# Date 2008-01-16 Time 05:59:03 PST -0800 (1200491943.20 s)
#phil __OFF__

Command line arguments: "../959.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5989
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 959

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 48.1033, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, 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: (70.9525, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97151
Completeness in resolution range: 0.927071
Completeness with d_max=infinity: 0.924315

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             d_min =   1.9715

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97151
Completeness in resolution range: 0.927071
Completeness with d_max=infinity: 0.924315

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.2192 [2224/2253]  2001   223  10.0%
  bin  2:  4.2192 -  3.3612 [2121/2144]  1909   212  10.0%
  bin  3:  3.3612 -  2.9399 [2094/2119]  1886   208   9.9%
  bin  4:  2.9399 -  2.6727 [2086/2102]  1879   207   9.9%
  bin  5:  2.6727 -  2.4821 [2081/2125]  1873   208  10.0%
  bin  6:  2.4821 -  2.3363 [2045/2073]  1845   200   9.8%
  bin  7:  2.3363 -  2.2197 [2043/2079]  1838   205  10.0%
  bin  8:  2.2197 -  2.1233 [2044/2086]  1834   210  10.3%
  bin  9:  2.1233 -  2.0418 [2012/2069]  1809   203  10.1%
  bin 10:  2.0418 -  1.9715 [ 839/2080]   756    83   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_959/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.39 -     2.09: 11
        2.09 -     2.79: 678
        2.79 -     3.50: 4446
        3.50 -     4.20: 9257
        4.20 -     4.90: 13713
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.389 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.424 3.040 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.629 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.691 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.695 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28100 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_959/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_959/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 48.10325 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4556   r_free= 0.4395   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.269696                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7061 0.99   1441  163 0.3655 0.3891      6.5469      6.5586|
|  2:  4.7061 -  3.7545 0.99   1381  148 0.3961 0.3983      6.8277      6.7712|
|  3:  3.7545 -  3.2856 0.99   1365  153 0.4316 0.3890      6.6512      6.6385|
|  4:  3.2856 -  2.9877 0.99   1346  149 0.4428 0.4373      6.4943      6.4713|
|  5:  2.9877 -  2.7750 0.99   1333  147 0.4691 0.4620       6.346      6.3258|
|  6:  2.7750 -  2.6123 0.99   1342  150 0.5032 0.4408      6.2704      6.1484|
|  7:  2.6123 -  2.4821 0.98   1340  148 0.4829 0.4134      6.2331      6.1539|
|  8:  2.4821 -  2.3745 0.98   1302  146 0.5034 0.5150      6.1305      6.1948|
|  9:  2.3745 -  2.2834 0.99   1344  147 0.5265 0.4822      6.1432      6.0724|
| 10:  2.2834 -  2.2048 0.98   1296  147 0.4819 0.5082      6.0656      6.1042|
| 11:  2.2048 -  2.1361 0.97   1315  142 0.5088 0.4889      6.0194      5.9874|
| 12:  2.1361 -  2.0752 0.99   1303  149 0.4951 0.5042      5.9186       5.975|
| 13:  2.0752 -  2.0207 0.89   1183  133 0.4910 0.4069       5.853      5.7844|
| 14:  2.0207 -  1.9715 0.25    339   37 0.5344 0.5031      5.8228       5.772|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.7061  1441   163  0.69  35.27   0.82     0.72      75908.57|
|  2:  4.7061 -  3.7545  1381   148  0.71  34.20   0.91     0.79      97428.91|
|  3:  3.7545 -  3.2856  1365   153  0.62  42.03   0.90     0.79     102411.63|
|  4:  3.2856 -  2.9877  1346   149  0.56  47.37   0.91     0.74      88995.40|
|  5:  2.9877 -  2.7750  1333   147  0.50  52.12   0.88     0.69      71415.54|
|  6:  2.7750 -  2.6123  1342   150  0.49  53.18   0.89     0.67      58300.17|
|  7:  2.6123 -  2.4821  1340   148  0.49  52.96   0.92     0.66      52921.92|
|  8:  2.4821 -  2.3745  1302   146  0.44  56.78   0.88     0.64      50832.39|
|  9:  2.3745 -  2.2834  1344   147  0.44  57.03   0.91     0.63      46789.75|
| 10:  2.2834 -  2.2048  1296   147  0.44  56.63   0.96     0.64      44439.59|
| 11:  2.2048 -  2.1361  1315   142  0.43  57.79   0.92     0.64      40740.00|
| 12:  2.1361 -  2.0752  1303   149  0.40  59.78   0.93     0.63      38332.08|
| 13:  2.0752 -  2.0207  1183   133  0.42  58.81   0.95     0.62      31340.93|
| 14:  2.0207 -  1.9715   339    37  0.44  57.10   0.91     0.66      25321.69|
|alpha:            min =        0.62 max =            0.79 mean =         0.68|
|beta:             min =    25321.69 max =       102411.63 mean =     61469.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.92|
|phase err.(test): min =        0.00 max =           89.96 mean =        50.93|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.119090              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.848   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.052273              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.334   (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 |  1.389 -  1.740:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.740 -  2.091:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.091 -  2.442:       24 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.442 -  2.793:      654 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.793 -  3.144:     2105 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.144 -  3.495:     2341 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.495 -  3.847:     4501 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.847 -  4.198:     4756 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.198 -  4.549:     6199 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.549 -  4.900:     7514 |
|-----------------------------------------------------------------------------|
|-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 |        0.181 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.389 |       0.442 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.095)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4556   r_free= 0.4395   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.269696                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4459   r_free= 0.4291   ksol= 0.29   Bsol= 20.48   scale= 0.930   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,4.73,-0.18,0.00,-0.00,-0.00); trace/3= 0.76                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.261675                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.080947              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.541   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.995507              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.206   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4459      final r-factor (work) = 0.3697          |
| start r-factor (free) = 0.4291      final r-factor (free) = 0.3939          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3434 = 7.08 * 0.50 * 6.2596 + 1.00 * 0.1815                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9079 = 7.08 * 0.50 * 6.1583 + 1.00 * 0.1048                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3697      final r-factor (work) = 0.3406          |
| start r-factor (free) = 0.3939      final r-factor (free) = 0.4053          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1367 = 1.00 * 1.00 * 6.1583 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0877 = 1.00 * 1.00 * 6.0960 + 1.00 * 0.0191                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.095)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.83   18.99    None  None   None       |
|    all(noH): 2823   0      0.00    96.83   18.99    None  None   None       |
|    Sol.    : 438    0      3.38    96.83   36.18    None  None   None       |
|    Mac.    : 2385   0      0.00    81.31   15.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.683:  803   |   5:    48.417 -  58.100:   71        |
|      1:     9.683 -  19.367:  961   |   6:    58.100 -  67.784:   46        |
|      2:    19.367 -  29.050:  513   |   7:    67.784 -  77.467:   18        |
|      3:    29.050 -  38.734:  272   |   8:    77.467 -  87.151:    5        |
