# Date 2008-01-16 Time 05:10:57 PST -0800 (1200489057.19 s)
#phil __OFF__

Command line arguments: "../623.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12624
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 623

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.9914, 87.2539, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 1.96309
Completeness in resolution range: 0.942322
Completeness with d_max=infinity: 0.93952

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   1.9631

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 1.96309
Completeness in resolution range: 0.942322
Completeness with d_max=infinity: 0.93952

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.2015 [2181/2206]  1961   220  10.1%
  bin  2:  4.2015 -  3.3469 [2101/2121]  1894   207   9.9%
  bin  3:  3.3469 -  2.9274 [2077/2096]  1870   207  10.0%
  bin  4:  2.9274 -  2.6614 [2043/2073]  1835   208  10.2%
  bin  5:  2.6614 -  2.4715 [2040/2059]  1843   197   9.7%
  bin  6:  2.4715 -  2.3263 [2033/2058]  1826   207  10.2%
  bin  7:  2.3263 -  2.2102 [2019/2047]  1812   207  10.3%
  bin  8:  2.2102 -  2.1143 [1997/2033]  1797   200  10.0%
  bin  9:  2.1143 -  2.0331 [2020/2062]  1823   197   9.8%
  bin 10:  2.0331 -  1.9631 [1078/2033]   969   109  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_623/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: 0.13 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:
        1.81 -     2.42: 41
        2.42 -     3.04: 2208
        3.04 -     3.66: 4726
        3.66 -     4.28: 9086
        4.28 -     4.90: 12365
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.836 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.943 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28421 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_623/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_623/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.9914 87.2539 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: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4038   r_free= 0.4031   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.216491                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.6865 0.99   1417  156 0.3351 0.3266      6.4967      6.4567|
|  2:  4.6865 -  3.7387 0.99   1369  155 0.3337 0.3212      6.6943      6.6024|
|  3:  3.7387 -  3.2716 0.99   1332  145 0.3590 0.3496      6.5728      6.5843|
|  4:  3.2716 -  2.9750 0.99   1343  150 0.3910 0.4149      6.4464      6.5014|
|  5:  2.9750 -  2.7632 0.99   1315  149 0.4248 0.3694      6.2843      6.2574|
|  6:  2.7632 -  2.6012 0.99   1318  144 0.4257 0.4521      6.1956      6.1444|
|  7:  2.6012 -  2.4715 0.99   1309  140 0.4315 0.4105      6.1788      6.1055|
|  8:  2.4715 -  2.3643 0.98   1294  151 0.4533 0.4829      6.1225      6.1646|
|  9:  2.3643 -  2.2736 0.98   1292  142 0.4372 0.4719      6.0741      6.1059|
| 10:  2.2736 -  2.1954 1.00   1295  148 0.4562 0.4566       6.047      6.0278|
| 11:  2.1954 -  2.1270 0.98   1314  144 0.4580 0.4771      5.9935      6.0343|
| 12:  2.1270 -  2.0663 0.98   1272  139 0.4530 0.4364      5.9187      5.9504|
| 13:  2.0663 -  2.0121 0.98   1276  139 0.4539 0.4453       5.834      5.7651|
| 14:  2.0121 -  1.9631 0.36    484   57 0.5212 0.5119      5.8821        5.85|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.6865  1417   156  0.77  28.25   0.84     0.82      52020.47|
|  2:  4.6865 -  3.7387  1369   155  0.78  27.91   0.93     0.89      74108.12|
|  3:  3.7387 -  3.2716  1332   145  0.70  35.34   0.97     0.88      79312.20|
|  4:  3.2716 -  2.9750  1343   150  0.63  41.02   0.95     0.83      73440.19|
|  5:  2.9750 -  2.7632  1315   149  0.57  46.45   0.93     0.77      57768.27|
|  6:  2.7632 -  2.6012  1318   144  0.55  48.31   0.93     0.73      51727.21|
|  7:  2.6012 -  2.4715  1309   140  0.52  50.79   0.96     0.69      49836.34|
|  8:  2.4715 -  2.3643  1294   151  0.48  53.86   0.94     0.67      47763.85|
|  9:  2.3643 -  2.2736  1292   142  0.48  53.58   0.98     0.67      44121.00|
| 10:  2.2736 -  2.1954  1295   148  0.49  53.12   0.98     0.68      38960.66|
| 11:  2.1954 -  2.1270  1314   144  0.47  54.26   0.99     0.70      38505.49|
| 12:  2.1270 -  2.0663  1272   139  0.45  56.04   0.98     0.69      36161.42|
| 13:  2.0663 -  2.0121  1276   139  0.42  58.43   0.98     0.67      32027.28|
| 14:  2.0121 -  1.9631   484    57  0.46  55.22   0.99     0.64      25000.38|
|alpha:            min =        0.64 max =            0.89 mean =         0.74|
|beta:             min =    25000.38 max =        79312.20 mean =     51482.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.98 mean =        46.69|
|phase err.(test): min =        0.00 max =           89.88 mean =        47.07|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.507456              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.032   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.484245              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.914   (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 |  1.806 -  2.115:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       30 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      199 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2009 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1885 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2841 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4680 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4406 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5644 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6721 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.335 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    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: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4038   r_free= 0.4031   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.216491                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3901   r_free= 0.3928   ksol= 0.35   Bsol= 50.00   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,3.24,0.15,0.00,0.00,0.00); trace/3= 0.05                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.203823                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.948594              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.078   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.757929              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.684   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3901      final r-factor (work) = 0.2777          |
| start r-factor (free) = 0.3928      final r-factor (free) = 0.3168          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8083 = 7.95 * 0.50 * 6.1988 + 1.00 * 0.1725                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0607 = 7.95 * 0.50 * 6.0242 + 1.00 * 0.1187                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2777      final r-factor (work) = 0.2519          |
| start r-factor (free) = 0.3168      final r-factor (free) = 0.3269          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5719 = 0.76 * 1.00 * 6.0242 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4553 = 0.76 * 1.00 * 5.8595 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.23   17.82    None  None   None       |
|    all(noH): 2823   0      0.00    95.23   17.82    None  None   None       |
|    Sol.    : 438    0      2.54    95.23   39.64    None  None   None       |
|    Mac.    : 2385   0      0.00    69.25   13.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.523:  869   |   5:    47.616 -  57.139:   97        |
|      1:     9.523 -  19.047: 1087   |   6:    57.139 -  66.663:   47        |
|      2:    19.047 -  28.570:  384   |   7:    66.663 -  76.186:   17        |
|      3:    28.570 -  38.093:  197   |   8:    76.186 -  85.709:    3        |
