# Date 2008-01-16 Time 03:50:25 PST -0800 (1200484225.28 s)
#phil __OFF__

Command line arguments: "../67.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3900
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 67

-------------------------------------------------------------------------------
  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: (68.4938, 47.1647, 84.6622, 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: 3.32, per 1000 atoms: 1.18


================================== 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: (68.4938, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7379 1.95061
Completeness in resolution range: 0.953375
Completeness with d_max=infinity: 0.950415

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7379
                             d_min =   1.9506

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: (68.4938, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7379 1.95061
Completeness in resolution range: 0.953375
Completeness with d_max=infinity: 0.950415

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7384 -  4.1736 [2163/2191]  1947   216  10.0%
  bin  2:  4.1736 -  3.3252 [2066/2089]  1859   207  10.0%
  bin  3:  3.3252 -  2.9086 [2045/2070]  1840   205  10.0%
  bin  4:  2.9086 -  2.6443 [2025/2041]  1823   202  10.0%
  bin  5:  2.6443 -  2.4557 [2004/2043]  1798   206  10.3%
  bin  6:  2.4557 -  2.3115 [2006/2038]  1814   192   9.6%
  bin  7:  2.3115 -  2.1961 [1986/2023]  1785   201  10.1%
  bin  8:  2.1961 -  2.1008 [1981/2023]  1784   197   9.9%
  bin  9:  2.1008 -  2.0202 [1975/2014]  1779   196   9.9%
  bin 10:  2.0202 -  1.9506 [1338/2015]  1201   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_67/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:
        1.12 -     1.87: 17
        1.87 -     2.63: 116
        2.63 -     3.39: 4385
        3.39 -     4.14: 9581
        4.14 -     4.90: 14846
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.117 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.196 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.208 3.040 -x+1,y-1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.493 3.270 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.494 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 28940 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_67/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_67/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.16465 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4329   r_free= 0.4354   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.233422                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7384 -  4.6549 0.99   1399  158 0.3483 0.3532       6.507      6.5549|
|  2:  4.6549 -  3.7142 0.99   1349  148 0.3619 0.3472      6.7003      6.7081|
|  3:  3.7142 -  3.2505 0.99   1321  149 0.3799 0.3896      6.5868      6.7118|
|  4:  3.2505 -  2.9559 0.99   1319  136 0.4106 0.4408      6.4462      6.4694|
|  5:  2.9559 -  2.7455 0.98   1298  147 0.4460 0.4297      6.3139      6.3089|
|  6:  2.7455 -  2.5845 0.99   1292  144 0.4606 0.4765      6.2258      6.1554|
|  7:  2.5845 -  2.4557 0.99   1289  154 0.4666 0.4348      6.2224      6.1587|
|  8:  2.4557 -  2.3493 0.99   1309  133 0.4752 0.4809      6.1467      6.1583|
|  9:  2.3493 -  2.2591 0.99   1273  148 0.4994 0.4910      6.0949      6.1404|
| 10:  2.2591 -  2.1814 0.98   1273  139 0.4860 0.5431      6.0864      6.0991|
| 11:  2.1814 -  2.1134 0.98   1276  147 0.5032 0.5128      6.0125      6.0708|
| 12:  2.1134 -  2.0532 1.00   1285  141 0.4914 0.4940      5.9498      5.9813|
| 13:  2.0532 -  1.9993 0.96   1269  132 0.4974 0.5028      5.8787      5.8618|
| 14:  1.9993 -  1.9506 0.54    678   83 0.5295 0.5071      5.8397      5.7351|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7384 -  4.6549  1399   158  0.71  33.27   0.85     0.72      64277.75|
|  2:  4.6549 -  3.7142  1349   148  0.72  33.64   0.94     0.83      94070.31|
|  3:  3.7142 -  3.2505  1321   149  0.65  39.96   0.97     0.85      99487.71|
|  4:  3.2505 -  2.9559  1319   136  0.57  46.09   0.97     0.80      86993.36|
|  5:  2.9559 -  2.7455  1298   147  0.52  50.17   0.92     0.75      68225.52|
|  6:  2.7455 -  2.5845  1292   144  0.49  52.75   0.92     0.70      58902.16|
|  7:  2.5845 -  2.4557  1289   154  0.50  52.17   0.93     0.68      54211.92|
|  8:  2.4557 -  2.3493  1309   133  0.45  55.77   0.96     0.66      51164.01|
|  9:  2.3493 -  2.2591  1273   148  0.42  58.26   0.94     0.63      48367.57|
| 10:  2.2591 -  2.1814  1273   139  0.42  58.43   1.00     0.61      44985.97|
| 11:  2.1814 -  2.1134  1276   147  0.39  60.97   0.97     0.59      42631.31|
| 12:  2.1134 -  2.0532  1285   141  0.38  61.26   0.99     0.61      40201.79|
| 13:  2.0532 -  1.9993  1269   132  0.36  63.23   0.99     0.56      35688.94|
| 14:  1.9993 -  1.9506   678    83  0.35  63.74   0.93     0.49      28340.97|
|alpha:            min =        0.49 max =            0.85 mean =         0.68|
|beta:             min =    28340.97 max =        99487.71 mean =     59779.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.48|
|phase err.(test): min =        0.00 max =           89.98 mean =        51.34|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.039569             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.075   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.963363              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.045   (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 |  1.117 -  1.495:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.495 -  1.873:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.873 -  2.252:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.252 -  2.630:       79 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.630 -  3.008:     1991 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.008 -  3.387:     2394 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.387 -  3.765:     4006 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.765 -  4.143:     5575 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.143 -  4.522:     6614 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.522 -  4.900:     8232 |
|-----------------------------------------------------------------------------|
|-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 |        0.245 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.117 |       1.444 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4329   r_free= 0.4354   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.233422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4242   r_free= 0.4247   ksol= 0.30   Bsol= 20.00   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.43,-2.35,1.75,-0.00,0.00,0.00); trace/3= -0.05                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.224692                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.743516             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.889   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.947013              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.776   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4242      final r-factor (work) = 0.2586          |
| start r-factor (free) = 0.4247      final r-factor (free) = 0.2808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.8010 = 11.74 * 0.50 * 6.2258 + 1.00 * 0.2445                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.5864 = 11.74 * 0.50 * 6.0384 + 1.00 * 0.1306                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2586      final r-factor (work) = 0.2326          |
| start r-factor (free) = 0.2808      final r-factor (free) = 0.2882          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7247 = 0.95 * 1.00 * 6.0384 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4663 = 0.95 * 1.00 * 5.7570 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.74   18.73    None  None   None       |
|    all(noH): 2823   0      0.00    97.74   18.73    None  None   None       |
|    Sol.    : 438    0      4.65    97.74   42.97    None  None   None       |
|    Mac.    : 2385   0      0.00    88.63   14.27    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 -   9.774:  941   |   5:    48.869 -  58.643:  105        |
