Z 215 " =    1.467
peak=    3.474 closest distance to " CB  LEU A 300 " =    0.901
peak=    3.465 closest distance to " O   HOH Z  58 " =    1.767
peak=    3.464 closest distance to " CD  ARG A 159 " =    0.852
peak=    3.460 closest distance to " CB  PHE A 225 " =    1.269
peak=    3.459 closest distance to " CG  GLU A 277 " =    1.984
peak=    3.457 closest distance to " CB  LYS A 290 " =    0.887
peak=    3.450 closest distance to " CB  GLN A 183 " =    1.177
peak=    3.447 closest distance to " O   HOH Z 394 " =    1.656
peak=    3.446 closest distance to " CB  PRO A  90 " =    1.003
peak=    3.445 closest distance to " CB  LEU A 228 " =    1.298
peak=    3.443 closest distance to " CB  ASP A 272 " =    1.003
peak=    3.441 closest distance to " CG2 VAL A 202 " =    1.543
peak=    3.434 closest distance to " CG  GLN A  11 " =    2.206
peak=    3.431 closest distance to " CA  ASN A 127 " =    1.115
peak=    3.426 closest distance to " CB  GLN A  89 " =    1.270
peak=    3.418 closest distance to " O   HOH Z 422 " =    2.155
peak=    3.415 closest distance to " NE2 GLN A  73 " =    1.595
peak=    3.408 closest distance to " CB  ASN A 215 " =    1.122
peak=    3.408 closest distance to " CZ  PHE A 218 " =    1.173
peak=    3.401 closest distance to " O   HOH Z  40 " =    2.132
peak=    3.397 closest distance to " O   HOH Z 119 " =    4.216
peak=    3.396 closest distance to " O   HOH Z 327 " =    1.787
peak=    3.395 closest distance to " CE  MET A  93 " =    1.435
peak=    3.394 closest distance to " CB  MET A  47 " =    1.103
peak=    3.394 closest distance to " O   HOH Z  88 " =    2.591
peak=    3.394 closest distance to " CB  ARG A 190 " =    1.733
peak=    3.392 closest distance to " N   ALA A   1 " =    1.534
peak=    3.384 closest distance to " CG  ARG A 159 " =    0.840
peak=    3.381 closest distance to " ND1 HIS A  86 " =    1.900
peak=    3.380 closest distance to " CB  ASN A 187 " =    0.971
peak=    3.378 closest distance to " O   HOH Z 172 " =    2.121
peak=    3.374 closest distance to " O   HOH Z 344 " =    3.166
peak=    3.371 closest distance to " OG BSER A  99 " =    2.285
peak=    3.370 closest distance to " CG2 ILE A  20 " =    1.641
peak=    3.369 closest distance to " CG2 ILE A 239 " =    1.061
peak=    3.366 closest distance to " CZ  PHE A  38 " =    1.331
peak=    3.364 closest distance to " CB  TYR A  30 " =    1.666
peak=    3.362 closest distance to " O   HOH Z  57 " =    1.102
peak=    3.358 closest distance to " O   HOH Z 156 " =    3.498
peak=    3.353 closest distance to " CA  GLU A 152 " =    0.946
peak=    3.349 closest distance to " O   HOH Z 357 " =    2.054
peak=    3.348 closest distance to " O   HOH Z 424 " =    3.000
peak=    3.346 closest distance to " CA  ILE A 234 " =    1.110
peak=    3.346 closest distance to " OE2 GLU A  53 " =    2.072
peak=    3.346 closest distance to " CB  TRP A 274 " =    1.123
peak=    3.342 closest distance to " O   HOH Z 219 " =    3.512
peak=    3.338 closest distance to " CB  SER A 210 " =    0.893
peak=    3.336 closest distance to " ND1 HIS A  81 " =    1.642
peak=    3.331 closest distance to " O   HOH Z  53 " =    2.294
peak=    3.331 closest distance to " CG2 VAL A 268 " =    0.897
peak=    3.325 closest distance to " O   VAL A  72 " =    0.919
peak=    3.322 closest distance to " O   HOH Z 104 " =    1.574
peak=    3.321 closest distance to " NH2AARG A 145 " =    2.360
peak=    3.317 closest distance to " CA  MET A 105 " =    0.916
peak=    3.316 closest distance to " O   HOH Z  44 " =    2.874
peak=    3.304 closest distance to " O   HOH Z 194 " =    2.419
peak=    3.300 closest distance to " CB  GLU A  46 " =    1.181
peak=    3.296 closest distance to " O   HOH Z  51 " =    1.802
peak=    3.293 closest distance to " O   HOH Z   6 " =    1.550
peak=    3.291 closest distance to " CG1 VAL A 296 " =    1.106
peak=    3.291 closest distance to " CB  ALA A  43 " =    0.903
peak=    3.290 closest distance to " C   GLN A  73 " =    1.041
peak=    3.286 closest distance to " O   HOH Z 189 " =    2.808
peak=    3.281 closest distance to " O   HOH Z 222 " =    2.299
peak=    3.275 closest distance to " OD2 ASP A 286 " =    2.402
peak=    3.271 closest distance to " CB  TYR A 116 " =    1.238
peak=    3.270 closest distance to " NZ  LYS A 166 " =    1.086