|      4:    38.093 -  47.616:  121   |   9:    85.709 -  95.232:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2519 r_free = 0.3269             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2515 r_free = 0.3272             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2515   r_free= 0.3272   ksol= 0.35   Bsol= 50.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,3.24,0.15,0.00,0.00,0.00); trace/3= 0.05                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.872043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2498   r_free= 0.3230   ksol= 0.34   Bsol= 63.93   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-0.12,-0.35,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.865924                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.098958              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.151   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.394  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2498      final r-factor (work) = 0.1981          |
| start r-factor (free) = 0.3230      final r-factor (free) = 0.2552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1968 = 3.10 * 0.50 * 5.8590 + 1.00 * 0.1184                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0035 = 3.10 * 0.50 * 5.7724 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1981      final r-factor (work) = 0.1872          |
| start r-factor (free) = 0.2552      final r-factor (free) = 0.2405          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5246 = 0.26 * 1.00 * 5.7724 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4813 = 0.26 * 1.00 * 5.6267 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.97   17.31    None  None   None       |
|    all(noH): 2823   0      0.00    90.97   17.31    None  None   None       |
|    Sol.    : 438    0      4.95    90.97   39.22    None  None   None       |
|    Mac.    : 2385   0      0.00    76.28   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.097:  796   |   5:    45.487 -  54.584:  108        |
|      1:     9.097 -  18.195: 1210   |   6:    54.584 -  63.682:   47        |
|      2:    18.195 -  27.292:  332   |   7:    63.682 -  72.779:   22        |
|      3:    27.292 -  36.390:  165   |   8:    72.779 -  81.876:    3        |
|      4:    36.390 -  45.487:  139   |   9:    81.876 -  90.974:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1872 r_free = 0.2405             target_work(ml) = 5.602         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1871 r_free = 0.2402             target_work(ml) = 5.601         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1871   r_free= 0.2402   ksol= 0.34   Bsol= 63.93   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-0.12,-0.35,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.601033                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1866   r_free= 0.2390   ksol= 0.33   Bsol= 56.55   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.40,-0.47,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.597913                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.844455              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.256  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.314575              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.361  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1866      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.2390      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0596 = 2.84 * 0.50 * 5.6252 + 1.00 * 0.0593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8467 = 2.84 * 0.50 * 5.4775 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1338          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7319 = 0.31 * 1.00 * 5.4775 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6834 = 0.31 * 1.00 * 5.3231 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    87.65   17.25    None  None   None       |
|    all(noH): 2823   0      0.52    87.65   17.25    None  None   None       |
|    Sol.    : 438    0      5.29    87.65   41.12    None  None   None       |
|    Mac.    : 2385   0      0.52    82.24   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:     0.522 -   9.235:  874   |   5:    44.086 -  52.799:  117        |
|      1:     9.235 -  17.948: 1188   |   6:    52.799 -  61.512:   79        |
|      2:    17.948 -  26.660:  283   |   7:    61.512 -  70.225:   34        |
|      3:    26.660 -  35.373:  132   |   8:    70.225 -  78.937:   14        |
|      4:    35.373 -  44.086:  100   |   9:    78.937 -  87.650:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1338 r_free = 0.1821             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1338 r_free = 0.1820             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1820   ksol= 0.33   Bsol= 56.55   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.40,-0.47,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.301482                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1812   ksol= 0.32   Bsol= 53.67   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.26,-0.74,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.299520                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.742633              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.495  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.201852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.425  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1340      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1812      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3583 = 2.74 * 0.50 * 5.3248 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2566 = 2.74 * 0.50 * 5.2488 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1655      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0683 = 0.20 * 1.00 * 5.2488 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0552 = 0.20 * 1.00 * 5.1888 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    86.20   16.83    None  None   None       |
|    all(noH): 2823   0      0.75    86.20   16.83    None  None   None       |
|    Sol.    : 438    0      3.62    83.03   39.42    None  None   None       |
|    Mac.    : 2385   0      0.75    86.20   12.69    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:     0.746 -   9.291:  864   |   5:    43.471 -  52.016:  104        |
|      1:     9.291 -  17.836: 1233   |   6:    52.016 -  60.561:   67        |
|      2:    17.836 -  26.381:  262   |   7:    60.561 -  69.106:   31        |
|      3:    26.381 -  34.926:  132   |   8:    69.106 -  77.651:   13        |
|      4:    34.926 -  43.471:  114   |   9:    77.651 -  86.196:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1627             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1627             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1627   ksol= 0.32   Bsol= 53.67   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.26,-0.74,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.179385                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1627   ksol= 0.32   Bsol= 49.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.43,-0.75,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.179102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.453466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.972  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.213981              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.538  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4236 = 2.45 * 0.50 * 5.1884 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3926 = 2.45 * 0.50 * 5.1624 + 1.00 * 0.0597                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1124 = 0.21 * 1.00 * 5.1624 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1086 = 0.21 * 1.00 * 5.1455 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    87.32   16.59    None  None   None       |
|    all(noH): 2823   0      0.96    87.32   16.59    None  None   None       |
|    Sol.    : 438    0      5.66    80.98   38.63    None  None   None       |
|    Mac.    : 2385   0      0.96    87.32   12.54    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:     0.961 -   9.598:  984   |   5:    44.143 -  52.779:  102        |
|      1:     9.598 -  18.234: 1144   |   6:    52.779 -  61.416:   57        |
|      2:    18.234 -  26.870:  245   |   7:    61.416 -  70.052:   25        |