|      1:     9.774 -  19.548: 1017   |   6:    58.643 -  68.416:   58        |
|      2:    19.548 -  29.321:  337   |   7:    68.416 -  78.190:   33        |
|      3:    29.321 -  39.095:  173   |   8:    78.190 -  87.964:    9        |
|      4:    39.095 -  48.869:  147   |   9:    87.964 -  97.737:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2326 r_free = 0.2882             target_work(ml) = 5.768         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2324 r_free = 0.2879             target_work(ml) = 5.768         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2324   r_free= 0.2879   ksol= 0.30   Bsol= 20.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.43,-2.35,1.75,-0.00,0.00,0.00); trace/3= -0.05                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.767600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2265   r_free= 0.2832   ksol= 0.31   Bsol= 30.07   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-0.72,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.753880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.913123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.469   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.288146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.166  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2265      final r-factor (work) = 0.1651          |
| start r-factor (free) = 0.2832      final r-factor (free) = 0.2142          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4006 = 3.91 * 0.50 * 5.7602 + 1.00 * 0.1304                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0804 = 3.91 * 0.50 * 5.6310 + 1.00 * 0.0630                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1651      final r-factor (work) = 0.1505          |
| start r-factor (free) = 0.2142      final r-factor (free) = 0.1994          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6369 = 0.29 * 1.00 * 5.6310 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5744 = 0.29 * 1.00 * 5.4331 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.28   17.89    None  None   None       |
|    all(noH): 2823   0      0.00    93.28   17.89    None  None   None       |
|    Sol.    : 438    0      6.90    85.99   41.36    None  None   None       |
|    Mac.    : 2385   0      0.00    93.28   13.58    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 -   9.328:  837   |   5:    46.638 -  55.966:  115        |
|      1:     9.328 -  18.655: 1221   |   6:    55.966 -  65.293:   54        |
|      2:    18.655 -  27.983:  278   |   7:    65.293 -  74.621:   25        |
|      3:    27.983 -  37.311:  143   |   8:    74.621 -  83.949:   14        |
|      4:    37.311 -  46.638:  134   |   9:    83.949 -  93.276:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1505 r_free = 0.1994             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1502 r_free = 0.1993             target_work(ml) = 5.387         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1502   r_free= 0.1993   ksol= 0.31   Bsol= 30.07   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-0.72,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.387127                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1498   r_free= 0.1971   ksol= 0.31   Bsol= 31.62   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.13,-1.59,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.382083                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.720900              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.620  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514252              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.393  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1498      final r-factor (work) = 0.1240          |
| start r-factor (free) = 0.1971      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4544 = 2.72 * 0.50 * 5.4331 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2739 = 2.72 * 0.50 * 5.3021 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1240      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7355 = 0.51 * 1.00 * 5.3021 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6855 = 0.51 * 1.00 * 5.2041 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.87  17.80    None  None   None       |
|    all(noH): 2823   0      0.00    100.87  17.80    None  None   None       |
|    Sol.    : 438    0      1.29    90.68   42.16    None  None   None       |
|    Mac.    : 2385   0      0.00    100.87  13.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.087:  995   |   5:    50.433 -  60.519:   98        |
|      1:    10.087 -  20.173: 1179   |   6:    60.519 -  70.606:   43        |
|      2:    20.173 -  30.260:  214   |   7:    70.606 -  80.692:   20        |
|      3:    30.260 -  40.346:  126   |   8:    80.692 -  90.779:    8        |
|      4:    40.346 -  50.433:  139   |   9:    90.779 - 100.865:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1664             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1663             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1663   ksol= 0.31   Bsol= 31.62   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.13,-1.59,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1661   ksol= 0.31   Bsol= 33.60   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.15,-1.84,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193550                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.381670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.049  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.197844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.941  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6570 = 1.38 * 0.50 * 5.2058 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6324 = 1.38 * 0.50 * 5.1862 + 1.00 * 0.0496                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0353 = 0.20 * 1.00 * 5.1862 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0328 = 0.20 * 1.00 * 5.1815 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.33    100.15  17.19    None  None   None       |
|    all(noH): 2823   0      2.33    100.15  17.19    None  None   None       |
|    Sol.    : 438    0      2.33    89.13   39.56    None  None   None       |
|    Mac.    : 2385   0      2.47    100.15  13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.330 -  12.113: 1453   |   5:    51.242 -  61.025:   82        |
|      1:    12.113 -  21.895:  801   |   6:    61.025 -  70.807:   16        |
|      2:    21.895 -  31.678:  178   |   7:    70.807 -  80.589:   13        |
|      3:    31.678 -  41.460:  133   |   8:    80.589 -  90.372:    4        |
|      4:    41.460 -  51.242:  142   |   9:    90.372 - 100.154:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1633             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1632             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1632   ksol= 0.31   Bsol= 33.60   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.15,-1.84,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1632   ksol= 0.32   Bsol= 33.84   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.04,-1.80,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175766                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.146812              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.020  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.179620              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.236  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6112 = 2.15 * 0.50 * 5.1812 + 1.00 * 0.0496                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5904 = 2.15 * 0.50 * 5.1515 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9330 = 0.18 * 1.00 * 5.1515 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9301 = 0.18 * 1.00 * 5.1380 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.29    99.18   16.93    None  None   None       |
|    all(noH): 2823   0      2.29    99.18   16.93    None  None   None       |
|    Sol.    : 438    0      4.03    88.78   38.58    None  None   None       |
|    Mac.    : 2385   0      2.29    99.18   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.291 -  11.979: 1446   |   5:    50.733 -  60.421:   77        |