peak=    3.270 closest distance to " CB  MET A 105 " =    1.254
peak=    3.263 closest distance to " O   HOH Z 220 " =    1.481
peak=    3.262 closest distance to " N   ILE A  33 " =    1.029
peak=    3.259 closest distance to " CB  GLU A 152 " =    1.219
peak=    3.259 closest distance to " CD  ARG A 195 " =    3.621
peak=    3.259 closest distance to " OD1 ASN A  45 " =    1.346
peak=    3.255 closest distance to " O   HOH Z 258 " =    1.169
peak=    3.254 closest distance to " O   HOH Z 122 " =    2.106
peak=    3.254 closest distance to " O   HOH Z 371 " =    1.985
peak=    3.254 closest distance to " CB  GLU A 277 " =    1.054
peak=    3.249 closest distance to " CD  ARG A 138 " =    0.811
peak=    3.247 closest distance to " CB  ARG A 138 " =    0.899
peak=    3.245 closest distance to " CG  LYS A 119 " =    1.164
peak=    3.238 closest distance to " CG AARG A 275 " =    1.239
peak=    3.234 closest distance to " O   HOH Z 289 " =    1.077
peak=    3.230 closest distance to " O   HOH Z 399 " =    0.855
peak=    3.230 closest distance to " CB  TRP A 150 " =    0.900
peak=    3.230 closest distance to " CA  ASN A 217 " =    1.175
peak=    3.226 closest distance to " O   HOH Z  83 " =    1.190
peak=    3.226 closest distance to " CB  SER A  62 " =    1.115
peak=    3.226 closest distance to " CB  ALA A 114 " =    1.051
peak=    3.226 closest distance to " NH2 ARG A 219 " =    1.743
peak=    3.223 closest distance to " O   HOH Z 411 " =    3.653
peak=    3.222 closest distance to " CA  MET A  40 " =    1.218
peak=    3.219 closest distance to " CD1 LEU A 300 " =    1.016
peak=    3.218 closest distance to " CD2 TRP A 179 " =    1.546
peak=    3.217 closest distance to " N   PHE A 155 " =    1.520
peak=    3.217 closest distance to " O   HOH Z 385 " =    2.647
peak=    3.217 closest distance to " O   MET A 105 " =    1.758
peak=    3.216 closest distance to " O   THR A 294 " =    1.022
peak=    3.211 closest distance to " OD1 ASN A 217 " =    1.400
peak=    3.206 closest distance to " NH2 ARG A  36 " =    0.938
peak=    3.200 closest distance to " N   SER A 210 " =    1.011
peak=    3.200 closest distance to " O   HOH Z  32 " =    2.239
peak=    3.199 closest distance to " NH2BARG A 145 " =    1.892
peak=    3.187 closest distance to " CA  SER A  87 " =    1.023
peak=    3.186 closest distance to " NE2 GLN A  58 " =    4.309
peak=    3.185 closest distance to " CB  MET A  40 " =    0.793
peak=    3.185 closest distance to " C   GLU A 277 " =    1.318
peak=    3.183 closest distance to " CA  ILE A 106 " =    0.704
peak=    3.183 closest distance to " CE3 TRP A  85 " =    0.946
peak=    3.179 closest distance to " N   ASN A 127 " =    1.395
peak=    3.178 closest distance to " O   HOH Z 157 " =    1.628
peak=    3.174 closest distance to " NZ  LYS A 119 " =    2.016
peak=    3.174 closest distance to " O   HOH Z 323 " =    1.661
peak=    3.170 closest distance to " NZ  LYS A 119 " =    1.327
peak=    3.169 closest distance to " O   ALA A 165 " =    1.332
peak=    3.165 closest distance to " CA  ARG A 159 " =    1.298
peak=    3.162 closest distance to " CA  PRO A 280 " =    1.368
peak=    3.161 closest distance to " CB  ALA A 292 " =    0.912
peak=    3.159 closest distance to " OG1 THR A 221 " =    1.361
peak=    3.156 closest distance to " CB  ARG A  79 " =    0.894
peak=    3.154 closest distance to " O   ASN A  69 " =    1.674
peak=    3.152 closest distance to " O   HOH Z 390 " =    2.366
peak=    3.149 closest distance to " CD  GLU A 236 " =    0.835
peak=    3.138 closest distance to " O   ASN A 142 " =    1.075
peak=    3.137 closest distance to " CA  ASN A 215 " =    1.000
peak=    3.136 closest distance to " N   ALA A   1 " =    2.776
peak=    3.135 closest distance to " CB  ASP A 171 " =    0.747
peak=    3.135 closest distance to " O   HOH Z  76 " =    1.019
peak=    3.135 closest distance to " CA  ALA A 154 " =    0.979
peak=    3.134 closest distance to " O   HOH Z 362 " =    1.559
peak=    3.123 closest distance to " O   GLY A 302 " =    2.525
peak=    3.117 closest distance to " O   HOH Z 303 " =    1.401
peak=    3.116 closest distance to " O   HOH Z 132 " =    2.362
peak=    3.112 closest distance to " O   HOH Z 248 " =    1.695
peak=    3.112 closest distance to " CB  GLN A  88 " =    1.357