|      3:    26.870 -  35.507:  133   |   8:    70.052 -  78.688:    9        |
|      4:    35.507 -  44.143:  121   |   9:    78.688 -  87.325:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1566             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1567             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1567   ksol= 0.32   Bsol= 49.89   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.43,-0.75,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143469                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.6865 0.99   1417  156 0.0970 0.1251       5.368      5.5605|
|  2:  4.6865 -  3.7387 0.99   1369  155 0.0854 0.1160      5.4387      5.6281|
|  3:  3.7387 -  3.2716 0.99   1332  145 0.1092 0.1538       5.491       5.825|
|  4:  3.2716 -  2.9750 0.99   1343  150 0.1234 0.1663      5.4512      5.6018|
|  5:  2.9750 -  2.7632 0.99   1315  149 0.1346 0.1727      5.3257      5.5597|
|  6:  2.7632 -  2.6012 0.99   1318  144 0.1210 0.1908      5.1891      5.4673|
|  7:  2.6012 -  2.4715 0.99   1309  140 0.1265 0.1549      5.1705      5.3037|
|  8:  2.4715 -  2.3643 0.98   1294  151 0.1162 0.1602      5.0515      5.3086|
|  9:  2.3643 -  2.2736 0.98   1292  142 0.1170 0.1725      5.0262      5.2794|
| 10:  2.2736 -  2.1954 1.00   1295  148 0.1094 0.1735      4.9218      5.1998|
| 11:  2.1954 -  2.1270 0.98   1314  144 0.1094 0.1808      4.9232      5.3131|
| 12:  2.1270 -  2.0663 0.98   1272  139 0.1138 0.1623      4.8564      5.1082|
| 13:  2.0663 -  2.0121 0.98   1276  139 0.1067 0.1700      4.7592      5.0132|
| 14:  2.0121 -  1.9631 0.36    484   57 0.0989 0.1425      4.6658      4.8365|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.6865  1417   156  0.94   8.81   0.98     0.95       6767.53|
|  2:  4.6865 -  3.7387  1369   155  0.95   7.78   1.02     1.01       9033.72|
|  3:  3.7387 -  3.2716  1332   145  0.93  11.53   1.02     1.02      10582.83|
|  4:  3.2716 -  2.9750  1343   150  0.92  13.99   1.01     0.98      10169.05|
|  5:  2.9750 -  2.7632  1315   149  0.90  15.56   1.00     0.98       8132.38|
|  6:  2.7632 -  2.6012  1318   144  0.90  15.99   0.98     0.96       6714.94|
|  7:  2.6012 -  2.4715  1309   140  0.91  15.45   0.99     0.96       6159.81|
|  8:  2.4715 -  2.3643  1294   151  0.91  15.31   0.99     0.97       5167.89|
|  9:  2.3643 -  2.2736  1292   142  0.91  15.27   1.00     0.97       4899.64|
| 10:  2.2736 -  2.1954  1295   148  0.91  15.13   1.00     0.97       4121.49|
| 11:  2.1954 -  2.1270  1314   144  0.90  15.77   0.99     0.94       4176.53|
| 12:  2.1270 -  2.0663  1272   139  0.91  15.38   1.01     1.01       3774.75|
| 13:  2.0663 -  2.0121  1276   139  0.90  16.34   1.00     0.99       3292.48|
| 14:  2.0121 -  1.9631   484    57  0.92  13.81   0.99     0.96       2636.57|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2636.57 max =        10582.83 mean =      6321.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.95|
|phase err.(test): min =        0.00 max =           88.58 mean =        13.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1564   ksol= 0.32   Bsol= 49.85   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.45,-0.66,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143373                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1564   ksol= 0.32   Bsol= 49.85   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.45,-0.66,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143373                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.6865 0.99   1417  156 0.0969 0.1241      5.3622      5.5419|
|  2:  4.6865 -  3.7387 0.99   1369  155 0.0860 0.1136      5.4384      5.6236|
|  3:  3.7387 -  3.2716 0.99   1332  145 0.1096 0.1522      5.4924      5.8188|
|  4:  3.2716 -  2.9750 0.99   1343  150 0.1232 0.1672      5.4518      5.6073|
|  5:  2.9750 -  2.7632 0.99   1315  149 0.1345 0.1725      5.3271      5.5587|
|  6:  2.7632 -  2.6012 0.99   1318  144 0.1210 0.1910      5.1899      5.4687|
|  7:  2.6012 -  2.4715 0.99   1309  140 0.1267 0.1553      5.1709      5.3052|
|  8:  2.4715 -  2.3643 0.98   1294  151 0.1159 0.1603      5.0513      5.3091|
|  9:  2.3643 -  2.2736 0.98   1292  142 0.1169 0.1722      5.0262      5.2806|
| 10:  2.2736 -  2.1954 1.00   1295  148 0.1093 0.1737      4.9224      5.2021|
| 11:  2.1954 -  2.1270 0.98   1314  144 0.1094 0.1811      4.9239      5.3151|
| 12:  2.1270 -  2.0663 0.98   1272  139 0.1137 0.1624      4.8565      5.1078|
| 13:  2.0663 -  2.0121 0.98   1276  139 0.1066 0.1700      4.7588      5.0133|
| 14:  2.0121 -  1.9631 0.36    484   57 0.0989 0.1415       4.665       4.833|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.6865  1417   156  0.94   8.61   0.98     0.95       6530.89|
|  2:  4.6865 -  3.7387  1369   155  0.96   7.64   1.02     1.01       8830.11|
|  3:  3.7387 -  3.2716  1332   145  0.93  11.47   1.02     1.02      10526.98|
|  4:  3.2716 -  2.9750  1343   150  0.92  14.04   1.01     0.98      10187.05|
|  5:  2.9750 -  2.7632  1315   149  0.90  15.58   1.00     0.98       8157.72|
|  6:  2.7632 -  2.6012  1318   144  0.90  16.00   0.98     0.96       6730.89|
|  7:  2.6012 -  2.4715  1309   140  0.91  15.46   0.99     0.96       6170.29|
|  8:  2.4715 -  2.3643  1294   151  0.91  15.33   0.99     0.97       5180.91|
|  9:  2.3643 -  2.2736  1292   142  0.91  15.29   1.00     0.97       4907.42|
| 10:  2.2736 -  2.1954  1295   148  0.91  15.16   1.01     0.97       4136.17|
| 11:  2.1954 -  2.1270  1314   144  0.90  15.80   0.99     0.94       4189.41|
| 12:  2.1270 -  2.0663  1272   139  0.91  15.42   1.01     1.01       3783.93|
| 13:  2.0663 -  2.0121  1276   139  0.90  16.34   1.01     0.99       3292.60|
| 14:  2.0121 -  1.9631   484    57  0.92  13.78   0.99     0.96       2629.50|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2629.50 max =        10526.98 mean =      6291.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.94|
|phase err.(test): min =        0.00 max =           88.39 mean =        13.48|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    87.29   16.56    None  None   None       |
|    all(noH): 2823   0      0.93    87.29   16.56    None  None   None       |
|    Sol.    : 438    0      5.62    80.95   38.60    None  None   None       |
|    Mac.    : 2385   0      0.93    87.29   12.51    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:     0.928 -   9.564:  984   |   5:    44.110 -  52.746:  102        |
|      1:     9.564 -  18.201: 1144   |   6:    52.746 -  61.382:   57        |
|      2:    18.201 -  26.837:  245   |   7:    61.382 -  70.019:   25        |
|      3:    26.837 -  35.473:  133   |   8:    70.019 -  78.655:    9        |
|      4:    35.473 -  44.110:  121   |   9:    78.655 -  87.291:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.613 - 4.766
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 310
   mapped sites are within: 0.716 - 4.766

peak=    6.336 closest distance to " NE2 GLN A  11 " =    1.274
peak=    5.670 closest distance to " O   HOH Z 144 " =    1.901
peak=    5.439 closest distance to " CG  PRO A  54 " =    1.327
peak=    5.393 closest distance to " O   HOH Z 126 " =    2.004
peak=    5.380 closest distance to " NH2 ARG A  56 " =    2.103
peak=    5.373 closest distance to " O   HOH Z  63 " =    1.630
peak=    5.193 closest distance to " O   HOH Z 423 " =    1.895
peak=    5.103 closest distance to " O   HOH Z 417 " =    1.891
peak=    5.029 closest distance to " O   HOH Z 287 " =    2.091
peak=    5.024 closest distance to " O   HOH Z   9 " =    1.544
peak=    4.860 closest distance to " O   HOH Z 371 " =    2.173
peak=    4.837 closest distance to " O   HOH Z  57 " =    2.287
peak=    4.815 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.813 closest distance to " CB  PRO A  54 " =    0.985
peak=    4.797 closest distance to " CB  GLN A 223 " =    1.495
peak=    4.759 closest distance to " CB  SER A  63 " =    1.213
peak=    4.675 closest distance to " CB  ARG A 275 " =    0.900
peak=    4.674 closest distance to " O   HOH Z  78 " =    1.636
peak=    4.618 closest distance to " O   HOH Z 380 " =    1.832
peak=    4.566 closest distance to " O   HOH Z 427 " =    2.553
