# Date 2008-01-16 Time 05:43:05 PST -0800 (1200490985.76 s)
#phil __OFF__

Command line arguments: "../855.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26425
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 855

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 45.7567, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 1.95405
Completeness in resolution range: 0.91993
Completeness with d_max=infinity: 0.917303

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   1.9540

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 1.95405
Completeness in resolution range: 0.91993
Completeness with d_max=infinity: 0.917303

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1646 -  4.1832 [2230/2256]  2007   223  10.0%
  bin  2:  4.1832 -  3.3319 [2161/2181]  1948   213   9.9%
  bin  3:  3.3319 -  2.9141 [2104/2123]  1890   214  10.2%
  bin  4:  2.9141 -  2.6492 [2098/2128]  1882   216  10.3%
  bin  5:  2.6492 -  2.4602 [2100/2119]  1896   204   9.7%
  bin  6:  2.4602 -  2.3157 [2078/2103]  1868   210  10.1%
  bin  7:  2.3157 -  2.2001 [2067/2095]  1858   209  10.1%
  bin  8:  2.2001 -  2.1046 [2054/2090]  1848   206  10.0%
  bin  9:  2.1046 -  2.0237 [2045/2097]  1850   195   9.5%
  bin 10:  2.0237 -  1.9540 [ 652/2102]   583    69  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_855/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 29
        2.32 -     2.97: 1780
        2.97 -     3.61: 4571
        3.61 -     4.26: 9168
        4.26 -     4.90: 12777
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.774 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28320 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_855/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_855/model_refine_001.geo

CPU time processing inputs: 9.41


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 45.75675 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4645   r_free= 0.4656   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281536                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.6667 0.99   1451  162 0.3863 0.3771      6.5945      6.5707|
|  2:  4.6667 -  3.7221 0.99   1391  153 0.4064 0.3921      6.8232      6.7788|
|  3:  3.7221 -  3.2569 0.99   1373  153 0.4313 0.4229      6.6595       6.669|
|  4:  3.2569 -  2.9615 0.99   1364  154 0.4632 0.4920      6.5289      6.5325|
|  5:  2.9615 -  2.7506 0.99   1349  148 0.4963 0.4879      6.3549      6.3877|
|  6:  2.7506 -  2.5893 0.99   1351  151 0.4970 0.5047      6.2642      6.2083|
|  7:  2.5893 -  2.4602 0.99   1344  149 0.4916 0.4914      6.2214      6.1617|
|  8:  2.4602 -  2.3535 0.98   1329  148 0.5127 0.5234       6.164      6.1507|
|  9:  2.3535 -  2.2632 0.98   1326  147 0.4992 0.5419      6.1189      6.1939|
| 10:  2.2632 -  2.1853 1.00   1331  156 0.5167 0.5343      6.0528      6.0563|
| 11:  2.1853 -  2.1172 0.98   1328  143 0.4968 0.5057      6.0207      6.0425|
| 12:  2.1172 -  2.0568 0.98   1322  140 0.5074 0.4912      5.9227      5.9343|
| 13:  2.0568 -  2.0028 0.83   1116  125 0.5133 0.4910      5.8747      5.7955|
| 14:  2.0028 -  1.9540 0.19    255   30 0.5170 0.5139      5.8603      5.8702|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.6667  1451   162  0.71  33.22   0.81     0.77      70069.22|
|  2:  4.6667 -  3.7221  1391   153  0.69  35.99   0.89     0.80     113465.00|
|  3:  3.7221 -  3.2569  1373   153  0.55  47.75   0.92     0.74     124713.75|
|  4:  3.2569 -  2.9615  1364   154  0.44  56.27   0.89     0.63     117232.55|
|  5:  2.9615 -  2.7506  1349   148  0.39  60.88   0.88     0.57      87747.40|
|  6:  2.7506 -  2.5893  1351   151  0.36  62.53   0.89     0.53      73936.04|
|  7:  2.5893 -  2.4602  1344   149  0.37  62.60   0.91     0.52      65193.49|
|  8:  2.4602 -  2.3535  1329   148  0.34  64.77   0.90     0.49      59832.23|
|  9:  2.3535 -  2.2632  1326   147  0.33  65.32   0.93     0.49      56972.98|
| 10:  2.2632 -  2.1853  1331   156  0.31  66.45   0.91     0.48      50519.73|
| 11:  2.1853 -  2.1172  1328   143  0.31  66.52   0.97     0.49      49228.92|
| 12:  2.1172 -  2.0568  1322   140  0.32  66.01   0.93     0.51      42887.94|
| 13:  2.0568 -  2.0028  1116   125  0.33  65.33   0.95     0.55      36786.54|
| 14:  2.0028 -  1.9540   255    30  0.43  58.03   1.02     0.61      27280.50|
|alpha:            min =        0.48 max =            0.80 mean =         0.59|
|beta:             min =    27280.50 max =       124713.75 mean =     73108.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.62|
|phase err.(test): min =        0.00 max =           89.83 mean =        58.07|
|-----------------------------------------------------------------------------|