|      4:    38.734 -  48.417:  132   |   9:    87.151 -  96.834:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3406 r_free = 0.4053             target_work(ml) = 6.103         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3403 r_free = 0.4054             target_work(ml) = 6.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3403   r_free= 0.4054   ksol= 0.29   Bsol= 20.48   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,4.73,-0.18,0.00,-0.00,-0.00); trace/3= 0.76                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.102076                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3402   r_free= 0.4040   ksol= 0.30   Bsol= 50.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,2.62,-0.65,0.00,-0.00,-0.00); trace/3= 0.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.103641                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.314637             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.842  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.657931              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.770  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3402      final r-factor (work) = 0.2724          |
| start r-factor (free) = 0.4040      final r-factor (free) = 0.3303          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6459 = 12.31 * 0.50 * 6.0970 + 1.00 * 0.1048                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.1480 = 12.31 * 0.50 * 6.0115 + 1.00 * 0.1330                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2724      final r-factor (work) = 0.2492          |
| start r-factor (free) = 0.3303      final r-factor (free) = 0.3146          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9736 = 0.66 * 1.00 * 6.0115 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8718 = 0.66 * 1.00 * 5.8650 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.095)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.54   18.41    None  None   None       |
|    all(noH): 2823   0      0.00    91.54   18.41    None  None   None       |
|    Sol.    : 438    0      3.22    89.34   39.12    None  None   None       |
|    Mac.    : 2385   0      0.00    91.54   14.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.155:  894   |   5:    45.772 -  54.927:  106        |
|      1:     9.155 -  18.309:  938   |   6:    54.927 -  64.081:   59        |
|      2:    18.309 -  27.463:  412   |   7:    64.081 -  73.236:   23        |
|      3:    27.463 -  36.618:  233   |   8:    73.236 -  82.390:   15        |
|      4:    36.618 -  45.772:  134   |   9:    82.390 -  91.545:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2492 r_free = 0.3146             target_work(ml) = 5.850         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2489 r_free = 0.3138             target_work(ml) = 5.849         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2489   r_free= 0.3138   ksol= 0.30   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,2.62,-0.65,0.00,-0.00,-0.00); trace/3= 0.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.848795                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2484   r_free= 0.3121   ksol= 0.32   Bsol= 60.74   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.95,-0.83,0.00,-0.00,-0.00); trace/3= -0.41                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.847103                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.670895              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.669   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.322930              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.903  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2484      final r-factor (work) = 0.2073          |
| start r-factor (free) = 0.3121      final r-factor (free) = 0.2620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8976 = 3.67 * 0.50 * 5.8648 + 1.00 * 0.1330                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6551 = 3.67 * 0.50 * 5.7748 + 1.00 * 0.0558                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2073      final r-factor (work) = 0.1971          |
| start r-factor (free) = 0.2620      final r-factor (free) = 0.2463          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8779 = 0.32 * 1.00 * 5.7748 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8363 = 0.32 * 1.00 * 5.6548 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.095)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.16   17.89    None  None   None       |
|    all(noH): 2823   0      0.00    90.16   17.89    None  None   None       |
|    Sol.    : 438    0      4.31    90.16   40.24    None  None   None       |
|    Mac.    : 2385   0      0.00    87.73   13.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.016:  878   |   5:    45.082 -  54.099:  118        |
|      1:     9.016 -  18.033: 1064   |   6:    54.099 -  63.115:   58        |
|      2:    18.033 -  27.049:  345   |   7:    63.115 -  72.131:   24        |
|      3:    27.049 -  36.066:  175   |   8:    72.131 -  81.148:   13        |
|      4:    36.066 -  45.082:  138   |   9:    81.148 -  90.164:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1971 r_free = 0.2463             target_work(ml) = 5.633         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1969 r_free = 0.2462             target_work(ml) = 5.633         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1969   r_free= 0.2462   ksol= 0.32   Bsol= 60.74   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.95,-0.83,0.00,-0.00,-0.00); trace/3= -0.41                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.632767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1970   r_free= 0.2458   ksol= 0.32   Bsol= 66.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-0.11,-1.50,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.633419                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.292930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.262  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.694  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1970      final r-factor (work) = 0.1555          |
| start r-factor (free) = 0.2458      final r-factor (free) = 0.1989          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3713 = 3.29 * 0.50 * 5.6579 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1704 = 3.29 * 0.50 * 5.5284 + 1.00 * 0.0681                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1555      final r-factor (work) = 0.1435          |
| start r-factor (free) = 0.1989      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4662 = 0.63 * 1.00 * 5.5284 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3765 = 0.63 * 1.00 * 5.3820 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.095)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    106.43  18.14    None  None   None       |
|    all(noH): 2823   0      0.57    106.43  18.14    None  None   None       |
|    Sol.    : 438    0      4.13    106.43  44.59    None  None   None       |
|    Mac.    : 2385   0      0.57    101.66  13.29    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:     0.572 -  11.158: 1302   |   5:    53.501 -  64.087:   99        |
|      1:    11.158 -  21.743:  886   |   6:    64.087 -  74.672:   53        |
|      2:    21.743 -  32.329:  215   |   7:    74.672 -  85.258:   23        |
|      3:    32.329 -  42.915:  121   |   8:    85.258 -  95.844:   10        |
|      4:    42.915 -  53.501:  109   |   9:    95.844 - 106.430:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1435 r_free = 0.1902             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1435 r_free = 0.1901             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1901   ksol= 0.32   Bsol= 66.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-0.11,-1.50,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.360612                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1437   r_free= 0.1904   ksol= 0.33   Bsol= 67.60   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.85,-1.55,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.361966                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.884921              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.959  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.213311              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.560  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1904      final r-factor (free) = 0.1808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1414 = 1.88 * 0.50 * 5.3830 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0739 = 1.88 * 0.50 * 5.3264 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1318          |
| start r-factor (free) = 0.1808      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1480 = 0.21 * 1.00 * 5.3264 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1390 = 0.21 * 1.00 * 5.2945 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.095)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    107.58  17.44    None  None   None       |
|    all(noH): 2823   0      1.48    107.58  17.44    None  None   None       |
|    Sol.    : 438    0      4.90    107.58  42.18    None  None   None       |