|      1:    11.979 -  21.668:  821   |   6:    60.421 -  70.110:   16        |
|      2:    21.668 -  31.356:  166   |   7:    70.110 -  79.798:   11        |
|      3:    31.356 -  41.045:  144   |   8:    79.798 -  89.487:    5        |
|      4:    41.045 -  50.733:  136   |   9:    89.487 -  99.175:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1590             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1589             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1589   ksol= 0.32   Bsol= 33.84   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.04,-1.80,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135730                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7384 -  4.6549 0.99   1399  158 0.0983 0.1311      5.3734      5.5627|
|  2:  4.6549 -  3.7142 0.99   1349  148 0.0834 0.1101      5.4186      5.6082|
|  3:  3.7142 -  3.2505 0.99   1321  149 0.1021 0.1512      5.4446       5.812|
|  4:  3.2505 -  2.9559 0.99   1319  136 0.1189 0.1622      5.4336      5.6333|
|  5:  2.9559 -  2.7455 0.98   1298  147 0.1273 0.1623      5.3017      5.4588|
|  6:  2.7455 -  2.5845 0.99   1292  144 0.1255 0.1933      5.2133       5.457|
|  7:  2.5845 -  2.4557 0.99   1289  154 0.1151 0.1661      5.1253      5.3738|
|  8:  2.4557 -  2.3493 0.99   1309  133 0.1173 0.1716      5.0738      5.3123|
|  9:  2.3493 -  2.2591 0.99   1273  148 0.1185 0.1898      5.0276      5.3227|
| 10:  2.2591 -  2.1814 0.98   1273  139 0.1120 0.1807      4.9718      5.1856|
| 11:  2.1814 -  2.1134 0.98   1276  147 0.1119 0.1742      4.9214      5.2449|
| 12:  2.1134 -  2.0532 1.00   1285  141 0.1081 0.1669      4.8365      5.1279|
| 13:  2.0532 -  1.9993 0.96   1269  132 0.1127 0.1746       4.786       5.039|
| 14:  1.9993 -  1.9506 0.54    678   83 0.1111 0.1709      4.7107       4.911|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7384 -  4.6549  1399   158  0.94   9.02   0.99     0.97       7020.87|
|  2:  4.6549 -  3.7142  1349   148  0.95   7.85   1.03     1.02       8798.69|
|  3:  3.7142 -  3.2505  1321   149  0.94  10.74   1.04     1.03       9798.11|
|  4:  3.2505 -  2.9559  1319   136  0.92  13.21   1.02     1.02       9954.69|
|  5:  2.9559 -  2.7455  1298   147  0.90  15.57   1.00     0.97       7905.79|
|  6:  2.7455 -  2.5845  1292   144  0.90  16.03   0.98     0.95       6916.13|
|  7:  2.5845 -  2.4557  1289   154  0.91  14.79   0.99     0.96       5791.07|
|  8:  2.4557 -  2.3493  1309   133  0.91  15.03   1.01     1.00       5431.98|
|  9:  2.3493 -  2.2591  1273   148  0.90  15.87   1.01     0.98       4967.65|
| 10:  2.2591 -  2.1814  1273   139  0.90  15.72   1.01     0.98       4572.45|
| 11:  2.1814 -  2.1134  1276   147  0.91  15.75   1.01     0.97       4234.88|
| 12:  2.1134 -  2.0532  1285   141  0.91  14.94   1.02     1.01       3659.73|
| 13:  2.0532 -  1.9993  1269   132  0.90  15.88   1.02     1.01       3289.04|
| 14:  1.9993 -  1.9506   678    83  0.91  15.14   1.00     0.96       2719.09|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2719.09 max =         9954.69 mean =      6228.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.78 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.24 mean =        13.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1589   ksol= 0.32   Bsol= 35.78   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.94,-1.67,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135748                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1589   ksol= 0.32   Bsol= 35.78   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.94,-1.67,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135748                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7384 -  4.6549 0.99   1399  158 0.0984 0.1319      5.3769      5.5669|
|  2:  4.6549 -  3.7142 0.99   1349  148 0.0834 0.1102      5.4201      5.6085|
|  3:  3.7142 -  3.2505 0.99   1321  149 0.1021 0.1512      5.4449      5.8125|
|  4:  3.2505 -  2.9559 0.99   1319  136 0.1189 0.1621      5.4336      5.6329|
|  5:  2.9559 -  2.7455 0.98   1298  147 0.1273 0.1623      5.3014      5.4591|
|  6:  2.7455 -  2.5845 0.99   1292  144 0.1255 0.1930      5.2128      5.4556|
|  7:  2.5845 -  2.4557 0.99   1289  154 0.1151 0.1660      5.1244       5.373|
|  8:  2.4557 -  2.3493 0.99   1309  133 0.1172 0.1715      5.0728      5.3106|
|  9:  2.3493 -  2.2591 0.99   1273  148 0.1185 0.1899      5.0269       5.323|
| 10:  2.2591 -  2.1814 0.98   1273  139 0.1119 0.1807      4.9715      5.1851|
| 11:  2.1814 -  2.1134 0.98   1276  147 0.1118 0.1742       4.921       5.245|
| 12:  2.1134 -  2.0532 1.00   1285  141 0.1080 0.1668      4.8361      5.1275|
| 13:  2.0532 -  1.9993 0.96   1269  132 0.1127 0.1746      4.7857      5.0389|
| 14:  1.9993 -  1.9506 0.54    678   83 0.1110 0.1707      4.7097      4.9102|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7384 -  4.6549  1399   158  0.94   9.07   0.99     0.97       7108.15|
|  2:  4.6549 -  3.7142  1349   148  0.95   7.89   1.03     1.02       8842.96|
|  3:  3.7142 -  3.2505  1321   149  0.94  10.74   1.04     1.03       9798.83|
|  4:  3.2505 -  2.9559  1319   136  0.92  13.22   1.02     1.02       9956.35|
|  5:  2.9559 -  2.7455  1298   147  0.90  15.57   1.00     0.97       7899.72|
|  6:  2.7455 -  2.5845  1292   144  0.90  16.02   0.98     0.95       6909.53|
|  7:  2.5845 -  2.4557  1289   154  0.91  14.75   0.99     0.96       5776.94|
|  8:  2.4557 -  2.3493  1309   133  0.91  15.00   1.01     1.00       5420.09|
|  9:  2.3493 -  2.2591  1273   148  0.90  15.85   1.01     0.98       4959.65|
| 10:  2.2591 -  2.1814  1273   139  0.90  15.72   1.01     0.98       4570.79|
| 11:  2.1814 -  2.1134  1276   147  0.91  15.75   1.01     0.97       4231.80|
| 12:  2.1134 -  2.0532  1285   141  0.91  14.93   1.02     1.01       3658.14|
| 13:  2.0532 -  1.9993  1269   132  0.90  15.87   1.02     1.02       3286.03|
| 14:  1.9993 -  1.9506   678    83  0.91  15.13   1.00     0.96       2713.75|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2713.75 max =         9956.35 mean =      6234.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.16 mean =        13.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.21    99.09   16.84    None  None   None       |
|    all(noH): 2823   0      2.21    99.09   16.84    None  None   None       |
|    Sol.    : 438    0      3.95    88.70   38.49    None  None   None       |
|    Mac.    : 2385   0      2.21    99.09   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.208 -  11.896: 1446   |   5:    50.650 -  60.339:   77        |
|      1:    11.896 -  21.585:  821   |   6:    60.339 -  70.027:   16        |
|      2:    21.585 -  31.273:  166   |   7:    70.027 -  79.715:   11        |
|      3:    31.273 -  40.962:  144   |   8:    79.715 -  89.404:    5        |
|      4:    40.962 -  50.650:  136   |   9:    89.404 -  99.092:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.648 - 4.478
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 300
   mapped sites are within: 0.713 - 4.478

peak=    8.219 closest distance to " O   HOH Z  92 " =    1.879
peak=    6.460 closest distance to " O   HOH Z 178 " =    0.990
peak=    5.727 closest distance to " CB  ASN A 187 " =    1.910
peak=    5.647 closest distance to " O   HOH Z 142 " =    1.696
peak=    5.455 closest distance to " NH2 ARG A  56 " =    2.081
peak=    5.403 closest distance to " O   HOH Z 193 " =    1.853
peak=    5.354 closest distance to " O   HOH Z  52 " =    1.648
peak=    5.289 closest distance to " CB  ARG A 275 " =    0.971
peak=    5.276 closest distance to " O   HOH Z 124 " =    1.488
peak=    5.220 closest distance to " NE2 GLN A  11 " =    1.103
peak=    5.157 closest distance to " CB  SER A  63 " =    1.103
peak=    5.020 closest distance to " C   PRO A 198 " =    1.577
peak=    5.010 closest distance to " O   HOH Z 401 " =    1.200
peak=    4.852 closest distance to " O   HOH Z 132 " =    1.326
peak=    4.826 closest distance to " CG  PRO A 213 " =    1.303
peak=    4.815 closest distance to " CG  PRO A  54 " =    1.235
peak=    4.793 closest distance to " O   HOH Z 272 " =    1.811
peak=    4.775 closest distance to " CB  GLN A 183 " =    1.302
peak=    4.755 closest distance to " O   HOH Z  97 " =    2.368