peak=    4.483 closest distance to " O   HOH Z 298 " =    1.961
peak=    4.459 closest distance to " CB  GLN A 183 " =    1.199
peak=    4.449 closest distance to " CB  ASN A 148 " =    1.370
peak=    4.394 closest distance to " CG  PRO A 213 " =    1.278
peak=    4.378 closest distance to " CB  ARG A 190 " =    1.659
peak=    4.371 closest distance to " ND2 ASN A 187 " =    1.619
peak=    4.274 closest distance to " O   HOH Z 403 " =    1.440
peak=    4.262 closest distance to " CD  ARG A 159 " =    0.817
peak=    4.254 closest distance to " O   HOH Z   7 " =    1.321
peak=    4.241 closest distance to " O   HOH Z   2 " =    1.562
peak=    4.224 closest distance to " NZ  LYS A 119 " =    2.518
peak=    4.202 closest distance to " CA  TYR A  30 " =    0.992
peak=    4.197 closest distance to " O   HOH Z 209 " =    2.243
peak=    4.186 closest distance to " O   HOH Z 405 " =    1.423
peak=    4.184 closest distance to " CG2 VAL A 257 " =    0.878
peak=    4.173 closest distance to " O   HOH Z   1 " =    1.875
peak=    4.169 closest distance to " O   HOH Z   1 " =    1.852
peak=    4.159 closest distance to " O   HOH Z 425 " =    1.400
peak=    4.150 closest distance to " O   HOH Z  78 " =    2.062
peak=    4.148 closest distance to " CB  ASN A 187 " =    1.051
peak=    4.129 closest distance to " O   HOH Z 158 " =    2.984
peak=    4.129 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.127 closest distance to " C   PRO A 198 " =    1.489
peak=    4.124 closest distance to " CB  ARG A  79 " =    1.360
peak=    4.122 closest distance to " O   HOH Z  68 " =    2.147
peak=    4.122 closest distance to " O   HOH Z 144 " =    2.246
peak=    4.105 closest distance to " CB  GLU A 152 " =    1.286
peak=    4.078 closest distance to " CG  TRP A 179 " =    2.101
peak=    4.068 closest distance to " CB  SER A   3 " =    1.353
peak=    4.024 closest distance to " O   HOH Z 362 " =    2.057
peak=    4.023 closest distance to " CB  VAL A 265 " =    1.318
peak=    4.020 closest distance to " CD  ARG A  66 " =    2.179
peak=    3.980 closest distance to " O   HOH Z  44 " =    1.733
peak=    3.975 closest distance to " O   SER A  87 " =    2.219
peak=    3.939 closest distance to " O   HOH Z  61 " =    1.527
peak=    3.932 closest distance to " CB  TRP A 266 " =    1.040
peak=    3.931 closest distance to " CG  PRO A 243 " =    1.095
peak=    3.930 closest distance to " O   HOH Z  10 " =    1.747
peak=    3.918 closest distance to " O   HOH Z  61 " =    1.606
peak=    3.914 closest distance to " CZ  PHE A 218 " =    1.064
peak=    3.913 closest distance to " CB  SER A 212 " =    1.247
peak=    3.902 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.888 closest distance to " CB  GLU A 277 " =    3.563
peak=    3.872 closest distance to " O   HOH Z 352 " =    1.832
peak=    3.867 closest distance to " O   HOH Z 116 " =    3.032
peak=    3.863 closest distance to " CB  SER A 216 " =    0.840
peak=    3.856 closest distance to " CG  LEU A 167 " =    1.268
peak=    3.853 closest distance to " O   HOH Z 365 " =    2.791
peak=    3.844 closest distance to " OG ASER A 258 " =    3.024
peak=    3.841 closest distance to " CB  ASN A  39 " =    0.915
peak=    3.831 closest distance to " CB  LEU A 228 " =    1.076
peak=    3.827 closest distance to " O   HOH Z 128 " =    2.124
peak=    3.825 closest distance to " CB  TYR A 169 " =    0.780
peak=    3.821 closest distance to " CB  GLU A 128 " =    0.939
peak=    3.803 closest distance to " O   HOH Z 346 " =    1.770
peak=    3.795 closest distance to " O   HOH Z  30 " =    1.714
peak=    3.781 closest distance to " CG  PRO A  90 " =    1.313
peak=    3.775 closest distance to " O   HOH Z 327 " =    1.637
peak=    3.768 closest distance to " ND1 HIS A  86 " =    1.680
peak=    3.753 closest distance to " OD1 ASN A  69 " =    2.604
peak=    3.729 closest distance to " CA  SER A  87 " =    1.000
peak=    3.719 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.714 closest distance to " CB  ASN A 142 " =    0.961
peak=    3.708 closest distance to " OG BSER A 164 " =    2.242
peak=    3.704 closest distance to " CB  ARG A  79 " =    0.892
peak=    3.699 closest distance to " O   HOH Z 368 " =    3.603
peak=    3.698 closest distance to " O   HOH Z 128 " =    1.899
peak=    3.698 closest distance to " CB  ARG A 139 " =    1.065
peak=    3.687 closest distance to " CD  PRO A 243 " =    1.713
peak=    3.684 closest distance to " CB  ILE A 120 " =    1.283
peak=    3.676 closest distance to " O   HOH Z 236 " =    1.493
peak=    3.670 closest distance to " O   HOH Z 375 " =    1.055
peak=    3.669 closest distance to " O   HOH Z 394 " =    1.688
peak=    3.668 closest distance to " NH2AARG A 190 " =    1.833
peak=    3.665 closest distance to " CA  ARG A 195 " =    1.195
peak=    3.663 closest distance to " O   HOH Z 250 " =    1.494
peak=    3.661 closest distance to " O   HOH Z 132 " =    2.560
peak=    3.659 closest distance to " O   HOH Z 214 " =    2.261
peak=    3.654 closest distance to " CB  THR A 157 " =    1.140
peak=    3.653 closest distance to " O   HOH Z 234 " =    3.723
peak=    3.644 closest distance to " O   HOH Z 145 " =    1.359
peak=    3.641 closest distance to " O   HOH Z 225 " =    1.490
peak=    3.633 closest distance to " O   HOH Z 175 " =    2.121
peak=    3.631 closest distance to " CA  ALA A 233 " =    1.088
peak=    3.624 closest distance to " N   PHE A 130 " =    1.246
peak=    3.622 closest distance to " O   HOH Z 257 " =    2.209
peak=    3.613 closest distance to " O   HOH Z 422 " =    2.628
peak=    3.612 closest distance to " O   HOH Z  44 " =    2.880
peak=    3.609 closest distance to " N   CYS A 260 " =    0.801
peak=    3.606 closest distance to " O   HOH Z 172 " =    2.487
peak=    3.600 closest distance to " NH1AARG A 145 " =    1.204
peak=    3.596 closest distance to " CB  GLN A  88 " =    1.240
peak=    3.588 closest distance to " O   HOH Z 305 " =    3.491
peak=    3.586 closest distance to " NE2 GLN A  73 " =    3.718
peak=    3.584 closest distance to " O   HOH Z 437 " =    1.806
peak=    3.577 closest distance to " O   HOH Z 425 " =    1.977
peak=    3.574 closest distance to " O   HOH Z 371 " =    1.747
peak=    3.568 closest distance to " CG1BVAL A  72 " =    1.450
peak=    3.558 closest distance to " O   HOH Z 272 " =    1.804
peak=    3.552 closest distance to " O   HOH Z 128 " =    2.010
peak=    3.550 closest distance to " NZ  LYS A 117 " =    3.181
peak=    3.548 closest distance to " O   HOH Z 193 " =    1.823
peak=    3.543 closest distance to " CD2 LEU A 297 " =    0.940
peak=    3.542 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.540 closest distance to " O   HOH Z 368 " =    1.845
peak=    3.532 closest distance to " O   HOH Z 189 " =    2.471
peak=    3.532 closest distance to " CG2 THR A 221 " =    1.083
peak=    3.528 closest distance to " O   HOH Z 148 " =    3.412
peak=    3.527 closest distance to " O   HOH Z 392 " =    1.244
peak=    3.526 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.520 closest distance to " CG  GLN A  11 " =    1.935
peak=    3.515 closest distance to " CA  ASN A 215 " =    1.116
peak=    3.507 closest distance to " CE  LYS A 119 " =    1.198
peak=    3.504 closest distance to " NE2 HIS A 207 " =    1.200
peak=    3.501 closest distance to " CD2 TRP A 179 " =    1.242
peak=    3.500 closest distance to " CA  ALA A  84 " =    1.379
peak=    3.492 closest distance to " N   SER A  97 " =    0.871
peak=    3.485 closest distance to " O   HOH Z 188 " =    2.047
peak=    3.485 closest distance to " CB  ALA A 114 " =    1.404
peak=    3.482 closest distance to " NH1BARG A 145 " =    1.257
peak=    3.481 closest distance to " O   HOH Z 183 " =    1.424
peak=    3.477 closest distance to " N   GLN A 278 " =    1.217
peak=    3.476 closest distance to " O   HOH Z  40 " =    2.135
peak=    3.472 closest distance to " CB  THR A  31 " =    1.725
peak=    3.457 closest distance to " CA  TYR A 116 " =    1.345
peak=    3.457 closest distance to " O   HOH Z  97 " =    2.067
peak=    3.456 closest distance to " CB  ALA A   1 " =    4.766
peak=    3.444 closest distance to " CB  LYS A 117 " =    1.243
peak=    3.442 closest distance to " OG  SER A  62 " =    2.924