peak=    3.107 closest distance to " OE1 GLN A 240 " =    1.623
peak=    3.101 closest distance to " O   HOH Z 171 " =    2.203
peak=    3.101 closest distance to " CA  ARG A 156 " =    1.116
peak=    3.095 closest distance to " O   HOH Z 251 " =    1.337
peak=    3.093 closest distance to " CB  ASP A 200 " =    1.074
peak=    3.088 closest distance to " O   HOH Z 128 " =    2.265
peak=    3.086 closest distance to " O   HOH Z  67 " =    1.363
peak=    3.086 closest distance to " CB  ASP A 140 " =    1.018
peak=    3.085 closest distance to " CG2 VAL A 232 " =    1.167
peak=    3.084 closest distance to " O   HOH Z 234 " =    3.666
peak=    3.081 closest distance to " O   HOH Z 373 " =    1.405
peak=    3.081 closest distance to " CA  ALA A 158 " =    1.158
peak=    3.077 closest distance to " CA  ALA A 129 " =    1.184
peak=    3.069 closest distance to " CB  LEU A 237 " =    0.783
peak=    3.067 closest distance to " CB  LEU A  83 " =    0.715
peak=    3.055 closest distance to " N   VAL A 296 " =    1.788
peak=    3.040 closest distance to " CA  ALA A 160 " =    1.414
peak=    3.037 closest distance to " O   HOH Z 356 " =    2.275
peak=    3.016 closest distance to " NE1 TRP A  85 " =    1.001

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.764 - 5.781
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 214
   mapped sites are within: 0.764 - 5.781

peak=   -4.829 closest distance to " OG  SER A  32 " =    0.906
peak=   -4.333 closest distance to " OD1 ASP A 191 " =    1.927
peak=   -4.297 closest distance to " O   PRO A 198 " =    1.089
peak=   -4.249 closest distance to " O   HOH Z 385 " =    1.320
peak=   -4.230 closest distance to " O   HOH Z  28 " =    1.258
peak=   -4.202 closest distance to " N   THR A 157 " =    1.639
peak=   -4.178 closest distance to " OG  SER A  63 " =    1.338
peak=   -4.153 closest distance to " O   ALA A  10 " =    1.611
peak=   -4.114 closest distance to " O   HOH Z  39 " =    1.007
peak=   -4.071 closest distance to " CD  ARG A  14 " =    3.268
peak=   -4.027 closest distance to " CD  LYS A 166 " =    2.605
peak=   -4.002 closest distance to " NE1 TRP A 179 " =    1.216
peak=   -3.973 closest distance to " OG BSER A 134 " =    1.574
peak=   -3.963 closest distance to " O   SER A 135 " =    1.532
peak=   -3.927 closest distance to " CB  GLN A  55 " =    1.191
peak=   -3.908 closest distance to " OG  SER A  97 " =    2.101
peak=   -3.891 closest distance to " O   PHE A 218 " =    1.510
peak=   -3.887 closest distance to " O   HOH Z  69 " =    1.536
peak=   -3.874 closest distance to " O   HOH Z  24 " =    1.019
peak=   -3.873 closest distance to " O   SER A  22 " =    2.676
peak=   -3.865 closest distance to " O   HOH Z 185 " =    1.902
peak=   -3.856 closest distance to " CB  PRO A 243 " =    2.548
peak=   -3.848 closest distance to " OE1 GLN A 223 " =    2.350
peak=   -3.844 closest distance to " O   HOH Z 131 " =    3.917
peak=   -3.839 closest distance to " CG  MET A 105 " =    0.984
peak=   -3.819 closest distance to " O   HOH Z 415 " =    1.101
peak=   -3.803 closest distance to " O   HOH Z 111 " =    1.837
peak=   -3.801 closest distance to " O   HOH Z  60 " =    1.658
peak=   -3.800 closest distance to " O   ILE A  49 " =    1.691
peak=   -3.797 closest distance to " CA  GLY A  98 " =    1.826
peak=   -3.793 closest distance to " NE2 GLN A 122 " =    1.019
peak=   -3.788 closest distance to " O   HOH Z 105 " =    1.890
peak=   -3.783 closest distance to " CE2 TYR A  30 " =    2.604
peak=   -3.782 closest distance to " O   HOH Z 298 " =    2.680
peak=   -3.781 closest distance to " CZ2 TRP A 274 " =    0.897
peak=   -3.721 closest distance to " O   HOH Z 313 " =    1.191
peak=   -3.719 closest distance to " O   HOH Z 129 " =    3.649
peak=   -3.708 closest distance to " CG1BVAL A  41 " =    2.757
peak=   -3.696 closest distance to " C   VAL A  72 " =    0.951
peak=   -3.690 closest distance to " CB  ALA A   9 " =    2.396
peak=   -3.681 closest distance to " CD2 TYR A 116 " =    2.130
peak=   -3.659 closest distance to " CA  ASP A  27 " =    2.485
peak=   -3.654 closest distance to " N   ALA A  43 " =    2.644
peak=   -3.650 closest distance to " O   GLU A 152 " =    1.422
peak=   -3.650 closest distance to " OE1 GLU A 277 " =    2.210