============================== 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 = 12.221747             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.588   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.233346              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.459   (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 |  1.681 -  2.003:       12 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       79 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1701 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1907 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2664 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4748 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4420 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5832 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6945 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.503 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4645   r_free= 0.4656   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281536                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4558   r_free= 0.4604   ksol= 0.30   Bsol= 50.00   scale= 0.919   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,1.95,1.00,0.00,0.00,0.00); trace/3= 0.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.277652                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.971729              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.471   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.512569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.172   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4558      final r-factor (work) = 0.3829          |
| start r-factor (free) = 0.4604      final r-factor (free) = 0.4231          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.4562 = 9.97 * 0.50 * 6.2721 + 1.00 * 0.1845                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0088 = 9.97 * 0.50 * 6.1969 + 1.00 * 0.1118                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3829      final r-factor (work) = 0.3510          |
| start r-factor (free) = 0.4231      final r-factor (free) = 0.4287          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3793 = 1.51 * 1.00 * 6.1969 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2871 = 1.51 * 1.00 * 6.1256 + 1.00 * 0.0217                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.07  19.76    None  None   None       |
|    all(noH): 2823   0      0.00    104.07  19.76    None  None   None       |
|    Sol.    : 438    0      0.00    104.07  37.13    None  None   None       |
|    Mac.    : 2385   0      0.00    82.77   16.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.407:  881   |   5:    52.036 -  62.443:   72        |
|      1:    10.407 -  20.814:  881   |   6:    62.443 -  72.850:   40        |
|      2:    20.814 -  31.221:  540   |   7:    72.850 -  83.257:   18        |
|      3:    31.221 -  41.628:  260   |   8:    83.257 -  93.664:    6        |
|      4:    41.628 -  52.036:  124   |   9:    93.664 - 104.071:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3510 r_free = 0.4287             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3508 r_free = 0.4287             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3508   r_free= 0.4287   ksol= 0.30   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,1.95,1.00,0.00,0.00,0.00); trace/3= 0.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.128795                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3513   r_free= 0.4279   ksol= 0.36   Bsol= 82.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,0.48,0.52,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.131645                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.482855             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.832  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.567441              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.751  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3513      final r-factor (work) = 0.2905          |
| start r-factor (free) = 0.4279      final r-factor (free) = 0.3740          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.3570 = 12.48 * 0.50 * 6.1276 + 1.00 * 0.1118                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.9603 = 12.48 * 0.50 * 6.0650 + 1.00 * 0.1059                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2905      final r-factor (work) = 0.2740          |
| start r-factor (free) = 0.3740      final r-factor (free) = 0.3610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4632 = 0.57 * 1.00 * 6.0650 + 1.00 * 0.0216                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3980 = 0.57 * 1.00 * 5.9666 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.70   19.08    None  None   None       |
|    all(noH): 2823   0      0.00    99.70   19.08    None  None   None       |
|    Sol.    : 438    0      0.00    99.70   37.63    None  None   None       |
|    Mac.    : 2385   0      0.00    84.39   15.67    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 -   9.970:  835   |   5:    49.851 -  59.821:   68        |
|      1:     9.970 -  19.940: 1004   |   6:    59.821 -  69.791:   45        |
|      2:    19.940 -  29.910:  473   |   7:    69.791 -  79.761:    7        |
|      3:    29.910 -  39.881:  260   |   8:    79.761 -  89.731:    3        |
|      4:    39.881 -  49.851:  126   |   9:    89.731 -  99.701:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2740 r_free = 0.3610             target_work(ml) = 5.951         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2738 r_free = 0.3606             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2738   r_free= 0.3606   ksol= 0.36   Bsol= 82.80   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,0.48,0.52,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.949940                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2738   r_free= 0.3588   ksol= 0.35   Bsol= 80.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-0.89,0.01,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.947384                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.809127              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.053  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.222057              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.851  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2738      final r-factor (work) = 0.2208          |
| start r-factor (free) = 0.3588      final r-factor (free) = 0.2864          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4191 = 6.81 * 0.50 * 5.9665 + 1.00 * 0.1059                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0573 = 6.81 * 0.50 * 5.8690 + 1.00 * 0.0758                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2208      final r-factor (work) = 0.1957          |
| start r-factor (free) = 0.2864      final r-factor (free) = 0.2647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1845 = 1.22 * 1.00 * 5.8690 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9668 = 1.22 * 1.00 * 5.6882 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.63  19.82    None  None   None       |
|    all(noH): 2823   0      0.00    104.63  19.82    None  None   None       |
|    Sol.    : 438    0      4.19    104.63  47.86    None  None   None       |
|    Mac.    : 2385   0      0.00    102.51  14.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.463: 1023   |   5:    52.313 -  62.776:   99        |
|      1:    10.463 -  20.925:  968   |   6:    62.776 -  73.239:   75        |
|      2:    20.925 -  31.388:  318   |   7:    73.239 -  83.701:   36        |
|      3:    31.388 -  41.851:  176   |   8:    83.701 -  94.164:   14        |
|      4:    41.851 -  52.313:  110   |   9:    94.164 - 104.627:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1957 r_free = 0.2647             target_work(ml) = 5.652         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1956 r_free = 0.2646             target_work(ml) = 5.651         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1956   r_free= 0.2646   ksol= 0.35   Bsol= 80.00   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-0.89,0.01,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.651435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1952   r_free= 0.2641   ksol= 0.34   Bsol= 80.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.11,-0.57,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.649438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.994196              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.015   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.420173              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.290  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1952      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2641      final r-factor (free) = 0.2128          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1307 = 5.99 * 0.50 * 5.6905 + 1.00 * 0.0758                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7334 = 5.99 * 0.50 * 5.5584 + 1.00 * 0.0744                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1543      final r-factor (work) = 0.1417          |
| start r-factor (free) = 0.2128      final r-factor (free) = 0.1962          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3508 = 0.42 * 1.00 * 5.5584 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2808 = 0.42 * 1.00 * 5.4012 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.58  18.79    None  None   None       |
|    all(noH): 2823   0      0.00    102.58  18.79    None  None   None       |
|    Sol.    : 438    0      4.98    101.31  47.15    None  None   None       |
|    Mac.    : 2385   0      0.00    102.58  13.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.258: 1049   |   5:    51.289 -  61.547:  106        |
|      1:    10.258 -  20.516: 1087   |   6:    61.547 -  71.804:   69        |
|      2:    20.516 -  30.773:  224   |   7:    71.804 -  82.062:   39        |
|      3:    30.773 -  41.031:  131   |   8:    82.062 -  92.320:   14        |
|      4:    41.031 -  51.289:  100   |   9:    92.320 - 102.578:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1417 r_free = 0.1962             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1416 r_free = 0.1960             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1416   r_free= 0.1960   ksol= 0.34   Bsol= 80.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.11,-0.57,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.356176                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1418   r_free= 0.1957   ksol= 0.32   Bsol= 65.80   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.76,-0.86,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.353530                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.226156              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.816  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.615487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.789  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.1957      final r-factor (free) = 0.1812          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0870 = 2.23 * 0.50 * 5.4018 + 1.00 * 0.0744                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9843 = 2.23 * 0.50 * 5.3289 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1812      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6201 = 1.62 * 1.00 * 5.3289 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5337 = 1.62 * 1.00 * 5.2748 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.45  18.71    None  None   None       |
|    all(noH): 2823   0      0.00    106.45  18.71    None  None   None       |
|    Sol.    : 438    0      5.08    104.62  48.21    None  None   None       |
|    Mac.    : 2385   0      0.00    106.45  13.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.645: 1153   |   5:    53.226 -  63.871:   78        |
|      1:    10.645 -  21.290: 1024   |   6:    63.871 -  74.516:   63        |
|      2:    21.290 -  31.936:  219   |   7:    74.516 -  85.162:   44        |
|      3:    31.936 -  42.581:  121   |   8:    85.162 -  95.807:   18        |
|      4:    42.581 -  53.226:   95   |   9:    95.807 - 106.452:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1796             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1283 r_free = 0.1795             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1795   ksol= 0.32   Bsol= 65.80   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.76,-0.86,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.267457                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.6667 0.99   1451  162 0.0998 0.1364      5.4094      5.6317|
|  2:  4.6667 -  3.7221 0.99   1391  153 0.0897 0.1198      5.4865      5.7072|
|  3:  3.7221 -  3.2569 0.99   1373  153 0.1186 0.1638      5.5544      5.8481|
|  4:  3.2569 -  2.9615 0.99   1364  154 0.1507 0.1973      5.5944      5.7405|
|  5:  2.9615 -  2.7506 0.99   1349  148 0.1544 0.2065      5.4635      5.7116|
|  6:  2.7506 -  2.5893 0.99   1351  151 0.1459 0.2175      5.3254      5.5586|
|  7:  2.5893 -  2.4602 0.99   1344  149 0.1432 0.1895      5.2824      5.4402|
|  8:  2.4602 -  2.3535 0.98   1329  148 0.1404 0.1989      5.1978      5.4785|
|  9:  2.3535 -  2.2632 0.98   1326  147 0.1400 0.1977      5.1693        5.42|
| 10:  2.2632 -  2.1853 1.00   1331  156 0.1282 0.1820      5.0366      5.2683|
| 11:  2.1853 -  2.1172 0.98   1328  143 0.1288 0.1991      5.0387      5.3926|
| 12:  2.1172 -  2.0568 0.98   1322  140 0.1355 0.2206      4.9995      5.2775|
| 13:  2.0568 -  2.0028 0.83   1116  125 0.1306 0.1857      4.9102       5.094|
| 14:  2.0028 -  1.9540 0.19    255   30 0.1118 0.1885      4.7709        5.12|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.6667  1451   162  0.93   9.86   0.96     0.93       7940.76|
|  2:  4.6667 -  3.7221  1391   153  0.95   8.36   1.02     1.00       9834.71|
|  3:  3.7221 -  3.2569  1373   153  0.92  12.91   1.04     1.04      12179.42|
|  4:  3.2569 -  2.9615  1364   154  0.89  17.14   1.02     0.99      13496.45|
|  5:  2.9615 -  2.7506  1349   148  0.88  18.70   1.00     0.98      11146.29|
|  6:  2.7506 -  2.5893  1351   151  0.87  18.99   0.99     0.96       8914.04|
|  7:  2.5893 -  2.4602  1344   149  0.88  18.09   1.00     0.96       8010.50|
|  8:  2.4602 -  2.3535  1329   148  0.88  18.68   1.00     0.97       6944.01|
|  9:  2.3535 -  2.2632  1326   147  0.88  18.42   0.99     0.93       6352.74|
| 10:  2.2632 -  2.1853  1331   156  0.89  17.68   1.00     0.97       5230.80|
| 11:  2.1853 -  2.1172  1328   143  0.88  18.14   0.99     0.93       5288.83|
| 12:  2.1172 -  2.0568  1322   140  0.88  19.26   1.00     0.98       5207.74|
| 13:  2.0568 -  2.0028  1116   125  0.87  19.96   0.98     0.96       4523.84|
| 14:  2.0028 -  1.9540   255    30  0.92  15.08   0.99     0.96       3213.01|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3213.01 max =        13496.45 mean =      8086.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.49|
|phase err.(test): min =        0.00 max =           89.99 mean =        15.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1795   ksol= 0.31   Bsol= 61.75   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.82,-0.81,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.267360                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1795   ksol= 0.31   Bsol= 61.75   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.82,-0.81,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.267360                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.6667 0.99   1451  162 0.0996 0.1363      5.4089       5.632|
|  2:  4.6667 -  3.7221 0.99   1391  153 0.0895 0.1198      5.4858      5.7059|
|  3:  3.7221 -  3.2569 0.99   1373  153 0.1184 0.1636      5.5537       5.847|
|  4:  3.2569 -  2.9615 0.99   1364  154 0.1508 0.1973      5.5944      5.7408|
|  5:  2.9615 -  2.7506 0.99   1349  148 0.1545 0.2065      5.4636      5.7119|
|  6:  2.7506 -  2.5893 0.99   1351  151 0.1459 0.2174      5.3252      5.5584|
|  7:  2.5893 -  2.4602 0.99   1344  149 0.1432 0.1896      5.2826      5.4405|
|  8:  2.4602 -  2.3535 0.98   1329  148 0.1405 0.1992      5.1982      5.4796|
|  9:  2.3535 -  2.2632 0.98   1326  147 0.1400 0.1975      5.1699      5.4195|
| 10:  2.2632 -  2.1853 1.00   1331  156 0.1282 0.1822      5.0368      5.2693|
| 11:  2.1853 -  2.1172 0.98   1328  143 0.1287 0.1993      5.0387      5.3937|
| 12:  2.1172 -  2.0568 0.98   1322  140 0.1354 0.2205      4.9995      5.2773|
| 13:  2.0568 -  2.0028 0.83   1116  125 0.1305 0.1854      4.9098       5.093|
| 14:  2.0028 -  1.9540 0.19    255   30 0.1119 0.1884      4.7699      5.1191|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.6667  1451   162  0.93   9.86   0.96     0.93       7940.69|
|  2:  4.6667 -  3.7221  1391   153  0.95   8.36   1.02     1.00       9825.09|
|  3:  3.7221 -  3.2569  1373   153  0.92  12.89   1.04     1.04      12157.50|
|  4:  3.2569 -  2.9615  1364   154  0.89  17.13   1.02     0.99      13485.34|
|  5:  2.9615 -  2.7506  1349   148  0.88  18.69   1.00     0.98      11144.52|
|  6:  2.7506 -  2.5893  1351   151  0.87  18.99   0.99     0.96       8913.13|
|  7:  2.5893 -  2.4602  1344   149  0.88  18.09   1.00     0.96       8014.05|
|  8:  2.4602 -  2.3535  1329   148  0.88  18.69   1.00     0.97       6952.24|
|  9:  2.3535 -  2.2632  1326   147  0.88  18.43   0.99     0.93       6359.87|
| 10:  2.2632 -  2.1853  1331   156  0.89  17.70   1.00     0.97       5236.41|
| 11:  2.1853 -  2.1172  1328   143  0.88  18.15   0.99     0.93       5295.41|
| 12:  2.1172 -  2.0568  1322   140  0.88  19.27   1.00     0.98       5210.80|
| 13:  2.0568 -  2.0028  1116   125  0.87  19.95   0.99     0.96       4521.28|
| 14:  2.0028 -  1.9540   255    30  0.92  15.04   0.99     0.96       3204.00|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3204.00 max =        13485.34 mean =      8085.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.94 mean =        16.49|
|phase err.(test): min =        0.00 max =           89.53 mean =        15.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.45  18.72    None  None   None       |
|    all(noH): 2823   0      0.00    106.45  18.72    None  None   None       |
|    Sol.    : 438    0      5.09    104.62  48.21    None  None   None       |
|    Mac.    : 2385   0      0.00    106.45  13.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.648: 1153   |   5:    53.229 -  63.874:   78        |
|      1:    10.648 -  21.293: 1024   |   6:    63.874 -  74.519:   63        |
|      2:    21.293 -  31.939:  219   |   7:    74.519 -  85.165:   44        |
|      3:    31.939 -  42.584:  121   |   8:    85.165 -  95.810:   18        |
|      4:    42.584 -  53.229:   95   |   9:    95.810 - 106.455:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 353         
Filter by distance & map next to the model:
   mapped sites are within: 0.615 - 5.453
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 351 from: 353
   mapped sites are within: 0.721 - 5.453