peak=    4.719 closest distance to " O   HOH Z 234 " =    3.578
peak=    4.619 closest distance to " O   HOH Z  54 " =    1.684
peak=    4.619 closest distance to " O   HOH Z  97 " =    1.894
peak=    4.612 closest distance to " O   HOH Z 232 " =    2.309
peak=    4.612 closest distance to " O   HOH Z 416 " =    1.043
peak=    4.606 closest distance to " O   HOH Z 403 " =    1.894
peak=    4.554 closest distance to " CB  ASN A 148 " =    1.749
peak=    4.543 closest distance to " O   HOH Z 209 " =    2.313
peak=    4.537 closest distance to " O   HOH Z 298 " =    1.843
peak=    4.474 closest distance to " CB  GLU A 152 " =    1.183
peak=    4.460 closest distance to " O   SER A  87 " =    2.304
peak=    4.458 closest distance to " O   HOH Z 402 " =    1.487
peak=    4.405 closest distance to " ND2 ASN A 187 " =    1.455
peak=    4.400 closest distance to " O   HOH Z 327 " =    1.822
peak=    4.388 closest distance to " CB  GLN A 223 " =    1.449
peak=    4.381 closest distance to " O   HOH Z 346 " =    1.624
peak=    4.357 closest distance to " O   HOH Z  78 " =    1.763
peak=    4.345 closest distance to " CA  TYR A  30 " =    0.968
peak=    4.316 closest distance to " O   HOH Z 368 " =    1.976
peak=    4.263 closest distance to " CG  GLN A  77 " =    2.095
peak=    4.250 closest distance to " NZ  LYS A 117 " =    3.087
peak=    4.240 closest distance to " NZ  LYS A 119 " =    1.727
peak=    4.197 closest distance to " CG1 ILE A  33 " =    1.244
peak=    4.192 closest distance to " O   HOH Z 236 " =    1.960
peak=    4.189 closest distance to " O   HOH Z 207 " =    1.812
peak=    4.179 closest distance to " O   HOH Z   6 " =    2.251
peak=    4.169 closest distance to " O   HOH Z 128 " =    1.890
peak=    4.168 closest distance to " O   HOH Z 389 " =    1.889
peak=    4.155 closest distance to " CB  ARG A  79 " =    1.379
peak=    4.155 closest distance to " O   HOH Z 427 " =    2.716
peak=    4.141 closest distance to " CA  ALA A  21 " =    1.119
peak=    4.117 closest distance to " CG  PRO A  90 " =    1.288
peak=    4.092 closest distance to " CD2 TRP A 179 " =    1.392
peak=    4.087 closest distance to " O   HOH Z 128 " =    2.062
peak=    4.072 closest distance to " O   HOH Z 134 " =    1.495
peak=    4.058 closest distance to " O   HOH Z 426 " =    1.520
peak=    4.038 closest distance to " N   ASN A  39 " =    1.245
peak=    4.031 closest distance to " O   HOH Z 278 " =    1.076
peak=    4.027 closest distance to " CB  SER A   3 " =    1.210
peak=    4.008 closest distance to " O   HOH Z 365 " =    2.759
peak=    4.005 closest distance to " NH2BARG A 145 " =    2.055
peak=    4.001 closest distance to " O   HOH Z  85 " =    1.535
peak=    3.995 closest distance to " O   HOH Z 380 " =    1.970
peak=    3.987 closest distance to " CG  PRO A 243 " =    1.188
peak=    3.956 closest distance to " O   HOH Z 408 " =    1.641
peak=    3.953 closest distance to " CB  TYR A 169 " =    0.713
peak=    3.945 closest distance to " O   HOH Z 334 " =    1.380
peak=    3.944 closest distance to " O   HOH Z  92 " =    1.091
peak=    3.931 closest distance to " O   HOH Z  63 " =    1.957
peak=    3.924 closest distance to " OD2 ASP A 286 " =    2.630
peak=    3.924 closest distance to " O   HOH Z 303 " =    2.068
peak=    3.902 closest distance to " O   HOH Z  44 " =    1.981
peak=    3.877 closest distance to " CB  VAL A 265 " =    1.288
peak=    3.873 closest distance to " CG  ARG A  66 " =    1.048
peak=    3.870 closest distance to " O   HOH Z  59 " =    2.258
peak=    3.870 closest distance to " O   HOH Z 345 " =    2.655
peak=    3.867 closest distance to " O   HOH Z 250 " =    1.472
peak=    3.852 closest distance to " O   HOH Z 411 " =    3.643
peak=    3.851 closest distance to " CD  ARG A 269 " =    1.065
peak=    3.849 closest distance to " CE  LYS A 119 " =    1.170
peak=    3.848 closest distance to " O   HOH Z  15 " =    2.140
peak=    3.845 closest distance to " O   HOH Z 173 " =    2.005
peak=    3.841 closest distance to " O   HOH Z  78 " =    2.437
peak=    3.840 closest distance to " O   HOH Z 315 " =    1.845
peak=    3.836 closest distance to " O   HOH Z  47 " =    1.590
peak=    3.833 closest distance to " O   HOH Z 425 " =    1.362
peak=    3.829 closest distance to " O  BHOH Z  74 " =    1.363
peak=    3.819 closest distance to " O   HOH Z 392 " =    2.470
peak=    3.817 closest distance to " O   HOH Z 380 " =    2.001
peak=    3.816 closest distance to " O   HOH Z 130 " =    2.786
peak=    3.810 closest distance to " CB  SER A  26 " =    1.612
peak=    3.805 closest distance to " CB  GLU A 128 " =    1.147
peak=    3.802 closest distance to " O   HOH Z 203 " =    1.711
peak=    3.801 closest distance to " O   HOH Z 227 " =    1.597
peak=    3.798 closest distance to " O   HOH Z  10 " =    1.801
peak=    3.797 closest distance to " CB  LEU A 228 " =    1.140
peak=    3.796 closest distance to " CG AARG A 275 " =    1.115
peak=    3.795 closest distance to " O   HOH Z  49 " =    2.164
peak=    3.791 closest distance to " O   HOH Z 427 " =    3.055
peak=    3.790 closest distance to " O   HOH Z 416 " =    2.978
peak=    3.789 closest distance to " CA  ASN A 176 " =    1.062
peak=    3.786 closest distance to " OG BSER A 164 " =    2.376
peak=    3.776 closest distance to " O   HOH Z 260 " =    1.180
peak=    3.754 closest distance to " O   HOH Z 316 " =    2.916
peak=    3.752 closest distance to " C   ALA A   1 " =    1.584
peak=    3.743 closest distance to " O   MET A 105 " =    1.902
peak=    3.736 closest distance to " O   HOH Z 279 " =    2.077
peak=    3.736 closest distance to " O   HOH Z 144 " =    2.016
peak=    3.734 closest distance to " O   HOH Z 245 " =    1.389
peak=    3.724 closest distance to " O   HOH Z 406 " =    1.666
peak=    3.724 closest distance to " O   HOH Z  43 " =    2.096
peak=    3.723 closest distance to " O   HOH Z 421 " =    1.580
peak=    3.713 closest distance to " O   HOH Z 286 " =    2.149
peak=    3.706 closest distance to " O   HOH Z 344 " =    2.728
peak=    3.694 closest distance to " O   HOH Z 423 " =    1.973
peak=    3.685 closest distance to " OD1 ASP A 253 " =    1.899
peak=    3.683 closest distance to " O   HOH Z 299 " =    2.288
peak=    3.681 closest distance to " O   HOH Z 369 " =    2.258
peak=    3.676 closest distance to " O   HOH Z 261 " =    1.732
peak=    3.672 closest distance to " CB  ASN A  39 " =    0.802
peak=    3.667 closest distance to " O   HOH Z  61 " =    1.540
peak=    3.662 closest distance to " CB  VAL A 202 " =    1.602
peak=    3.647 closest distance to " CG  PRO A 198 " =    1.236
peak=    3.642 closest distance to " O   HOH Z 180 " =    2.210
peak=    3.641 closest distance to " O   HOH Z  80 " =    1.697
peak=    3.640 closest distance to " O   HOH Z 326 " =    1.514
peak=    3.634 closest distance to " CB  PRO A  54 " =    0.912
peak=    3.633 closest distance to " O   HOH Z 118 " =    1.309
peak=    3.629 closest distance to " CA  ALA A  84 " =    1.223
peak=    3.629 closest distance to " CB  TRP A 179 " =    1.065
peak=    3.619 closest distance to " O   HOH Z 214 " =    2.280
peak=    3.618 closest distance to " O   HOH Z 425 " =    1.930
peak=    3.611 closest distance to " O   HOH Z  66 " =    2.170
peak=    3.611 closest distance to " O   HOH Z 251 " =    1.612
peak=    3.568 closest distance to " CB  THR A  31 " =    1.784
peak=    3.566 closest distance to " O   ALA A 165 " =    1.399
peak=    3.564 closest distance to " CG2 ILE A  20 " =    1.429
peak=    3.560 closest distance to " O   HOH Z 183 " =    1.631
peak=    3.558 closest distance to " CB  TYR A 169 " =    0.739
peak=    3.555 closest distance to " CB  GLU A 277 " =    3.490
peak=    3.550 closest distance to " N   ASP A 162 " =    1.195
peak=    3.545 closest distance to " CA  MET A  40 " =    1.082
peak=    3.544 closest distance to " CB  TRP A 266 " =    1.107
peak=    3.541 closest distance to " O   HOH Z 118 " =    1.096
peak=    3.537 closest distance to " NH2AARG A 190 " =    1.288
peak=    3.534 closest distance to " O   HOH Z 108 " =    2.224
peak=    3.533 closest distance to " O   HOH Z   1 " =    1.951
peak=    3.522 closest distance to " CA  GLY A  80 " =    0.730
peak=    3.519 closest distance to " CG  MET A 185 " =    1.185
peak=    3.517 closest distance to " O   HOH Z  95 " =    1.559