peak=   -3.649 closest distance to " N   GLN A  58 " =    1.280
peak=   -3.644 closest distance to " OE1 GLU A  44 " =    2.001
peak=   -3.639 closest distance to " O   HOH Z 351 " =    1.639
peak=   -3.631 closest distance to " O   HOH Z 275 " =    1.685
peak=   -3.623 closest distance to " CE BMET A  47 " =    1.156
peak=   -3.622 closest distance to " O   HOH Z 198 " =    1.744
peak=   -3.618 closest distance to " CZ  PHE A  59 " =    1.438
peak=   -3.614 closest distance to " CA  HIS A 207 " =    1.232
peak=   -3.592 closest distance to " NE2 GLN A  55 " =    0.941
peak=   -3.574 closest distance to " O   HOH Z 425 " =    0.927
peak=   -3.568 closest distance to " O   HOH Z 163 " =    1.798
peak=   -3.567 closest distance to " O   HOH Z 231 " =    1.909
peak=   -3.567 closest distance to " CD  ARG A 156 " =    1.964
peak=   -3.563 closest distance to " CG2 ILE A 120 " =    1.156
peak=   -3.562 closest distance to " CZ  TYR A 169 " =    2.005
peak=   -3.552 closest distance to " CG  TRP A 266 " =    1.887
peak=   -3.542 closest distance to " CD2 PHE A  61 " =    1.974
peak=   -3.541 closest distance to " CB  ALA A 291 " =    2.134
peak=   -3.533 closest distance to " O   HOH Z 266 " =    4.996
peak=   -3.533 closest distance to " O   PRO A 163 " =    1.827
peak=   -3.531 closest distance to " CD2 TYR A 293 " =    1.767
peak=   -3.515 closest distance to " NE2 GLN A  77 " =    1.657
peak=   -3.511 closest distance to " O   HOH Z 231 " =    1.264
peak=   -3.487 closest distance to " CB  ALA A 131 " =    1.873
peak=   -3.485 closest distance to " O   ARG A 145 " =    1.181
peak=   -3.484 closest distance to " O   HOH Z  22 " =    2.472
peak=   -3.466 closest distance to " OD2 ASP A 272 " =    1.473
peak=   -3.462 closest distance to " O   HOH Z 428 " =    2.033
peak=   -3.458 closest distance to " O   GLN A 240 " =    3.147
peak=   -3.458 closest distance to " NE2 GLN A 223 " =    1.826
peak=   -3.453 closest distance to " O   HOH Z 384 " =    3.628
peak=   -3.449 closest distance to " O   HOH Z 276 " =    1.260
peak=   -3.443 closest distance to " CB  TYR A  15 " =    2.173
peak=   -3.442 closest distance to " O   HOH Z 196 " =    2.021
peak=   -3.439 closest distance to " NH2 ARG A 219 " =    2.011
peak=   -3.436 closest distance to " OD2 ASP A 171 " =    2.210
peak=   -3.434 closest distance to " CA  GLY A 133 " =    2.084
peak=   -3.431 closest distance to " O   HOH Z 286 " =    1.574
peak=   -3.430 closest distance to " CE3 TRP A 179 " =    1.396
peak=   -3.427 closest distance to " OE1 GLN A 183 " =    1.687
peak=   -3.426 closest distance to " O   HOH Z 348 " =    1.841
peak=   -3.423 closest distance to " CG2 ILE A  49 " =    2.786
peak=   -3.421 closest distance to " OE2 GLU A 152 " =    1.214
peak=   -3.418 closest distance to " CE3 TRP A 274 " =    2.305
peak=   -3.414 closest distance to " O   HOH Z 105 " =    1.328
peak=   -3.412 closest distance to " O   HOH Z 288 " =    1.412
peak=   -3.411 closest distance to " CB  ALA A  43 " =    2.366
peak=   -3.404 closest distance to " ND2 ASN A 249 " =    2.141
peak=   -3.401 closest distance to " O   GLY A  80 " =    2.542
peak=   -3.400 closest distance to " O   HOH Z 251 " =    1.043
peak=   -3.395 closest distance to " O   HOH Z 323 " =    2.154
peak=   -3.392 closest distance to " CG1 VAL A 265 " =    2.320
peak=   -3.390 closest distance to " ND2 ASN A 209 " =    1.957
peak=   -3.389 closest distance to " O   HOH Z 102 " =    1.693
peak=   -3.383 closest distance to " CA  GLY A 241 " =    2.243
peak=   -3.381 closest distance to " CG  LEU A  83 " =    2.157
peak=   -3.378 closest distance to " OG BSER A  99 " =    1.418
peak=   -3.366 closest distance to " CA  ILE A 120 " =    1.266
peak=   -3.365 closest distance to " O   HOH Z 165 " =    2.445
peak=   -3.358 closest distance to " OE1 GLU A 236 " =    1.117
peak=   -3.350 closest distance to " O   HOH Z 100 " =    1.228
peak=   -3.349 closest distance to " CA  GLY A 203 " =    2.439
peak=   -3.349 closest distance to " O   HOH Z 211 " =    1.094
peak=   -3.344 closest distance to " CG2 ILE A  20 " =    2.684
peak=   -3.340 closest distance to " N   VAL A 232 " =    2.204
peak=   -3.331 closest distance to " CB  ASN A  45 " =    2.061
peak=   -3.330 closest distance to " CG2 THR A  52 " =    3.162
