# Date 2008-01-16 Time 05:14:27 PST -0800 (1200489267.43 s)
#phil __OFF__

Command line arguments: "../655.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30431
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 655

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 86.822, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.99194
Completeness in resolution range: 0.974238
Completeness with d_max=infinity: 0.971195

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   1.9919

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.99194
Completeness in resolution range: 0.974238
Completeness with d_max=infinity: 0.971195

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2619 [2114/2138]  1901   213  10.1%
  bin  2:  4.2619 -  3.3956 [2029/2049]  1827   202  10.0%
  bin  3:  3.3956 -  2.9702 [2000/2019]  1802   198   9.9%
  bin  4:  2.9702 -  2.7003 [1982/2012]  1781   201  10.1%
  bin  5:  2.7003 -  2.5077 [1977/1996]  1779   198  10.0%
  bin  6:  2.5077 -  2.3605 [1966/1991]  1767   199  10.1%
  bin  7:  2.3605 -  2.2427 [1936/1964]  1747   189   9.8%
  bin  8:  2.2427 -  2.1453 [1952/1988]  1756   196  10.0%
  bin  9:  2.1453 -  2.0630 [1938/1980]  1744   194  10.0%
  bin 10:  2.0630 -  1.9919 [1695/1970]  1526   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_655/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2204
        3.04 -     3.66: 4653
        3.66 -     4.28: 9065
        4.28 -     4.90: 12339
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.213 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.283 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28265 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_655/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_655/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 86.82195 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: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2177   r_free= 0.2165   ksol= 0.00   Bsol= 0.00   scale= 1.008    |
|                                                                             |
| 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:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.670899                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7532 0.99   1376  152 0.2477 0.2372      6.2389      6.1663|
|  2:  4.7532 -  3.7928 0.99   1316  148 0.1673 0.1607      6.0476      6.0266|
|  3:  3.7928 -  3.3193 0.99   1293  144 0.1752 0.1915      5.9193      6.0553|
|  4:  3.3193 -  3.0185 0.99   1285  142 0.1841 0.2014       5.812      5.8446|
|  5:  3.0185 -  2.8036 0.99   1270  141 0.2157 0.1795      5.7174       5.584|
|  6:  2.8036 -  2.6393 0.99   1286  141 0.2063 0.2172      5.6181      5.5563|
|  7:  2.6393 -  2.5077 0.99   1264  144 0.2156 0.2184       5.594      5.6058|
|  8:  2.5077 -  2.3990 0.98   1262  136 0.2241 0.2117      5.5844       5.573|
|  9:  2.3990 -  2.3070 0.98   1258  141 0.2214 0.2413      5.5122      5.5321|
| 10:  2.3070 -  2.2277 1.00   1255  143 0.2311 0.2173      5.5356      5.4237|
| 11:  2.2277 -  2.1582 0.97   1255  136 0.2327 0.2293      5.4898      5.4802|
| 12:  2.1582 -  2.0967 0.98   1245  138 0.2393 0.2315       5.452      5.5162|
| 13:  2.0967 -  2.0416 0.99   1252  139 0.2402 0.2410      5.3472      5.3654|
| 14:  2.0416 -  1.9919 0.80   1013  114 0.2536 0.2442      5.3846      5.2309|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7532  1376   152  0.83  22.30   0.87     0.84      31736.75|
|  2:  4.7532 -  3.7928  1316   148  0.90  15.75   1.00     0.95      24474.37|
|  3:  3.7928 -  3.3193  1293   144  0.90  16.01   1.03     1.01      18697.11|
|  4:  3.3193 -  3.0185  1285   142  0.90  15.90   1.03     1.01      14474.79|
|  5:  3.0185 -  2.8036  1270   141  0.88  18.43   1.05     1.01      11260.62|
|  6:  2.8036 -  2.6393  1286   141  0.88  18.39   1.04     1.01       9504.22|
|  7:  2.6393 -  2.5077  1264   144  0.87  19.54   1.06     1.02       9109.73|
|  8:  2.5077 -  2.3990  1262   136  0.87  19.85   1.06     1.03       8889.00|
|  9:  2.3990 -  2.3070  1258   141  0.87  19.98   1.09     1.05       8360.51|
| 10:  2.3070 -  2.2277  1255   143  0.86  20.67   1.11     1.06       7843.62|
| 11:  2.2277 -  2.1582  1255   136  0.86  21.07   1.10     1.08       7569.08|
| 12:  2.1582 -  2.0967  1245   138  0.86  21.06   1.12     1.09       7233.82|
| 13:  2.0967 -  2.0416  1252   139  0.85  22.06   1.11     1.08       6245.69|
| 14:  2.0416 -  1.9919  1013   114  0.87  20.22   1.11     1.04       4726.97|
|alpha:            min =        0.84 max =            1.09 mean =         1.02|
|beta:             min =     4726.97 max =        31736.75 mean =     12443.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.89 mean =        19.35|
|phase err.(test): min =        0.00 max =           89.18 mean =        19.22|
|-----------------------------------------------------------------------------|