peak=    3.512 closest distance to " O   HOH Z 236 " =    1.388
peak=    3.512 closest distance to " O   HOH Z  19 " =    1.787
peak=    3.507 closest distance to " O   HOH Z 284 " =    2.805
peak=    3.507 closest distance to " O   HOH Z  88 " =    2.813
peak=    3.506 closest distance to " OG  SER A  62 " =    2.816
peak=    3.498 closest distance to " O   HOH Z  35 " =    2.441
peak=    3.498 closest distance to " CA  THR A 221 " =    0.990
peak=    3.491 closest distance to " O   HOH Z 108 " =    1.046
peak=    3.490 closest distance to " CB  ALA A   1 " =    1.180
peak=    3.484 closest distance to " O   HOH Z 255 " =    1.738
peak=    3.480 closest distance to " CD  GLN A 194 " =    1.473
peak=    3.474 closest distance to " O   HOH Z 257 " =    2.092
peak=    3.473 closest distance to " CA  ALA A 248 " =    1.418
peak=    3.470 closest distance to " CE BLYS A 290 " =    1.017
peak=    3.468 closest distance to " O   HOH Z  40 " =    1.506
peak=    3.465 closest distance to " O   HOH Z 106 " =    2.429
peak=    3.465 closest distance to " O   HOH Z 194 " =    1.946
peak=    3.463 closest distance to " CG2BVAL A  41 " =    0.781
peak=    3.462 closest distance to " O   HOH Z 172 " =    3.916
peak=    3.457 closest distance to " CG2 ILE A 120 " =    1.196
peak=    3.455 closest distance to " CG  GLU A 277 " =    2.246
peak=    3.450 closest distance to " O   HOH Z 111 " =    1.570
peak=    3.445 closest distance to " CA  ALA A 291 " =    0.884
peak=    3.443 closest distance to " O   HOH Z 313 " =    1.636
peak=    3.440 closest distance to " CB  ALA A 291 " =    1.228
peak=    3.432 closest distance to " CA  ASN A 215 " =    1.138
peak=    3.431 closest distance to " N   ASN A 127 " =    1.255
peak=    3.431 closest distance to " CA  ASP A 140 " =    1.085
peak=    3.429 closest distance to " CB  ARG A 190 " =    1.762
peak=    3.428 closest distance to " O   GLY A  91 " =    1.523
peak=    3.418 closest distance to " CA  SER A 146 " =    1.902
peak=    3.418 closest distance to " CB  ARG A 139 " =    1.041
peak=    3.415 closest distance to " CD2 LEU A 297 " =    0.951
peak=    3.409 closest distance to " CB  SER A 141 " =    1.116
peak=    3.408 closest distance to " O   HOH Z 291 " =    1.655
peak=    3.407 closest distance to " O   HOH Z 156 " =    3.207
peak=    3.407 closest distance to " CG1BVAL A  72 " =    1.530
peak=    3.402 closest distance to " CA  LYS A 117 " =    1.246
peak=    3.393 closest distance to " O   HOH Z  94 " =    2.012
peak=    3.391 closest distance to " O   HOH Z 299 " =    4.159
peak=    3.386 closest distance to " O   HOH Z  71 " =    1.364
peak=    3.385 closest distance to " CD  ARG A 139 " =    1.524
peak=    3.379 closest distance to " OG  SER A  62 " =    3.523
peak=    3.378 closest distance to " CZ2 TRP A 179 " =    1.790
peak=    3.376 closest distance to " O   HOH Z  89 " =    2.189
peak=    3.366 closest distance to " CA  ALA A 233 " =    1.192
peak=    3.365 closest distance to " O   HOH Z 273 " =    2.696
peak=    3.364 closest distance to " CB  SER A  62 " =    1.037
peak=    3.362 closest distance to " O   HOH Z 357 " =    1.755
peak=    3.355 closest distance to " O   HOH Z 214 " =    2.254
peak=    3.351 closest distance to " N   ARG A 156 " =    1.360
peak=    3.347 closest distance to " O   HOH Z 261 " =    1.986
peak=    3.332 closest distance to " O   HOH Z  88 " =    2.579
peak=    3.330 closest distance to " O   HOH Z 359 " =    1.475
peak=    3.324 closest distance to " CA  ASP A 162 " =    1.084
peak=    3.323 closest distance to " O   HOH Z 132 " =    2.321
peak=    3.322 closest distance to " CB  GLU A  46 " =    1.024
peak=    3.320 closest distance to " O   HOH Z  71 " =    1.562
peak=    3.318 closest distance to " O   HOH Z 189 " =    1.527
peak=    3.317 closest distance to " NE2 GLN A 223 " =    1.897
peak=    3.316 closest distance to " O   HOH Z   9 " =    2.050
peak=    3.308 closest distance to " O   HOH Z 371 " =    2.490
peak=    3.306 closest distance to " CA  ALA A  51 " =    0.844
peak=    3.296 closest distance to " O   HOH Z 305 " =    3.588
peak=    3.296 closest distance to " CB  PRO A 163 " =    3.868
peak=    3.294 closest distance to " CG  LYS A 119 " =    1.179
peak=    3.294 closest distance to " CB  SER A  62 " =    1.410
peak=    3.288 closest distance to " CG2 THR A 294 " =    1.555
peak=    3.284 closest distance to " O   HOH Z  85 " =    2.355
peak=    3.281 closest distance to " CB  ASN A  45 " =    1.054
peak=    3.278 closest distance to " O   HOH Z 374 " =    2.428
peak=    3.278 closest distance to " CG  LYS A 166 " =    1.631
peak=    3.276 closest distance to " CG  MET A 185 " =    0.979
peak=    3.276 closest distance to " O   HOH Z   3 " =    1.723
peak=    3.272 closest distance to " O   HOH Z 394 " =    1.714
peak=    3.270 closest distance to " OD1 ASN A  69 " =    2.656
peak=    3.269 closest distance to " NH1 ARG A  66 " =    1.707
peak=    3.269 closest distance to " O   HOH Z 163 " =    1.415
peak=    3.266 closest distance to " CG1 ILE A 120 " =    1.235
peak=    3.266 closest distance to " O   HOH Z 132 " =    2.166
peak=    3.266 closest distance to " CB  ILE A 120 " =    1.310
peak=    3.265 closest distance to " CG2 THR A 221 " =    1.092
peak=    3.261 closest distance to " O   HOH Z 125 " =    2.463
peak=    3.260 closest distance to " CG  LYS A  76 " =    1.053
peak=    3.258 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.256 closest distance to " OG1 THR A 294 " =    2.306
peak=    3.252 closest distance to " O   HOH Z 147 " =    1.751
peak=    3.236 closest distance to " O   HOH Z 342 " =    0.880
peak=    3.233 closest distance to " N   TRP A 150 " =    1.601
peak=    3.233 closest distance to " O   HOH Z 106 " =    2.322
peak=    3.231 closest distance to " O   HOH Z 337 " =    3.296
peak=    3.229 closest distance to " O   HOH Z 353 " =    2.575
peak=    3.227 closest distance to " CG2 VAL A 257 " =    0.867
peak=    3.227 closest distance to " CA  THR A 264 " =    0.827
peak=    3.222 closest distance to " O   HOH Z 119 " =    4.478
peak=    3.220 closest distance to " NH1BARG A 145 " =    1.292
peak=    3.216 closest distance to " OD1 ASP A 238 " =    1.104
peak=    3.214 closest distance to " CD BLYS A 290 " =    1.155
peak=    3.214 closest distance to " O   HOH Z 381 " =    1.539
peak=    3.212 closest distance to " O   HOH Z 145 " =    2.306
peak=    3.208 closest distance to " CA  ASN A 217 " =    1.280
peak=    3.201 closest distance to " O   HOH Z 391 " =    2.207
peak=    3.196 closest distance to " NZ  LYS A  76 " =    1.822
peak=    3.194 closest distance to " N   CYS A 260 " =    0.774
peak=    3.193 closest distance to " O   HOH Z 428 " =    3.778
peak=    3.192 closest distance to " O   HOH Z  30 " =    2.129
peak=    3.191 closest distance to " O   HOH Z 194 " =    1.884
peak=    3.189 closest distance to " O   HOH Z  63 " =    1.950
peak=    3.188 closest distance to " CB  TYR A  30 " =    1.442
peak=    3.185 closest distance to " CZ2 TRP A 274 " =    1.622
peak=    3.184 closest distance to " O   HOH Z 361 " =    3.521
peak=    3.183 closest distance to " O   HOH Z  85 " =    2.146
peak=    3.183 closest distance to " O   HOH Z  39 " =    2.551
peak=    3.183 closest distance to " O   HOH Z 417 " =    3.080
peak=    3.178 closest distance to " O   HOH Z 325 " =    3.428
peak=    3.177 closest distance to " O   HOH Z 345 " =    1.689
peak=    3.177 closest distance to " CB  GLN A 205 " =    1.203
peak=    3.177 closest distance to " O   HOH Z  59 " =    2.158
peak=    3.176 closest distance to " CA  ALA A 299 " =    0.952
peak=    3.175 closest distance to " OG BSER A 210 " =    1.344
peak=    3.174 closest distance to " CB  ALA A  34 " =    0.976
peak=    3.173 closest distance to " CB  GLN A 278 " =    0.747
peak=    3.170 closest distance to " O   HOH Z 234 " =    2.195
peak=    3.168 closest distance to " NZ  LYS A  76 " =    1.354
peak=    3.164 closest distance to " O   HOH Z 234 " =    1.736
peak=    3.163 closest distance to " O   HOH Z 299 " =    2.104
peak=    3.157 closest distance to " CA  ARG A  36 " =    1.023
peak=    3.152 closest distance to " CG  MET A  93 " =    1.008
peak=    3.146 closest distance to " N   PHE A 130 " =    1.376
peak=    3.146 closest distance to " CH2 TRP A  92 " =    2.092