peak=   -3.328 closest distance to " CZ  PHE A 130 " =    1.023
peak=   -3.325 closest distance to " CD1 LEU A 101 " =    2.213
peak=   -3.325 closest distance to " N   ALA A   1 " =    1.554
peak=   -3.321 closest distance to " O   HOH Z 200 " =    3.551
peak=   -3.319 closest distance to " OE2 GLU A 152 " =    2.164
peak=   -3.318 closest distance to " CG2 VAL A 189 " =    1.936
peak=   -3.314 closest distance to " O   HOH Z 389 " =    1.063
peak=   -3.307 closest distance to " O   HOH Z 404 " =    1.333
peak=   -3.304 closest distance to " O   HOH Z   5 " =    1.409
peak=   -3.303 closest distance to " O   VAL A 125 " =    2.044
peak=   -3.299 closest distance to " O   HOH Z 377 " =    1.926
peak=   -3.299 closest distance to " N   ALA A  84 " =    1.651
peak=   -3.297 closest distance to " O   HOH Z  56 " =    1.830
peak=   -3.297 closest distance to " OG  SER A  87 " =    1.750
peak=   -3.297 closest distance to " O   HOH Z 216 " =    1.728
peak=   -3.297 closest distance to " CG  ARG A 269 " =    2.310
peak=   -3.290 closest distance to " CB  SER A 210 " =    1.082
peak=   -3.289 closest distance to " O   HOH Z 123 " =    2.467
peak=   -3.289 closest distance to " C   GLU A   2 " =    1.869
peak=   -3.286 closest distance to " O   HOH Z  65 " =    1.212
peak=   -3.285 closest distance to " O   HOH Z 389 " =    2.219
peak=   -3.285 closest distance to " O   HOH Z 318 " =    1.774
peak=   -3.283 closest distance to " NZ  LYS A 166 " =    1.510
peak=   -3.282 closest distance to " O   HOH Z 412 " =    5.781
peak=   -3.281 closest distance to " CG  PRO A 243 " =    1.687
peak=   -3.281 closest distance to " CB  PRO A 213 " =    1.934
peak=   -3.279 closest distance to " O   HOH Z  53 " =    1.653
peak=   -3.276 closest distance to " O   HOH Z 412 " =    3.666
peak=   -3.275 closest distance to " O   HOH Z 147 " =    1.112
peak=   -3.275 closest distance to " ND2 ASN A 187 " =    1.629
peak=   -3.273 closest distance to " N   ARG A 159 " =    2.086
peak=   -3.267 closest distance to " O   HOH Z 372 " =    2.608
peak=   -3.262 closest distance to " O   HOH Z 407 " =    3.057
peak=   -3.261 closest distance to " CB  LYS A 289 " =    2.947
peak=   -3.259 closest distance to " O   HOH Z 250 " =    1.150
peak=   -3.255 closest distance to " CD  GLN A  77 " =    1.268
peak=   -3.253 closest distance to " CG  GLU A 128 " =    1.494
peak=   -3.253 closest distance to " OG  SER A 245 " =    1.497
peak=   -3.251 closest distance to " CB  ALA A 100 " =    2.008
peak=   -3.249 closest distance to " O   HOH Z 128 " =    2.446
peak=   -3.247 closest distance to " ND2 ASN A  60 " =    3.908
peak=   -3.242 closest distance to " CG  LEU A 281 " =    1.767
peak=   -3.240 closest distance to " O   HOH Z 324 " =    0.764
peak=   -3.234 closest distance to " O   HOH Z 359 " =    1.533
peak=   -3.232 closest distance to " O   TRP A  70 " =    1.417
peak=   -3.226 closest distance to " O   HOH Z 130 " =    0.970
peak=   -3.224 closest distance to " O   HOH Z 337 " =    1.660
peak=   -3.222 closest distance to " O   HOH Z 218 " =    3.723
peak=   -3.218 closest distance to " OE1 GLN A  88 " =    1.077
peak=   -3.212 closest distance to " O   HOH Z 357 " =    1.905
peak=   -3.208 closest distance to " CD1 ILE A  49 " =    1.408
peak=   -3.208 closest distance to " O   HOH Z 435 " =    3.233
peak=   -3.204 closest distance to " O   HOH Z 429 " =    1.851
peak=   -3.203 closest distance to " O   HOH Z 275 " =    1.497
peak=   -3.194 closest distance to " C   PHE A  59 " =    1.129
peak=   -3.191 closest distance to " O   HOH Z 166 " =    1.200
peak=   -3.189 closest distance to " CB  CYS A 254 " =    1.926
peak=   -3.189 closest distance to " OG  SER A  87 " =    1.294
peak=   -3.188 closest distance to " O   ASP A 298 " =    1.816
peak=   -3.184 closest distance to " O   HOH Z  52 " =    0.998
peak=   -3.181 closest distance to " O   HOH Z 328 " =    1.037
peak=   -3.180 closest distance to " O   HOH Z 368 " =    1.569
peak=   -3.178 closest distance to " CD1 ILE A 239 " =    2.367
peak=   -3.174 closest distance to " O   HOH Z  11 " =    1.796
peak=   -3.164 closest distance to " CB  PRO A  54 " =    2.400
peak=   -3.161 closest distance to " O   HOH Z 217 " =    1.686
peak=   -3.158 closest distance to " O   LYS A  76 " =    2.343