peak=    3.432 closest distance to " O   HOH Z 265 " =    2.036
peak=    3.431 closest distance to " O   ASN A  74 " =    1.479
peak=    3.430 closest distance to " CA  ASN A 127 " =    1.022
peak=    3.422 closest distance to " O   HOH Z 406 " =    1.623
peak=    3.416 closest distance to " O   HOH Z 368 " =    4.273
peak=    3.414 closest distance to " O   HOH Z 248 " =    1.528
peak=    3.413 closest distance to " O   HOH Z 391 " =    2.936
peak=    3.412 closest distance to " CB  SER A  62 " =    1.115
peak=    3.412 closest distance to " O   HOH Z 195 " =    1.275
peak=    3.412 closest distance to " CA  ILE A 234 " =    0.967
peak=    3.405 closest distance to " O   HOH Z 344 " =    3.166
peak=    3.400 closest distance to " CE1 TYR A 186 " =    1.413
peak=    3.400 closest distance to " CB  ASN A 110 " =    1.029
peak=    3.395 closest distance to " CA  ALA A 299 " =    0.874
peak=    3.391 closest distance to " CB  ALA A 114 " =    1.122
peak=    3.384 closest distance to " O   HOH Z 181 " =    2.112
peak=    3.383 closest distance to " CA  VAL A 125 " =    1.123
peak=    3.382 closest distance to " N   ALA A   1 " =    1.986
peak=    3.380 closest distance to " O   HOH Z 291 " =    1.561
peak=    3.378 closest distance to " CD1 ILE A 263 " =    1.346
peak=    3.372 closest distance to " CB  SER A 210 " =    0.727
peak=    3.371 closest distance to " O   HOH Z  88 " =    3.794
peak=    3.368 closest distance to " CD  ARG A 138 " =    0.771
peak=    3.367 closest distance to " O   HOH Z 126 " =    1.496
peak=    3.366 closest distance to " CA  THR A 264 " =    0.869
peak=    3.362 closest distance to " O   HOH Z 213 " =    2.069
peak=    3.361 closest distance to " O   HOH Z 345 " =    1.814
peak=    3.357 closest distance to " N   ARG A 156 " =    1.292
peak=    3.355 closest distance to " N   GLU A   2 " =    1.370
peak=    3.354 closest distance to " CG1 ILE A  33 " =    1.296
peak=    3.353 closest distance to " CB  GLU A  46 " =    0.986
peak=    3.353 closest distance to " O   HOH Z 294 " =    1.466
peak=    3.351 closest distance to " O   HOH Z 147 " =    1.772
peak=    3.349 closest distance to " O   TYR A 116 " =    1.332
peak=    3.347 closest distance to " CG  LYS A 119 " =    1.179
peak=    3.345 closest distance to " CB  MET A 188 " =    1.746
peak=    3.343 closest distance to " O   HOH Z 109 " =    2.410
peak=    3.341 closest distance to " CA  SER A  95 " =    1.018
peak=    3.339 closest distance to " O   HOH Z 357 " =    1.952
peak=    3.339 closest distance to " O   HOH Z 371 " =    2.964
peak=    3.336 closest distance to " O   GLY A 302 " =    1.647
peak=    3.336 closest distance to " O   HOH Z 219 " =    2.139
peak=    3.335 closest distance to " OD1BASN A 224 " =    2.317
peak=    3.323 closest distance to " O   HOH Z 421 " =    2.063
peak=    3.317 closest distance to " CB  ASN A 215 " =    1.021
peak=    3.317 closest distance to " CB  TRP A 179 " =    1.429
peak=    3.315 closest distance to " CA  ARG A 102 " =    1.113
peak=    3.309 closest distance to " O   HOH Z  85 " =    2.120
peak=    3.308 closest distance to " O   HOH Z 112 " =    1.025
peak=    3.304 closest distance to " O   HOH Z 359 " =    1.381
peak=    3.301 closest distance to " O   HOH Z 244 " =    1.759
peak=    3.301 closest distance to " O   HOH Z 274 " =    2.000
peak=    3.299 closest distance to " O   HOH Z 411 " =    3.809
peak=    3.296 closest distance to " O   HOH Z 435 " =    1.909
peak=    3.295 closest distance to " O   HOH Z 343 " =    3.239
peak=    3.294 closest distance to " CB  SER A 276 " =    1.197
peak=    3.290 closest distance to " O   HOH Z 272 " =    2.058
peak=    3.290 closest distance to " CB  ARG A 138 " =    0.952
peak=    3.288 closest distance to " O   HOH Z 218 " =    2.081
peak=    3.288 closest distance to " CG1 ILE A 151 " =    1.035
peak=    3.288 closest distance to " O   PHE A 192 " =    1.398
peak=    3.282 closest distance to " O   HOH Z 119 " =    1.620
peak=    3.280 closest distance to " O   HOH Z 386 " =    2.957
peak=    3.279 closest distance to " O   HOH Z 325 " =    3.817
peak=    3.276 closest distance to " O   HOH Z  89 " =    2.062
peak=    3.272 closest distance to " CB  VAL A 202 " =    1.614
peak=    3.266 closest distance to " O   HOH Z  93 " =    2.444
peak=    3.262 closest distance to " CZ3 TRP A 266 " =    1.159
peak=    3.261 closest distance to " O   HOH Z 245 " =    1.350
peak=    3.260 closest distance to " CG  GLN A 278 " =    1.326
peak=    3.259 closest distance to " CE3 TRP A  85 " =    0.989
peak=    3.258 closest distance to " O   HOH Z   9 " =    1.853
peak=    3.258 closest distance to " CB  ALA A 180 " =    1.315
peak=    3.255 closest distance to " CD  LYS A 166 " =    1.283
peak=    3.254 closest distance to " NH2BARG A 145 " =    1.969
peak=    3.253 closest distance to " OG BSER A  99 " =    2.354
peak=    3.250 closest distance to " CG1 VAL A 189 " =    1.792
peak=    3.249 closest distance to " O   HOH Z 432 " =    1.814
peak=    3.242 closest distance to " OE2 GLU A  53 " =    1.989
peak=    3.242 closest distance to " CA  ALA A 158 " =    1.147
peak=    3.241 closest distance to " CE3 TRP A 274 " =    1.288
peak=    3.239 closest distance to " O   HOH Z 402 " =    1.480
peak=    3.237 closest distance to " CA  ALA A  51 " =    0.963
peak=    3.235 closest distance to " O   HOH Z 273 " =    2.858
peak=    3.233 closest distance to " O   HOH Z 389 " =    1.831
peak=    3.230 closest distance to " O   HOH Z  88 " =    2.617
peak=    3.230 closest distance to " CB  ALA A  34 " =    1.175
peak=    3.229 closest distance to " CD1 LEU A 300 " =    1.117
peak=    3.224 closest distance to " O   HOH Z 193 " =    2.059
peak=    3.222 closest distance to " N   TYR A 116 " =    1.366
peak=    3.220 closest distance to " O   HOH Z 415 " =    3.800
peak=    3.219 closest distance to " O   PRO A  90 " =    1.625
peak=    3.218 closest distance to " O   HOH Z 286 " =    2.158
peak=    3.212 closest distance to " CD2 TYR A 186 " =    1.076
peak=    3.210 closest distance to " O   HOH Z 219 " =    4.523
peak=    3.210 closest distance to " CB  ASP A 124 " =    0.782
peak=    3.209 closest distance to " CB  TYR A 116 " =    0.869
peak=    3.205 closest distance to " CB  ALA A 160 " =    1.427
peak=    3.204 closest distance to " ND2 ASN A 249 " =    0.830
peak=    3.203 closest distance to " CB  SER A  99 " =    0.954
peak=    3.199 closest distance to " CA  MET A 105 " =    0.828
peak=    3.198 closest distance to " NZ  LYS A 117 " =    1.349
peak=    3.197 closest distance to " CA  GLY A 136 " =    1.015
peak=    3.197 closest distance to " O   HOH Z 154 " =    1.955
peak=    3.197 closest distance to " O   HOH Z 153 " =    3.747
peak=    3.195 closest distance to " O   HOH Z  47 " =    1.847
peak=    3.194 closest distance to " CB  LEU A 143 " =    1.092
peak=    3.192 closest distance to " CG1 VAL A 153 " =    0.925
peak=    3.188 closest distance to " O   HOH Z 434 " =    1.297
peak=    3.185 closest distance to " O   HOH Z 234 " =    1.876
peak=    3.184 closest distance to " CB  PHE A 204 " =    0.716
peak=    3.180 closest distance to " O   HOH Z   3 " =    2.660
peak=    3.178 closest distance to " O   HOH Z 325 " =    2.321
peak=    3.176 closest distance to " CD BLYS A 290 " =    1.222
peak=    3.170 closest distance to " O   HOH Z  50 " =    1.634
peak=    3.169 closest distance to " O   HOH Z 388 " =    2.102
peak=    3.167 closest distance to " O   HOH Z 130 " =    3.758
peak=    3.165 closest distance to " O   HOH Z 156 " =    2.518
peak=    3.157 closest distance to " O   HOH Z 336 " =    1.928
peak=    3.154 closest distance to " CB  PRO A 243 " =    1.232
peak=    3.153 closest distance to " CG  MET A 113 " =    1.127
peak=    3.151 closest distance to " O   HOH Z  17 " =    1.786
peak=    3.150 closest distance to " O   HOH Z 238 " =    3.694
peak=    3.150 closest distance to " CB  ASP A 140 " =    0.851
peak=    3.148 closest distance to " O   HOH Z 286 " =    2.396
peak=    3.147 closest distance to " OD2 ASP A 286 " =    3.249
peak=    3.144 closest distance to " CA  LEU A 101 " =    1.795
peak=    3.143 closest distance to " CA  ALA A 129 " =    1.278
peak=    3.142 closest distance to " CA  ALA A 291 " =    0.827