peak=    3.145 closest distance to " CA  ARG A  66 " =    1.179
peak=    3.142 closest distance to " O   TRP A 274 " =    1.822
peak=    3.141 closest distance to " CG2 VAL A 126 " =    1.726
peak=    3.139 closest distance to " O   HOH Z 109 " =    2.207
peak=    3.138 closest distance to " O   HOH Z 217 " =    2.157
peak=    3.136 closest distance to " CH2 TRP A 274 " =    2.238
peak=    3.131 closest distance to " O   HOH Z 417 " =    1.991
peak=    3.115 closest distance to " O  BHOH Z  74 " =    1.151
peak=    3.113 closest distance to " O   HOH Z 189 " =    2.622
peak=    3.111 closest distance to " O   HOH Z 113 " =    1.834
peak=    3.110 closest distance to " O   HOH Z 164 " =    1.998
peak=    3.099 closest distance to " O   HOH Z 185 " =    1.618
peak=    3.082 closest distance to " O   HOH Z  68 " =    1.582
peak=    3.080 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.077 closest distance to " CD2 HIS A  81 " =    1.158
peak=    3.071 closest distance to " CD  LYS A 119 " =    2.032
peak=    3.055 closest distance to " O   HOH Z 435 " =    1.999
peak=    3.054 closest distance to " O   HOH Z 154 " =    1.981
peak=    3.046 closest distance to " CB  GLN A 103 " =    0.831

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.443 - 5.609
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.711 - 5.609

peak=   -4.859 closest distance to " C   HIS A 108 " =    1.160
peak=   -4.687 closest distance to " O   HOH Z 266 " =    4.317
peak=   -4.381 closest distance to " O   HOH Z 290 " =    0.881
peak=   -4.366 closest distance to " N   ALA A 248 " =    1.747
peak=   -4.255 closest distance to " N   GLN A  58 " =    1.699
peak=   -4.246 closest distance to " OXT GLY A 302 " =    2.751
peak=   -4.239 closest distance to " SG  CYS A 254 " =    3.186
peak=   -4.224 closest distance to " OG BSER A 134 " =    1.286
peak=   -4.194 closest distance to " CA  VAL A  67 " =    2.844
peak=   -4.192 closest distance to " O   HOH Z  13 " =    1.619
peak=   -4.127 closest distance to " O   HOH Z 407 " =    2.680
peak=   -4.099 closest distance to " CD2 LEU A 237 " =    2.570
peak=   -4.081 closest distance to " O   HOH Z 401 " =    0.763
peak=   -4.075 closest distance to " NH2 ARG A  79 " =    1.966
peak=   -4.026 closest distance to " CG  MET A  93 " =    2.369
peak=   -3.990 closest distance to " CD  ARG A 156 " =    2.018
peak=   -3.952 closest distance to " O   HOH Z  92 " =    1.659
peak=   -3.948 closest distance to " O   PRO A 163 " =    1.883
peak=   -3.929 closest distance to " O   HOH Z 372 " =    2.270
peak=   -3.926 closest distance to " O   SER A 146 " =    0.937
peak=   -3.918 closest distance to " O   HOH Z 102 " =    1.053
peak=   -3.886 closest distance to " OD2 ASP A 171 " =    2.340
peak=   -3.874 closest distance to " CB  PRO A 243 " =    2.642
peak=   -3.872 closest distance to " O   HOH Z 234 " =    3.954
peak=   -3.870 closest distance to " CB  ALA A 291 " =    2.317
peak=   -3.853 closest distance to " CZ  TYR A 169 " =    1.808
peak=   -3.830 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.812 closest distance to " O   HOH Z 198 " =    1.714
peak=   -3.799 closest distance to " O   HOH Z  11 " =    1.931
peak=   -3.797 closest distance to " ND2 ASN A  39 " =    1.153
peak=   -3.787 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.781 closest distance to " CD  GLN A  58 " =    1.363
peak=   -3.779 closest distance to " N   ASP A 286 " =    2.146
peak=   -3.770 closest distance to " O   HOH Z 126 " =    1.891
peak=   -3.762 closest distance to " O   VAL A 174 " =    1.975
peak=   -3.756 closest distance to " ND2 ASN A  45 " =    1.271
peak=   -3.756 closest distance to " N   HIS A 115 " =    1.984
peak=   -3.752 closest distance to " ND2 ASN A 187 " =    1.377
peak=   -3.744 closest distance to " OD1 ASN A  39 " =    2.162
peak=   -3.744 closest distance to " O   HOH Z  52 " =    1.859
peak=   -3.731 closest distance to " O   ALA A 161 " =    1.662
peak=   -3.715 closest distance to " CB  ASN A  39 " =    2.268
peak=   -3.703 closest distance to " CD  ARG A 139 " =    1.508
peak=   -3.701 closest distance to " O   HOH Z 166 " =    1.575
peak=   -3.691 closest distance to " O   VAL A  67 " =    2.727
peak=   -3.690 closest distance to " O   MET A  40 " =    2.770
peak=   -3.689 closest distance to " CD2 LEU A 300 " =    2.824
peak=   -3.688 closest distance to " CG1 VAL A  67 " =    3.069
peak=   -3.684 closest distance to " CZ3 TRP A 274 " =    1.079
peak=   -3.682 closest distance to " CB  ALA A 161 " =    2.488
peak=   -3.682 closest distance to " C   ALA A 158 " =    1.212
peak=   -3.680 closest distance to " CB  PHE A 192 " =    1.926
peak=   -3.677 closest distance to " N   GLN A 122 " =    1.450
peak=   -3.668 closest distance to " O   HOH Z 250 " =    1.438
peak=   -3.651 closest distance to " CD1 LEU A 228 " =    2.027
peak=   -3.638 closest distance to " O   HOH Z 362 " =    5.602
peak=   -3.623 closest distance to " NH2 ARG A  66 " =    4.588
peak=   -3.623 closest distance to " O   HOH Z 165 " =    2.007
peak=   -3.619 closest distance to " CD1 LEU A  25 " =    2.471
peak=   -3.618 closest distance to " CD  GLN A 223 " =    0.711
peak=   -3.614 closest distance to " OD2 ASP A 191 " =    1.385
peak=   -3.606 closest distance to " C   GLY A  91 " =    1.383
peak=   -3.604 closest distance to " O   HOH Z 197 " =    4.945
peak=   -3.584 closest distance to " O   HOH Z 395 " =    5.101
peak=   -3.580 closest distance to " OXT GLY A 302 " =    3.274
peak=   -3.580 closest distance to " CE2 TYR A  30 " =    2.869
peak=   -3.574 closest distance to " N   SER A 276 " =    1.232
peak=   -3.573 closest distance to " OG  SER A  97 " =    2.021
peak=   -3.556 closest distance to " O   TRP A  92 " =    1.803
peak=   -3.554 closest distance to " N   SER A 206 " =    1.807
peak=   -3.547 closest distance to " O   HOH Z 435 " =    2.687
peak=   -3.544 closest distance to " CD  GLN A  88 " =    0.958
peak=   -3.542 closest distance to " N   ALA A 248 " =    2.200
peak=   -3.539 closest distance to " O   PHE A 218 " =    1.627
peak=   -3.538 closest distance to " CB  PRO A 163 " =    2.639
peak=   -3.535 closest distance to " CG  ASP A 132 " =    2.238
peak=   -3.531 closest distance to " CD  GLN A  58 " =    1.223
peak=   -3.529 closest distance to " N   THR A 220 " =    2.216
peak=   -3.512 closest distance to " O   HOH Z 367 " =    2.553
peak=   -3.508 closest distance to " OG BSER A 134 " =    1.628
peak=   -3.508 closest distance to " O   HOH Z 427 " =    1.441
peak=   -3.506 closest distance to " O   SER A 273 " =    1.214
peak=   -3.505 closest distance to " O   HOH Z 326 " =    1.676
peak=   -3.503 closest distance to " CZ3 TRP A 179 " =    1.387
peak=   -3.497 closest distance to " OG  SER A   3 " =    1.480
peak=   -3.496 closest distance to " CA  GLY A 133 " =    1.776
peak=   -3.492 closest distance to " CG  GLU A   2 " =    1.903
peak=   -3.490 closest distance to " CG  GLU A  53 " =    1.393
peak=   -3.486 closest distance to " O   ASN A  45 " =    1.800
peak=   -3.478 closest distance to " O   HOH Z 174 " =    4.079
peak=   -3.476 closest distance to " O   HOH Z  11 " =    1.730
peak=   -3.467 closest distance to " CG  GLN A 223 " =    2.071
peak=   -3.466 closest distance to " O   GLY A  80 " =    2.342
peak=   -3.464 closest distance to " OG ASER A 134 " =    1.325
peak=   -3.461 closest distance to " O   HOH Z 166 " =    2.075
peak=   -3.460 closest distance to " O   HOH Z 114 " =    3.161
peak=   -3.453 closest distance to " O   HOH Z  88 " =    4.260
peak=   -3.449 closest distance to " C   ASP A 231 " =    2.499
peak=   -3.434 closest distance to " O   HOH Z 423 " =    2.224
peak=   -3.432 closest distance to " O   SER A 210 " =    1.894
peak=   -3.428 closest distance to " O   HOH Z 388 " =    2.003
peak=   -3.427 closest distance to " OG  SER A  87 " =    1.172
peak=   -3.423 closest distance to " CD1 PHE A 130 " =    2.202
peak=   -3.419 closest distance to " CB  PRO A 280 " =    2.169
peak=   -3.417 closest distance to " SG ACYS A 201 " =    2.001
peak=   -3.412 closest distance to " O   ALA A  51 " =    1.274
peak=   -3.404 closest distance to " CG  ASN A 110 " =    1.098
peak=   -3.395 closest distance to " CG1 VAL A 112 " =    2.736
peak=   -3.394 closest distance to " O   HOH Z  43 " =    1.822