peak=   -3.156 closest distance to " O   HOH Z 426 " =    2.140
peak=   -3.155 closest distance to " OG  SER A   3 " =    1.648
peak=   -3.155 closest distance to " O   HOH Z 268 " =    3.018
peak=   -3.155 closest distance to " CB  ASP A 132 " =    2.301
peak=   -3.150 closest distance to " CD2 HIS A 207 " =    1.566
peak=   -3.147 closest distance to " CB  TRP A  85 " =    2.330
peak=   -3.146 closest distance to " C   HIS A 108 " =    1.312
peak=   -3.144 closest distance to " O   HOH Z 374 " =    1.864
peak=   -3.142 closest distance to " O   ASP A  27 " =    1.906
peak=   -3.139 closest distance to " CA  ASN A 127 " =    1.245
peak=   -3.134 closest distance to " CA  GLY A  80 " =    1.339
peak=   -3.134 closest distance to " O   HOH Z 234 " =    4.655
peak=   -3.133 closest distance to " O   HOH Z 397 " =    1.341
peak=   -3.131 closest distance to " O   HOH Z 416 " =    1.167
peak=   -3.128 closest distance to " O   HOH Z 244 " =    1.745
peak=   -3.128 closest distance to " CH2 TRP A 123 " =    1.749
peak=   -3.127 closest distance to " CD1 TYR A 214 " =    1.456
peak=   -3.126 closest distance to " O   HOH Z  88 " =    1.720
peak=   -3.124 closest distance to " N   ASP A 171 " =    2.580
peak=   -3.121 closest distance to " OG  SER A 206 " =    1.936
peak=   -3.120 closest distance to " O   ALA A  34 " =    2.481
peak=   -3.102 closest distance to " N   HIS A  81 " =    1.168
peak=   -3.101 closest distance to " CD2 PHE A 130 " =    2.949
peak=   -3.099 closest distance to " CG1 VAL A  78 " =    2.525
peak=   -3.093 closest distance to " ND2 ASN A 173 " =    1.616
peak=   -3.090 closest distance to " O   HOH Z 340 " =    2.097
peak=   -3.085 closest distance to " O   HOH Z  68 " =    1.472
peak=   -3.081 closest distance to " O   HOH Z 390 " =    2.506
peak=   -3.067 closest distance to " O   HOH Z 174 " =    2.997
peak=   -3.065 closest distance to " CG  ARG A 219 " =    2.172
peak=   -3.061 closest distance to " O   HOH Z 298 " =    1.117
peak=   -3.060 closest distance to " CA  GLY A  57 " =    2.068
peak=   -3.050 closest distance to " CG2 ILE A 151 " =    2.529
peak=   -3.045 closest distance to " CG1 VAL A 125 " =    2.233
peak=   -3.033 closest distance to " CD2 LEU A  25 " =    2.098

================= 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    :  0.4506 0.4517   6.271163e+00   6.261039e+00
   1_bss:  0.4390 0.4433   6.264758e+00   6.251766e+00
   1_xyz:  0.3770 0.4129   6.161799e+00   6.212268e+00
   1_adp:  0.3471 0.4190   6.122447e+00   6.220593e+00
   1_occ:  0.3469 0.4195   6.122089e+00   6.221202e+00
   2_bss:  0.3470 0.4176   6.125191e+00   6.223350e+00
   2_xyz:  0.2899 0.3737   5.987478e+00   6.135289e+00
   2_adp:  0.2767 0.3628   5.958954e+00   6.113135e+00
   2_occ:  0.2764 0.3626   5.958534e+00   6.112982e+00
   3_bss:  0.2767 0.3614   5.957134e+00   6.110784e+00
   3_xyz:  0.2222 0.2863   5.747714e+00   5.926334e+00
   3_adp:  0.1975 0.2714   5.664038e+00   5.882843e+00
   3_occ:  0.1975 0.2711   5.663292e+00   5.882399e+00
   4_bss:  0.1972 0.2708   5.661295e+00   5.880255e+00
   4_xyz:  0.1589 0.2228   5.466857e+00   5.718239e+00
   4_adp:  0.1452 0.2038   5.385301e+00   5.635833e+00
   4_occ:  0.1452 0.2035   5.384417e+00   5.634435e+00
   5_bss:  0.1455 0.2032   5.383114e+00   5.631984e+00
   5_xyz:  0.1358 0.1886   5.316945e+00   5.559465e+00
   5_adp:  0.1312 0.1829   5.287398e+00   5.527443e+00
   5_occ:  0.1311 0.1828   5.287224e+00   5.527244e+00
   5_bss:  0.1311 0.1828   5.287224e+00   5.527244e+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:  0.343  41.152  -3.404   2.538   1.234   0.000   0.000   0.000
   1_xyz:  0.343  41.152  -3.404   2.538   1.234   0.000   0.000   0.000
   1_adp:  0.343  41.152  -3.404   2.538   1.234   0.000   0.000   0.000
   1_occ:  0.343  41.152  -3.404   2.538   1.234   0.000   0.000   0.000
   2_bss:  0.354  67.235  -1.660   0.995   0.608   0.000   0.000   0.000
   2_xyz:  0.354  67.235  -1.660   0.995   0.608   0.000   0.000   0.000
   2_adp:  0.354  67.235  -1.660   0.995   0.608   0.000   0.000   0.000
   2_occ:  0.354  67.235  -1.660   0.995   0.608   0.000   0.000   0.000
   3_bss:  0.327  54.950  -1.397  -0.317   0.396  -0.000   0.000   0.000
   3_xyz:  0.327  54.950  -1.397  -0.317   0.396  -0.000   0.000   0.000