|    Mac.    : 2385   0      1.48    98.45   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.482 -  12.091: 1490   |   5:    54.529 -  65.138:   69        |
|      1:    12.091 -  22.701:  778   |   6:    65.138 -  75.747:   46        |
|      2:    22.701 -  33.310:  176   |   7:    75.747 -  86.357:   10        |
|      3:    33.310 -  43.919:  122   |   8:    86.357 -  96.966:    6        |
|      4:    43.919 -  54.529:  121   |   9:    96.966 - 107.575:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1318 r_free = 0.1773             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1317 r_free = 0.1773             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1773   ksol= 0.33   Bsol= 67.60   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.85,-1.55,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.284685                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7061 0.99   1441  163 0.1019 0.1335      5.4174      5.5777|
|  2:  4.7061 -  3.7545 0.99   1381  148 0.0924 0.1158      5.4974      5.6957|
|  3:  3.7545 -  3.2856 0.99   1365  153 0.1214 0.1722      5.5779      5.9475|
|  4:  3.2856 -  2.9877 0.99   1346  149 0.1491 0.1783      5.5997      5.7499|
|  5:  2.9877 -  2.7750 0.99   1333  147 0.1613 0.1962      5.4928      5.6187|
|  6:  2.7750 -  2.6123 0.99   1342  150 0.1540 0.2275      5.3734      5.5916|
|  7:  2.6123 -  2.4821 0.98   1340  148 0.1447 0.1974      5.3047      5.5246|
|  8:  2.4821 -  2.3745 0.98   1302  146 0.1493 0.1961      5.2228      5.4168|
|  9:  2.3745 -  2.2834 0.99   1344  147 0.1422 0.1997      5.1795      5.4053|
| 10:  2.2834 -  2.2048 0.98   1296  147 0.1352 0.1944       5.111      5.3655|
| 11:  2.2048 -  2.1361 0.97   1315  142 0.1352 0.2014       5.049      5.2996|
| 12:  2.1361 -  2.0752 0.99   1303  149 0.1372 0.1921      4.9882      5.2218|
| 13:  2.0752 -  2.0207 0.89   1183  133 0.1401 0.1916      4.9209      5.1092|
| 14:  2.0207 -  1.9715 0.25    339   37 0.1370 0.1934      4.8154      5.1163|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.7061  1441   163  0.93   9.76   0.96     0.94       7813.08|
|  2:  4.7061 -  3.7545  1381   148  0.95   8.91   1.01     0.99      10149.59|
|  3:  3.7545 -  3.2856  1365   153  0.92  13.26   1.02     1.01      12568.77|
|  4:  3.2856 -  2.9877  1346   149  0.90  16.58   1.00     0.98      13497.97|
|  5:  2.9877 -  2.7750  1333   147  0.87  19.61   1.00     0.98      11640.63|
|  6:  2.7750 -  2.6123  1342   150  0.88  18.78   0.99     0.95       9260.72|
|  7:  2.6123 -  2.4821  1340   148  0.88  18.37   0.99     0.96       8215.03|
|  8:  2.4821 -  2.3745  1302   146  0.88  18.81   1.00     0.96       7174.39|
|  9:  2.3745 -  2.2834  1344   147  0.88  18.82   0.99     0.93       6497.88|
| 10:  2.2834 -  2.2048  1296   147  0.88  18.12   0.99     0.95       5962.96|
| 11:  2.2048 -  2.1361  1315   142  0.88  18.64   0.99     0.95       5352.67|
| 12:  2.1361 -  2.0752  1303   149  0.89  18.07   0.98     0.97       4834.47|
| 13:  2.0752 -  2.0207  1183   133  0.88  18.78   0.98     0.98       4234.65|
| 14:  2.0207 -  1.9715   339    37  0.87  19.28   0.97     0.93       3482.44|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3482.44 max =        13497.97 mean =      8218.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.61|
|phase err.(test): min =        0.00 max =           87.37 mean =        15.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1773   ksol= 0.32   Bsol= 62.18   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.05,-1.48,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.284577                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1773   ksol= 0.32   Bsol= 62.18   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.05,-1.48,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.284577                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7061 0.99   1441  163 0.1018 0.1336      5.4171      5.5753|
|  2:  4.7061 -  3.7545 0.99   1381  148 0.0921 0.1154      5.4943      5.6913|
|  3:  3.7545 -  3.2856 0.99   1365  153 0.1213 0.1721      5.5764      5.9476|
|  4:  3.2856 -  2.9877 0.99   1346  149 0.1492 0.1782      5.6001      5.7497|
|  5:  2.9877 -  2.7750 0.99   1333  147 0.1616 0.1963      5.4935      5.6188|
|  6:  2.7750 -  2.6123 0.99   1342  150 0.1540 0.2273      5.3735      5.5911|
|  7:  2.6123 -  2.4821 0.98   1340  148 0.1448 0.1972      5.3049      5.5241|
|  8:  2.4821 -  2.3745 0.98   1302  146 0.1493 0.1964      5.2236      5.4182|
|  9:  2.3745 -  2.2834 0.99   1344  147 0.1421 0.2000      5.1794      5.4058|
| 10:  2.2834 -  2.2048 0.98   1296  147 0.1353 0.1946      5.1118      5.3663|
| 11:  2.2048 -  2.1361 0.97   1315  142 0.1351 0.2014      5.0488      5.2995|
| 12:  2.1361 -  2.0752 0.99   1303  149 0.1371 0.1928      4.9891      5.2236|
| 13:  2.0752 -  2.0207 0.89   1183  133 0.1401 0.1917      4.9212      5.1087|
| 14:  2.0207 -  1.9715 0.25    339   37 0.1371 0.1931      4.8157      5.1133|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.7061  1441   163  0.93   9.75   0.96     0.94       7804.67|
|  2:  4.7061 -  3.7545  1381   148  0.95   8.88   1.01     0.99      10091.84|
|  3:  3.7545 -  3.2856  1365   153  0.92  13.21   1.02     1.01      12489.13|
|  4:  3.2856 -  2.9877  1346   149  0.90  16.56   1.00     0.98      13495.97|
|  5:  2.9877 -  2.7750  1333   147  0.87  19.59   1.00     0.98      11624.76|
|  6:  2.7750 -  2.6123  1342   150  0.88  18.77   0.98     0.95       9257.96|
|  7:  2.6123 -  2.4821  1340   148  0.88  18.35   0.99     0.95       8214.33|
|  8:  2.4821 -  2.3745  1302   146  0.88  18.83   1.00     0.96       7190.48|
|  9:  2.3745 -  2.2834  1344   147  0.88  18.85   0.98     0.93       6516.33|
| 10:  2.2834 -  2.2048  1296   147  0.88  18.14   0.98     0.94       5976.13|
| 11:  2.2048 -  2.1361  1315   142  0.88  18.64   0.98     0.94       5354.17|
| 12:  2.1361 -  2.0752  1303   149  0.89  18.08   0.98     0.96       4844.33|
| 13:  2.0752 -  2.0207  1183   133  0.88  18.79   0.98     0.97       4235.48|
| 14:  2.0207 -  1.9715   339    37  0.87  19.28   0.97     0.92       3474.23|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3474.23 max =        13495.97 mean =      8209.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.60|
|phase err.(test): min =        0.00 max =           87.51 mean =        15.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.095)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    107.52  17.39    None  None   None       |
|    all(noH): 2823   0      1.43    107.52  17.39    None  None   None       |
|    Sol.    : 438    0      4.85    107.52  42.13    None  None   None       |
|    Mac.    : 2385   0      1.43    98.40   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.429 -  12.039: 1490   |   5:    54.476 -  65.085:   69        |
|      1:    12.039 -  22.648:  778   |   6:    65.085 -  75.695:   46        |
|      2:    22.648 -  33.257:  176   |   7:    75.695 -  86.304:   10        |
|      3:    33.257 -  43.867:  122   |   8:    86.304 -  96.913:    6        |
|      4:    43.867 -  54.476:  121   |   9:    96.913 - 107.523:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 361         
Filter by distance & map next to the model:
   mapped sites are within: 0.440 - 5.615
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 358 from: 361
   mapped sites are within: 0.714 - 5.615

peak=    7.302 closest distance to " O   HOH Z  41 " =    1.149
peak=    5.435 closest distance to " O   HOH Z 210 " =    1.570
peak=    5.228 closest distance to " CB  SER A  63 " =    1.290
peak=    5.128 closest distance to " CB  GLN A 223 " =    1.364
peak=    5.050 closest distance to " O   HOH Z 111 " =    2.219
peak=    4.963 closest distance to " CB  ARG A 275 " =    0.910
peak=    4.869 closest distance to " CG  PRO A  54 " =    1.292
peak=    4.759 closest distance to " O   HOH Z 134 " =    2.052
peak=    4.745 closest distance to " O   PRO A 198 " =    1.602
peak=    4.744 closest distance to " CG  PRO A 198 " =    1.338
peak=    4.739 closest distance to " O   HOH Z 126 " =    1.851
peak=    4.736 closest distance to " CA  TYR A  30 " =    0.999
peak=    4.717 closest distance to " O   HOH Z 120 " =    1.065
peak=    4.672 closest distance to " O   HOH Z 272 " =    1.302
peak=    4.669 closest distance to " CG  GLN A  77 " =    0.915
peak=    4.653 closest distance to " CG  PRO A 280 " =    0.871
peak=    4.639 closest distance to " O   ARG A 275 " =    0.772
peak=    4.614 closest distance to " O   HOH Z 433 " =    1.982
peak=    4.605 closest distance to " O   HOH Z  15 " =    2.072
peak=    4.593 closest distance to " CG  PRO A  90 " =    1.269
peak=    4.554 closest distance to " CB  PRO A  54 " =    0.857
peak=    4.513 closest distance to " O   HOH Z 232 " =    2.303
peak=    4.481 closest distance to " NH2BARG A 102 " =    1.014
peak=    4.476 closest distance to " O   HOH Z  47 " =    1.657