peak=    3.138 closest distance to " OG  SER A  62 " =    2.842
peak=    3.137 closest distance to " CB  LEU A  83 " =    0.718
peak=    3.136 closest distance to " CZ3 TRP A 123 " =    1.504
peak=    3.136 closest distance to " NZ  LYS A 119 " =    1.409
peak=    3.132 closest distance to " O   HOH Z 184 " =    1.633
peak=    3.131 closest distance to " CG BARG A 102 " =    1.821
peak=    3.126 closest distance to " O   HOH Z 407 " =    2.196
peak=    3.126 closest distance to " O   HOH Z 132 " =    3.858
peak=    3.120 closest distance to " O   ASN A 209 " =    1.408
peak=    3.113 closest distance to " CB  TRP A 150 " =    1.251
peak=    3.112 closest distance to " CD2 LEU A 255 " =    1.605
peak=    3.104 closest distance to " CB  LEU A 300 " =    0.925
peak=    3.104 closest distance to " CB  TYR A  30 " =    1.398
peak=    3.101 closest distance to " NH1 ARG A 138 " =    1.054
peak=    3.092 closest distance to " NH2BARG A 190 " =    1.455
peak=    3.088 closest distance to " O   HOH Z 285 " =    2.338
peak=    3.087 closest distance to " CG2 ILE A 120 " =    1.270
peak=    3.078 closest distance to " CD1 LEU A 261 " =    1.272
peak=    3.077 closest distance to " O   GLY A 302 " =    2.081
peak=    3.077 closest distance to " O   HOH Z 371 " =    3.163
peak=    3.075 closest distance to " O   HOH Z 303 " =    3.195
peak=    3.065 closest distance to " N   TYR A  15 " =    0.764
peak=    3.057 closest distance to " O  BHOH Z 338 " =    2.379
peak=    3.056 closest distance to " O   HOH Z 438 " =    1.985
peak=    3.040 closest distance to " ND1 HIS A  81 " =    1.683
peak=    3.032 closest distance to " CA  ILE A 106 " =    0.757
peak=    3.019 closest distance to " O   HOH Z 217 " =    1.515
peak=    3.003 closest distance to " O   HOH Z 113 " =    1.989

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.461 - 5.480
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 192
   mapped sites are within: 0.782 - 5.480

peak=   -4.634 closest distance to " CB  PRO A 243 " =    2.595
peak=   -4.417 closest distance to " O   HOH Z 377 " =    1.993
peak=   -4.308 closest distance to " CD  ARG A  14 " =    3.352
peak=   -4.274 closest distance to " CB  ALA A  43 " =    2.418
peak=   -4.165 closest distance to " O   HOH Z 290 " =    1.081
peak=   -4.136 closest distance to " CD1 LEU A 255 " =    2.909
peak=   -4.116 closest distance to " CA  GLY A  98 " =    1.719
peak=   -4.112 closest distance to " CD  ARG A 156 " =    2.107
peak=   -4.079 closest distance to " O   PRO A 198 " =    1.234
peak=   -4.079 closest distance to " OG BSER A 134 " =    1.316
peak=   -4.076 closest distance to " O   HOH Z 185 " =    2.165
peak=   -4.048 closest distance to " O   VAL A  67 " =    2.612
peak=   -4.042 closest distance to " O   HOH Z 131 " =    4.051
peak=   -4.026 closest distance to " O   HOH Z 266 " =    4.975
peak=   -4.022 closest distance to " O   HOH Z 351 " =    1.541
peak=   -3.933 closest distance to " CE2 PHE A 218 " =    2.445
peak=   -3.932 closest distance to " N   THR A 157 " =    1.562
peak=   -3.919 closest distance to " CD  GLN A  58 " =    0.956
peak=   -3.895 closest distance to " CB  ALA A 291 " =    2.214
peak=   -3.892 closest distance to " O   HOH Z 372 " =    2.451
peak=   -3.872 closest distance to " CZ3 TRP A 179 " =    1.246
peak=   -3.861 closest distance to " O   SER A 135 " =    1.448
peak=   -3.861 closest distance to " O   SER A  22 " =    2.546
peak=   -3.844 closest distance to " O   HOH Z 231 " =    2.014
peak=   -3.840 closest distance to " CG  GLN A 223 " =    1.703
peak=   -3.828 closest distance to " C   HIS A 108 " =    1.182
peak=   -3.822 closest distance to " CB  ALA A 248 " =    2.100
peak=   -3.800 closest distance to " O   PRO A 198 " =    1.315
peak=   -3.794 closest distance to " CG1 VAL A 112 " =    2.936
peak=   -3.792 closest distance to " ND2 ASN A 249 " =    2.310
peak=   -3.776 closest distance to " O   HOH Z 389 " =    2.066
peak=   -3.775 closest distance to " CB  PHE A 192 " =    1.944
peak=   -3.767 closest distance to " O   HOH Z 152 " =    4.845
peak=   -3.763 closest distance to " O   HOH Z 385 " =    2.046
peak=   -3.743 closest distance to " CE  MET A 105 " =    2.538
peak=   -3.721 closest distance to " O   HOH Z  65 " =    1.104
peak=   -3.714 closest distance to " CG  GLN A 223 " =    0.986
peak=   -3.694 closest distance to " O   PRO A 243 " =    2.433
peak=   -3.692 closest distance to " CE2 TYR A  30 " =    2.586
peak=   -3.676 closest distance to " O   HOH Z 317 " =    1.313
peak=   -3.672 closest distance to " CD2 LEU A 237 " =    2.877
peak=   -3.671 closest distance to " CB  ASP A 132 " =    2.376
peak=   -3.665 closest distance to " CA  GLY A 241 " =    2.255
peak=   -3.661 closest distance to " O   HOH Z 140 " =    1.387
peak=   -3.645 closest distance to " CD2 TYR A 293 " =    1.926
peak=   -3.630 closest distance to " CG  ASN A  39 " =    1.654
peak=   -3.624 closest distance to " ND2 ASN A  45 " =    2.034
peak=   -3.619 closest distance to " CE BMET A  47 " =    1.270
peak=   -3.617 closest distance to " CB  ASN A  39 " =    2.310
peak=   -3.597 closest distance to " OG  SER A  87 " =    1.247
peak=   -3.591 closest distance to " CG  PHE A 283 " =    2.581
peak=   -3.583 closest distance to " N   ALA A  43 " =    2.521
peak=   -3.576 closest distance to " N   GLN A  58 " =    1.691
peak=   -3.570 closest distance to " O   HOH Z 282 " =    4.662
peak=   -3.564 closest distance to " CB  PRO A 163 " =    2.431
peak=   -3.564 closest distance to " O   HOH Z 407 " =    3.063
peak=   -3.562 closest distance to " O   HOH Z 313 " =    1.776
peak=   -3.549 closest distance to " CG1 VAL A 112 " =    2.601
peak=   -3.547 closest distance to " CG2 THR A  18 " =    2.744
peak=   -3.543 closest distance to " CB  ALA A 158 " =    1.707
peak=   -3.542 closest distance to " OG BSER A 134 " =    1.721
peak=   -3.533 closest distance to " O   ALA A  10 " =    1.694
peak=   -3.530 closest distance to " CD1 LEU A 101 " =    2.195
peak=   -3.530 closest distance to " CA  GLY A 203 " =    2.298
peak=   -3.527 closest distance to " CE  LYS A  76 " =    2.776
peak=   -3.524 closest distance to " CZ2 TRP A 274 " =    0.970
peak=   -3.524 closest distance to " O   VAL A 189 " =    2.540
peak=   -3.522 closest distance to " O   HOH Z 191 " =    5.480
peak=   -3.521 closest distance to " ND2 ASN A  60 " =    4.113
peak=   -3.521 closest distance to " O   HOH Z 211 " =    1.506
peak=   -3.516 closest distance to " OXT GLY A 302 " =    3.075
peak=   -3.516 closest distance to " OG  SER A  97 " =    2.199
peak=   -3.514 closest distance to " O   HOH Z  11 " =    1.807
peak=   -3.511 closest distance to " O   HOH Z  15 " =    1.476
peak=   -3.509 closest distance to " O   HOH Z   1 " =    1.467
peak=   -3.507 closest distance to " O   HOH Z 316 " =    1.912
peak=   -3.506 closest distance to " O   PRO A 163 " =    1.888
peak=   -3.500 closest distance to " CA  VAL A  67 " =    2.952
peak=   -3.483 closest distance to " O   ARG A 145 " =    1.375
peak=   -3.482 closest distance to " O   HOH Z 298 " =    1.133
peak=   -3.480 closest distance to " O   ALA A   1 " =    1.633
peak=   -3.477 closest distance to " O   HOH Z 198 " =    1.722
peak=   -3.469 closest distance to " O   SER A  95 " =    1.446
peak=   -3.465 closest distance to " O   ILE A  49 " =    1.703
peak=   -3.464 closest distance to " O   HOH Z 286 " =    1.738
peak=   -3.464 closest distance to " O   HOH Z  90 " =    2.521
peak=   -3.464 closest distance to " CB  TRP A  85 " =    2.434
peak=   -3.462 closest distance to " O   HOH Z 282 " =    0.782
peak=   -3.462 closest distance to " O   HOH Z 351 " =    1.694
peak=   -3.459 closest distance to " O   HOH Z 298 " =    2.520
peak=   -3.457 closest distance to " O   HOH Z  28 " =    1.697
peak=   -3.450 closest distance to " O   HOH Z  51 " =    1.029
peak=   -3.447 closest distance to " OD1 ASP A 171 " =    1.652
peak=   -3.440 closest distance to " CB  ASP A  27 " =    2.349
peak=   -3.433 closest distance to " ND2 ASN A 187 " =    1.439
peak=   -3.430 closest distance to " CB  TYR A  15 " =    2.254
peak=   -3.430 closest distance to " CA  GLY A 133 " =    1.982
peak=   -3.429 closest distance to " O   HOH Z  52 " =    1.132