peak=    8.247 closest distance to " O   HOH Z 390 " =    1.309
peak=    7.014 closest distance to " O   HOH Z 385 " =    1.668
peak=    6.612 closest distance to " O   HOH Z 245 " =    1.322
peak=    5.571 closest distance to " O   HOH Z 222 " =    1.338
peak=    5.557 closest distance to " NE2 GLN A  11 " =    1.361
peak=    5.536 closest distance to " O   HOH Z 431 " =    1.753
peak=    5.314 closest distance to " O   HOH Z  65 " =    1.451
peak=    5.289 closest distance to " O   HOH Z 417 " =    2.636
peak=    5.245 closest distance to " O   HOH Z 287 " =    2.183
peak=    5.241 closest distance to " O   HOH Z 424 " =    1.996
peak=    5.107 closest distance to " CG  PRO A  90 " =    1.342
peak=    4.994 closest distance to " O   HOH Z  63 " =    2.138
peak=    4.917 closest distance to " CG  PRO A  54 " =    1.431
peak=    4.887 closest distance to " O   HOH Z  29 " =    1.317
peak=    4.781 closest distance to " CB  SER A 216 " =    1.080
peak=    4.742 closest distance to " CB  GLN A 223 " =    1.557
peak=    4.720 closest distance to " O   HOH Z 130 " =    0.863
peak=    4.664 closest distance to " O   HOH Z 142 " =    1.974
peak=    4.663 closest distance to " O   HOH Z  11 " =    1.164
peak=    4.640 closest distance to " O   HOH Z 105 " =    1.351
peak=    4.633 closest distance to " O   HOH Z 145 " =    2.094
peak=    4.627 closest distance to " O   HOH Z 427 " =    1.267
peak=    4.623 closest distance to " O   HOH Z  69 " =    1.464
peak=    4.590 closest distance to " O   HOH Z 232 " =    2.120
peak=    4.583 closest distance to " O   HOH Z  63 " =    1.780
peak=    4.539 closest distance to " O   HOH Z 427 " =    2.080
peak=    4.515 closest distance to " O   HOH Z 139 " =    1.335
peak=    4.508 closest distance to " CG  PRO A 198 " =    1.275
peak=    4.498 closest distance to " O   HOH Z 276 " =    1.352
peak=    4.483 closest distance to " O   HOH Z   9 " =    1.717
peak=    4.459 closest distance to " CB  PRO A  54 " =    1.176
peak=    4.441 closest distance to " O   HOH Z 316 " =    3.084
peak=    4.436 closest distance to " O   HOH Z 293 " =    1.552
peak=    4.410 closest distance to " O   HOH Z  66 " =    1.108
peak=    4.403 closest distance to " O   HOH Z 414 " =    1.523
peak=    4.389 closest distance to " O   HOH Z 361 " =    1.525
peak=    4.383 closest distance to " O   ASP A 286 " =    2.550
peak=    4.353 closest distance to " CB  SER A  63 " =    1.342
peak=    4.328 closest distance to " O   HOH Z 225 " =    1.792
peak=    4.305 closest distance to " O   HOH Z 380 " =    2.196
peak=    4.298 closest distance to " O   HOH Z 425 " =    1.557
peak=    4.296 closest distance to " O   PRO A 198 " =    1.234
peak=    4.295 closest distance to " O   HOH Z 403 " =    1.588
peak=    4.274 closest distance to " CG  PRO A 213 " =    1.326
peak=    4.262 closest distance to " O   HOH Z 211 " =    1.359
peak=    4.257 closest distance to " O   HOH Z 158 " =    1.326
peak=    4.247 closest distance to " O   HOH Z  49 " =    1.387
peak=    4.223 closest distance to " O   HOH Z 369 " =    1.971
peak=    4.204 closest distance to " O   HOH Z 359 " =    1.508
peak=    4.200 closest distance to " CE3 TRP A 274 " =    1.445
peak=    4.199 closest distance to " O   HOH Z 424 " =    1.308
peak=    4.190 closest distance to " NZ  LYS A 119 " =    2.453
peak=    4.156 closest distance to " CB  ASN A 148 " =    1.390
peak=    4.152 closest distance to " CG2 ILE A 120 " =    1.114
peak=    4.148 closest distance to " O   HOH Z  78 " =    1.732
peak=    4.135 closest distance to " O   HOH Z 418 " =    1.052
peak=    4.132 closest distance to " O   HOH Z 298 " =    1.976
peak=    4.113 closest distance to " O   HOH Z  46 " =    1.031
peak=    4.073 closest distance to " O   HOH Z 423 " =    2.068
peak=    4.070 closest distance to " O   HOH Z 295 " =    1.151
peak=    4.067 closest distance to " O   HOH Z  39 " =    1.098
peak=    4.059 closest distance to " O   HOH Z  57 " =    1.304
peak=    4.056 closest distance to " NH1AARG A 145 " =    1.221
peak=    4.048 closest distance to " CA  TYR A  30 " =    1.122
peak=    4.047 closest distance to " CA  ALA A  51 " =    1.075
peak=    4.027 closest distance to " O   HOH Z 392 " =    1.370
peak=    4.022 closest distance to " N   TYR A  15 " =    1.072
peak=    4.000 closest distance to " CZ3 TRP A 266 " =    1.143
peak=    3.997 closest distance to " O   HOH Z  59 " =    1.808
peak=    3.995 closest distance to " O   HOH Z 103 " =    0.848
peak=    3.993 closest distance to " CB  SER A 276 " =    1.133
peak=    3.990 closest distance to " O   HOH Z  92 " =    1.314
peak=    3.975 closest distance to " O   HOH Z  77 " =    1.252
peak=    3.973 closest distance to " O   HOH Z 111 " =    2.036
peak=    3.972 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.961 closest distance to " O   HOH Z 133 " =    1.226
peak=    3.953 closest distance to " O   HOH Z 426 " =    1.022
peak=    3.953 closest distance to " N   GLN A 278 " =    1.131
peak=    3.951 closest distance to " ND2 ASN A  60 " =    2.958
peak=    3.940 closest distance to " CB  SER A   3 " =    1.391
peak=    3.939 closest distance to " CB  ASN A  39 " =    0.939
peak=    3.934 closest distance to " NZ BLYS A 290 " =    0.916
peak=    3.928 closest distance to " CB  ARG A 275 " =    1.098
peak=    3.922 closest distance to " O   HOH Z 437 " =    2.074
peak=    3.918 closest distance to " CB  ASP A 124 " =    0.862
peak=    3.907 closest distance to " CE3 TRP A 150 " =    1.148
peak=    3.893 closest distance to " CB  GLU A 128 " =    1.056
peak=    3.883 closest distance to " O   HOH Z 422 " =    0.824
peak=    3.865 closest distance to " CG2 VAL A 257 " =    0.831
peak=    3.862 closest distance to " CB  ALA A 114 " =    0.930
peak=    3.855 closest distance to " O   HOH Z  27 " =    0.964
peak=    3.839 closest distance to " CG  LEU A 167 " =    1.306
peak=    3.835 closest distance to " CG2 THR A 221 " =    1.271
peak=    3.829 closest distance to " CB  VAL A 202 " =    1.628
peak=    3.825 closest distance to " O   HOH Z 193 " =    1.806
peak=    3.819 closest distance to " CG  GLU A 277 " =    1.892
peak=    3.817 closest distance to " CG  TRP A 179 " =    2.116
peak=    3.811 closest distance to " O   HOH Z 201 " =    2.054
peak=    3.808 closest distance to " O   HOH Z 346 " =    1.842
peak=    3.804 closest distance to " CD  ARG A 159 " =    0.812
peak=    3.801 closest distance to " O   HOH Z 393 " =    1.273
peak=    3.788 closest distance to " CA  ALA A 160 " =    0.955
peak=    3.787 closest distance to " O   HOH Z 368 " =    3.671
peak=    3.784 closest distance to " O   HOH Z 403 " =    1.660
peak=    3.752 closest distance to " O   HOH Z 352 " =    1.619
peak=    3.751 closest distance to " O   HOH Z  44 " =    1.962
peak=    3.741 closest distance to " O   HOH Z 218 " =    1.752
peak=    3.732 closest distance to " O   HOH Z  78 " =    1.919
peak=    3.721 closest distance to " N   GLU A   2 " =    1.425
peak=    3.719 closest distance to " O  BHOH Z  74 " =    1.333
peak=    3.719 closest distance to " O   TYR A 116 " =    1.258
peak=    3.715 closest distance to " CD  ARG A  66 " =    2.293
peak=    3.708 closest distance to " NZ  LYS A 117 " =    1.249
peak=    3.702 closest distance to " O   HOH Z  88 " =    3.965
peak=    3.698 closest distance to " O   HOH Z 112 " =    1.303
peak=    3.686 closest distance to " CB  GLN A 183 " =    1.194
peak=    3.683 closest distance to " CG2 ILE A  20 " =    1.579