peak=    4.471 closest distance to " O   HOH Z  80 " =    2.120
peak=    4.445 closest distance to " CG  PRO A 213 " =    1.344
peak=    4.432 closest distance to " O   HOH Z 133 " =    1.966
peak=    4.429 closest distance to " O   HOH Z 247 " =    1.487
peak=    4.392 closest distance to " CG2BVAL A  41 " =    1.011
peak=    4.376 closest distance to " O   HOH Z 196 " =    2.032
peak=    4.371 closest distance to " O   HOH Z 350 " =    1.047
peak=    4.339 closest distance to " O   HOH Z 422 " =    1.090
peak=    4.314 closest distance to " O   HOH Z 209 " =    2.397
peak=    4.311 closest distance to " O   HOH Z 142 " =    1.589
peak=    4.305 closest distance to " O   HOH Z 234 " =    3.788
peak=    4.295 closest distance to " NE2 HIS A 115 " =    1.081
peak=    4.288 closest distance to " O   HOH Z 214 " =    1.369
peak=    4.265 closest distance to " O   HOH Z 124 " =    1.360
peak=    4.261 closest distance to " O   HOH Z 404 " =    1.616
peak=    4.247 closest distance to " OE1 GLN A  77 " =    1.004
peak=    4.247 closest distance to " O   HOH Z  97 " =    1.959
peak=    4.220 closest distance to " CB  TRP A 179 " =    1.365
peak=    4.218 closest distance to " O   HOH Z  78 " =    2.182
peak=    4.210 closest distance to " O   HOH Z 411 " =    3.078
peak=    4.201 closest distance to " O   HOH Z  61 " =    1.600
peak=    4.167 closest distance to " O   HOH Z 389 " =    2.041
peak=    4.160 closest distance to " CB  GLN A  73 " =    1.030
peak=    4.142 closest distance to " N   ASN A  39 " =    1.252
peak=    4.124 closest distance to " O   GLY A  91 " =    1.161
peak=    4.118 closest distance to " CB  GLU A 128 " =    1.111
peak=    4.117 closest distance to " O   HOH Z  67 " =    2.005
peak=    4.107 closest distance to " CB  GLN A 183 " =    1.323
peak=    4.062 closest distance to " CB  ARG A 190 " =    1.742
peak=    4.052 closest distance to " O   HOH Z 324 " =    1.638
peak=    4.050 closest distance to " CG1 ILE A 120 " =    1.122
peak=    4.047 closest distance to " O   HOH Z 394 " =    1.729
peak=    4.032 closest distance to " O   HOH Z 369 " =    2.035
peak=    4.025 closest distance to " O   THR A 251 " =    1.328
peak=    4.013 closest distance to " O   HOH Z 271 " =    2.358
peak=    4.009 closest distance to " O   HOH Z 133 " =    1.812
peak=    4.005 closest distance to " CB  ASN A 148 " =    1.336
peak=    4.004 closest distance to " CB  SER A  62 " =    0.864
peak=    4.002 closest distance to " CG2 THR A 221 " =    1.066
peak=    3.996 closest distance to " O   HOH Z 132 " =    1.237
peak=    3.991 closest distance to " CB  LEU A 228 " =    1.193
peak=    3.987 closest distance to " CG  ARG A  66 " =    2.865
peak=    3.983 closest distance to " O   HOH Z 357 " =    2.108
peak=    3.947 closest distance to " O   HOH Z 193 " =    1.986
peak=    3.925 closest distance to " CE  LYS A 119 " =    1.161
peak=    3.919 closest distance to " O   HOH Z 406 " =    1.532
peak=    3.914 closest distance to " CB  ASN A 285 " =    0.857
peak=    3.909 closest distance to " NH2 ARG A 156 " =    1.241
peak=    3.897 closest distance to " O   HOH Z  49 " =    1.141
peak=    3.897 closest distance to " O   HOH Z 426 " =    1.337
peak=    3.896 closest distance to " CB  TRP A 266 " =    0.963
peak=    3.893 closest distance to " N   SER A 164 " =    1.028
peak=    3.891 closest distance to " CA  VAL A  41 " =    0.801
peak=    3.891 closest distance to " CB  SER A 141 " =    1.056
peak=    3.886 closest distance to " OE1 GLN A  11 " =    2.013
peak=    3.881 closest distance to " CA  GLU A 152 " =    0.908
peak=    3.876 closest distance to " N   ILE A  33 " =    1.102
peak=    3.874 closest distance to " CA  ASP A 191 " =    0.855
peak=    3.871 closest distance to " O   HOH Z 189 " =    2.286
peak=    3.870 closest distance to " O   HOH Z  44 " =    1.805
peak=    3.867 closest distance to " O   HOH Z   7 " =    1.187
peak=    3.866 closest distance to " CG AARG A 275 " =    1.070
peak=    3.862 closest distance to " O   HOH Z  40 " =    2.239
peak=    3.861 closest distance to " O   HOH Z 203 " =    1.879
peak=    3.853 closest distance to " O   HOH Z  48 " =    1.688
peak=    3.852 closest distance to " CB  ALA A   1 " =    1.290
peak=    3.836 closest distance to " CB  GLU A 277 " =    1.039
peak=    3.821 closest distance to " CG1 ILE A  33 " =    1.359
peak=    3.787 closest distance to " CB  MET A 105 " =    1.182
peak=    3.784 closest distance to " CA  GLY A 196 " =    0.985
peak=    3.774 closest distance to " O   VAL A  72 " =    1.357
peak=    3.765 closest distance to " O   HOH Z 418 " =    1.753
peak=    3.764 closest distance to " O   HOH Z 336 " =    1.624
peak=    3.753 closest distance to " O   HOH Z 437 " =    1.811
peak=    3.740 closest distance to " O   HOH Z 163 " =    1.714
peak=    3.733 closest distance to " CG2 VAL A 197 " =    1.333
peak=    3.727 closest distance to " NH1 ARG A 269 " =    0.824
peak=    3.726 closest distance to " CB  GLU A 152 " =    1.205
peak=    3.720 closest distance to " O  BHOH Z 338 " =    0.936
peak=    3.716 closest distance to " O   HOH Z 431 " =    1.380
peak=    3.712 closest distance to " O   HOH Z 192 " =    2.040
peak=    3.711 closest distance to " CB  GLN A  58 " =    0.914
peak=    3.703 closest distance to " CB  TYR A 169 " =    0.811
peak=    3.697 closest distance to " O   GLY A  23 " =    2.443
peak=    3.689 closest distance to " CD  ARG A 269 " =    0.994
peak=    3.689 closest distance to " OG  SER A  97 " =    3.507
peak=    3.686 closest distance to " O   HOH Z  11 " =    1.309
peak=    3.681 closest distance to " O   HOH Z 118 " =    1.819
peak=    3.676 closest distance to " CZ3 TRP A 274 " =    2.101
peak=    3.674 closest distance to " CB  PRO A 198 " =    0.984
peak=    3.670 closest distance to " O   HOH Z 327 " =    1.613
peak=    3.662 closest distance to " CB  PHE A 283 " =    0.960
peak=    3.653 closest distance to " CZ  PHE A 218 " =    1.030
peak=    3.649 closest distance to " CB  ARG A  79 " =    1.413
peak=    3.648 closest distance to " O   HOH Z 301 " =    1.602
peak=    3.644 closest distance to " O   HOH Z 265 " =    2.148
peak=    3.643 closest distance to " O   HOH Z 200 " =    1.426
peak=    3.638 closest distance to " O   HOH Z 174 " =    1.898
peak=    3.637 closest distance to " NH1 ARG A  36 " =    1.164
peak=    3.630 closest distance to " O   HOH Z  22 " =    2.508
peak=    3.630 closest distance to " CG2 VAL A  78 " =    1.023
peak=    3.625 closest distance to " O   HOH Z 387 " =    2.504
peak=    3.624 closest distance to " CB  VAL A 202 " =    1.553
peak=    3.623 closest distance to " CA  GLN A 223 " =    0.878
peak=    3.618 closest distance to " O   HOH Z 358 " =    1.480
peak=    3.618 closest distance to " O   HOH Z 145 " =    2.066
peak=    3.617 closest distance to " CB  PHE A  16 " =    1.262
peak=    3.617 closest distance to " O   HOH Z 119 " =    2.294
peak=    3.610 closest distance to " CA  LYS A  48 " =    1.460
peak=    3.600 closest distance to " CG2 THR A 220 " =    0.796
peak=    3.595 closest distance to " CD  ARG A 159 " =    0.795
peak=    3.587 closest distance to " CA  ARG A 195 " =    1.103
peak=    3.586 closest distance to " OD1 ASN A 301 " =    1.104
peak=    3.585 closest distance to " O   HOH Z 132 " =    2.591
peak=    3.584 closest distance to " O   HOH Z 432 " =    2.002
peak=    3.583 closest distance to " O   HOH Z 362 " =    3.281
peak=    3.575 closest distance to " O   HOH Z 139 " =    4.284
peak=    3.571 closest distance to " CD1 LEU A 222 " =    0.887
peak=    3.559 closest distance to " O   HOH Z  88 " =    3.576
peak=    3.557 closest distance to " CB  MET A  47 " =    1.017
peak=    3.554 closest distance to " CD2 LEU A 297 " =    1.012
peak=    3.549 closest distance to " O   HOH Z 374 " =    2.649
peak=    3.547 closest distance to " CG  PRO A 243 " =    1.211
peak=    3.546 closest distance to " O   HOH Z 298 " =    1.951
peak=    3.542 closest distance to " O   HOH Z  48 " =    1.852
peak=    3.540 closest distance to " O   ILE A 106 " =    1.778
peak=    3.539 closest distance to " CG  GLN A  11 " =    1.312
peak=    3.535 closest distance to " O   HOH Z 428 " =    1.145
peak=    3.521 closest distance to " O   HOH Z  20 " =    1.883
peak=    3.520 closest distance to " O   HOH Z  83 " =    1.228
peak=    3.513 closest distance to " CD  LYS A 166 " =    1.485
peak=    3.505 closest distance to " O   HOH Z  66 " =    2.118
peak=    3.503 closest distance to " O   HOH Z 352 " =    1.342
peak=    3.496 closest distance to " ND2 ASN A 301 " =    1.090
peak=    3.493 closest distance to " O   HOH Z 150 " =    1.741
peak=    3.491 closest distance to " CA  ASP A 124 " =    0.837
peak=    3.490 closest distance to " CA  ALA A  21 " =    1.497
peak=    3.488 closest distance to " O   HOH Z   1 " =    3.211
peak=    3.487 closest distance to " O   HOH Z 245 " =    1.406
peak=    3.487 closest distance to " CB  GLN A 194 " =    0.950