============================== 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 = 2.656130              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.962   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.551   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      200 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2004 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1832 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2821 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4653 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4412 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5654 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6685 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.140 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.910)------------------------------------------|
|    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: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2177   r_free= 0.2165   ksol= 0.00   Bsol= 0.00   scale= 1.008    |
|                                                                             |
| 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:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.670899                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1980   r_free= 0.1977   ksol= 0.33   Bsol= 50.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.00,-0.96,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.626878                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.381199              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.009   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.164016              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.441   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1980      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1977      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9360 = 2.38 * 0.50 * 5.6913 + 1.00 * 0.1600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4094 = 2.38 * 0.50 * 5.3316 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8806 = 0.16 * 1.00 * 5.3316 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8702 = 0.16 * 1.00 * 5.1590 + 1.00 * 0.0240                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.910)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.81   16.40    None  None   None       |
|    all(noH): 2823   0      0.00    62.81   16.40    None  None   None       |
|    Sol.    : 438    0      6.96    62.81   36.92    None  None   None       |
|    Mac.    : 2385   0      0.00    60.32   12.64    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 -   6.282:  139   |   5:    31.407 -  37.689:   99        |
|      1:     6.282 -  12.563: 1367   |   6:    37.689 -  43.970:  101        |
|      2:    12.563 -  18.844:  661   |   7:    43.970 -  50.252:   74        |
|      3:    18.844 -  25.126:  191   |   8:    50.252 -  56.533:   51        |
|      4:    25.126 -  31.407:  117   |   9:    56.533 -  62.815:   23        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1523             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1524             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1524   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.00,-0.96,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.163378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1521   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.57,-1.30,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.164862                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.253051              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.952  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.154166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.396   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1498          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2945 = 1.25 * 0.50 * 5.1600 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2759 = 1.25 * 0.50 * 5.1453 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1498      final r-factor (free) = 0.1494          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9228 = 0.15 * 1.00 * 5.1453 + 1.00 * 0.1296                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7968 = 0.15 * 1.00 * 5.1247 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.910)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    66.02   16.54    None  None   None       |
|    all(noH): 2823   0      1.84    66.02   16.54    None  None   None       |
|    Sol.    : 438    0      5.93    66.02   36.79    None  None   None       |
|    Mac.    : 2385   0      1.84    62.91   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.845 -   8.262:  519   |   5:    33.933 -  40.350:  119        |
|      1:     8.262 -  14.680: 1316   |   6:    40.350 -  46.768:   87        |
|      2:    14.680 -  21.098:  400   |   7:    46.768 -  53.186:   91        |
|      3:    21.098 -  27.515:  149   |   8:    53.186 -  59.603:   35        |