peak=    3.677 closest distance to " O   HOH Z  58 " =    1.842
peak=    3.674 closest distance to " O   HOH Z 217 " =    3.194
peak=    3.673 closest distance to " CA  ARG A 102 " =    1.070
peak=    3.670 closest distance to " O   HOH Z 411 " =    3.366
peak=    3.659 closest distance to " O   HOH Z 383 " =    2.658
peak=    3.654 closest distance to " O   HOH Z  88 " =    3.218
peak=    3.654 closest distance to " CB  LYS A 117 " =    1.286
peak=    3.649 closest distance to " O   HOH Z 422 " =    2.418
peak=    3.641 closest distance to " O   HOH Z  40 " =    2.173
peak=    3.631 closest distance to " O   HOH Z  61 " =    1.706
peak=    3.628 closest distance to " O   HOH Z 126 " =    1.401
peak=    3.627 closest distance to " CB  TRP A 179 " =    1.462
peak=    3.626 closest distance to " CB  LEU A 228 " =    1.273
peak=    3.626 closest distance to " CG  ARG A 159 " =    0.796
peak=    3.623 closest distance to " CA  ARG A 195 " =    1.392
peak=    3.622 closest distance to " O   HOH Z 358 " =    1.225
peak=    3.621 closest distance to " CB  TRP A 150 " =    0.966
peak=    3.616 closest distance to " O   HOH Z 104 " =    1.680
peak=    3.610 closest distance to " O   HOH Z 434 " =    1.510
peak=    3.608 closest distance to " CA  ARG A  36 " =    1.214
peak=    3.596 closest distance to " N   ALA A   1 " =    1.551
peak=    3.591 closest distance to " O   HOH Z  97 " =    1.437
peak=    3.581 closest distance to " O   HOH Z 215 " =    1.495
peak=    3.581 closest distance to " CB  ASN A 187 " =    1.012
peak=    3.581 closest distance to " O   HOH Z 284 " =    1.432
peak=    3.577 closest distance to " O   HOH Z 405 " =    1.629
peak=    3.576 closest distance to " O   HOH Z 327 " =    1.857
peak=    3.568 closest distance to " CA  MET A 105 " =    0.944
peak=    3.567 closest distance to " N   CYS A 260 " =    0.949
peak=    3.561 closest distance to " CB  GLU A 277 " =    3.645
peak=    3.555 closest distance to " CA  ARG A 159 " =    1.384
peak=    3.554 closest distance to " CB  ALA A 114 " =    1.057
peak=    3.548 closest distance to " CB  SER A 212 " =    1.559
peak=    3.547 closest distance to " O   HOH Z 143 " =    1.303
peak=    3.536 closest distance to " O   HOH Z 106 " =    4.081
peak=    3.533 closest distance to " O   HOH Z 258 " =    1.991
peak=    3.529 closest distance to " CB  SER A 210 " =    0.935
peak=    3.528 closest distance to " CA  ILE A 234 " =    1.075
peak=    3.525 closest distance to " O   HOH Z 214 " =    2.172
peak=    3.509 closest distance to " O   HOH Z 146 " =    1.515
peak=    3.506 closest distance to " CD  GLN A  77 " =    1.262
peak=    3.505 closest distance to " O   HOH Z 132 " =    2.409
peak=    3.498 closest distance to " CZ  PHE A  38 " =    1.238
peak=    3.498 closest distance to " CB  THR A 157 " =    1.104
peak=    3.483 closest distance to " CG2BVAL A  41 " =    1.150
peak=    3.478 closest distance to " CA  ASN A 127 " =    1.180
peak=    3.471 closest distance to " NE1 TRP A 274 " =    0.985
peak=    3.471 closest distance to " CA  VAL A 125 " =    1.120
peak=    3.470 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.466 closest distance to " CB  ALA A  43 " =    0.818
peak=    3.466 closest distance to " CZ  PHE A 218 " =    1.224
peak=    3.459 closest distance to " O   HOH Z 272 " =    1.783
peak=    3.459 closest distance to " O   HOH Z  11 " =    2.101
peak=    3.458 closest distance to " OD1 ASP A 238 " =    1.020
peak=    3.456 closest distance to " O   HOH Z 425 " =    2.087
peak=    3.455 closest distance to " O   HOH Z 378 " =    0.998
peak=    3.446 closest distance to " O   HOH Z 371 " =    3.223
peak=    3.443 closest distance to " OG BSER A 134 " =    2.704
peak=    3.436 closest distance to " CB  ARG A 190 " =    1.745
peak=    3.432 closest distance to " CD2 PHE A  59 " =    1.918
peak=    3.429 closest distance to " ND2BASN A 224 " =    0.882
peak=    3.429 closest distance to " CB  SER A  99 " =    0.843
peak=    3.429 closest distance to " NH2AARG A 190 " =    1.791
peak=    3.426 closest distance to " O   HOH Z 299 " =    2.938
peak=    3.425 closest distance to " O   HOH Z  68 " =    1.837
peak=    3.424 closest distance to " O   HOH Z  91 " =    2.419
peak=    3.423 closest distance to " CB  PRO A  90 " =    1.095
peak=    3.421 closest distance to " O   HOH Z  30 " =    1.724
peak=    3.417 closest distance to " ND1 HIS A  81 " =    1.741
peak=    3.413 closest distance to " O   HOH Z   2 " =    1.787
peak=    3.410 closest distance to " CA  THR A 264 " =    0.812
peak=    3.409 closest distance to " CD  LYS A  76 " =    1.976
peak=    3.409 closest distance to " OE1 GLN A 240 " =    1.692
peak=    3.408 closest distance to " O   HOH Z  22 " =    1.292
peak=    3.407 closest distance to " O   HOH Z 280 " =    2.798
peak=    3.403 closest distance to " CD  LYS A 166 " =    1.485
peak=    3.403 closest distance to " CB  GLU A  46 " =    1.155
peak=    3.401 closest distance to " O   HOH Z 365 " =    2.666
peak=    3.401 closest distance to " CA  ALA A 180 " =    1.302
peak=    3.395 closest distance to " O   HOH Z 153 " =    3.545
peak=    3.393 closest distance to " CG  GLN A  89 " =    1.521
peak=    3.391 closest distance to " CB  GLN A  89 " =    1.230
peak=    3.391 closest distance to " O   HOH Z 424 " =    3.115
peak=    3.380 closest distance to " O   HOH Z 244 " =    1.564
peak=    3.380 closest distance to " CG  LEU A 281 " =    2.066
peak=    3.379 closest distance to " O   HOH Z 389 " =    1.781
peak=    3.377 closest distance to " O   HOH Z  32 " =    2.207
peak=    3.375 closest distance to " O   HOH Z 115 " =    1.712
peak=    3.375 closest distance to " O   HOH Z  42 " =    1.544
peak=    3.373 closest distance to " O   HOH Z 236 " =    1.465
peak=    3.373 closest distance to " CB  TRP A 274 " =    1.269
peak=    3.372 closest distance to " OG BSER A  99 " =    2.347
peak=    3.372 closest distance to " CD1 LEU A 300 " =    1.107
peak=    3.371 closest distance to " CB  LEU A 237 " =    0.876
peak=    3.369 closest distance to " CA  LEU A 282 " =    1.197
peak=    3.365 closest distance to " CB  GLU A 152 " =    1.187
peak=    3.365 closest distance to " O   HOH Z 128 " =    2.347
peak=    3.363 closest distance to " O   HOH Z 130 " =    2.036
peak=    3.361 closest distance to " NE2 GLN A  73 " =    1.586
peak=    3.361 closest distance to " O   HOH Z   6 " =    1.572
peak=    3.356 closest distance to " O   HOH Z 368 " =    1.768
peak=    3.354 closest distance to " CE  MET A  93 " =    1.460
peak=    3.354 closest distance to " CB  THR A  31 " =    1.556
peak=    3.349 closest distance to " O   HOH Z 357 " =    2.025
peak=    3.348 closest distance to " O   HOH Z 399 " =    0.774
peak=    3.348 closest distance to " OD2 ASP A 286 " =    2.577
peak=    3.347 closest distance to " CA  GLY A 267 " =    1.255
peak=    3.344 closest distance to " CG  GLN A 278 " =    3.809
peak=    3.340 closest distance to " CB  MET A  40 " =    0.775
peak=    3.335 closest distance to " O   ALA A  71 " =    1.205
peak=    3.335 closest distance to " O   HOH Z 119 " =    1.508
peak=    3.332 closest distance to " CB  TYR A  30 " =    1.478
peak=    3.330 closest distance to " O   HOH Z 222 " =    2.367
peak=    3.329 closest distance to " N   VAL A 296 " =    1.780
peak=    3.325 closest distance to " CG  GLN A  11 " =    2.170
peak=    3.323 closest distance to " CG1 VAL A 296 " =    1.194
peak=    3.323 closest distance to " CG  PRO A 243 " =    1.056