peak=   -3.428 closest distance to " CD  GLU A 277 " =    1.070
peak=   -3.419 closest distance to " O   HOH Z  60 " =    2.316
peak=   -3.418 closest distance to " O   HOH Z 359 " =    3.262
peak=   -3.400 closest distance to " C   ALA A 114 " =    2.259
peak=   -3.399 closest distance to " CB  ALA A 114 " =    2.461
peak=   -3.397 closest distance to " ND2BASN A 224 " =    1.681
peak=   -3.395 closest distance to " CD1 ILE A 239 " =    2.314
peak=   -3.392 closest distance to " ND2 ASN A  45 " =    1.193
peak=   -3.389 closest distance to " CB  ALA A 291 " =    1.963
peak=   -3.389 closest distance to " CB  PHE A 208 " =    2.275
peak=   -3.383 closest distance to " OD1 ASN A 187 " =    1.666
peak=   -3.379 closest distance to " CA  ASP A 298 " =    1.089
peak=   -3.378 closest distance to " O   HOH Z  38 " =    1.732
peak=   -3.378 closest distance to " OD2 ASP A 171 " =    2.229
peak=   -3.377 closest distance to " CD1 PHE A  59 " =    2.069
peak=   -3.365 closest distance to " O   HOH Z  49 " =    1.225
peak=   -3.360 closest distance to " O   HOH Z 111 " =    2.006
peak=   -3.359 closest distance to " NH1AARG A 275 " =    1.884
peak=   -3.356 closest distance to " CG2 ILE A 263 " =    2.310
peak=   -3.355 closest distance to " O   HOH Z 166 " =    1.878
peak=   -3.351 closest distance to " O   HOH Z 174 " =    2.666
peak=   -3.348 closest distance to " O   HOH Z 253 " =    3.857
peak=   -3.345 closest distance to " CE3 TRP A 274 " =    2.375
peak=   -3.344 closest distance to " O   HOH Z  60 " =    1.855
peak=   -3.343 closest distance to " O   HOH Z 412 " =    4.140
peak=   -3.339 closest distance to " CZ  PHE A  59 " =    1.455
peak=   -3.339 closest distance to " CE  LYS A  76 " =    2.855
peak=   -3.329 closest distance to " O   HOH Z  63 " =    2.302
peak=   -3.328 closest distance to " NE2 GLN A 278 " =    1.644
peak=   -3.327 closest distance to " CA  GLY A  57 " =    2.151
peak=   -3.326 closest distance to " O   HOH Z 348 " =    1.844
peak=   -3.310 closest distance to " O   HOH Z  43 " =    1.795
peak=   -3.310 closest distance to " CG1 VAL A 230 " =    2.116
peak=   -3.309 closest distance to " CG2 ILE A  49 " =    2.761
peak=   -3.301 closest distance to " OD1 ASN A 148 " =    1.539
peak=   -3.297 closest distance to " OE1 GLN A  88 " =    1.209
peak=   -3.289 closest distance to " OD2 ASP A 191 " =    1.504
peak=   -3.287 closest distance to " CG  GLN A  88 " =    0.782
peak=   -3.282 closest distance to " O   HOH Z 134 " =    3.663
peak=   -3.281 closest distance to " CB  ALA A 248 " =    2.350
peak=   -3.276 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.275 closest distance to " OE1 GLN A 183 " =    1.583
peak=   -3.261 closest distance to " O   HOH Z 384 " =    2.922
peak=   -3.261 closest distance to " O   ALA A 161 " =    1.606
peak=   -3.258 closest distance to " CE1 PHE A  59 " =    2.147
peak=   -3.252 closest distance to " CB  CYS A 201 " =    2.224
peak=   -3.237 closest distance to " CG  GLN A 240 " =    2.432
peak=   -3.233 closest distance to " CG2 THR A 178 " =    2.160
peak=   -3.228 closest distance to " O   PHE A 218 " =    1.447
peak=   -3.227 closest distance to " CG  GLU A 152 " =    1.123
peak=   -3.224 closest distance to " CG  LEU A  83 " =    1.935
peak=   -3.222 closest distance to " N   SER A 212 " =    1.931
peak=   -3.220 closest distance to " O   GLN A 240 " =    1.997
peak=   -3.219 closest distance to " CB  SER A 245 " =    2.128
peak=   -3.216 closest distance to " CG2 ILE A 151 " =    2.572
peak=   -3.215 closest distance to " O   HOH Z 250 " =    1.386
peak=   -3.214 closest distance to " ND2 ASN A 285 " =    2.098
peak=   -3.214 closest distance to " O   HOH Z 100 " =    1.167
peak=   -3.211 closest distance to " NH2 ARG A  79 " =    2.101
peak=   -3.206 closest distance to " CG1 VAL A 197 " =    2.193
peak=   -3.198 closest distance to " O   HOH Z  24 " =    1.294
peak=   -3.197 closest distance to " CB  ALA A 131 " =    1.978
peak=   -3.194 closest distance to " CG  ARG A 139 " =    2.187
peak=   -3.183 closest distance to " CD2 PHE A 225 " =    1.105
peak=   -3.176 closest distance to " O   HOH Z 414 " =    2.089
peak=   -3.175 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.171 closest distance to " CZ  TYR A 169 " =    1.635
peak=   -3.171 closest distance to " O   GLU A 152 " =    1.434
peak=   -3.170 closest distance to " O   HOH Z 281 " =    2.747
peak=   -3.170 closest distance to " O   HOH Z 152 " =    0.899
peak=   -3.168 closest distance to " O   LYS A 181 " =    2.943
peak=   -3.158 closest distance to " N   VAL A 232 " =    2.218
peak=   -3.154 closest distance to " O   HOH Z 189 " =    1.665
peak=   -3.153 closest distance to " CB  GLN A  55 " =    1.332
peak=   -3.152 closest distance to " NH2BARG A 275 " =    1.587
peak=   -3.150 closest distance to " O   HOH Z 281 " =    2.963
peak=   -3.144 closest distance to " N   ASP A 270 " =    1.409
peak=   -3.138 closest distance to " CG  TRP A 266 " =    1.765
peak=   -3.134 closest distance to " CG  PRO A 163 " =    2.580
peak=   -3.131 closest distance to " CG1 VAL A  78 " =    2.636
peak=   -3.130 closest distance to " CD2 PHE A  61 " =    2.050
peak=   -3.119 closest distance to " CE3 TRP A 123 " =    1.355
peak=   -3.118 closest distance to " NE2 GLN A  58 " =    2.924
peak=   -3.111 closest distance to " O   HOH Z 200 " =    3.619
peak=   -3.107 closest distance to " SG BCYS A 201 " =    1.921
peak=   -3.104 closest distance to " O   HOH Z 256 " =    1.520
peak=   -3.066 closest distance to " CB  ALA A 180 " =    1.596
peak=   -3.062 closest distance to " CE3 TRP A 150 " =    2.173
peak=   -3.060 closest distance to " C   MET A 188 " =    1.586
peak=   -3.060 closest distance to " N   ASP A 171 " =    2.397
peak=   -3.046 closest distance to " SD  MET A 188 " =    2.267
peak=   -3.045 closest distance to " CD1 TRP A 179 " =    0.996

================= 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    :  0.4038 0.4031   6.216491e+00   6.203839e+00
   1_bss:  0.3901 0.3928   6.203823e+00   6.188807e+00
   1_xyz:  0.2777 0.3168   5.921820e+00   6.001786e+00
   1_adp:  0.2519 0.3269   5.872348e+00   6.028561e+00
   1_occ:  0.2515 0.3272   5.872043e+00   6.029143e+00
   2_bss:  0.2498 0.3230   5.865924e+00   6.023184e+00
   2_xyz:  0.1981 0.2552   5.649866e+00   5.834585e+00
   2_adp:  0.1872 0.2405   5.601788e+00   5.785884e+00
   2_occ:  0.1871 0.2402   5.601033e+00   5.785141e+00
   3_bss:  0.1866 0.2390   5.597913e+00   5.781664e+00
   3_xyz:  0.1437 0.1910   5.356951e+00   5.567354e+00
   3_adp:  0.1338 0.1821   5.301787e+00   5.522799e+00
   3_occ:  0.1338 0.1820   5.301482e+00   5.522399e+00
   4_bss:  0.1340 0.1812   5.299520e+00   5.519136e+00
   4_xyz:  0.1186 0.1655   5.194787e+00   5.430940e+00
   4_adp:  0.1166 0.1627   5.179522e+00   5.413834e+00
   4_occ:  0.1166 0.1627   5.179385e+00   5.413688e+00
   5_bss:  0.1166 0.1627   5.179102e+00   5.413351e+00
   5_xyz:  0.1122 0.1576   5.148291e+00   5.390095e+00
   5_adp:  0.1115 0.1566   5.143641e+00   5.386248e+00
   5_occ:  0.1114 0.1567   5.143469e+00   5.386104e+00
   5_bss:  0.1115 0.1564   5.143373e+00   5.384679e+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:  0.348  50.001  -3.257   3.243   0.155   0.000   0.000   0.000
   1_xyz:  0.348  50.001  -3.257   3.243   0.155   0.000   0.000   0.000
   1_adp:  0.348  50.001  -3.257   3.243   0.155   0.000   0.000   0.000
   1_occ:  0.348  50.001  -3.257   3.243   0.155   0.000   0.000   0.000
   2_bss:  0.341  63.927  -2.451  -0.118  -0.351  -0.000  -0.000  -0.000
   2_xyz:  0.341  63.927  -2.451  -0.118  -0.351  -0.000  -0.000  -0.000
   2_adp:  0.341  63.927  -2.451  -0.118  -0.351  -0.000  -0.000  -0.000
   2_occ:  0.341  63.927  -2.451  -0.118  -0.351  -0.000  -0.000  -0.000
   3_bss:  0.332  56.552  -2.331  -1.401  -0.470  -0.000  -0.000  -0.000
   3_xyz:  0.332  56.552  -2.331  -1.401  -0.470  -0.000  -0.000  -0.000
   3_adp:  0.332  56.552  -2.331  -1.401  -0.470  -0.000  -0.000  -0.000
   3_occ:  0.332  56.552  -2.331  -1.401  -0.470  -0.000  -0.000  -0.000
   4_bss:  0.321  53.666  -2.480  -2.259  -0.743  -0.000  -0.000  -0.000
   4_xyz:  0.321  53.666  -2.480  -2.259  -0.743  -0.000  -0.000  -0.000