   3_adp:  0.327  54.950  -1.397  -0.317   0.396  -0.000   0.000   0.000
   3_occ:  0.327  54.950  -1.397  -0.317   0.396  -0.000   0.000   0.000
   4_bss:  0.329  65.844  -1.881  -1.463  -0.027  -0.000  -0.000  -0.000
   4_xyz:  0.329  65.844  -1.881  -1.463  -0.027  -0.000  -0.000  -0.000
   4_adp:  0.329  65.844  -1.881  -1.463  -0.027  -0.000  -0.000  -0.000
   4_occ:  0.329  65.844  -1.881  -1.463  -0.027  -0.000  -0.000  -0.000
   5_bss:  0.321  63.473  -1.900  -1.931  -0.090  -0.000  -0.000  -0.000
   5_xyz:  0.321  63.473  -1.900  -1.931  -0.090  -0.000  -0.000  -0.000
   5_adp:  0.321  63.473  -1.900  -1.931  -0.090  -0.000  -0.000  -0.000
   5_occ:  0.321  63.473  -1.900  -1.931  -0.090  -0.000  -0.000  -0.000
   5_bss:  0.321  63.476  -1.903  -1.934  -0.093  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.363 0.4665  0.6390    67433.583
   1_bss:  53.440 0.4771  0.6606    65000.734
   1_xyz:  48.177 0.5425  0.7364    53678.367
   1_adp:  48.984 0.5319  0.7326    55283.148
   1_occ:  49.029 0.5313  0.7312    55429.390
   2_bss:  48.885 0.5331  0.7314    55342.616
   2_xyz:  41.367 0.6245  0.8500    40125.213
   2_adp:  39.400 0.6487  0.8697    37764.764
   2_occ:  39.392 0.6488  0.8696    37735.450
   3_bss:  39.208 0.6507  0.8594    37328.314
   3_xyz:  29.424 0.7630  0.9688    21940.256
   3_adp:  27.396 0.7853  0.9686    19261.665
   3_occ:  27.371 0.7855  0.9685    19212.944
   4_bss:  27.261 0.7865  0.9463    19067.309
   4_xyz:  22.096 0.8394  0.9804    12644.610
   4_adp:  19.754 0.8633  0.9798    10606.275
   4_occ:  19.719 0.8636  0.9798    10568.704
   5_bss:  19.647 0.8641  0.9737    10473.877
   5_xyz:  17.737 0.8824  0.9824     8933.231
   5_adp:  16.887 0.8907  0.9767     8444.198
   5_occ:  16.879 0.8907  0.9765     8435.366
   5_bss:  16.879 0.8907  0.9765     8435.366
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8758e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8758e-01
   1_xyz:   1.375  0.010  0.093 15.449  0.006  4.105   1.0356e-01
   1_adp:   1.375  0.010  0.093 15.449  0.006  4.105   1.0356e-01
   1_occ:   1.375  0.010  0.093 15.449  0.006  4.105   1.0356e-01
   2_bss:   1.375  0.010  0.093 15.449  0.006  4.105   1.0356e-01
   2_xyz:   1.306  0.010  0.094 15.262  0.005  4.105   9.9665e-02
   2_adp:   1.306  0.010  0.094 15.262  0.005  4.105   9.9665e-02
   2_occ:   1.306  0.010  0.094 15.262  0.005  4.105   9.9665e-02
   3_bss:   1.306  0.010  0.094 15.262  0.005  4.105   9.9665e-02
   3_xyz:   1.160  0.009  0.079 14.808  0.004  4.108   7.9477e-02
   3_adp:   1.160  0.009  0.079 14.808  0.004  4.108   7.9477e-02
   3_occ:   1.160  0.009  0.079 14.808  0.004  4.108   7.9477e-02
   4_bss:   1.160  0.009  0.079 14.808  0.004  4.108   7.9477e-02
   4_xyz:   1.062  0.007  0.079 14.542  0.003  4.118   6.4813e-02
   4_adp:   1.062  0.007  0.079 14.542  0.003  4.118   6.4813e-02
   4_occ:   1.062  0.007  0.079 14.542  0.003  4.118   6.4813e-02
   5_bss:   1.062  0.007  0.079 14.542  0.003  4.118   6.4813e-02
   5_xyz:   0.862  0.005  0.063 14.100  0.003  4.111   4.6482e-02
   5_adp:   0.862  0.005  0.063 14.100  0.003  4.111   4.6482e-02
   5_occ:   0.862  0.005  0.063 14.100  0.003  4.111   4.6482e-02
   5_bss:   0.862  0.005  0.063 14.100  0.003  4.111   4.6482e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.680   2.4088e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.680   2.4088e-01
   1_xyz:   8.687  0.060  0.347 81.455  0.055  2.063   8.2998e-02
   1_adp:   8.687  0.060  0.347 81.455  0.055  2.063   8.2998e-02
   1_occ:   8.687  0.060  0.347 81.455  0.055  2.063   8.2998e-02
   2_bss:   8.687  0.060  0.347 81.455  0.055  2.063   8.2998e-02
   2_xyz:   9.369  0.056  0.316 77.893  0.037  2.008   1.5636e-01
   2_adp:   9.369  0.056  0.316 77.893  0.037  2.008   1.5636e-01
   2_occ:   9.369  0.056  0.316 77.893  0.037  2.008   1.5636e-01
   3_bss:   9.369  0.056  0.316 77.893  0.037  2.008   1.5636e-01
   3_xyz:   7.414  0.046  0.236 76.839  0.027  2.231   1.1298e-01
   3_adp:   7.414  0.046  0.236 76.839  0.027  2.231   1.1298e-01
   3_occ:   7.414  0.046  0.236 76.839  0.027  2.231   1.1298e-01
   4_bss:   7.414  0.046  0.236 76.839  0.027  2.231   1.1298e-01
   4_xyz:   6.622  0.053  0.242 83.882  0.028  2.291   5.2367e-02