peak=    3.319 closest distance to " CG1 ILE A 151 " =    1.086
peak=    3.315 closest distance to " CB  ARG A 219 " =    0.759
peak=    3.312 closest distance to " CB  LYS A 290 " =    0.837
peak=    3.312 closest distance to " O   HOH Z 390 " =    2.499
peak=    3.311 closest distance to " O   ASN A  69 " =    1.701
peak=    3.310 closest distance to " OE2 GLU A  53 " =    1.872
peak=    3.307 closest distance to " O   HOH Z   7 " =    2.929
peak=    3.304 closest distance to " O   THR A 294 " =    1.070
peak=    3.303 closest distance to " NZ  LYS A 119 " =    1.351
peak=    3.301 closest distance to " OG BSER A 164 " =    2.137
peak=    3.291 closest distance to " O   HOH Z  44 " =    2.811
peak=    3.290 closest distance to " N   ALA A 292 " =    1.154
peak=    3.288 closest distance to " N   SER A 271 " =    1.068
peak=    3.288 closest distance to " ND2 ASN A 249 " =    0.776
peak=    3.284 closest distance to " ND2 ASN A 187 " =    1.541
peak=    3.283 closest distance to " CB  PHE A  61 " =    1.271
peak=    3.283 closest distance to " ND1 HIS A  86 " =    1.866
peak=    3.281 closest distance to " N   SER A  97 " =    0.857
peak=    3.280 closest distance to " O   ASN A 209 " =    1.824
peak=    3.279 closest distance to " OE1 GLU A   2 " =    1.435
peak=    3.278 closest distance to " CE3 TRP A  85 " =    0.962
peak=    3.274 closest distance to " CA  GLU A 152 " =    1.021
peak=    3.271 closest distance to " O   HOH Z  17 " =    1.806
peak=    3.267 closest distance to " CB  SER A 273 " =    0.979
peak=    3.263 closest distance to " O   HOH Z 155 " =    1.602
peak=    3.262 closest distance to " C   GLN A  73 " =    1.081
peak=    3.259 closest distance to " CB  TYR A 116 " =    1.245
peak=    3.258 closest distance to " O   HOH Z 250 " =    1.446
peak=    3.253 closest distance to " CA  SER A  87 " =    1.150
peak=    3.252 closest distance to " NE2 HIS A 207 " =    1.115
peak=    3.248 closest distance to " O   HOH Z  43 " =    1.161
peak=    3.246 closest distance to " NE2 GLN A  58 " =    4.413
peak=    3.244 closest distance to " CA  ASP A 124 " =    0.721
peak=    3.243 closest distance to " NH2AARG A 145 " =    1.165
peak=    3.241 closest distance to " CA  ALA A 129 " =    1.225
peak=    3.240 closest distance to " OG BSER A 258 " =    0.941
peak=    3.239 closest distance to " O   HOH Z 407 " =    1.551
peak=    3.238 closest distance to " CA  PHE A 283 " =    1.316
peak=    3.236 closest distance to " O   ASN A 142 " =    1.003
peak=    3.235 closest distance to " O   HOH Z   1 " =    1.663
peak=    3.235 closest distance to " OE2 GLU A  44 " =    1.165
peak=    3.234 closest distance to " CB  ARG A  79 " =    1.160
peak=    3.232 closest distance to " CD BLYS A 290 " =    1.024
peak=    3.230 closest distance to " CG2 VAL A 197 " =    1.092
peak=    3.228 closest distance to " O   ASN A  74 " =    1.748
peak=    3.227 closest distance to " O   HOH Z 394 " =    1.652
peak=    3.226 closest distance to " O   MET A 105 " =    1.675
peak=    3.221 closest distance to " CG2 VAL A 202 " =    1.400
peak=    3.220 closest distance to " CD  ARG A 269 " =    1.006
peak=    3.215 closest distance to " O   HOH Z 302 " =    1.596
peak=    3.215 closest distance to " O   HOH Z 425 " =    2.064
peak=    3.212 closest distance to " NH2 ARG A  66 " =    5.453
peak=    3.210 closest distance to " CA  ILE A 106 " =    0.741
peak=    3.208 closest distance to " O   HOH Z 344 " =    3.241
peak=    3.202 closest distance to " CD  ARG A 259 " =    1.759
peak=    3.202 closest distance to " N   GLY A 133 " =    3.938
peak=    3.202 closest distance to " O   GLN A 240 " =    1.774
peak=    3.201 closest distance to " O   HOH Z  88 " =    2.711
peak=    3.200 closest distance to " O   HOH Z 147 " =    1.526
peak=    3.197 closest distance to " CG  GLN A  58 " =    1.156
peak=    3.194 closest distance to " O   HOH Z 154 " =    1.930
peak=    3.193 closest distance to " CA  ARG A 156 " =    1.258
peak=    3.189 closest distance to " N   ARG A  66 " =    1.073
peak=    3.185 closest distance to " O   HOH Z 413 " =    1.624
peak=    3.182 closest distance to " O   HOH Z 157 " =    1.687
peak=    3.181 closest distance to " O   HOH Z 175 " =    2.148
peak=    3.179 closest distance to " O   ALA A 165 " =    1.426
peak=    3.179 closest distance to " O   HOH Z 172 " =    2.226
peak=    3.179 closest distance to " O   HOH Z 189 " =    2.782
peak=    3.175 closest distance to " CA  ASN A 215 " =    1.053
peak=    3.174 closest distance to " CD  ARG A 195 " =    3.548
peak=    3.166 closest distance to " O   HOH Z 180 " =    2.267
peak=    3.164 closest distance to " O   HOH Z 119 " =    4.263
peak=    3.161 closest distance to " O   HOH Z 371 " =    1.744
peak=    3.161 closest distance to " CG1 VAL A 189 " =    1.344
peak=    3.157 closest distance to " O   TRP A  70 " =    1.374
peak=    3.155 closest distance to " N   VAL A 125 " =    1.496
peak=    3.154 closest distance to " O   HOH Z 113 " =    1.910
peak=    3.150 closest distance to " O   GLU A   2 " =    1.801
peak=    3.144 closest distance to " O   HOH Z 362 " =    1.548
peak=    3.143 closest distance to " CB  THR A 235 " =    0.991
peak=    3.141 closest distance to " CE1 PHE A  61 " =    1.812
peak=    3.140 closest distance to " CB  ASN A 215 " =    1.135
peak=    3.130 closest distance to " CD2 LEU A   5 " =    1.408
peak=    3.130 closest distance to " O   HOH Z 158 " =    2.599
peak=    3.130 closest distance to " O   HOH Z 145 " =    1.933
peak=    3.126 closest distance to " CA  ALA A 299 " =    0.864
peak=    3.125 closest distance to " O   HOH Z 368 " =    4.510
peak=    3.120 closest distance to " C   VAL A 153 " =    1.091
peak=    3.115 closest distance to " O   HOH Z 418 " =    1.665
peak=    3.109 closest distance to " CB  ALA A 161 " =    1.030
peak=    3.108 closest distance to " CB  VAL A 268 " =    0.888
peak=    3.106 closest distance to " CB  PHE A 130 " =    1.032
peak=    3.106 closest distance to " CG1 ILE A  33 " =    1.334
peak=    3.106 closest distance to " O   HOH Z 251 " =    1.349
peak=    3.104 closest distance to " CB  ARG A 138 " =    0.925
peak=    3.103 closest distance to " CB  ASN A 142 " =    0.853
peak=    3.103 closest distance to " O   HOH Z 303 " =    1.011
peak=    3.098 closest distance to " N   ASP A 162 " =    1.406
peak=    3.097 closest distance to " OG1 THR A 221 " =    1.242
peak=    3.087 closest distance to " O   HOH Z  61 " =    1.655
peak=    3.082 closest distance to " O   HOH Z  51 " =    1.916
peak=    3.081 closest distance to " C   GLU A 277 " =    1.339
peak=    3.079 closest distance to " O   HOH Z  55 " =    1.611
peak=    3.078 closest distance to " O   HOH Z 373 " =    1.402
peak=    3.076 closest distance to " O   HOH Z 288 " =    1.983
peak=    3.074 closest distance to " N   ASN A 127 " =    1.344
peak=    3.070 closest distance to " O   HOH Z 283 " =    2.504
peak=    3.069 closest distance to " OG ASER A 212 " =    2.044
peak=    3.063 closest distance to " CA  ALA A 292 " =    0.995
peak=    3.056 closest distance to " O   HOH Z 130 " =    3.559
peak=    3.052 closest distance to " OD1 ASN A 217 " =    1.524
peak=    3.050 closest distance to " CG1 VAL A 153 " =    0.954
peak=    3.048 closest distance to " CB  PHE A 225 " =    1.358
peak=    3.043 closest distance to " O   HOH Z 281 " =    1.947
peak=    3.042 closest distance to " CB  ALA A 242 " =    0.816
peak=    3.041 closest distance to " O   HOH Z 431 " =    1.291