peak=    3.478 closest distance to " CG1 VAL A 153 " =    1.099
peak=    3.477 closest distance to " CB  GLN A  88 " =    1.118
peak=    3.474 closest distance to " O   HOH Z  30 " =    1.773
peak=    3.474 closest distance to " O   HOH Z 250 " =    1.433
peak=    3.474 closest distance to " O   HOH Z 141 " =    1.647
peak=    3.472 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.467 closest distance to " O   HOH Z  89 " =    3.537
peak=    3.467 closest distance to " O   HOH Z 377 " =    1.493
peak=    3.465 closest distance to " O   HOH Z 371 " =    3.382
peak=    3.465 closest distance to " O   HOH Z 343 " =    2.330
peak=    3.457 closest distance to " N   LYS A 166 " =    0.842
peak=    3.456 closest distance to " CB  ARG A 269 " =    1.063
peak=    3.456 closest distance to " CA  ASN A 127 " =    1.082
peak=    3.447 closest distance to " CG  ARG A  66 " =    0.894
peak=    3.443 closest distance to " CD BLYS A 290 " =    1.014
peak=    3.439 closest distance to " O   HOH Z  43 " =    1.635
peak=    3.434 closest distance to " CB  PRO A  90 " =    1.178
peak=    3.434 closest distance to " CB  ILE A 199 " =    1.084
peak=    3.433 closest distance to " OG  SER A  62 " =    3.080
peak=    3.433 closest distance to " CG2 THR A  42 " =    0.924
peak=    3.431 closest distance to " O   HOH Z  26 " =    1.466
peak=    3.429 closest distance to " CB  ASP A 140 " =    0.776
peak=    3.429 closest distance to " O   HOH Z  88 " =    1.621
peak=    3.428 closest distance to " O   HOH Z  63 " =    1.903
peak=    3.428 closest distance to " CB  ASN A 187 " =    1.144
peak=    3.427 closest distance to " O   HOH Z 215 " =    1.364
peak=    3.427 closest distance to " CB  ALA A 100 " =    1.502
peak=    3.426 closest distance to " CA  LEU A  83 " =    1.441
peak=    3.425 closest distance to " O   HOH Z 403 " =    1.844
peak=    3.425 closest distance to " CA  THR A 294 " =    1.810
peak=    3.424 closest distance to " N   ASN A 252 " =    1.150
peak=    3.423 closest distance to " CG AARG A 275 " =    1.066
peak=    3.414 closest distance to " OG  SER A 245 " =    1.613
peak=    3.412 closest distance to " CA  ARG A  66 " =    1.194
peak=    3.409 closest distance to " CA  ALA A  51 " =    0.909
peak=    3.407 closest distance to " CB  ALA A 256 " =    1.321
peak=    3.402 closest distance to " CA  ALA A 248 " =    1.209
peak=    3.399 closest distance to " CA  ASN A 176 " =    1.530
peak=    3.390 closest distance to " O   HOH Z 395 " =    1.475
peak=    3.384 closest distance to " O   HOH Z 104 " =    3.218
peak=    3.375 closest distance to " N   TYR A 116 " =    1.808
peak=    3.374 closest distance to " C   GLY A  80 " =    1.344
peak=    3.373 closest distance to " O   HOH Z 380 " =    1.875
peak=    3.372 closest distance to " CB  ALA A  71 " =    1.248
peak=    3.370 closest distance to " CA  GLU A 277 " =    1.106
peak=    3.370 closest distance to " NZ  LYS A 117 " =    3.140
peak=    3.364 closest distance to " O   HOH Z 155 " =    3.002
peak=    3.363 closest distance to " O   HOH Z 416 " =    1.160
peak=    3.363 closest distance to " CG2 ILE A 120 " =    1.071
peak=    3.362 closest distance to " CE1 TYR A 186 " =    1.329
peak=    3.360 closest distance to " O   HOH Z 373 " =    1.675
peak=    3.360 closest distance to " O   SER A  87 " =    2.333
peak=    3.359 closest distance to " O   ALA A 165 " =    1.305
peak=    3.359 closest distance to " O   HOH Z   4 " =    1.145
peak=    3.358 closest distance to " CB  TRP A 123 " =    1.227
peak=    3.357 closest distance to " CD1 TRP A 274 " =    1.022
peak=    3.353 closest distance to " CD1 LEU A 167 " =    1.298
peak=    3.352 closest distance to " O   HOH Z 425 " =    1.485
peak=    3.351 closest distance to " CB  PRO A 213 " =    1.926
peak=    3.339 closest distance to " O   HOH Z 272 " =    1.987
peak=    3.337 closest distance to " CB  ARG A 275 " =    1.273
peak=    3.335 closest distance to " ND1 HIS A  81 " =    1.399
peak=    3.329 closest distance to " CD1 LEU A  96 " =    0.714
peak=    3.325 closest distance to " O   HOH Z  39 " =    1.733
peak=    3.325 closest distance to " O   HOH Z 345 " =    3.020
peak=    3.325 closest distance to " CA  ALA A 100 " =    1.332
peak=    3.312 closest distance to " OH  TYR A 169 " =    0.927
peak=    3.312 closest distance to " CB  SER A 276 " =    1.234
peak=    3.308 closest distance to " O   HOH Z 344 " =    3.291
peak=    3.308 closest distance to " O   HOH Z 400 " =    0.906
peak=    3.306 closest distance to " CA  THR A 221 " =    1.525
peak=    3.304 closest distance to " O   HOH Z 279 " =    2.282
peak=    3.303 closest distance to " O   HOH Z 227 " =    1.763
peak=    3.300 closest distance to " CG2AVAL A 121 " =    1.913
peak=    3.296 closest distance to " CG2 ILE A  20 " =    1.240
peak=    3.295 closest distance to " CA  SER A  12 " =    1.462
peak=    3.294 closest distance to " O   HOH Z 409 " =    3.212
peak=    3.293 closest distance to " CB  PHE A  61 " =    0.719
peak=    3.292 closest distance to " OE1 GLU A   2 " =    1.858
peak=    3.292 closest distance to " O   HOH Z  48 " =    1.681
peak=    3.291 closest distance to " CA  ARG A  36 " =    1.074
peak=    3.290 closest distance to " O   HOH Z 108 " =    1.100
peak=    3.290 closest distance to " CZ  PHE A 192 " =    0.941
peak=    3.288 closest distance to " CA  SER A  87 " =    0.933
peak=    3.278 closest distance to " OD1 ASP A 238 " =    0.913
peak=    3.278 closest distance to " CB  GLU A  46 " =    1.011
peak=    3.278 closest distance to " O   HOH Z 261 " =    1.972
peak=    3.276 closest distance to " CB  PRO A 243 " =    1.154
peak=    3.273 closest distance to " N   TRP A 150 " =    1.006
peak=    3.272 closest distance to " CB  SER A   3 " =    1.380
peak=    3.272 closest distance to " CD2 TRP A 179 " =    1.255
peak=    3.272 closest distance to " CE BMET A  47 " =    1.414
peak=    3.269 closest distance to " O   ASN A  74 " =    1.678
peak=    3.269 closest distance to " O   HOH Z 215 " =    2.322
peak=    3.269 closest distance to " O   HOH Z 214 " =    2.305
peak=    3.264 closest distance to " O   SER A 276 " =    1.169
peak=    3.264 closest distance to " O   HOH Z 155 " =    1.460
peak=    3.262 closest distance to " CA  ALA A 160 " =    1.026
peak=    3.256 closest distance to " O   HOH Z 316 " =    2.891
peak=    3.256 closest distance to " NE AARG A 275 " =    1.466
peak=    3.254 closest distance to " O   HOH Z 207 " =    2.472
peak=    3.253 closest distance to " CB  TRP A 179 " =    1.973
peak=    3.252 closest distance to " CB  ALA A 154 " =    1.062
peak=    3.247 closest distance to " OD1 ASN A  69 " =    2.347
peak=    3.243 closest distance to " O   HOH Z 146 " =    1.639
peak=    3.241 closest distance to " CG2 VAL A 112 " =    1.482
peak=    3.239 closest distance to " O   HOH Z 363 " =    1.080
peak=    3.239 closest distance to " O   HOH Z 289 " =    1.612
peak=    3.239 closest distance to " O   SER A 273 " =    1.707
peak=    3.238 closest distance to " N   PHE A 130 " =    1.325
peak=    3.238 closest distance to " CA  LEU A 282 " =    1.182
peak=    3.236 closest distance to " CB  GLU A 277 " =    3.775
peak=    3.236 closest distance to " CA  ILE A 106 " =    0.758
peak=    3.231 closest distance to " O   HOH Z 327 " =    2.552
peak=    3.227 closest distance to " O   HOH Z 287 " =    1.912
peak=    3.224 closest distance to " CA  ILE A 263 " =    0.951
peak=    3.223 closest distance to " N   ASN A 110 " =    1.289
peak=    3.223 closest distance to " CB  SER A  26 " =    0.867
peak=    3.222 closest distance to " CB  SER A  28 " =    0.905
peak=    3.221 closest distance to " O   HOH Z 417 " =    2.961
peak=    3.219 closest distance to " CB  ASN A 148 " =    2.015
peak=    3.219 closest distance to " CB  VAL A 265 " =    1.331
peak=    3.218 closest distance to " CA  GLU A  46 " =    1.000
peak=    3.218 closest distance to " CA  THR A 246 " =    1.125
peak=    3.216 closest distance to " OE1 GLN A  58 " =    3.311
peak=    3.216 closest distance to " CB  VAL A 126 " =    0.800
peak=    3.213 closest distance to " O   HOH Z 162 " =    1.858
peak=    3.210 closest distance to " O   HOH Z  50 " =    3.363
peak=    3.208 closest distance to " CA  PRO A  90 " =    0.993
peak=    3.207 closest distance to " ND2 ASN A  45 " =    1.163
peak=    3.204 closest distance to " O   HOH Z 128 " =    1.951
peak=    3.202 closest distance to " NH1 ARG A  14 " =    1.261
peak=    3.201 closest distance to " CD  PRO A 280 " =    1.001
peak=    3.201 closest distance to " O   HOH Z 124 " =    3.474
peak=    3.198 closest distance to " O   HOH Z 126 " =    1.889
peak=    3.197 closest distance to " O   HOH Z  21 " =    1.881
peak=    3.196 closest distance to " CB  ALA A  34 " =    0.839
peak=    3.195 closest distance to " O   HOH Z 183 " =    1.437
peak=    3.192 closest distance to " OG1 THR A 294 " =    2.552
peak=    3.192 closest distance to " O   SER A  26 " =    1.732