|      4:    27.515 -  33.933:  100   |   9:    59.603 -  66.021:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1494             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1494             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1494   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.57,-1.30,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125732                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1493   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.53,-1.20,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125249                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.008301              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.185  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.992410              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.608  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1493      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7605 = 3.01 * 0.50 * 5.1247 + 1.00 * 0.0522                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7395 = 3.01 * 0.50 * 5.0963 + 1.00 * 0.0738                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1050          |
| start r-factor (free) = 0.1506      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0643 = 0.99 * 1.00 * 5.0963 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0588 = 0.99 * 1.00 * 5.0888 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.910)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    77.59   16.92    None  None   None       |
|    all(noH): 2823   0      0.98    77.59   16.92    None  None   None       |
|    Sol.    : 438    0      6.19    71.03   39.05    None  None   None       |
|    Mac.    : 2385   0      0.98    77.59   12.86    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:     0.983 -   8.644:  685   |   5:    39.288 -  46.949:  101        |
|      1:     8.644 -  16.305: 1279   |   6:    46.949 -  54.609:   83        |
|      2:    16.305 -  23.966:  349   |   7:    54.609 -  62.270:   63        |
|      3:    23.966 -  31.627:  119   |   8:    62.270 -  69.931:   26        |
|      4:    31.627 -  39.288:  112   |   9:    69.931 -  77.592:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1050 r_free = 0.1513             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1049 r_free = 0.1513             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1513   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.53,-1.20,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.093430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1048   r_free= 0.1513   ksol= 0.32   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.31,-0.96,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.093328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.465306              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.656  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.124534              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.333  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1048      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8030 = 1.47 * 0.50 * 5.0903 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7970 = 1.47 * 0.50 * 5.1087 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6449 = 0.12 * 1.00 * 5.1087 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6448 = 0.12 * 1.00 * 5.1228 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.910)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.26    76.10   16.38    None  None   None       |
|    all(noH): 2823   0      2.26    76.10   16.38    None  None   None       |
|    Sol.    : 438    0      6.50    70.92   36.89    None  None   None       |
|    Mac.    : 2385   0      2.26    76.10   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.262 -   9.645:  970   |   5:    39.179 -  46.562:   98        |
|      1:     9.645 -  17.028: 1094   |   6:    46.562 -  53.946:   76        |
|      2:    17.028 -  24.412:  273   |   7:    53.946 -  61.329:   43        |
|      3:    24.412 -  31.795:  135   |   8:    61.329 -  68.713:   20        |
|      4:    31.795 -  39.179:  110   |   9:    68.713 -  76.096:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1517             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1517             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1517   ksol= 0.32   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.31,-0.96,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118744                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1518   ksol= 0.32   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.25,-0.89,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118823                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.091386              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.761  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.221454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.949  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1518          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4112 = 2.09 * 0.50 * 5.1230 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4040 = 2.09 * 0.50 * 5.1099 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.5782 = 4.22 * 1.00 * 5.1099 + 1.00 * 0.0068                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.5425 = 4.22 * 1.00 * 5.1009 + 1.00 * 0.0092                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.910)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    83.65   16.68    None  None   None       |