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.879 - 5.573
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.879 - 5.573

peak=   -4.735 closest distance to " O   PRO A 198 " =    1.203
peak=   -4.688 closest distance to " N   THR A 157 " =    1.653
peak=   -4.365 closest distance to " OD1 ASP A 191 " =    1.895
peak=   -4.332 closest distance to " O   HOH Z  28 " =    1.166
peak=   -4.306 closest distance to " CD  LYS A 166 " =    2.572
peak=   -4.223 closest distance to " O   HOH Z  60 " =    1.561
peak=   -4.126 closest distance to " O   ALA A  10 " =    1.615
peak=   -4.095 closest distance to " CB  PRO A 243 " =    2.551
peak=   -4.061 closest distance to " O   HOH Z 111 " =    1.687
peak=   -4.054 closest distance to " CD  ARG A  14 " =    3.387
peak=   -4.030 closest distance to " O   HOH Z 185 " =    1.958
peak=   -4.025 closest distance to " O   HOH Z 231 " =    1.050
peak=   -4.014 closest distance to " CD1 TRP A 179 " =    1.172
peak=   -4.001 closest distance to " OG  SER A  97 " =    2.095
peak=   -3.996 closest distance to " O   HOH Z  77 " =    1.875
peak=   -3.993 closest distance to " O   HOH Z 385 " =    1.319
peak=   -3.986 closest distance to " CE2 TYR A  30 " =    2.549
peak=   -3.983 closest distance to " O   SER A  22 " =    2.776
peak=   -3.954 closest distance to " N   ALA A  43 " =    2.688
peak=   -3.927 closest distance to " O   HOH Z 298 " =    2.693
peak=   -3.897 closest distance to " O   HOH Z  39 " =    0.879
peak=   -3.886 closest distance to " CG1BVAL A  41 " =    2.698
peak=   -3.883 closest distance to " CG  MET A 105 " =    0.981
peak=   -3.862 closest distance to " CD  ARG A 156 " =    1.986
peak=   -3.851 closest distance to " O   HOH Z  24 " =    0.969
peak=   -3.848 closest distance to " O   HOH Z 313 " =    1.356
peak=   -3.833 closest distance to " CA  GLY A  98 " =    1.850
peak=   -3.815 closest distance to " O   PRO A 163 " =    1.881
peak=   -3.782 closest distance to " O   HOH Z 404 " =    1.208
peak=   -3.763 closest distance to " O   GLY A  80 " =    2.424
peak=   -3.761 closest distance to " CB  GLN A  55 " =    1.237
peak=   -3.741 closest distance to " O   HOH Z 242 " =    1.519
peak=   -3.717 closest distance to " CB  ALA A 291 " =    2.143
peak=   -3.711 closest distance to " OG BSER A 134 " =    1.643
peak=   -3.705 closest distance to " OG  SER A  32 " =    0.966
peak=   -3.702 closest distance to " OG  SER A  63 " =    1.436
peak=   -3.670 closest distance to " O   HOH Z 351 " =    1.622
peak=   -3.667 closest distance to " O   HOH Z 198 " =    1.956
peak=   -3.647 closest distance to " CB  ASP A  27 " =    2.460
peak=   -3.646 closest distance to " O   GLY A 203 " =    2.551
peak=   -3.643 closest distance to " O   HOH Z 377 " =    1.947
peak=   -3.638 closest distance to " O   HOH Z 105 " =    2.025
peak=   -3.635 closest distance to " NE2 GLN A 223 " =    1.739
peak=   -3.634 closest distance to " CA  GLY A 241 " =    2.271
peak=   -3.631 closest distance to " CZ3 TRP A 179 " =    1.337
peak=   -3.627 closest distance to " O   HOH Z 275 " =    1.606
peak=   -3.623 closest distance to " CD2 PHE A  61 " =    2.008
peak=   -3.608 closest distance to " O   HOH Z 323 " =    2.043
peak=   -3.607 closest distance to " N   LEU A 282 " =    2.185
peak=   -3.601 closest distance to " CG  ARG A 219 " =    2.475
peak=   -3.600 closest distance to " NE2 GLN A  55 " =    0.880
peak=   -3.597 closest distance to " CB  ALA A  43 " =    2.486
peak=   -3.597 closest distance to " O   GLN A 240 " =    3.080
peak=   -3.591 closest distance to " CA  GLY A 203 " =    2.438
peak=   -3.586 closest distance to " O   HOH Z 415 " =    1.181
peak=   -3.585 closest distance to " CZ  PHE A  59 " =    1.399
peak=   -3.573 closest distance to " CZ2 TRP A 274 " =    0.956
peak=   -3.570 closest distance to " O   HOH Z 286 " =    1.540
peak=   -3.565 closest distance to " OG  SER A 245 " =    1.428
peak=   -3.561 closest distance to " O   HOH Z 143 " =    1.053
peak=   -3.559 closest distance to " CD2 TYR A 116 " =    2.126
peak=   -3.551 closest distance to " CB  ALA A 100 " =    2.015
peak=   -3.537 closest distance to " OE1 GLU A 277 " =    2.352
peak=   -3.533 closest distance to " CB  ASP A 132 " =    2.547
peak=   -3.531 closest distance to " O   HOH Z 131 " =    3.963
peak=   -3.531 closest distance to " NZ  LYS A 166 " =    1.100
peak=   -3.528 closest distance to " CB  ALA A   9 " =    2.365
peak=   -3.526 closest distance to " O   HOH Z 211 " =    1.079
peak=   -3.525 closest distance to " CG  GLN A  88 " =    0.890
peak=   -3.523 closest distance to " O   ALA A   1 " =    1.301
peak=   -3.518 closest distance to " O   PHE A 218 " =    1.512
peak=   -3.510 closest distance to " CG2 THR A  52 " =    3.201
peak=   -3.509 closest distance to " O   HOH Z 276 " =    1.339
peak=   -3.501 closest distance to " CB  ALA A 131 " =    1.894
peak=   -3.499 closest distance to " O   HOH Z 389 " =    1.093
peak=   -3.493 closest distance to " O   HOH Z 231 " =    1.938
peak=   -3.488 closest distance to " O   HOH Z 348 " =    1.872
peak=   -3.487 closest distance to " O   HOH Z  69 " =    1.537
peak=   -3.483 closest distance to " ND2 ASN A 209 " =    1.892
peak=   -3.475 closest distance to " O   HOH Z  65 " =    1.347
peak=   -3.474 closest distance to " O   LEU A 261 " =    1.214
peak=   -3.473 closest distance to " O   HOH Z 275 " =    1.746
peak=   -3.472 closest distance to " O   ILE A  49 " =    1.600
peak=   -3.469 closest distance to " O   ASN A 301 " =    1.322
peak=   -3.467 closest distance to " ND2 ASN A 249 " =    2.129
peak=   -3.466 closest distance to " O   GLU A 152 " =    1.359
peak=   -3.462 closest distance to " CG  ARG A 269 " =    2.399
peak=   -3.460 closest distance to " CB  TRP A  85 " =    2.260
peak=   -3.452 closest distance to " CD2 TYR A 293 " =    1.838
peak=   -3.451 closest distance to " O   HOH Z 384 " =    3.497
peak=   -3.440 closest distance to " NH2 ARG A 219 " =    2.024
peak=   -3.437 closest distance to " CZ2 TRP A  92 " =    2.775
peak=   -3.434 closest distance to " O   HOH Z 425 " =    0.928
peak=   -3.433 closest distance to " CZ  PHE A 130 " =    1.087
peak=   -3.433 closest distance to " O   HOH Z 200 " =    3.642
peak=   -3.428 closest distance to " O   HOH Z 390 " =    2.498
peak=   -3.404 closest distance to " O   HOH Z 251 " =    1.069
peak=   -3.400 closest distance to " CB  ALA A 158 " =    1.639
peak=   -3.397 closest distance to " O   HOH Z 129 " =    3.751
peak=   -3.396 closest distance to " O   HOH Z  88 " =    1.852