   4_adp:  0.321  53.666  -2.480  -2.259  -0.743  -0.000  -0.000  -0.000
   4_occ:  0.321  53.666  -2.480  -2.259  -0.743  -0.000  -0.000  -0.000
   5_bss:  0.318  49.886  -2.463  -2.432  -0.749  -0.000  -0.000  -0.000
   5_xyz:  0.318  49.886  -2.463  -2.432  -0.749  -0.000  -0.000  -0.000
   5_adp:  0.318  49.886  -2.463  -2.432  -0.749  -0.000  -0.000  -0.000
   5_occ:  0.318  49.886  -2.463  -2.432  -0.749  -0.000  -0.000  -0.000
   5_bss:  0.319  49.853  -2.359  -2.450  -0.655  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.733 0.5621  0.7442    51482.319
   1_bss:  45.894 0.5708  0.7597    48834.246
   1_xyz:  32.407 0.7319  0.9314    26703.785
   1_adp:  33.972 0.7131  0.9123    28904.847
   1_occ:  34.054 0.7121  0.9102    28935.229
   2_bss:  33.426 0.7192  0.8885    28133.282
   2_xyz:  25.527 0.8049  0.9628    16867.209
   2_adp:  23.451 0.8276  0.9727    14886.660
   2_occ:  23.427 0.8278  0.9725    14856.538
   3_bss:  23.273 0.8292  0.9589    14674.938
   3_xyz:  18.135 0.8787  0.9900     9227.781
   3_adp:  17.052 0.8890  0.9884     8498.500
   3_occ:  17.043 0.8891  0.9881     8484.334
   4_bss:  16.956 0.8898  0.9738     8412.161
   4_xyz:  14.963 0.9068  0.9830     6932.291
   4_adp:  14.547 0.9106  0.9814     6745.085
   4_occ:  14.548 0.9106  0.9813     6738.920
   5_bss:  14.543 0.9106  0.9794     6734.359
   5_xyz:  14.014 0.9150  0.9798     6382.686
   5_adp:  13.906 0.9159  0.9755     6324.746
   5_occ:  13.906 0.9159  0.9755     6320.708
   5_bss:  13.892 0.9160  0.9767     6290.930
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7253e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7253e-01
   1_xyz:   1.471  0.011  0.099 15.933  0.006  4.107   1.1871e-01
   1_adp:   1.471  0.011  0.099 15.933  0.006  4.107   1.1871e-01
   1_occ:   1.471  0.011  0.099 15.933  0.006  4.107   1.1871e-01
   2_bss:   1.471  0.011  0.099 15.933  0.006  4.107   1.1871e-01
   2_xyz:   1.036  0.006  0.074 14.533  0.004  4.108   5.9288e-02
   2_adp:   1.036  0.006  0.074 14.533  0.004  4.108   5.9288e-02
   2_occ:   1.036  0.006  0.074 14.533  0.004  4.108   5.9288e-02
   3_bss:   1.036  0.006  0.074 14.533  0.004  4.108   5.9288e-02
   3_xyz:   0.983  0.006  0.070 14.660  0.004  4.112   5.6365e-02
   3_adp:   0.983  0.006  0.070 14.660  0.004  4.112   5.6365e-02
   3_occ:   0.983  0.006  0.070 14.660  0.004  4.112   5.6365e-02
   4_bss:   0.983  0.006  0.070 14.660  0.004  4.112   5.6365e-02
   4_xyz:   0.986  0.007  0.074 14.638  0.004  4.109   5.8817e-02
   4_adp:   0.986  0.007  0.074 14.638  0.004  4.109   5.8817e-02
   4_occ:   0.986  0.007  0.074 14.638  0.004  4.109   5.8817e-02
   5_bss:   0.986  0.007  0.074 14.638  0.004  4.109   5.8817e-02
   5_xyz:   0.996  0.007  0.075 14.632  0.004  4.111   5.9746e-02
   5_adp:   0.996  0.007  0.075 14.632  0.004  4.111   5.9746e-02
   5_occ:   0.996  0.007  0.075 14.632  0.004  4.111   5.9746e-02
   5_bss:   0.996  0.007  0.075 14.632  0.004  4.111   5.9746e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4033e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4033e-01
   1_xyz:  10.740  0.058  0.311 82.035  0.044  2.079   1.1676e-01
   1_adp:  10.740  0.058  0.311 82.035  0.044  2.079   1.1676e-01
   1_occ:  10.740  0.058  0.311 82.035  0.044  2.079   1.1676e-01
   2_bss:  10.740  0.058  0.311 82.035  0.044  2.079   1.1676e-01
   2_xyz:   7.007  0.033  0.248 81.387  0.040  2.341   5.4121e-02
   2_adp:   7.007  0.033  0.248 81.387  0.040  2.341   5.4121e-02
   2_occ:   7.007  0.033  0.248 81.387  0.040  2.341   5.4121e-02
   3_bss:   7.007  0.033  0.248 81.387  0.040  2.341   5.4121e-02
   3_xyz:   6.042  0.041  0.239 82.102  0.032  2.325   5.0687e-02
   3_adp:   6.042  0.041  0.239 82.102  0.032  2.325   5.0687e-02
   3_occ:   6.042  0.041  0.239 82.102  0.032  2.325   5.0687e-02
   4_bss:   6.042  0.041  0.239 82.102  0.032  2.325   5.0687e-02
   4_xyz:   6.569  0.043  0.236 82.871  0.034  2.317   5.9575e-02
   4_adp:   6.569  0.043  0.236 82.871  0.034  2.317   5.9575e-02
   4_occ:   6.569  0.043  0.236 82.871  0.034  2.317   5.9575e-02
   5_bss:   6.569  0.043  0.236 82.871  0.034  2.317   5.9575e-02
   5_xyz:   6.544  0.044  0.240 84.707  0.036  2.306   4.3561e-02
   5_adp:   6.544  0.044  0.240 84.707  0.036  2.306   4.3561e-02
   5_occ:   6.544  0.044  0.240 84.707  0.036  2.306   4.3561e-02
   5_bss:   6.544  0.044  0.240 84.707  0.036  2.306   4.3561e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  95.23   0.00  17.82  69.25   0.00  13.81  95.23   2.54  39.64
   1_occ:  95.23   0.00  17.82  69.25   0.00  13.81  95.23   2.54  39.64
   2_bss:  95.23   0.00  17.82  69.25   0.00  13.81  95.23   2.54  39.64
   2_xyz:  95.23   0.00  17.82  69.25   0.00  13.81  95.23   2.54  39.64
   2_adp:  90.97   0.00  17.31  76.28   0.00  13.29  90.97   4.95  39.22
   2_occ:  90.97   0.00  17.31  76.28   0.00  13.29  90.97   4.95  39.22
   3_bss:  90.97   0.00  17.31  76.28   0.00  13.29  90.97   4.95  39.22
   3_xyz:  90.97   0.00  17.31  76.28   0.00  13.29  90.97   4.95  39.22
   3_adp:  87.65   0.52  17.25  82.24   0.52  12.87  87.65   5.29  41.12
   3_occ:  87.65   0.52  17.25  82.24   0.52  12.87  87.65   5.29  41.12
   4_bss:  87.65   0.52  17.25  82.24   0.52  12.87  87.65   5.29  41.12
   4_xyz:  87.65   0.52  17.25  82.24   0.52  12.87  87.65   5.29  41.12
   4_adp:  86.20   0.75  16.83  86.20   0.75  12.69  83.03   3.62  39.42
   4_occ:  86.20   0.75  16.83  86.20   0.75  12.69  83.03   3.62  39.42
   5_bss:  86.20   0.75  16.83  86.20   0.75  12.69  83.03   3.62  39.42
   5_xyz:  86.20   0.75  16.83  86.20   0.75  12.69  83.03   3.62  39.42
   5_adp:  87.32   0.96  16.59  87.32   0.96  12.54  80.98   5.66  38.63
   5_occ:  87.32   0.96  16.59  87.32   0.96  12.54  80.98   5.66  38.63
   5_bss:  87.29   0.93  16.56  87.29   0.93  12.51  80.95   5.62  38.60
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.550    0.014    0.405
   1_adp:    1.550    0.014    0.405
   1_occ:    1.550    0.014    0.405
   2_bss:    1.550    0.014    0.405
   2_xyz:    1.261    0.034    0.474
   2_adp:    1.261    0.034    0.474
   2_occ:    1.261    0.034    0.474
   3_bss:    1.261    0.034    0.474
   3_xyz:    1.266    0.015    0.591
   3_adp:    1.266    0.015    0.591
   3_occ:    1.266    0.015    0.591
   4_bss:    1.266    0.015    0.591
   4_xyz:    1.395    0.037    0.626
   4_adp:    1.395    0.037    0.626
   4_occ:    1.395    0.037    0.626
   5_bss:    1.395    0.037    0.626
   5_xyz:    1.497    0.062    0.644
   5_adp:    1.497    0.062    0.644
   5_occ:    1.497    0.062    0.644
   5_bss:    1.497    0.062    0.644
------------------------------------------------------------------------

CPU time actual refinement: 330.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_623/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_623/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_623/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_623/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_623/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.64 
  Macro-tasks:
    bulk solvent and scale       = 37.91  
    individual site refinement   = 138.32 
    weights calculation          = 29.23  
    collect and process          = 6.61   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 212.15 
  Micro-tasks:
    mask                            = 2.34   
    f_calc                          = 104.96 
    alpha_beta                      = 8.22   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 114.57 
    fmodel                         = 6.47   
    r_factors                      = 0.27   
    phase_errors                   = 11.02  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 249.22 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.643 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    659 calls, 104.55 s
gradients_fft:          604 calls, 100.65 s

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

# Date 2008-01-16 Time 05:16:41 PST -0800 (1200489401.05 s)
Start R-work = 0.4038, R-free = 0.4031 (no bulk solvent and anisotropic scale)
Final R-work = 0.1356, R-free = 0.1772 (no bulk solvent and anisotropic scale)

Start R-work = 0.3901, R-free = 0.3928
Final R-work = 0.1115, R-free = 0.1564