|    all(noH): 2823   0      0.22    83.65   16.68    None  None   None       |
|    Sol.    : 438    0      6.10    72.74   39.04    None  None   None       |
|    Mac.    : 2385   0      0.22    83.65   12.57    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:     0.223 -   8.566:  752   |   5:    41.935 -  50.277:  110        |
|      1:     8.566 -  16.908: 1299   |   6:    50.277 -  58.620:   75        |
|      2:    16.908 -  25.250:  285   |   7:    58.620 -  66.962:   42        |
|      3:    25.250 -  33.593:  130   |   8:    66.962 -  75.304:   15        |
|      4:    33.593 -  41.935:  111   |   9:    75.304 -  83.646:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1536             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1067 r_free = 0.1536             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1536   ksol= 0.32   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.25,-0.89,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109261                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7532 0.99   1376  152 0.0981 0.1272      5.3776      5.5102|
|  2:  4.7532 -  3.7928 0.99   1316  148 0.0834 0.1128      5.4213      5.6277|
|  3:  3.7928 -  3.3193 0.99   1293  144 0.1023 0.1449      5.4544      5.8223|
|  4:  3.3193 -  3.0185 0.99   1285  142 0.1160 0.1555       5.415        5.56|
|  5:  3.0185 -  2.8036 0.99   1270  141 0.1265 0.1632      5.3045      5.5233|
|  6:  2.8036 -  2.6393 0.99   1286  141 0.1147 0.1924      5.1856       5.463|
|  7:  2.6393 -  2.5077 0.99   1264  144 0.1208 0.1527      5.1326      5.3123|
|  8:  2.5077 -  2.3990 0.98   1262  136 0.1101 0.1696        5.03      5.3345|
|  9:  2.3990 -  2.3070 0.98   1258  141 0.1101 0.1698       4.991      5.2501|
| 10:  2.3070 -  2.2277 1.00   1255  143 0.1060 0.1669      4.9278      5.2116|
| 11:  2.2277 -  2.1582 0.97   1255  136 0.1065 0.1656       4.902      5.1905|
| 12:  2.1582 -  2.0967 0.98   1245  138 0.1046 0.1650      4.8375      5.2031|
| 13:  2.0967 -  2.0416 0.99   1252  139 0.1020 0.1639      4.7509      5.0198|
| 14:  2.0416 -  1.9919 0.80   1013  114 0.0969 0.1775      4.6441      4.9469|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7532  1376   152  0.94   9.10   0.98     0.95       7035.47|
|  2:  4.7532 -  3.7928  1316   148  0.95   7.74   1.01     1.00       8836.51|
|  3:  3.7928 -  3.3193  1293   144  0.94  10.69   1.02     1.02       9837.80|
|  4:  3.3193 -  3.0185  1285   142  0.93  12.86   1.00     0.98       9507.41|
|  5:  3.0185 -  2.8036  1270   141  0.91  15.20   0.99     0.97       8037.09|
|  6:  2.8036 -  2.6393  1286   141  0.90  15.56   0.98     0.95       6840.27|
|  7:  2.6393 -  2.5077  1264   144  0.91  15.19   0.98     0.96       5907.85|
|  8:  2.5077 -  2.3990  1262   136  0.92  14.07   0.98     0.96       4855.06|
|  9:  2.3990 -  2.3070  1258   141  0.92  14.57   1.00     0.96       4636.59|
| 10:  2.3070 -  2.2277  1255   143  0.91  14.86   0.99     0.95       4116.25|
| 11:  2.2277 -  2.1582  1255   136  0.90  15.61   0.98     0.95       4161.68|
| 12:  2.1582 -  2.0967  1245   138  0.92  14.46   1.00     0.98       3659.03|
| 13:  2.0967 -  2.0416  1252   139  0.91  15.21   0.99     0.97       3188.02|
| 14:  2.0416 -  1.9919  1013   114  0.92  14.02   0.96     0.92       2517.19|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2517.19 max =         9837.80 mean =      6021.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.67 mean =        13.02|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1535   ksol= 0.32   Bsol= 49.99   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.00,-0.66,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109220                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1535   ksol= 0.32   Bsol= 49.99   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.00,-0.66,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109220                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7532 0.99   1376  152 0.0980 0.1272      5.3769      5.5097|
|  2:  4.7532 -  3.7928 0.99   1316  148 0.0835 0.1128      5.4219      5.6281|
|  3:  3.7928 -  3.3193 0.99   1293  144 0.1024 0.1449      5.4546      5.8226|
|  4:  3.3193 -  3.0185 0.99   1285  142 0.1160 0.1555      5.4149        5.56|
|  5:  3.0185 -  2.8036 0.99   1270  141 0.1264 0.1631      5.3042      5.5229|
|  6:  2.8036 -  2.6393 0.99   1286  141 0.1146 0.1925      5.1854      5.4629|