peak=   -3.386 closest distance to " CZ  TYR A 169 " =    1.906
peak=   -3.385 closest distance to " NE2 GLN A  77 " =    1.691
peak=   -3.381 closest distance to " CB  ASN A  45 " =    2.189
peak=   -3.371 closest distance to " O   HOH Z 166 " =    1.227
peak=   -3.368 closest distance to " O   ARG A 145 " =    1.259
peak=   -3.367 closest distance to " CG2 VAL A 189 " =    1.996
peak=   -3.366 closest distance to " NE2 GLN A 122 " =    1.054
peak=   -3.359 closest distance to " CG1 VAL A  78 " =    2.496
peak=   -3.353 closest distance to " NH1 ARG A 195 " =    2.400
peak=   -3.351 closest distance to " O   HOH Z 357 " =    2.085
peak=   -3.347 closest distance to " O   HOH Z 359 " =    1.510
peak=   -3.344 closest distance to " CG  TRP A 266 " =    1.967
peak=   -3.343 closest distance to " O   ILE A 106 " =    2.098
peak=   -3.340 closest distance to " O   ALA A   1 " =    1.766
peak=   -3.338 closest distance to " CZ  ARG A  36 " =    1.524
peak=   -3.335 closest distance to " O   HOH Z 163 " =    1.601
peak=   -3.334 closest distance to " CG1 VAL A 112 " =    2.582
peak=   -3.328 closest distance to " CB  ALA A 248 " =    2.129
peak=   -3.326 closest distance to " CD  GLN A  77 " =    1.384
peak=   -3.322 closest distance to " O   HOH Z 368 " =    1.485
peak=   -3.317 closest distance to " O   HOH Z  49 " =    1.305
peak=   -3.317 closest distance to " O   HOH Z 102 " =    1.688
peak=   -3.312 closest distance to " CB  PRO A  54 " =    2.361
peak=   -3.309 closest distance to " O   HOH Z 165 " =    2.323
peak=   -3.307 closest distance to " CG  GLN A  58 " =    1.161
peak=   -3.306 closest distance to " N   ARG A 159 " =    2.108
peak=   -3.305 closest distance to " O   HOH Z 123 " =    2.509
peak=   -3.304 closest distance to " OD2 ASP A 132 " =    2.243
peak=   -3.303 closest distance to " CG  GLU A 128 " =    1.520
peak=   -3.303 closest distance to " O   HOH Z 282 " =    4.605
peak=   -3.301 closest distance to " O   HOH Z 412 " =    3.922
peak=   -3.300 closest distance to " N   GLN A  58 " =    1.364
peak=   -3.298 closest distance to " CA  GLY A 133 " =    2.015
peak=   -3.292 closest distance to " CG1 VAL A 125 " =    2.261
peak=   -3.286 closest distance to " O   HOH Z 389 " =    2.253
peak=   -3.282 closest distance to " O   ALA A  34 " =    2.560
peak=   -3.277 closest distance to " CD1 ILE A 239 " =    2.439
peak=   -3.276 closest distance to " CG2 THR A 178 " =    2.153
peak=   -3.269 closest distance to " C   PHE A  59 " =    1.132
peak=   -3.264 closest distance to " CD1 LEU A 101 " =    2.269
peak=   -3.262 closest distance to " CG  LEU A  83 " =    2.134
peak=   -3.261 closest distance to " O   ASP A  27 " =    1.967
peak=   -3.258 closest distance to " OG  SER A  87 " =    1.332
peak=   -3.257 closest distance to " OE1 GLN A  88 " =    1.054
peak=   -3.247 closest distance to " OD2 ASP A 272 " =    1.640
peak=   -3.247 closest distance to " CD  LYS A 289 " =    2.337
peak=   -3.246 closest distance to " CB  TYR A  15 " =    2.062
peak=   -3.241 closest distance to " CG1BVAL A  72 " =    2.265
peak=   -3.238 closest distance to " O   LYS A  76 " =    1.264
peak=   -3.232 closest distance to " OH  TYR A 247 " =    1.548
peak=   -3.230 closest distance to " O   HOH Z   1 " =    1.276
peak=   -3.227 closest distance to " O   HOH Z  22 " =    2.533
peak=   -3.225 closest distance to " O   HOH Z 352 " =    1.874
peak=   -3.223 closest distance to " O   HOH Z  53 " =    1.692
peak=   -3.223 closest distance to " O   HOH Z 259 " =    3.901
peak=   -3.220 closest distance to " CD2 PHE A 130 " =    2.881
peak=   -3.210 closest distance to " CB  CYS A 254 " =    1.929
peak=   -3.206 closest distance to " OD2 ASP A 171 " =    2.134
peak=   -3.204 closest distance to " O   HOH Z  52 " =    0.920
peak=   -3.192 closest distance to " O   LYS A 117 " =    2.229
peak=   -3.188 closest distance to " CD2 HIS A 207 " =    1.554
peak=   -3.186 closest distance to " O   HOH Z  27 " =    1.108
peak=   -3.185 closest distance to " O   HOH Z 128 " =    2.491
peak=   -3.184 closest distance to " O   HOH Z 130 " =    1.014
peak=   -3.184 closest distance to " CG1 VAL A 265 " =    2.425
peak=   -3.184 closest distance to " O   HOH Z 407 " =    3.197
peak=   -3.181 closest distance to " CB  SER A 210 " =    1.152
peak=   -3.180 closest distance to " O   HOH Z 270 " =    3.040
peak=   -3.179 closest distance to " O   HOH Z 155 " =    1.081
peak=   -3.178 closest distance to " CA  HIS A  86 " =    2.246
peak=   -3.178 closest distance to " CE  LYS A  76 " =    3.008
peak=   -3.170 closest distance to " O   HOH Z 114 " =    0.916
peak=   -3.168 closest distance to " CB  ALA A 227 " =    2.351
peak=   -3.167 closest distance to " O   HOH Z 428 " =    2.049
peak=   -3.166 closest distance to " O   HOH Z 238 " =    0.976
peak=   -3.155 closest distance to " OE1 GLN A 183 " =    1.646
peak=   -3.154 closest distance to " O   HOH Z  73 " =    2.294
peak=   -3.149 closest distance to " O   HOH Z  90 " =    2.786
peak=   -3.143 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.142 closest distance to " O   HOH Z 105 " =    1.266
peak=   -3.140 closest distance to " OD1 ASN A 301 " =    1.728
peak=   -3.133 closest distance to " O   HOH Z 147 " =    1.284
peak=   -3.133 closest distance to " OG  SER A 206 " =    2.008
peak=   -3.130 closest distance to " O   SER A  87 " =    2.000
peak=   -3.120 closest distance to " O   HOH Z 281 " =    2.876
peak=   -3.116 closest distance to " ND2 ASN A 187 " =    1.554
peak=   -3.115 closest distance to " CG2 ILE A 120 " =    0.938
peak=   -3.112 closest distance to " N   LYS A 166 " =    1.821
peak=   -3.110 closest distance to " CZ  PHE A  16 " =    2.208
peak=   -3.099 closest distance to " CD2 LEU A 297 " =    2.147
peak=   -3.090 closest distance to " OE1 GLU A 236 " =    1.131
peak=   -3.084 closest distance to " O   VAL A  67 " =    2.907
peak=   -3.081 closest distance to " C   SER A  62 " =    2.373
peak=   -3.080 closest distance to " O   TRP A  70 " =    1.423
peak=   -3.080 closest distance to " CA  ILE A 120 " =    1.209
peak=   -3.066 closest distance to " O   HOH Z 410 " =    1.252
peak=   -3.053 closest distance to " CD2 LEU A 237 " =    2.877
peak=   -3.049 closest distance to " CA  GLY A 241 " =    3.315
peak=   -3.048 closest distance to " CB  ALA A  10 " =    2.301
peak=   -3.045 closest distance to " NH2AARG A 275 " =    5.573
peak=   -3.031 closest distance to " O   HOH Z 134 " =    3.761
peak=   -3.021 closest distance to " O   HOH Z 217 " =    1.631