   4_adp:   6.622  0.053  0.242 83.882  0.028  2.291   5.2367e-02
   4_occ:   6.622  0.053  0.242 83.882  0.028  2.291   5.2367e-02
   5_bss:   6.622  0.053  0.242 83.882  0.028  2.291   5.2367e-02
   5_xyz:   7.265  0.041  0.188 79.576  0.032  2.421   3.1709e-02
   5_adp:   7.265  0.041  0.188 79.576  0.032  2.421   3.1709e-02
   5_occ:   7.265  0.041  0.188 79.576  0.032  2.421   3.1709e-02
   5_bss:   7.265  0.041  0.188 79.576  0.032  2.421   3.1709e-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: 100.93   0.00  18.89  83.50   0.00  15.99 100.93   0.00  34.70
   1_occ: 100.93   0.00  18.89  83.50   0.00  15.99 100.93   0.00  34.70
   2_bss: 100.93   0.00  18.89  83.50   0.00  15.99 100.93   0.00  34.70
   2_xyz: 100.93   0.00  18.89  83.50   0.00  15.99 100.93   0.00  34.70
   2_adp: 101.36   0.00  18.39  84.08   0.00  15.26 101.36   1.24  35.41
   2_occ: 101.36   0.00  18.39  84.08   0.00  15.26 101.36   1.24  35.41
   3_bss: 101.36   0.00  18.39  84.08   0.00  15.26 101.36   1.24  35.41
   3_xyz: 101.36   0.00  18.39  84.08   0.00  15.26 101.36   1.24  35.41
   3_adp: 108.76   0.00  19.55 103.04   0.00  14.56 108.76   2.92  46.70
   3_occ: 108.76   0.00  19.55 103.04   0.00  14.56 108.76   2.92  46.70
   4_bss: 108.76   0.00  19.55 103.04   0.00  14.56 108.76   2.92  46.70
   4_xyz: 108.76   0.00  19.55 103.04   0.00  14.56 108.76   2.92  46.70
   4_adp: 112.35   0.00  18.84 105.42   0.00  13.39 112.35   5.21  48.48
   4_occ: 112.35   0.00  18.84 105.42   0.00  13.39 112.35   5.21  48.48
   5_bss: 112.35   0.00  18.84 105.42   0.00  13.39 112.35   5.21  48.48
   5_xyz: 112.35   0.00  18.84 105.42   0.00  13.39 112.35   5.21  48.48
   5_adp: 115.09   0.00  18.35 107.14   0.00  12.85 115.09   5.36  48.30
   5_occ: 115.09   0.00  18.35 107.14   0.00  12.85 115.09   5.36  48.30
   5_bss: 115.09   0.00  18.35 107.14   0.00  12.85 115.09   5.36  48.30
------------------------------------------------------------------------
 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:    1.730    0.022    0.271
   1_adp:    1.730    0.022    0.271
   1_occ:    1.730    0.022    0.271
   2_bss:    1.730    0.022    0.271
   2_xyz:    1.535    0.023    0.497
   2_adp:    1.535    0.023    0.497
   2_occ:    1.535    0.023    0.497
   3_bss:    1.535    0.023    0.497
   3_xyz:    1.733    0.061    0.681
   3_adp:    1.733    0.061    0.681
   3_occ:    1.733    0.061    0.681
   4_bss:    1.733    0.061    0.681
   4_xyz:    1.647    0.055    0.766
   4_adp:    1.647    0.055    0.766
   4_occ:    1.647    0.055    0.766
   5_bss:    1.647    0.055    0.766
   5_xyz:    1.610    0.072    0.796
   5_adp:    1.610    0.072    0.796
   5_occ:    1.610    0.072    0.796
   5_bss:    1.610    0.072    0.796
------------------------------------------------------------------------

CPU time actual refinement: 337.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_613/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_613/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_613/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_613/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_613/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.53 
  Macro-tasks:
    bulk solvent and scale       = 39.01  
    individual site refinement   = 146.23 
    weights calculation          = 29.18  
    collect and process          = 6.59   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 221.10 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 107.77 
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 118.24 
    fmodel                         = 6.61   
    r_factors                      = 0.21   
    phase_errors                   = 10.34  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 255.27 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.759 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    641 calls, 107.48 s
gradients_fft:          586 calls, 104.41 s

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

# Date 2008-01-16 Time 05:14:14 PST -0800 (1200489254.04 s)
Start R-work = 0.4506, R-free = 0.4517 (no bulk solvent and anisotropic scale)
Final R-work = 0.1498, R-free = 0.1977 (no bulk solvent and anisotropic scale)

Start R-work = 0.4390, R-free = 0.4433
Final R-work = 0.1311, R-free = 0.1828