|  7:  2.6393 -  2.5077 0.99   1264  144 0.1208 0.1527      5.1326      5.3122|
|  8:  2.5077 -  2.3990 0.98   1262  136 0.1101 0.1695      5.0301      5.3343|
|  9:  2.3990 -  2.3070 0.98   1258  141 0.1101 0.1698      4.9911      5.2502|
| 10:  2.3070 -  2.2277 1.00   1255  143 0.1060 0.1669      4.9278      5.2115|
| 11:  2.2277 -  2.1582 0.97   1255  136 0.1065 0.1655      4.9019      5.1901|
| 12:  2.1582 -  2.0967 0.98   1245  138 0.1046 0.1650      4.8374      5.2028|
| 13:  2.0967 -  2.0416 0.99   1252  139 0.1020 0.1639      4.7509      5.0197|
| 14:  2.0416 -  1.9919 0.80   1013  114 0.0969 0.1774      4.6442       4.947|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7532  1376   152  0.94   9.09   0.98     0.95       7022.74|
|  2:  4.7532 -  3.7928  1316   148  0.95   7.74   1.02     1.00       8836.47|
|  3:  3.7928 -  3.3193  1293   144  0.94  10.69   1.03     1.02       9841.39|
|  4:  3.3193 -  3.0185  1285   142  0.93  12.85   1.01     0.99       9503.81|
|  5:  3.0185 -  2.8036  1270   141  0.91  15.19   1.00     0.97       8033.49|
|  6:  2.8036 -  2.6393  1286   141  0.90  15.55   0.99     0.96       6836.34|
|  7:  2.6393 -  2.5077  1264   144  0.91  15.19   0.99     0.97       5906.75|
|  8:  2.5077 -  2.3990  1262   136  0.92  14.07   0.99     0.97       4854.93|
|  9:  2.3990 -  2.3070  1258   141  0.92  14.57   1.01     0.97       4637.74|
| 10:  2.3070 -  2.2277  1255   143  0.91  14.86   1.00     0.96       4115.56|
| 11:  2.2277 -  2.1582  1255   136  0.90  15.61   1.00     0.96       4159.93|
| 12:  2.1582 -  2.0967  1245   138  0.92  14.46   1.01     1.00       3657.59|
| 13:  2.0967 -  2.0416  1252   139  0.91  15.21   1.00     0.99       3187.38|
| 14:  2.0416 -  1.9919  1013   114  0.92  14.02   0.98     0.94       2517.33|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2517.33 max =         9841.39 mean =      6019.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.69 mean =        13.02|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.910)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    83.64   16.67    None  None   None       |
|    all(noH): 2823   0      0.22    83.64   16.67    None  None   None       |
|    Sol.    : 438    0      6.10    72.73   39.04    None  None   None       |
|    Mac.    : 2385   0      0.22    83.64   12.57    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:     0.218 -   8.560:  752   |   5:    41.929 -  50.272:  110        |
|      1:     8.560 -  16.902: 1299   |   6:    50.272 -  58.614:   75        |
|      2:    16.902 -  25.245:  285   |   7:    58.614 -  66.956:   42        |
|      3:    25.245 -  33.587:  130   |   8:    66.956 -  75.299:   15        |
|      4:    33.587 -  41.929:  111   |   9:    75.299 -  83.641:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 285         
Filter by distance & map next to the model:
   mapped sites are within: 0.521 - 4.752
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 280 from: 285
   mapped sites are within: 0.705 - 4.752

peak=    5.903 closest distance to " NH2 ARG A  56 " =    2.219
peak=    5.584 closest distance to " CG  PRO A  54 " =    1.293
peak=    5.364 closest distance to " O   HOH Z 232 " =    2.367
peak=    5.241 closest distance to " O   HOH Z 126 " =    1.912
peak=    5.082 closest distance to " CB  ARG A 275 " =    0.920
peak=    5.078 closest distance to " CB  GLN A 223 " =    1.420
peak=    4.986 closest distance to " O   HOH Z 144 " =    1.773
peak=    4.952 closest distance to " NE2 GLN A  11 " =    1.093
peak=    4.851 closest distance to " CB  SER A  63 " =    1.181
peak=    4.762 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.574 closest distance to " CB  PRO A  54 " =    0.944
peak=    4.548 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.529 closest distance to " CB  ARG A  79 " =    1.353
peak=    4.515 closest distance to " C   PRO A 198 " =    1.455
peak=    4.508 closest distance to " CB  GLU A 152 " =    1.239
peak=    4.485 closest distance to " O   HOH Z  15 " =    2.234
peak=    4.479 closest distance to " O   HOH Z 298 " =    1.917
peak=    4.454 closest distance to " O   HOH Z 236 " =    2.093
peak=    4.436 closest distance to " CG2 VAL A 257 " =    0.899
peak=    4.403 closest distance to " O   HOH Z 427 " =    2.889
peak=    4.395 closest distance to " O   HOH Z  78 " =    1.729
peak=    4.334 closest distance to " CB  ARG A 190 " =    1.619
peak=    4.286 closest distance to " O   HOH Z 250 " =    1.531
peak=    4.256 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.252 closest distance to " O   HOH Z 234 " =    3.692
peak=    4.249 closest distance to " O   HOH Z 369 " =    2.182
peak=    4.241 closest distance to " O   HOH Z 158 " =    2.999
peak=    4.239 closest distance to " CB  ASN A 148 " =    1.404
peak=    4.237 closest distance to " O   HOH Z 189 " =    2.489
peak=    4.236 closest distance to " O   HOH Z  61 " =    1.607
peak=    4.232 closest distance to " CB  LEU A 228 " =    1.104
peak=    4.228 closest distance to " O   HOH Z 303 " =    2.111