peak=    3.190 closest distance to " NE2 GLN A  11 " =    1.013
peak=    3.190 closest distance to " CE3 TRP A  85 " =    1.222
peak=    3.188 closest distance to " O   HOH Z 271 " =    1.167
peak=    3.186 closest distance to " C   VAL A 265 " =    1.119
peak=    3.185 closest distance to " CA  GLY A  75 " =    1.076
peak=    3.184 closest distance to " CB  SER A  97 " =    2.040
peak=    3.181 closest distance to " O   HOH Z 402 " =    1.546
peak=    3.176 closest distance to " O   HOH Z 109 " =    2.013
peak=    3.175 closest distance to " O   HOH Z 240 " =    1.924
peak=    3.171 closest distance to " N   THR A  52 " =    1.100
peak=    3.171 closest distance to " CG2 THR A  29 " =    1.547
peak=    3.169 closest distance to " CB  ALA A 137 " =    1.198
peak=    3.162 closest distance to " O   HOH Z 403 " =    1.398
peak=    3.162 closest distance to " O   HOH Z 284 " =    3.056
peak=    3.158 closest distance to " CB  GLU A 175 " =    1.313
peak=    3.153 closest distance to " O   HOH Z 303 " =    2.296
peak=    3.148 closest distance to " O   HOH Z 154 " =    1.324
peak=    3.147 closest distance to " CG2 ILE A 151 " =    0.855
peak=    3.145 closest distance to " CA  GLN A  11 " =    1.107
peak=    3.143 closest distance to " CD  ARG A  56 " =    1.321
peak=    3.143 closest distance to " O   HOH Z 325 " =    3.458
peak=    3.141 closest distance to " O   HOH Z 420 " =    5.615
peak=    3.137 closest distance to " O   HOH Z  52 " =    1.537
peak=    3.135 closest distance to " O   HOH Z 152 " =    1.802
peak=    3.135 closest distance to " CB  LEU A  83 " =    0.794
peak=    3.129 closest distance to " O   HOH Z   6 " =    1.244
peak=    3.128 closest distance to " O   HOH Z  20 " =    2.274
peak=    3.123 closest distance to " O   ASP A 231 " =    1.823
peak=    3.122 closest distance to " CA  GLY A 229 " =    0.843
peak=    3.121 closest distance to " CD  GLU A 236 " =    1.163
peak=    3.121 closest distance to " CB  VAL A 257 " =    0.971
peak=    3.120 closest distance to " O   HOH Z 435 " =    1.920
peak=    3.119 closest distance to " CD2 HIS A  81 " =    1.388
peak=    3.117 closest distance to " O   HOH Z   2 " =    1.736
peak=    3.113 closest distance to " O   HOH Z 423 " =    1.805
peak=    3.113 closest distance to " CG2 VAL A 126 " =    1.040
peak=    3.111 closest distance to " O   HOH Z 142 " =    1.457
peak=    3.102 closest distance to " ND2 ASN A 110 " =    1.563
peak=    3.099 closest distance to " CZ3 TRP A  85 " =    0.984
peak=    3.099 closest distance to " N   ARG A 156 " =    1.497
peak=    3.090 closest distance to " CB  GLN A 240 " =    1.660
peak=    3.087 closest distance to " CA  ARG A 139 " =    1.471
peak=    3.087 closest distance to " CA  GLU A 152 " =    1.440
peak=    3.076 closest distance to " CA  ALA A 291 " =    0.976
peak=    3.067 closest distance to " O   HOH Z 420 " =    2.292
peak=    3.061 closest distance to " O   HOH Z 146 " =    1.277
peak=    3.055 closest distance to " CA  LYS A 117 " =    1.303
peak=    3.055 closest distance to " CA  ALA A 299 " =    1.282
peak=    3.053 closest distance to " CA  ASP A 132 " =    1.293
peak=    3.041 closest distance to " CA  ASP A 162 " =    1.200
peak=    3.037 closest distance to " CB  ALA A 248 " =    1.254
peak=    3.036 closest distance to " N   ALA A 256 " =    1.132
peak=    3.036 closest distance to " NH2AARG A 190 " =    1.508
peak=    3.035 closest distance to " CD  ARG A  36 " =    0.966

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.353 - 5.513
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 200
   mapped sites are within: 0.720 - 5.513

peak=   -4.539 closest distance to " N   ARG A 275 " =    0.956
peak=   -4.395 closest distance to " O   HOH Z 266 " =    4.718
peak=   -4.384 closest distance to " C   ASN A 285 " =    2.509
peak=   -4.348 closest distance to " O   HOH Z 221 " =    1.229
peak=   -4.299 closest distance to " O   HOH Z 196 " =    1.656
peak=   -4.175 closest distance to " CB  LEU A 167 " =    2.165
peak=   -4.148 closest distance to " CB  SER A 146 " =    2.079
peak=   -4.138 closest distance to " NH2 ARG A  66 " =    1.044
peak=   -4.113 closest distance to " O   HOH Z 290 " =    0.898
peak=   -4.051 closest distance to " CD1 PHE A  59 " =    1.873
peak=   -4.044 closest distance to " OG  SER A  97 " =    2.265
peak=   -3.986 closest distance to " O   HOH Z 348 " =    2.368
peak=   -3.950 closest distance to " O   HOH Z  58 " =    0.896
peak=   -3.946 closest distance to " N   ARG A 275 " =    1.222
peak=   -3.944 closest distance to " N   ALA A  43 " =    2.673
peak=   -3.942 closest distance to " O   HOH Z  52 " =    1.883
peak=   -3.934 closest distance to " O   HOH Z 377 " =    0.782
peak=   -3.930 closest distance to " O   HOH Z  93 " =    1.419
peak=   -3.929 closest distance to " CA  VAL A 197 " =    0.948
peak=   -3.916 closest distance to " O   HOH Z 155 " =    1.441
peak=   -3.903 closest distance to " O   HOH Z 120 " =    0.897
peak=   -3.879 closest distance to " OG  SER A  32 " =    1.075
peak=   -3.868 closest distance to " CG  PRO A 243 " =    1.519
peak=   -3.860 closest distance to " O   HOH Z  15 " =    1.663
peak=   -3.852 closest distance to " C   THR A 279 " =    1.112
peak=   -3.842 closest distance to " O   PRO A 198 " =    1.365
peak=   -3.821 closest distance to " O   HOH Z 151 " =    1.461
peak=   -3.819 closest distance to " CA  GLU A 277 " =    1.190
peak=   -3.786 closest distance to " O   ALA A   1 " =    2.085
peak=   -3.785 closest distance to " O   HOH Z 407 " =    0.720
peak=   -3.779 closest distance to " OD2 ASP A 171 " =    1.850
peak=   -3.779 closest distance to " CG  ASP A 231 " =    0.805
peak=   -3.767 closest distance to " CZ  ARG A  66 " =    1.122
peak=   -3.759 closest distance to " OXT GLY A 302 " =    2.921
peak=   -3.756 closest distance to " O   HOH Z  11 " =    1.113
peak=   -3.749 closest distance to " C   SER A 271 " =    1.242
peak=   -3.736 closest distance to " C   SER A 206 " =    1.461
peak=   -3.725 closest distance to " O   HOH Z 210 " =    0.910
peak=   -3.723 closest distance to " O   PHE A 218 " =    1.344
peak=   -3.712 closest distance to " OH  TYR A 169 " =    0.923
peak=   -3.688 closest distance to " O   HOH Z  37 " =    1.500
peak=   -3.680 closest distance to " CA  GLY A 203 " =    2.280
peak=   -3.674 closest distance to " CD  GLN A  77 " =    1.010
peak=   -3.672 closest distance to " CG2 ILE A  49 " =    2.588
peak=   -3.671 closest distance to " O   HOH Z 185 " =    2.352
peak=   -3.670 closest distance to " O   HOH Z 350 " =    0.973
peak=   -3.647 closest distance to " CG2BVAL A  41 " =    2.708
peak=   -3.636 closest distance to " CG2 THR A 221 " =    2.235
peak=   -3.625 closest distance to " CA  SER A 164 " =    2.169
peak=   -3.620 closest distance to " CD  GLN A 223 " =    0.868
peak=   -3.620 closest distance to " C   HIS A 108 " =    1.087
peak=   -3.604 closest distance to " O   GLY A 196 " =    1.132
peak=   -3.603 closest distance to " O   HOH Z 118 " =    5.513
peak=   -3.597 closest distance to " CD  GLN A  88 " =    0.878
peak=   -3.592 closest distance to " O   HOH Z  71 " =    1.551
peak=   -3.589 closest distance to " NH2 ARG A  36 " =    1.002
peak=   -3.584 closest distance to " O  BHOH Z 338 " =    1.417
peak=   -3.581 closest distance to " O   ASP A 171 " =    1.031
peak=   -3.574 closest distance to " O   HOH Z 325 " =    1.707
peak=   -3.568 closest distance to " N   SER A 134 " =    1.214
peak=   -3.567 closest distance to " O   HOH Z 109 " =    3.474
peak=   -3.566 closest distance to " CA  SER A 276 " =    1.357
peak=   -3.556 closest distance to " CG  ASP A  50 " =    2.544
peak=   -3.551 closest distance to " O   HOH Z  19 " =    2.320
peak=   -3.540 closest distance to " CA  VAL A  67 " =    2.884
peak=   -3.530 closest distance to " O   TRP A  92 " =    1.904
peak=   -3.527 closest distance to " O   HOH Z 418 " =    1.453
peak=   -3.523 closest distance to " CD2 LEU A 300 " =    2.891
peak=   -3.520 closest distance to " CE2 TYR A  30 " =    2.721
peak=   -3.519 closest distance to " OD2 ASP A 171 " =    2.248
peak=   -3.514 closest distance to " NE2 GLN A 223 " =    1.037
peak=   -3.512 closest distance to " O   HOH Z 351 " =    1.575
peak=   -3.498 closest distance to " O   HOH Z   7 " =    1.110
peak=   -3.495 closest distance to " CD2 LEU A 237 " =    2.310
peak=   -3.487 closest distance to " O   HOH Z 184 " =    1.311
peak=   -3.479 closest distance to " CD2 PHE A  61 " =    1.900
peak=   -3.477 closest distance to " CE  MET A  93 " =    1.320
peak=   -3.473 closest distance to " O   HOH Z 176 " =    1.679
peak=   -3.465 closest distance to " CD1 LEU A  25 " =    2.503
peak=   -3.458 closest distance to " NH1 ARG A 195 " =    2.340
peak=   -3.455 closest distance to " O   HOH Z  91 " =    2.169
peak=   -3.453 closest distance to " CD  GLN A 223 " =    1.614
peak=   -3.448 closest distance to " O   HOH Z 308 " =    1.673