peak=   -3.391 closest distance to " O   SER A 135 " =    1.547
peak=   -3.386 closest distance to " O   SER A   3 " =    1.030
peak=   -3.385 closest distance to " O   HOH Z 417 " =    2.498
peak=   -3.376 closest distance to " CG  ASP A 231 " =    0.792
peak=   -3.374 closest distance to " CG  GLU A 152 " =    0.980
peak=   -3.371 closest distance to " O   HOH Z  71 " =    1.193
peak=   -3.370 closest distance to " OD1 ASP A 191 " =    1.513
peak=   -3.356 closest distance to " CE  MET A  93 " =    1.106
peak=   -3.352 closest distance to " O   HOH Z 351 " =    1.516
peak=   -3.349 closest distance to " O   THR A 182 " =    1.229
peak=   -3.345 closest distance to " CG1AVAL A  41 " =    2.687
peak=   -3.333 closest distance to " CG  PHE A 283 " =    2.558
peak=   -3.328 closest distance to " ND2 ASN A 209 " =    1.723
peak=   -3.318 closest distance to " O   HOH Z  41 " =    2.258
peak=   -3.317 closest distance to " O   HOH Z  56 " =    1.034
peak=   -3.317 closest distance to " O   HOH Z  60 " =    1.902
peak=   -3.298 closest distance to " N   ALA A 226 " =    1.850
peak=   -3.296 closest distance to " C   THR A 279 " =    1.212
peak=   -3.294 closest distance to " O   HOH Z 385 " =    2.056
peak=   -3.290 closest distance to " O   ARG A  56 " =    1.654
peak=   -3.286 closest distance to " O   ASP A 162 " =    2.129
peak=   -3.282 closest distance to " O   HOH Z  10 " =    1.308
peak=   -3.279 closest distance to " O   HOH Z 193 " =    1.769
peak=   -3.279 closest distance to " OD2 ASP A  50 " =    1.295
peak=   -3.277 closest distance to " O   HOH Z 251 " =    1.180
peak=   -3.270 closest distance to " O   LEU A 167 " =    1.604
peak=   -3.270 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.268 closest distance to " CB  PHE A 208 " =    2.222
peak=   -3.260 closest distance to " O   HOH Z 282 " =    1.480
peak=   -3.253 closest distance to " O   HOH Z  47 " =    1.635
peak=   -3.251 closest distance to " O   HOH Z 191 " =    5.609
peak=   -3.246 closest distance to " NH1 ARG A 195 " =    2.541
peak=   -3.241 closest distance to " O   HOH Z 384 " =    3.296
peak=   -3.240 closest distance to " O   HOH Z 421 " =    3.449
peak=   -3.240 closest distance to " O   HOH Z 377 " =    1.209
peak=   -3.229 closest distance to " CB  TRP A 274 " =    2.792
peak=   -3.227 closest distance to " CD1 TYR A 247 " =    2.405
peak=   -3.226 closest distance to " CZ  PHE A 130 " =    0.849
peak=   -3.223 closest distance to " CG  TRP A 266 " =    1.995
peak=   -3.222 closest distance to " OD1 ASP A 200 " =    1.241
peak=   -3.215 closest distance to " OH  TYR A 172 " =    1.705
peak=   -3.211 closest distance to " O   HOH Z 360 " =    2.348
peak=   -3.210 closest distance to " O   HOH Z 313 " =    2.014
peak=   -3.209 closest distance to " CB  GLN A  11 " =    1.723
peak=   -3.209 closest distance to " O   LEU A 222 " =    1.291
peak=   -3.205 closest distance to " O   PRO A 198 " =    1.203
peak=   -3.200 closest distance to " O   HOH Z 185 " =    2.193
peak=   -3.198 closest distance to " O   GLN A 194 " =    1.484
peak=   -3.198 closest distance to " OD1 ASP A 191 " =    1.549
peak=   -3.195 closest distance to " CG  GLU A 152 " =    2.499
peak=   -3.188 closest distance to " CD1 ILE A 199 " =    2.295
peak=   -3.188 closest distance to " O   HOH Z 310 " =    3.398
peak=   -3.187 closest distance to " O   GLY A 196 " =    0.963
peak=   -3.184 closest distance to " O   ALA A 256 " =    1.521
peak=   -3.184 closest distance to " O   HOH Z  97 " =    1.145
peak=   -3.183 closest distance to " O   HOH Z 281 " =    2.674
peak=   -3.182 closest distance to " O   ALA A 160 " =    1.410
peak=   -3.181 closest distance to " NH1 ARG A  66 " =    0.739
peak=   -3.178 closest distance to " CG2 VAL A 296 " =    1.991
peak=   -3.175 closest distance to " O   PRO A  54 " =    1.718
peak=   -3.171 closest distance to " O   VAL A 153 " =    2.459
peak=   -3.170 closest distance to " CA  ALA A 299 " =    2.231
peak=   -3.166 closest distance to " O   HOH Z 116 " =    1.351
peak=   -3.160 closest distance to " CG  ASP A  50 " =    2.321
peak=   -3.159 closest distance to " O   HOH Z 188 " =    4.732
peak=   -3.158 closest distance to " O   MET A 188 " =    1.741
peak=   -3.158 closest distance to " O   HOH Z 210 " =    0.985
peak=   -3.153 closest distance to " CD1 ILE A 239 " =    2.525
peak=   -3.149 closest distance to " O   HOH Z 377 " =    1.572
peak=   -3.140 closest distance to " CE  LYS A  76 " =    2.770
peak=   -3.139 closest distance to " CB  ALA A 248 " =    2.069
peak=   -3.134 closest distance to " CG  ARG A 269 " =    2.096
peak=   -3.129 closest distance to " C   LEU A 101 " =    1.474
peak=   -3.123 closest distance to " CG  PRO A 163 " =    2.562
peak=   -3.122 closest distance to " O   ASN A 249 " =    1.485
peak=   -3.121 closest distance to " O   HOH Z 424 " =    3.040
peak=   -3.117 closest distance to " N   SER A 210 " =    1.384
peak=   -3.117 closest distance to " ND2 ASN A 215 " =    2.125
peak=   -3.115 closest distance to " O   HOH Z  93 " =    1.452
peak=   -3.114 closest distance to " OE2 GLU A   2 " =    1.371
peak=   -3.111 closest distance to " OG  SER A  63 " =    1.182
peak=   -3.104 closest distance to " O   HOH Z 193 " =    1.486
peak=   -3.096 closest distance to " O   HOH Z 397 " =    1.247
peak=   -3.086 closest distance to " CG2 VAL A 202 " =    2.160
peak=   -3.081 closest distance to " CA  GLY A 133 " =    2.015
peak=   -3.078 closest distance to " O   HOH Z 265 " =    2.044
peak=   -3.078 closest distance to " O   HOH Z 298 " =    2.606
peak=   -3.077 closest distance to " OD1 ASN A 249 " =    1.915
peak=   -3.075 closest distance to " OD1 ASP A 171 " =    1.556
peak=   -3.064 closest distance to " N   SER A 245 " =    2.289
peak=   -3.048 closest distance to " N   VAL A 189 " =    1.598
peak=   -3.043 closest distance to " C   GLN A 144 " =    0.836
peak=   -3.032 closest distance to " CG  GLN A 223 " =    1.293
peak=   -3.019 closest distance to " CD2 LEU A 300 " =    2.605

================= 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    :  0.4329 0.4354   6.233422e+00   6.243881e+00
   1_bss:  0.4242 0.4247   6.224692e+00   6.226878e+00
   1_xyz:  0.2586 0.2808   5.829008e+00   5.911530e+00
   1_adp:  0.2326 0.2882   5.768268e+00   5.931941e+00
   1_occ:  0.2324 0.2879   5.767600e+00   5.931663e+00
   2_bss:  0.2265 0.2832   5.753880e+00   5.920090e+00
   2_xyz:  0.1651 0.2142   5.472356e+00   5.675138e+00
   2_adp:  0.1505 0.1994   5.388007e+00   5.594401e+00
   2_occ:  0.1502 0.1993   5.387127e+00   5.593815e+00
   3_bss:  0.1498 0.1971   5.382083e+00   5.586833e+00
   3_xyz:  0.1240 0.1691   5.224099e+00   5.446110e+00
   3_adp:  0.1187 0.1664   5.193691e+00   5.426025e+00
   3_occ:  0.1186 0.1663   5.193006e+00   5.425550e+00
   4_bss:  0.1190 0.1661   5.193550e+00   5.423949e+00
   4_xyz:  0.1163 0.1643   5.180225e+00   5.413961e+00
   4_adp:  0.1165 0.1633   5.176317e+00   5.406102e+00
   4_occ:  0.1164 0.1632   5.175504e+00   5.405588e+00
   5_bss:  0.1163 0.1632   5.175766e+00   5.405793e+00
   5_xyz:  0.1100 0.1596   5.137961e+00   5.382989e+00
   5_adp:  0.1100 0.1590   5.136185e+00   5.379769e+00
   5_occ:  0.1100 0.1589   5.135730e+00   5.379645e+00
   5_bss:  0.1099 0.1589   5.135748e+00   5.379682e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   0.429  -2.348   1.755  -0.000   0.000   0.000
   1_xyz:  0.300  20.000   0.429  -2.348   1.755  -0.000   0.000   0.000
   1_adp:  0.300  20.000   0.429  -2.348   1.755  -0.000   0.000   0.000
   1_occ:  0.300  20.000   0.429  -2.348   1.755  -0.000   0.000   0.000
   2_bss:  0.310  30.069  -2.154  -2.279  -0.720  -0.000  -0.000  -0.000
   2_xyz:  0.310  30.069  -2.154  -2.279  -0.720  -0.000  -0.000  -0.000
   2_adp:  0.310  30.069  -2.154  -2.279  -0.720  -0.000  -0.000  -0.000
   2_occ:  0.310  30.069  -2.154  -2.279  -0.720  -0.000  -0.000  -0.000
   3_bss:  0.314  31.620  -2.911  -2.130  -1.586  -0.000  -0.000  -0.000
   3_xyz:  0.314  31.620  -2.911  -2.130  -1.586  -0.000  -0.000  -0.000
   3_adp:  0.314  31.620  -2.911  -2.130  -1.586  -0.000  -0.000  -0.000
   3_occ:  0.314  31.620  -2.911  -2.130  -1.586  -0.000  -0.000  -0.000
   4_bss:  0.305  33.602  -3.148  -2.149  -1.840  -0.000  -0.000  -0.000
   4_xyz:  0.305  33.602  -3.148  -2.149  -1.840  -0.000  -0.000  -0.000