peak=    4.212 closest distance to " CA  ASN A 215 " =    1.164
peak=    4.206 closest distance to " O   HOH Z 193 " =    1.827
peak=    4.204 closest distance to " CB  TYR A 169 " =    0.757
peak=    4.174 closest distance to " O   HOH Z 346 " =    1.685
peak=    4.157 closest distance to " O   HOH Z 209 " =    2.305
peak=    4.147 closest distance to " OD1 ASN A  69 " =    2.576
peak=    4.141 closest distance to " NZ  LYS A 117 " =    3.174
peak=    4.139 closest distance to " ND2 ASN A 187 " =    1.412
peak=    4.121 closest distance to " CB  TRP A 266 " =    1.017
peak=    4.104 closest distance to " OG ASER A 258 " =    3.121
peak=    4.104 closest distance to " CB  VAL A 265 " =    1.268
peak=    4.073 closest distance to " CE  LYS A  76 " =    0.867
peak=    4.067 closest distance to " O   HOH Z 203 " =    1.718
peak=    4.034 closest distance to " O   HOH Z 392 " =    3.145
peak=    4.028 closest distance to " O   HOH Z  40 " =    1.696
peak=    4.007 closest distance to " CZ  PHE A 218 " =    1.051
peak=    3.994 closest distance to " O   HOH Z 272 " =    1.844
peak=    3.969 closest distance to " CB  ASP A 140 " =    0.980
peak=    3.967 closest distance to " CD2 TRP A 179 " =    1.357
peak=    3.887 closest distance to " CG  PRO A 243 " =    1.015
peak=    3.883 closest distance to " CD  ARG A 159 " =    0.731
peak=    3.847 closest distance to " O   SER A  87 " =    2.269
peak=    3.817 closest distance to " O   HOH Z  10 " =    1.809
peak=    3.817 closest distance to " O   HOH Z 214 " =    2.126
peak=    3.807 closest distance to " O   HOH Z 248 " =    1.571
peak=    3.804 closest distance to " O   HOH Z 280 " =    2.950
peak=    3.803 closest distance to " CB  SER A   3 " =    1.298
peak=    3.790 closest distance to " O   HOH Z 261 " =    2.152
peak=    3.776 closest distance to " O   HOH Z  19 " =    2.547
peak=    3.765 closest distance to " CB  GLU A 128 " =    1.043
peak=    3.764 closest distance to " CG  ARG A  66 " =    2.548
peak=    3.760 closest distance to " O   HOH Z 313 " =    1.961
peak=    3.758 closest distance to " O   HOH Z 180 " =    2.215
peak=    3.747 closest distance to " O   HOH Z  43 " =    1.855
peak=    3.743 closest distance to " NH1AARG A 145 " =    1.198
peak=    3.733 closest distance to " CA  ARG A  36 " =    1.029
peak=    3.721 closest distance to " O   HOH Z 368 " =    2.045
peak=    3.714 closest distance to " O   HOH Z 389 " =    1.849
peak=    3.714 closest distance to " O   HOH Z 172 " =    3.249
peak=    3.704 closest distance to " O   HOH Z 403 " =    1.631
peak=    3.701 closest distance to " CA  ARG A 195 " =    1.203
peak=    3.698 closest distance to " O   HOH Z   1 " =    1.968
peak=    3.693 closest distance to " O   HOH Z 419 " =    2.025
peak=    3.680 closest distance to " CB  VAL A 202 " =    1.569
peak=    3.673 closest distance to " O   HOH Z 291 " =    1.538
peak=    3.667 closest distance to " O   HOH Z  66 " =    2.169
peak=    3.660 closest distance to " CB  SER A 212 " =    1.103
peak=    3.655 closest distance to " O   HOH Z 402 " =    1.384
peak=    3.643 closest distance to " O   HOH Z 344 " =    3.141
peak=    3.638 closest distance to " O   HOH Z 371 " =    3.103
peak=    3.632 closest distance to " O   HOH Z 368 " =    3.573
peak=    3.631 closest distance to " OG BSER A 164 " =    2.309
peak=    3.631 closest distance to " CB  GLU A 277 " =    3.579
peak=    3.626 closest distance to " O   HOH Z 426 " =    1.864
peak=    3.625 closest distance to " CG1 ILE A  33 " =    1.206
peak=    3.620 closest distance to " N   ARG A 156 " =    1.312
peak=    3.609 closest distance to " O   HOH Z   9 " =    2.034
peak=    3.607 closest distance to " CB  HIS A 108 " =    0.785
peak=    3.604 closest distance to " O   HOH Z  59 " =    1.852
peak=    3.603 closest distance to " CA  ALA A  51 " =    0.925
peak=    3.603 closest distance to " O   HOH Z 425 " =    2.078
peak=    3.598 closest distance to " CB  ASN A 142 " =    1.043
peak=    3.582 closest distance to " O   HOH Z 423 " =    1.828
peak=    3.582 closest distance to " CB  ASN A  39 " =    0.889
peak=    3.576 closest distance to " CD BLYS A 290 " =    1.078
peak=    3.563 closest distance to " OD2 ASP A 286 " =    2.826
peak=    3.562 closest distance to " CB  TRP A 179 " =    1.364
peak=    3.559 closest distance to " O   HOH Z 245 " =    1.280
peak=    3.554 closest distance to " O   HOH Z 417 " =    3.264
peak=    3.549 closest distance to " CB  ALA A 291 " =    1.339
peak=    3.549 closest distance to " O   HOH Z 133 " =    2.560
peak=    3.545 closest distance to " CB  THR A  31 " =    1.640
peak=    3.534 closest distance to " O   HOH Z 371 " =    1.788
peak=    3.527 closest distance to " O   HOH Z  21 " =    1.737
peak=    3.520 closest distance to " O  BHOH Z 338 " =    2.347
peak=    3.517 closest distance to " O   HOH Z 305 " =    3.542
peak=    3.517 closest distance to " CD2 LEU A 255 " =    1.452
peak=    3.511 closest distance to " O   HOH Z 132 " =    2.469