peak=   -3.446 closest distance to " O   HOH Z 198 " =    1.502
peak=   -3.441 closest distance to " OD1 ASP A 191 " =    1.579
peak=   -3.439 closest distance to " O   HOH Z 210 " =    2.560
peak=   -3.436 closest distance to " O   HOH Z 222 " =    1.173
peak=   -3.433 closest distance to " O   HOH Z 422 " =    1.073
peak=   -3.427 closest distance to " ND2 ASN A  60 " =    1.291
peak=   -3.423 closest distance to " O   HOH Z  38 " =    1.121
peak=   -3.422 closest distance to " O   HOH Z 423 " =    2.372
peak=   -3.414 closest distance to " ND2 ASN A  45 " =    1.270
peak=   -3.407 closest distance to " CD  GLU A 236 " =    1.054
peak=   -3.405 closest distance to " N   GLN A  58 " =    1.631
peak=   -3.405 closest distance to " O   HOH Z  49 " =    0.941
peak=   -3.402 closest distance to " O   ALA A 256 " =    1.545
peak=   -3.399 closest distance to " OE2 GLU A   2 " =    1.386
peak=   -3.399 closest distance to " OE1 GLN A  88 " =    1.048
peak=   -3.393 closest distance to " CB  ALA A 161 " =    2.640
peak=   -3.391 closest distance to " O   HOH Z 407 " =    1.635
peak=   -3.386 closest distance to " O   HOH Z 313 " =    1.424
peak=   -3.383 closest distance to " O   HOH Z 234 " =    4.234
peak=   -3.376 closest distance to " O   GLN A  11 " =    1.117
peak=   -3.376 closest distance to " CD2 TRP A  85 " =    1.128
peak=   -3.369 closest distance to " O   HOH Z 401 " =    1.455
peak=   -3.369 closest distance to " CB  TYR A  15 " =    2.354
peak=   -3.368 closest distance to " O   HOH Z 423 " =    1.087
peak=   -3.367 closest distance to " O   HOH Z  10 " =    1.671
peak=   -3.364 closest distance to " O   HOH Z 388 " =    1.972
peak=   -3.361 closest distance to " CD2 LEU A 237 " =    2.648
peak=   -3.359 closest distance to " O   HOH Z  48 " =    0.903
peak=   -3.349 closest distance to " O   VAL A 174 " =    1.951
peak=   -3.348 closest distance to " CG  ARG A 269 " =    2.353
peak=   -3.347 closest distance to " O   GLY A 118 " =    2.276
peak=   -3.341 closest distance to " CD2 TRP A 274 " =    2.255
peak=   -3.340 closest distance to " CB  CYS A 254 " =    2.120
peak=   -3.334 closest distance to " O   ALA A  34 " =    1.960
peak=   -3.331 closest distance to " O   HOH Z  53 " =    2.414
peak=   -3.330 closest distance to " CD  PRO A 198 " =    1.089
peak=   -3.330 closest distance to " O   HOH Z 251 " =    1.664
peak=   -3.326 closest distance to " O   HOH Z 103 " =    1.903
peak=   -3.325 closest distance to " CD2 HIS A 115 " =    1.046
peak=   -3.321 closest distance to " O   TYR A  15 " =    1.428
peak=   -3.317 closest distance to " OG  SER A  87 " =    1.683
peak=   -3.316 closest distance to " SG  CYS A 254 " =    3.293
peak=   -3.315 closest distance to " O   HOH Z  76 " =    2.078
peak=   -3.310 closest distance to " CH2 TRP A 177 " =    1.988
peak=   -3.309 closest distance to " CB  ALA A 291 " =    2.505
peak=   -3.308 closest distance to " CA  TYR A  68 " =    2.682
peak=   -3.305 closest distance to " OG BSER A 210 " =    2.224
peak=   -3.303 closest distance to " CA  ASN A 127 " =    1.065
peak=   -3.303 closest distance to " CB  ALA A 131 " =    2.366
peak=   -3.302 closest distance to " OG1 THR A   4 " =    1.852
peak=   -3.302 closest distance to " OG1 THR A  82 " =    2.050
peak=   -3.300 closest distance to " CG1 VAL A 112 " =    2.640
peak=   -3.298 closest distance to " OE1 GLN A  88 " =    0.860
peak=   -3.296 closest distance to " N   ALA A 226 " =    2.046
peak=   -3.282 closest distance to " OG ASER A 134 " =    1.195
peak=   -3.278 closest distance to " CD  ARG A  14 " =    3.310
peak=   -3.277 closest distance to " CE2 PHE A 218 " =    2.603
peak=   -3.275 closest distance to " O   THR A  18 " =    1.599
peak=   -3.275 closest distance to " O   HOH Z 136 " =    1.685
peak=   -3.267 closest distance to " O   HOH Z   7 " =    1.572
peak=   -3.262 closest distance to " O   HOH Z 200 " =    1.180
peak=   -3.261 closest distance to " CA  GLY A 241 " =    2.274
peak=   -3.261 closest distance to " O   HOH Z 428 " =    1.047
peak=   -3.251 closest distance to " CD2 PHE A  59 " =    2.304
peak=   -3.246 closest distance to " NH1 ARG A  66 " =    4.464
peak=   -3.236 closest distance to " O   HOH Z 298 " =    2.956
peak=   -3.235 closest distance to " O   HOH Z 148 " =    3.243
peak=   -3.234 closest distance to " O   HOH Z 171 " =    2.536
peak=   -3.228 closest distance to " O   HOH Z 128 " =    4.460
peak=   -3.228 closest distance to " ND2 ASN A  60 " =    1.557
peak=   -3.225 closest distance to " O   HOH Z 117 " =    4.733
peak=   -3.225 closest distance to " O   HOH Z 196 " =    3.067
peak=   -3.224 closest distance to " O   ALA A 158 " =    1.102
peak=   -3.221 closest distance to " O   HOH Z 280 " =    1.841
peak=   -3.218 closest distance to " O   HOH Z 368 " =    2.175
peak=   -3.218 closest distance to " OG1 THR A  82 " =    1.223
peak=   -3.211 closest distance to " O   HOH Z 166 " =    2.257
peak=   -3.208 closest distance to " CD  PRO A 213 " =    2.278
peak=   -3.205 closest distance to " CB  PRO A 243 " =    2.738
peak=   -3.203 closest distance to " CB  PRO A 213 " =    1.579
peak=   -3.201 closest distance to " O   VAL A  67 " =    2.010
peak=   -3.196 closest distance to " CE2 PHE A  38 " =    1.917
peak=   -3.192 closest distance to " O   HOH Z 231 " =    0.884
peak=   -3.192 closest distance to " O   HOH Z 275 " =    1.567
peak=   -3.185 closest distance to " O   ARG A 275 " =    2.168
peak=   -3.185 closest distance to " CB  ALA A 291 " =    2.407
peak=   -3.183 closest distance to " OD1 ASN A 148 " =    1.575
peak=   -3.182 closest distance to " OD1 ASP A 298 " =    2.022
peak=   -3.180 closest distance to " CD  LYS A 289 " =    2.386
peak=   -3.173 closest distance to " O   HOH Z 165 " =    1.913
peak=   -3.167 closest distance to " CZ  ARG A  36 " =    2.143
peak=   -3.164 closest distance to " O   HOH Z 396 " =    1.386
peak=   -3.159 closest distance to " O   HOH Z 109 " =    3.484
peak=   -3.157 closest distance to " CG  GLN A  58 " =    1.186
peak=   -3.156 closest distance to " O   HOH Z 174 " =    2.078
peak=   -3.156 closest distance to " CE  LYS A 119 " =    0.999
peak=   -3.153 closest distance to " O   VAL A 121 " =    1.035
peak=   -3.143 closest distance to " C   ALA A 158 " =    1.254
peak=   -3.143 closest distance to " O   HOH Z 380 " =    4.290
peak=   -3.126 closest distance to " CE  MET A 105 " =    2.108
peak=   -3.115 closest distance to " O   HOH Z  25 " =    1.876
peak=   -3.111 closest distance to " O   HOH Z 231 " =    1.731
peak=   -3.110 closest distance to " NH2 ARG A  79 " =    1.916
peak=   -3.110 closest distance to " CE  MET A 105 " =    2.232
peak=   -3.107 closest distance to " CG  GLU A   2 " =    1.544
peak=   -3.099 closest distance to " CD  GLN A  73 " =    0.830
peak=   -3.092 closest distance to " N   GLY A  17 " =    1.741
peak=   -3.078 closest distance to " O   HOH Z  30 " =    0.925
peak=   -3.077 closest distance to " NE1 TRP A 150 " =    2.171
peak=   -3.077 closest distance to " CD  ARG A 139 " =    1.637
peak=   -3.070 closest distance to " CG  ARG A 219 " =    2.358
peak=   -3.069 closest distance to " O   HOH Z 422 " =    1.650
peak=   -3.053 closest distance to " O   HOH Z  17 " =    1.205
peak=   -3.052 closest distance to " O   HOH Z 134 " =    2.023

================= 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    :  0.4556 0.4395   6.269696e+00   6.243902e+00
   1_bss:  0.4459 0.4291   6.261675e+00   6.231211e+00
   1_xyz:  0.3697 0.3939   6.144480e+00   6.182435e+00
   1_adp:  0.3406 0.4053   6.102704e+00   6.193912e+00
   1_occ:  0.3403 0.4054   6.102076e+00   6.194306e+00
   2_bss:  0.3402 0.4040   6.103641e+00   6.193314e+00
   2_xyz:  0.2724 0.3303   5.905183e+00   6.045019e+00
   2_adp:  0.2492 0.3146   5.849731e+00   6.016718e+00
   2_occ:  0.2489 0.3138   5.848795e+00   6.015901e+00
   3_bss:  0.2484 0.3121   5.847103e+00   6.013953e+00
   3_xyz:  0.2073 0.2620   5.676953e+00   5.850896e+00
   3_adp:  0.1971 0.2463   5.633155e+00   5.805605e+00
   3_occ:  0.1969 0.2462   5.632767e+00   5.805028e+00
   4_bss:  0.1970 0.2458   5.633419e+00   5.804879e+00
   4_xyz:  0.1555 0.1989   5.417998e+00   5.614700e+00
   4_adp:  0.1435 0.1902   5.360719e+00   5.571703e+00
   4_occ:  0.1435 0.1901   5.360612e+00   5.571679e+00
   5_bss:  0.1437 0.1904   5.361966e+00   5.573221e+00
   5_xyz:  0.1331 0.1808   5.296595e+00   5.518111e+00
   5_adp:  0.1318 0.1773   5.284842e+00   5.499876e+00
   5_occ:  0.1317 0.1773   5.284685e+00   5.500133e+00
   5_bss:  0.1316 0.1773   5.284577e+00   5.499762e+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:  0.286  20.479  -2.281   4.733  -0.177   0.000  -0.000  -0.000
   1_xyz:  0.286  20.479  -2.281   4.733  -0.177   0.000  -0.000  -0.000
   1_adp:  0.286  20.479  -2.281   4.733  -0.177   0.000  -0.000  -0.000
   1_occ:  0.286  20.479  -2.281   4.733  -0.177   0.000  -0.000  -0.000
   2_bss:  0.300  50.000  -1.848   2.623  -0.650   0.000  -0.000  -0.000