   4_adp:  0.305  33.602  -3.148  -2.149  -1.840  -0.000  -0.000  -0.000
   4_occ:  0.305  33.602  -3.148  -2.149  -1.840  -0.000  -0.000  -0.000
   5_bss:  0.316  33.839  -3.151  -2.043  -1.805  -0.000  -0.000  -0.000
   5_xyz:  0.316  33.839  -3.151  -2.043  -1.805  -0.000  -0.000  -0.000
   5_adp:  0.316  33.839  -3.151  -2.043  -1.805  -0.000  -0.000  -0.000
   5_occ:  0.316  33.839  -3.151  -2.043  -1.805  -0.000  -0.000  -0.000
   5_bss:  0.323  35.777  -3.058  -1.942  -1.670  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.464 0.5033  0.6837    59763.744
   1_bss:  49.966 0.5203  0.7101    55561.277
   1_xyz:  28.248 0.7780  0.9926    20828.466
   1_adp:  29.512 0.7630  0.9809    21853.789
   1_occ:  29.504 0.7631  0.9811    21847.899
   2_bss:  28.952 0.7687  0.9286    21057.917
   2_xyz:  20.902 0.8519  0.9934    11605.851
   2_adp:  18.497 0.8761  1.0056     9831.776
   2_occ:  18.483 0.8762  1.0056     9812.883
   3_bss:  18.303 0.8777  0.9870     9597.008
   3_xyz:  15.398 0.9031  0.9978     7124.877
   3_adp:  14.908 0.9076  0.9946     6905.302
   3_occ:  14.894 0.9077  0.9945     6889.455
   4_bss:  14.862 0.9079  0.9886     6857.204
   4_xyz:  14.539 0.9108  0.9893     6658.151
   4_adp:  14.334 0.9126  0.9882     6584.583
   4_occ:  14.317 0.9128  0.9881     6570.647
   5_bss:  14.326 0.9127  0.9897     6579.877
   5_xyz:  13.922 0.9157  0.9906     6261.953
   5_adp:  13.831 0.9165  0.9885     6233.618
   5_occ:  13.824 0.9165  0.9884     6226.597
   5_bss:  13.823 0.9165  0.9895     6232.785
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.4454e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.4454e-01
   1_xyz:   1.530  0.012  0.093 16.243  0.007  4.102   1.3059e-01
   1_adp:   1.530  0.012  0.093 16.243  0.007  4.102   1.3059e-01
   1_occ:   1.530  0.012  0.093 16.243  0.007  4.102   1.3059e-01
   2_bss:   1.530  0.012  0.093 16.243  0.007  4.102   1.3059e-01
   2_xyz:   1.073  0.006  0.072 14.660  0.005  4.118   6.2986e-02
   2_adp:   1.073  0.006  0.072 14.660  0.005  4.118   6.2986e-02
   2_occ:   1.073  0.006  0.072 14.660  0.005  4.118   6.2986e-02
   3_bss:   1.073  0.006  0.072 14.660  0.005  4.118   6.2986e-02
   3_xyz:   1.031  0.006  0.070 14.731  0.004  4.108   6.0662e-02
   3_adp:   1.031  0.006  0.070 14.731  0.004  4.108   6.0662e-02
   3_occ:   1.031  0.006  0.070 14.731  0.004  4.108   6.0662e-02
   4_bss:   1.031  0.006  0.070 14.731  0.004  4.108   6.0662e-02
   4_xyz:   0.909  0.005  0.064 14.429  0.004  4.108   4.9626e-02
   4_adp:   0.909  0.005  0.064 14.429  0.004  4.108   4.9626e-02
   4_occ:   0.909  0.005  0.064 14.429  0.004  4.108   4.9626e-02
   5_bss:   0.909  0.005  0.064 14.429  0.004  4.108   4.9626e-02
   5_xyz:   1.036  0.006  0.072 14.686  0.004  4.108   6.0823e-02
   5_adp:   1.036  0.006  0.072 14.686  0.004  4.108   6.0823e-02
   5_occ:   1.036  0.006  0.072 14.686  0.004  4.108   6.0823e-02
   5_bss:   1.036  0.006  0.072 14.686  0.004  4.108   6.0823e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.117   2.4365e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.117   2.4365e-01
   1_xyz:  10.159  0.076  0.381 82.921  0.047  1.995   9.3623e-02
   1_adp:  10.159  0.076  0.381 82.921  0.047  1.995   9.3623e-02
   1_occ:  10.159  0.076  0.381 82.921  0.047  1.995   9.3623e-02
   2_bss:  10.159  0.076  0.381 82.921  0.047  1.995   9.3623e-02
   2_xyz:   7.949  0.042  0.248 85.066  0.051  2.229   5.8560e-02
   2_adp:   7.949  0.042  0.248 85.066  0.051  2.229   5.8560e-02
   2_occ:   7.949  0.042  0.248 85.066  0.051  2.229   5.8560e-02
   3_bss:   7.949  0.042  0.248 85.066  0.051  2.229   5.8560e-02
   3_xyz:   7.253  0.047  0.263 83.190  0.039  2.273   4.7948e-02
   3_adp:   7.253  0.047  0.263 83.190  0.039  2.273   4.7948e-02
   3_occ:   7.253  0.047  0.263 83.190  0.039  2.273   4.7948e-02
   4_bss:   7.253  0.047  0.263 83.190  0.039  2.273   4.7948e-02
   4_xyz:   6.543  0.038  0.201 82.657  0.034  2.366   3.5610e-02
   4_adp:   6.543  0.038  0.201 82.657  0.034  2.366   3.5610e-02
   4_occ:   6.543  0.038  0.201 82.657  0.034  2.366   3.5610e-02
   5_bss:   6.543  0.038  0.201 82.657  0.034  2.366   3.5610e-02
   5_xyz:   6.914  0.043  0.236 82.677  0.042  2.269   3.8893e-02
   5_adp:   6.914  0.043  0.236 82.677  0.042  2.269   3.8893e-02
   5_occ:   6.914  0.043  0.236 82.677  0.042  2.269   3.8893e-02
   5_bss:   6.914  0.043  0.236 82.677  0.042  2.269   3.8893e-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:  97.74   0.00  18.73  88.63   0.00  14.27  97.74   4.65  42.97
   1_occ:  97.74   0.00  18.73  88.63   0.00  14.27  97.74   4.65  42.97
   2_bss:  97.74   0.00  18.73  88.63   0.00  14.27  97.74   4.65  42.97
   2_xyz:  97.74   0.00  18.73  88.63   0.00  14.27  97.74   4.65  42.97
   2_adp:  93.28   0.00  17.89  93.28   0.00  13.58  85.99   6.90  41.36
   2_occ:  93.28   0.00  17.89  93.28   0.00  13.58  85.99   6.90  41.36
   3_bss:  93.28   0.00  17.89  93.28   0.00  13.58  85.99   6.90  41.36
   3_xyz:  93.28   0.00  17.89  93.28   0.00  13.58  85.99   6.90  41.36
   3_adp: 100.87   0.00  17.80 100.87   0.00  13.33  90.68   1.29  42.16
   3_occ: 100.87   0.00  17.80 100.87   0.00  13.33  90.68   1.29  42.16
   4_bss: 100.87   0.00  17.80 100.87   0.00  13.33  90.68   1.29  42.16
   4_xyz: 100.87   0.00  17.80 100.87   0.00  13.33  90.68   1.29  42.16
   4_adp: 100.15   2.33  17.19 100.15   2.47  13.08  89.13   2.33  39.56
   4_occ: 100.15   2.33  17.19 100.15   2.47  13.08  89.13   2.33  39.56
   5_bss: 100.15   2.33  17.19 100.15   2.47  13.08  89.13   2.33  39.56
   5_xyz: 100.15   2.33  17.19 100.15   2.47  13.08  89.13   2.33  39.56
   5_adp:  99.18   2.29  16.93  99.18   2.29  12.95  88.78   4.03  38.58
   5_occ:  99.18   2.29  16.93  99.18   2.29  12.95  88.78   4.03  38.58
   5_bss:  99.09   2.21  16.84  99.09   2.21  12.87  88.70   3.95  38.49
------------------------------------------------------------------------
 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:    3.469    0.020    0.473
   1_adp:    3.469    0.020    0.473
   1_occ:    3.469    0.020    0.473
   2_bss:    3.469    0.020    0.473
   2_xyz:    2.610    0.031    0.539
   2_adp:    2.610    0.031    0.539
   2_occ:    2.610    0.031    0.539
   3_bss:    2.610    0.031    0.539
   3_xyz:    2.337    0.047    0.603
   3_adp:    2.337    0.047    0.603
   3_occ:    2.337    0.047    0.603
   4_bss:    2.337    0.047    0.603
   4_xyz:    2.073    0.046    0.614
   4_adp:    2.073    0.046    0.614
   4_occ:    2.073    0.046    0.614
   5_bss:    2.073    0.046    0.614
   5_xyz:    1.804    0.090    0.628
   5_adp:    1.804    0.090    0.628
   5_occ:    1.804    0.090    0.628
   5_bss:    1.804    0.090    0.628
------------------------------------------------------------------------

CPU time actual refinement: 332.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_67/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_67/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_67/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_67/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_67/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.31 
  Macro-tasks:
    bulk solvent and scale       = 42.46  
    individual site refinement   = 130.95 
    weights calculation          = 29.85  
    collect and process          = 6.52   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 209.86 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 105.39 
    alpha_beta                      = 8.21   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 112.60 
    fmodel                         = 6.91   
    r_factors                      = 0.17   
    phase_errors                   = 10.84  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 247.27 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.774 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    637 calls, 105.06 s
gradients_fft:          582 calls,  99.95 s

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

# Date 2008-01-16 Time 03:56:10 PST -0800 (1200484570.07 s)
Start R-work = 0.4329, R-free = 0.4354 (no bulk solvent and anisotropic scale)
Final R-work = 0.1378, R-free = 0.1804 (no bulk solvent and anisotropic scale)

Start R-work = 0.4242, R-free = 0.4247
Final R-work = 0.1099, R-free = 0.1589