peak=    3.511 closest distance to " OG1 THR A 294 " =    2.405
peak=    3.504 closest distance to " O   HOH Z  97 " =    2.685
peak=    3.504 closest distance to " CB  ARG A 139 " =    0.979
peak=    3.503 closest distance to " CD1 LEU A 300 " =    1.238
peak=    3.500 closest distance to " CG1BVAL A  72 " =    1.625
peak=    3.496 closest distance to " O   HOH Z  44 " =    3.017
peak=    3.494 closest distance to " CB  ASN A 110 " =    1.126
peak=    3.493 closest distance to " CB  TYR A 116 " =    0.758
peak=    3.490 closest distance to " CB  ALA A  34 " =    1.059
peak=    3.482 closest distance to " O   HOH Z 265 " =    2.430
peak=    3.482 closest distance to " ND1 HIS A  86 " =    1.719
peak=    3.478 closest distance to " CB  SER A 216 " =    0.856
peak=    3.471 closest distance to " CB  GLU A  46 " =    0.986
peak=    3.468 closest distance to " CG2 ILE A 120 " =    1.125
peak=    3.464 closest distance to " O   HOH Z 193 " =    1.660
peak=    3.458 closest distance to " O   HOH Z  61 " =    1.462
peak=    3.453 closest distance to " CA  THR A 264 " =    0.886
peak=    3.452 closest distance to " O   HOH Z 213 " =    1.918
peak=    3.452 closest distance to " CB  ILE A 120 " =    1.274
peak=    3.451 closest distance to " CB  MET A  47 " =    1.057
peak=    3.450 closest distance to " O   MET A 105 " =    1.862
peak=    3.446 closest distance to " O   HOH Z 148 " =    3.390
peak=    3.433 closest distance to " O   HOH Z 193 " =    2.027
peak=    3.431 closest distance to " O   HOH Z  40 " =    1.323
peak=    3.431 closest distance to " NH2BARG A 145 " =    2.057
peak=    3.429 closest distance to " NE2 GLN A  73 " =    3.766
peak=    3.427 closest distance to " O   HOH Z 147 " =    1.802
peak=    3.424 closest distance to " CD1 ILE A 106 " =    0.767
peak=    3.423 closest distance to " CA  MET A  40 " =    1.139
peak=    3.423 closest distance to " CB  THR A 157 " =    1.125
peak=    3.420 closest distance to " O   HOH Z  44 " =    1.713
peak=    3.419 closest distance to " O   HOH Z 353 " =    2.653
peak=    3.418 closest distance to " CG  LEU A 167 " =    1.247
peak=    3.412 closest distance to " CD1 LEU A  96 " =    0.792
peak=    3.412 closest distance to " CA  THR A 221 " =    1.016
peak=    3.412 closest distance to " O   HOH Z 234 " =    1.898
peak=    3.406 closest distance to " O   HOH Z 411 " =    3.905
peak=    3.404 closest distance to " O   HOH Z 406 " =    1.506
peak=    3.396 closest distance to " OE1 GLU A   2 " =    2.182
peak=    3.392 closest distance to " CA  ALA A 158 " =    1.319
peak=    3.392 closest distance to " O   HOH Z 128 " =    2.119
peak=    3.390 closest distance to " CG2 THR A 221 " =    1.091
peak=    3.386 closest distance to " CG2 ILE A  20 " =    1.470
peak=    3.386 closest distance to " CA  ALA A  21 " =    1.144
peak=    3.386 closest distance to " O   HOH Z 407 " =    2.374
peak=    3.385 closest distance to " CD2 LEU A 297 " =    0.842
peak=    3.385 closest distance to " CD  LYS A 166 " =    1.214
peak=    3.382 closest distance to " CG1 VAL A 153 " =    0.988
peak=    3.379 closest distance to " N   ASN A  39 " =    1.247
peak=    3.378 closest distance to " O   ASN A  74 " =    1.532
peak=    3.377 closest distance to " O   HOH Z 250 " =    2.147
peak=    3.375 closest distance to " O   THR A 220 " =    1.287
peak=    3.373 closest distance to " O   HOH Z 128 " =    2.283
peak=    3.371 closest distance to " CE1 TYR A 186 " =    1.345
peak=    3.370 closest distance to " CZ2 TRP A 179 " =    1.730
peak=    3.370 closest distance to " CA  ALA A 291 " =    0.810
peak=    3.357 closest distance to " O   HOH Z 261 " =    1.511
peak=    3.345 closest distance to " O   HOH Z  88 " =    2.979
peak=    3.344 closest distance to " O   HOH Z 285 " =    2.763
peak=    3.340 closest distance to " O   HOH Z 337 " =    3.674
peak=    3.336 closest distance to " O   HOH Z 403 " =    1.388
peak=    3.330 closest distance to " O   HOH Z 359 " =    1.419
peak=    3.327 closest distance to " O   HOH Z 409 " =    2.898
peak=    3.321 closest distance to " CA  SER A  87 " =    1.061
peak=    3.320 closest distance to " O   HOH Z 391 " =    2.918
peak=    3.320 closest distance to " ND2 ASN A 110 " =    1.678
peak=    3.309 closest distance to " O   HOH Z 435 " =    1.954
peak=    3.308 closest distance to " O   HOH Z 185 " =    1.773
peak=    3.303 closest distance to " CG  LYS A  76 " =    0.974
peak=    3.302 closest distance to " CB  ALA A 248 " =    0.861
peak=    3.299 closest distance to " CD1 LEU A 228 " =    2.062
peak=    3.298 closest distance to " CA  ALA A  84 " =    1.272
peak=    3.296 closest distance to " O   HOH Z 327 " =    1.622
peak=    3.295 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.294 closest distance to " O   HOH Z 421 " =    1.822
peak=    3.293 closest distance to " O   HOH Z 219 " =    1.950
peak=    3.292 closest distance to " O   HOH Z 298 " =    2.509
peak=    3.291 closest distance to " ND2 ASN A 249 " =    0.850
peak=    3.287 closest distance to " O   HOH Z 173 " =    1.779