================= 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    :  0.4645 0.4656   6.281536e+00   6.273571e+00
   1_bss:  0.4558 0.4604   6.277652e+00   6.267665e+00
   1_xyz:  0.3829 0.4231   6.168140e+00   6.220198e+00
   1_adp:  0.3510 0.4287   6.129113e+00   6.228147e+00
   1_occ:  0.3508 0.4287   6.128795e+00   6.228455e+00
   2_bss:  0.3513 0.4279   6.131645e+00   6.229816e+00
   2_xyz:  0.2905 0.3740   5.983820e+00   6.130398e+00
   2_adp:  0.2740 0.3610   5.950503e+00   6.105931e+00
   2_occ:  0.2738 0.3606   5.949940e+00   6.105700e+00
   3_bss:  0.2738 0.3588   5.947384e+00   6.102973e+00
   3_xyz:  0.2208 0.2864   5.741464e+00   5.927342e+00
   3_adp:  0.1957 0.2647   5.651787e+00   5.867218e+00
   3_occ:  0.1956 0.2646   5.651435e+00   5.867167e+00
   4_bss:  0.1952 0.2641   5.649438e+00   5.864622e+00
   4_xyz:  0.1543 0.2128   5.430798e+00   5.674790e+00
   4_adp:  0.1417 0.1962   5.356865e+00   5.596286e+00
   4_occ:  0.1416 0.1960   5.356176e+00   5.595348e+00
   5_bss:  0.1418 0.1957   5.353530e+00   5.592760e+00
   5_xyz:  0.1322 0.1812   5.286933e+00   5.522549e+00
   5_adp:  0.1283 0.1796   5.267536e+00   5.507614e+00
   5_occ:  0.1283 0.1795   5.267457e+00   5.507565e+00
   5_bss:  0.1283 0.1795   5.267360e+00   5.507565e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -2.280   1.954   1.003   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -2.280   1.954   1.003   0.000   0.000   0.000
   1_adp:  0.300  50.000  -2.280   1.954   1.003   0.000   0.000   0.000
   1_occ:  0.300  50.000  -2.280   1.954   1.003   0.000   0.000   0.000
   2_bss:  0.359  82.799  -1.122   0.480   0.521   0.000   0.000   0.000
   2_xyz:  0.359  82.799  -1.122   0.480   0.521   0.000   0.000   0.000
   2_adp:  0.359  82.799  -1.122   0.480   0.521   0.000   0.000   0.000
   2_occ:  0.359  82.799  -1.122   0.480   0.521   0.000   0.000   0.000
   3_bss:  0.347  80.000  -1.286  -0.888   0.012  -0.000   0.000   0.000
   3_xyz:  0.347  80.000  -1.286  -0.888   0.012  -0.000   0.000   0.000
   3_adp:  0.347  80.000  -1.286  -0.888   0.012  -0.000   0.000   0.000
   3_occ:  0.347  80.000  -1.286  -0.888   0.012  -0.000   0.000   0.000
   4_bss:  0.340  80.000  -2.085  -2.107  -0.572  -0.000  -0.000  -0.000
   4_xyz:  0.340  80.000  -2.085  -2.107  -0.572  -0.000  -0.000  -0.000
   4_adp:  0.340  80.000  -2.085  -2.107  -0.572  -0.000  -0.000  -0.000
   4_occ:  0.340  80.000  -2.085  -2.107  -0.572  -0.000  -0.000  -0.000
   5_bss:  0.321  65.802  -2.369  -2.761  -0.864  -0.000  -0.000  -0.000
   5_xyz:  0.321  65.802  -2.369  -2.761  -0.864  -0.000  -0.000  -0.000
   5_adp:  0.321  65.802  -2.369  -2.761  -0.864  -0.000  -0.000  -0.000
   5_occ:  0.321  65.802  -2.369  -2.761  -0.864  -0.000  -0.000  -0.000
   5_bss:  0.314  61.747  -2.327  -2.821  -0.811  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.661 0.4240  0.5850    73111.883
   1_bss:  57.016 0.4312  0.6054    71386.346
   1_xyz:  49.425 0.5270  0.7220    56122.035
   1_adp:  50.292 0.5156  0.7200    57731.928
   1_occ:  50.315 0.5154  0.7192    57836.957
   2_bss:  50.237 0.5164  0.7153    57886.885
   2_xyz:  41.360 0.6248  0.8566    39969.435
   2_adp:  39.298 0.6500  0.8784    37355.126
   2_occ:  39.288 0.6500  0.8785    37300.566
   3_bss:  39.037 0.6527  0.8606    36780.882
   3_xyz:  29.480 0.7620  0.9652    21877.525
   3_adp:  26.830 0.7912  0.9724    18441.197
   3_occ:  26.823 0.7912  0.9720    18412.499
   4_bss:  26.708 0.7923  0.9439    18275.269
   4_xyz:  20.983 0.8506  0.9807    11536.945
   4_adp:  18.828 0.8723  0.9836     9889.158
   4_occ:  18.810 0.8725  0.9834     9856.629
   5_bss:  18.736 0.8729  0.9693     9744.598
   5_xyz:  16.868 0.8904  0.9767     8312.953
   5_adp:  16.430 0.8947  0.9698     8090.622
   5_occ:  16.431 0.8947  0.9696     8087.021
   5_bss:  16.433 0.8947  0.9700     8085.767
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8452e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8452e-01
   1_xyz:   1.411  0.010  0.096 15.814  0.006  4.106   1.1180e-01
   1_adp:   1.411  0.010  0.096 15.814  0.006  4.106   1.1180e-01
   1_occ:   1.411  0.010  0.096 15.814  0.006  4.106   1.1180e-01
   2_bss:   1.411  0.010  0.096 15.814  0.006  4.106   1.1180e-01
   2_xyz:   1.370  0.010  0.097 15.656  0.005  4.107   1.0587e-01
   2_adp:   1.370  0.010  0.097 15.656  0.005  4.107   1.0587e-01
   2_occ:   1.370  0.010  0.097 15.656  0.005  4.107   1.0587e-01
   3_bss:   1.370  0.010  0.097 15.656  0.005  4.107   1.0587e-01
   3_xyz:   1.124  0.009  0.083 14.726  0.004  4.108   7.5850e-02
   3_adp:   1.124  0.009  0.083 14.726  0.004  4.108   7.5850e-02
   3_occ:   1.124  0.009  0.083 14.726  0.004  4.108   7.5850e-02
   4_bss:   1.124  0.009  0.083 14.726  0.004  4.108   7.5850e-02
   4_xyz:   1.135  0.009  0.082 14.786  0.004  4.109   7.4372e-02
   4_adp:   1.135  0.009  0.082 14.786  0.004  4.109   7.4372e-02
   4_occ:   1.135  0.009  0.082 14.786  0.004  4.109   7.4372e-02
   5_bss:   1.135  0.009  0.082 14.786  0.004  4.109   7.4372e-02
   5_xyz:   0.924  0.006  0.068 14.407  0.003  4.113   5.2839e-02
   5_adp:   0.924  0.006  0.068 14.407  0.003  4.113   5.2839e-02
   5_occ:   0.924  0.006  0.068 14.407  0.003  4.113   5.2839e-02
   5_bss:   0.924  0.006  0.068 14.407  0.003  4.113   5.2839e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4161e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4161e-01
   1_xyz:   8.729  0.050  0.338 83.424  0.046  2.074   9.2167e-02
   1_adp:   8.729  0.050  0.338 83.424  0.046  2.074   9.2167e-02
   1_occ:   8.729  0.050  0.338 83.424  0.046  2.074   9.2167e-02
   2_bss:   8.729  0.050  0.338 83.424  0.046  2.074   9.2167e-02
   2_xyz:   7.965  0.057  0.310 78.201  0.042  1.963   7.6108e-02
   2_adp:   7.965  0.057  0.310 78.201  0.042  1.963   7.6108e-02
   2_occ:   7.965  0.057  0.310 78.201  0.042  1.963   7.6108e-02
   3_bss:   7.965  0.057  0.310 78.201  0.042  1.963   7.6108e-02
   3_xyz:   7.837  0.056  0.287 75.532  0.018  2.243   9.6822e-02
   3_adp:   7.837  0.056  0.287 75.532  0.018  2.243   9.6822e-02
   3_occ:   7.837  0.056  0.287 75.532  0.018  2.243   9.6822e-02
   4_bss:   7.837  0.056  0.287 75.532  0.018  2.243   9.6822e-02
   4_xyz:   6.651  0.062  0.256 81.180  0.035  2.246   7.6863e-02
   4_adp:   6.651  0.062  0.256 81.180  0.035  2.246   7.6863e-02
   4_occ:   6.651  0.062  0.256 81.180  0.035  2.246   7.6863e-02
   5_bss:   6.651  0.062  0.256 81.180  0.035  2.246   7.6863e-02
   5_xyz:   7.611  0.043  0.212 80.562  0.033  2.394   3.6688e-02
   5_adp:   7.611  0.043  0.212 80.562  0.033  2.394   3.6688e-02
   5_occ:   7.611  0.043  0.212 80.562  0.033  2.394   3.6688e-02
   5_bss:   7.611  0.043  0.212 80.562  0.033  2.394   3.6688e-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: 104.07   0.00  19.76  82.77   0.00  16.57 104.07   0.00  37.13
   1_occ: 104.07   0.00  19.76  82.77   0.00  16.57 104.07   0.00  37.13
   2_bss: 104.07   0.00  19.76  82.77   0.00  16.57 104.07   0.00  37.13
   2_xyz: 104.07   0.00  19.76  82.77   0.00  16.57 104.07   0.00  37.13
   2_adp:  99.70   0.00  19.08  84.39   0.00  15.67  99.70   0.00  37.63
   2_occ:  99.70   0.00  19.08  84.39   0.00  15.67  99.70   0.00  37.63
   3_bss:  99.70   0.00  19.08  84.39   0.00  15.67  99.70   0.00  37.63
   3_xyz:  99.70   0.00  19.08  84.39   0.00  15.67  99.70   0.00  37.63
   3_adp: 104.63   0.00  19.82 102.51   0.00  14.67 104.63   4.19  47.86
   3_occ: 104.63   0.00  19.82 102.51   0.00  14.67 104.63   4.19  47.86
   4_bss: 104.63   0.00  19.82 102.51   0.00  14.67 104.63   4.19  47.86
   4_xyz: 104.63   0.00  19.82 102.51   0.00  14.67 104.63   4.19  47.86
   4_adp: 102.58   0.00  18.79 102.58   0.00  13.59 101.31   4.98  47.15
   4_occ: 102.58   0.00  18.79 102.58   0.00  13.59 101.31   4.98  47.15
   5_bss: 102.58   0.00  18.79 102.58   0.00  13.59 101.31   4.98  47.15
   5_xyz: 102.58   0.00  18.79 102.58   0.00  13.59 101.31   4.98  47.15
   5_adp: 106.45   0.00  18.71 106.45   0.00  13.30 104.62   5.08  48.21
   5_occ: 106.45   0.00  18.71 106.45   0.00  13.30 104.62   5.08  48.21
   5_bss: 106.45   0.00  18.72 106.45   0.00  13.30 104.62   5.09  48.21
------------------------------------------------------------------------
 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:    1.706    0.006    0.299
   1_adp:    1.706    0.006    0.299
   1_occ:    1.706    0.006    0.299
   2_bss:    1.706    0.006    0.299
   2_xyz:    1.595    0.048    0.548
   2_adp:    1.595    0.048    0.548
   2_occ:    1.595    0.048    0.548
   3_bss:    1.595    0.048    0.548
   3_xyz:    1.695    0.067    0.712
   3_adp:    1.695    0.067    0.712
   3_occ:    1.695    0.067    0.712
   4_bss:    1.695    0.067    0.712
   4_xyz:    1.594    0.050    0.802
   4_adp:    1.594    0.050    0.802
   4_occ:    1.594    0.050    0.802
   5_bss:    1.594    0.050    0.802
   5_xyz:    1.627    0.079    0.822
   5_adp:    1.627    0.079    0.822
   5_occ:    1.627    0.079    0.822
   5_bss:    1.627    0.079    0.822
------------------------------------------------------------------------

CPU time actual refinement: 364.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_855/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_855/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_855/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_855/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_855/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 364.52 
  Macro-tasks:
    bulk solvent and scale       = 55.21  
    individual site refinement   = 148.05 
    weights calculation          = 29.43  
    collect and process          = 6.24   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 239.03 
  Micro-tasks:
    mask                            = 2.59   
    f_calc                          = 115.31 
    alpha_beta                      = 8.12   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 123.14 
    fmodel                         = 8.37   
    r_factors                      = 0.27   
    phase_errors                   = 9.93   
    foms                           = 0.29   
    TOTAL for micro-tasks          = 269.13 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.134 micro seconds
Total CPU time: 6.30 minutes
from_scatterers_fft:    635 calls, 114.97 s
gradients_fft:          580 calls, 109.87 s

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

# Date 2008-01-16 Time 05:49:22 PST -0800 (1200491362.34 s)
Start R-work = 0.4645, R-free = 0.4656 (no bulk solvent and anisotropic scale)
Final R-work = 0.1498, R-free = 0.1955 (no bulk solvent and anisotropic scale)

Start R-work = 0.4558, R-free = 0.4604
Final R-work = 0.1283, R-free = 0.1795