   2_xyz:  0.300  50.000  -1.848   2.623  -0.650   0.000  -0.000  -0.000
   2_adp:  0.300  50.000  -1.848   2.623  -0.650   0.000  -0.000  -0.000
   2_occ:  0.300  50.000  -1.848   2.623  -0.650   0.000  -0.000  -0.000
   3_bss:  0.318  60.737  -1.355   0.953  -0.829   0.000  -0.000  -0.000
   3_xyz:  0.318  60.737  -1.355   0.953  -0.829   0.000  -0.000  -0.000
   3_adp:  0.318  60.737  -1.355   0.953  -0.829   0.000  -0.000  -0.000
   3_occ:  0.318  60.737  -1.355   0.953  -0.829   0.000  -0.000  -0.000
   4_bss:  0.324  66.003  -2.007  -0.113  -1.500  -0.000  -0.000  -0.000
   4_xyz:  0.324  66.003  -2.007  -0.113  -1.500  -0.000  -0.000  -0.000
   4_adp:  0.324  66.003  -2.007  -0.113  -1.500  -0.000  -0.000  -0.000
   4_occ:  0.324  66.003  -2.007  -0.113  -1.500  -0.000  -0.000  -0.000
   5_bss:  0.327  67.603  -2.176  -0.853  -1.551  -0.000  -0.000  -0.000
   5_xyz:  0.327  67.603  -2.176  -0.853  -1.551  -0.000  -0.000  -0.000
   5_adp:  0.327  67.603  -2.176  -0.853  -1.551  -0.000  -0.000  -0.000
   5_occ:  0.327  67.603  -2.176  -0.853  -1.551  -0.000  -0.000  -0.000
   5_bss:  0.324  62.176  -2.173  -1.051  -1.480  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.924 0.5110  0.6840    61459.947
   1_bss:  50.024 0.5208  0.7125    57926.994
   1_xyz:  45.108 0.5812  0.7801    47869.351
   1_adp:  46.828 0.5591  0.7630    49911.639
   1_occ:  46.855 0.5587  0.7614    49906.974
   2_bss:  46.607 0.5618  0.7511    49590.673
   2_xyz:  36.086 0.6873  0.8950    30499.369
   2_adp:  33.882 0.7134  0.8970    27762.426
   2_occ:  33.836 0.7139  0.8968    27686.989
   3_bss:  33.618 0.7164  0.8874    27410.533
   3_xyz:  26.448 0.7959  0.9588    17885.761
   3_adp:  24.577 0.8165  0.9678    16133.789
   3_occ:  24.564 0.8166  0.9680    16125.789
   4_bss:  24.491 0.8173  0.9422    16057.982
   4_xyz:  19.342 0.8672  0.9728    10136.568
   4_adp:  18.201 0.8784  0.9710     9349.740
   4_occ:  18.203 0.8784  0.9710     9355.051
   5_bss:  18.228 0.8783  0.9607     9408.277
   5_xyz:  16.958 0.8899  0.9670     8436.217
   5_adp:  16.538 0.8939  0.9639     8209.616
   5_occ:  16.541 0.8939  0.9638     8216.905
   5_bss:  16.536 0.8939  0.9609     8208.225
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.8148e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.8148e-01
   1_xyz:   1.415  0.010  0.085 15.563  0.005  4.112   1.0476e-01
   1_adp:   1.415  0.010  0.085 15.563  0.005  4.112   1.0476e-01
   1_occ:   1.415  0.010  0.085 15.563  0.005  4.112   1.0476e-01
   2_bss:   1.415  0.010  0.085 15.563  0.005  4.112   1.0476e-01
   2_xyz:   1.495  0.011  0.097 15.609  0.006  4.116   1.3300e-01
   2_adp:   1.495  0.011  0.097 15.609  0.006  4.116   1.3300e-01
   2_occ:   1.495  0.011  0.097 15.609  0.006  4.116   1.3300e-01
   3_bss:   1.495  0.011  0.097 15.609  0.006  4.116   1.3300e-01
   3_xyz:   0.953  0.006  0.062 14.435  0.004  4.113   5.5792e-02
   3_adp:   0.953  0.006  0.062 14.435  0.004  4.113   5.5792e-02
   3_occ:   0.953  0.006  0.062 14.435  0.004  4.113   5.5792e-02
   4_bss:   0.953  0.006  0.062 14.435  0.004  4.113   5.5792e-02
   4_xyz:   1.111  0.008  0.079 14.389  0.004  4.127   6.8148e-02
   4_adp:   1.111  0.008  0.079 14.389  0.004  4.127   6.8148e-02
   4_occ:   1.111  0.008  0.079 14.389  0.004  4.127   6.8148e-02
   5_bss:   1.111  0.008  0.079 14.389  0.004  4.127   6.8148e-02
   5_xyz:   0.954  0.006  0.068 14.266  0.003  4.131   5.3986e-02
   5_adp:   0.954  0.006  0.068 14.266  0.003  4.131   5.3986e-02
   5_occ:   0.954  0.006  0.068 14.266  0.003  4.131   5.3986e-02
   5_bss:   0.954  0.006  0.068 14.266  0.003  4.131   5.3986e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.389   2.4345e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.389   2.4345e-01
   1_xyz:   9.453  0.056  0.326 85.709  0.020  2.093   9.0193e-02
   1_adp:   9.453  0.056  0.326 85.709  0.020  2.093   9.0193e-02
   1_occ:   9.453  0.056  0.326 85.709  0.020  2.093   9.0193e-02
   2_bss:   9.453  0.056  0.326 85.709  0.020  2.093   9.0193e-02
   2_xyz:   9.076  0.097  0.318 78.461  0.051  2.057   2.6993e-01
   2_adp:   9.076  0.097  0.318 78.461  0.051  2.057   2.6993e-01
   2_occ:   9.076  0.097  0.318 78.461  0.051  2.057   2.6993e-01
   3_bss:   9.076  0.097  0.318 78.461  0.051  2.057   2.6993e-01
   3_xyz:   7.509  0.044  0.228 86.019  0.021  2.268   5.2594e-02
   3_adp:   7.509  0.044  0.228 86.019  0.021  2.268   5.2594e-02
   3_occ:   7.509  0.044  0.228 86.019  0.021  2.268   5.2594e-02
   4_bss:   7.509  0.044  0.228 86.019  0.021  2.268   5.2594e-02
   4_xyz:   7.927  0.062  0.238 86.311  0.027  2.225   5.0835e-02
   4_adp:   7.927  0.062  0.238 86.311  0.027  2.225   5.0835e-02
   4_occ:   7.927  0.062  0.238 86.311  0.027  2.225   5.0835e-02
   5_bss:   7.927  0.062  0.238 86.311  0.027  2.225   5.0835e-02
   5_xyz:   7.058  0.037  0.225 82.037  0.034  2.362   3.3926e-02
   5_adp:   7.058  0.037  0.225 82.037  0.034  2.362   3.3926e-02
   5_occ:   7.058  0.037  0.225 82.037  0.034  2.362   3.3926e-02
   5_bss:   7.058  0.037  0.225 82.037  0.034  2.362   3.3926e-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:  96.83   0.00  18.99  81.31   0.00  15.84  96.83   3.38  36.18
   1_occ:  96.83   0.00  18.99  81.31   0.00  15.84  96.83   3.38  36.18
   2_bss:  96.83   0.00  18.99  81.31   0.00  15.84  96.83   3.38  36.18
   2_xyz:  96.83   0.00  18.99  81.31   0.00  15.84  96.83   3.38  36.18
   2_adp:  91.54   0.00  18.41  91.54   0.00  14.60  89.34   3.22  39.12
   2_occ:  91.54   0.00  18.41  91.54   0.00  14.60  89.34   3.22  39.12
   3_bss:  91.54   0.00  18.41  91.54   0.00  14.60  89.34   3.22  39.12
   3_xyz:  91.54   0.00  18.41  91.54   0.00  14.60  89.34   3.22  39.12
   3_adp:  90.16   0.00  17.89  87.73   0.00  13.79  90.16   4.31  40.24
   3_occ:  90.16   0.00  17.89  87.73   0.00  13.79  90.16   4.31  40.24
   4_bss:  90.16   0.00  17.89  87.73   0.00  13.79  90.16   4.31  40.24
   4_xyz:  90.16   0.00  17.89  87.73   0.00  13.79  90.16   4.31  40.24
   4_adp: 106.43   0.57  18.14 101.66   0.57  13.29 106.43   4.13  44.59
   4_occ: 106.43   0.57  18.14 101.66   0.57  13.29 106.43   4.13  44.59
   5_bss: 106.43   0.57  18.14 101.66   0.57  13.29 106.43   4.13  44.59
   5_xyz: 106.43   0.57  18.14 101.66   0.57  13.29 106.43   4.13  44.59
   5_adp: 107.58   1.48  17.44  98.45   1.48  12.89 107.58   4.90  42.18
   5_occ: 107.58   1.48  17.44  98.45   1.48  12.89 107.58   4.90  42.18
   5_bss: 107.52   1.43  17.39  98.40   1.43  12.84 107.52   4.85  42.13
------------------------------------------------------------------------
 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:    1.957    0.008    0.277
   1_adp:    1.957    0.008    0.277
   1_occ:    1.957    0.008    0.277
   2_bss:    1.957    0.008    0.277
   2_xyz:    1.663    0.034    0.607
   2_adp:    1.663    0.034    0.607
   2_occ:    1.663    0.034    0.607
   3_bss:    1.663    0.034    0.607
   3_xyz:    1.647    0.070    0.683
   3_adp:    1.647    0.070    0.683
   3_occ:    1.647    0.070    0.683
   4_bss:    1.647    0.070    0.683
   4_xyz:    1.690    0.087    0.784
   4_adp:    1.690    0.087    0.784
   4_occ:    1.690    0.087    0.784
   5_bss:    1.690    0.087    0.784
   5_xyz:    1.695    0.077    0.813
   5_adp:    1.695    0.077    0.813
   5_occ:    1.695    0.077    0.813
   5_bss:    1.695    0.077    0.813
------------------------------------------------------------------------

CPU time actual refinement: 339.66


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_959/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_959/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_959/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_959/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_959/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.50 
  Macro-tasks:
    bulk solvent and scale       = 44.27  
    individual site refinement   = 138.77 
    weights calculation          = 29.26  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 218.94 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 107.07 
    alpha_beta                      = 8.51   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 115.61 
    fmodel                         = 7.16   
    r_factors                      = 0.15   
    phase_errors                   = 10.61  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 252.95 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.820 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    636 calls, 106.75 s
gradients_fft:          581 calls, 102.52 s

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

# Date 2008-01-16 Time 06:04:56 PST -0800 (1200492296.03 s)
Start R-work = 0.4556, R-free = 0.4395 (no bulk solvent and anisotropic scale)
Final R-work = 0.1515, R-free = 0.1950 (no bulk solvent and anisotropic scale)

Start R-work = 0.4459, R-free = 0.4291
Final R-work = 0.1316, R-free = 0.1773