peak=    3.286 closest distance to " O   HOH Z 175 " =    2.190
peak=    3.283 closest distance to " NH1BARG A 145 " =    1.171
peak=    3.282 closest distance to " N   ASN A 127 " =    1.241
peak=    3.281 closest distance to " CA  MET A 105 " =    1.004
peak=    3.280 closest distance to " CB  ASN A 224 " =    0.987
peak=    3.275 closest distance to " CB  LYS A 290 " =    1.040
peak=    3.270 closest distance to " CB  ALA A 248 " =    1.404
peak=    3.267 closest distance to " N   PHE A 130 " =    1.247
peak=    3.267 closest distance to " O   HOH Z 411 " =    1.692
peak=    3.266 closest distance to " O   ALA A   1 " =    1.706
peak=    3.265 closest distance to " O   HOH Z   1 " =    1.671
peak=    3.264 closest distance to " O   HOH Z 433 " =    1.765
peak=    3.263 closest distance to " CA  ILE A 234 " =    0.964
peak=    3.262 closest distance to " NH2 ARG A 156 " =    1.199
peak=    3.262 closest distance to " CD  LYS A 119 " =    1.345
peak=    3.262 closest distance to " CA  TYR A 116 " =    1.324
peak=    3.258 closest distance to " CB  SER A 141 " =    1.025
peak=    3.256 closest distance to " CB  GLN A  88 " =    1.207
peak=    3.256 closest distance to " NE2 HIS A 207 " =    1.325
peak=    3.252 closest distance to " O   HOH Z 365 " =    2.962
peak=    3.252 closest distance to " O   HOH Z 329 " =    3.951
peak=    3.251 closest distance to " O   HOH Z 273 " =    2.853
peak=    3.246 closest distance to " O   HOH Z 188 " =    2.002
peak=    3.242 closest distance to " CA  VAL A 125 " =    1.058
peak=    3.241 closest distance to " CA  ALA A 233 " =    1.228
peak=    3.241 closest distance to " O   HOH Z 135 " =    1.667
peak=    3.239 closest distance to " CB  GLN A  89 " =    1.380
peak=    3.239 closest distance to " O   HOH Z  40 " =    1.931
peak=    3.238 closest distance to " OG  SER A  22 " =    2.724
peak=    3.233 closest distance to " CB  THR A 235 " =    1.104
peak=    3.230 closest distance to " CG1 ILE A  49 " =    1.474
peak=    3.227 closest distance to " O   ALA A 165 " =    1.550
peak=    3.222 closest distance to " CB  ALA A 242 " =    0.903
peak=    3.220 closest distance to " O   HOH Z 294 " =    1.512
peak=    3.220 closest distance to " CG  MET A 185 " =    1.109
peak=    3.219 closest distance to " CB  ALA A 114 " =    0.803
peak=    3.219 closest distance to " CB  ALA A   9 " =    1.518
peak=    3.212 closest distance to " CG2 VAL A 197 " =    1.072
peak=    3.212 closest distance to " O   HOH Z 271 " =    2.356
peak=    3.207 closest distance to " N   VAL A 126 " =    1.317
peak=    3.199 closest distance to " CD  ARG A  36 " =    0.998
peak=    3.194 closest distance to " O   THR A 251 " =    1.211
peak=    3.186 closest distance to " O   HOH Z 325 " =    3.845
peak=    3.186 closest distance to " CA  GLU A  46 " =    0.749
peak=    3.184 closest distance to " CG2 ILE A 234 " =    0.757
peak=    3.183 closest distance to " O   HOH Z 357 " =    1.869
peak=    3.180 closest distance to " O   HOH Z  97 " =    1.993
peak=    3.179 closest distance to " CB  MET A  40 " =    0.782
peak=    3.179 closest distance to " CB  PRO A  90 " =    1.188
peak=    3.178 closest distance to " OG BSER A  99 " =    2.228
peak=    3.175 closest distance to " O   HOH Z 423 " =    2.885
peak=    3.171 closest distance to " CG  ARG A 159 " =    0.835
peak=    3.171 closest distance to " N   GLN A 278 " =    1.286
peak=    3.169 closest distance to " CG  GLN A  11 " =    1.738
peak=    3.169 closest distance to " CB  SER A  62 " =    1.217
peak=    3.166 closest distance to " O   HOH Z 287 " =    2.298
peak=    3.165 closest distance to " O   HOH Z 345 " =    3.444
peak=    3.154 closest distance to " CB  LEU A 255 " =    0.777
peak=    3.150 closest distance to " CE  LYS A  48 " =    1.069
peak=    3.147 closest distance to " CB  ARG A 138 " =    0.937
peak=    3.147 closest distance to " O   HOH Z 299 " =    4.498
peak=    3.142 closest distance to " CB  PHE A 204 " =    0.705
peak=    3.141 closest distance to " CB  ALA A  21 " =    1.955
peak=    3.133 closest distance to " OD1BASN A 224 " =    2.385
peak=    3.132 closest distance to " CG  PRO A 213 " =    0.949
peak=    3.131 closest distance to " CD1 ILE A 263 " =    1.308
peak=    3.130 closest distance to " O   HOH Z 258 " =    1.625
peak=    3.124 closest distance to " O   TYR A 116 " =    1.335
peak=    3.121 closest distance to " CG  GLN A  89 " =    1.498
peak=    3.120 closest distance to " O   SER A 164 " =    1.282
peak=    3.119 closest distance to " O   HOH Z 290 " =    0.992
peak=    3.118 closest distance to " O   HOH Z 383 " =    1.818
peak=    3.114 closest distance to " O   HOH Z 437 " =    1.241
peak=    3.110 closest distance to " O   HOH Z  49 " =    2.942
peak=    3.109 closest distance to " O   HOH Z  88 " =    2.076
peak=    3.105 closest distance to " CB  ALA A   1 " =    4.752
peak=    3.098 closest distance to " CB  ASN A 215 " =    1.076
peak=    3.095 closest distance to " CD1AILE A 234 " =    0.867
peak=    3.095 closest distance to " O   HOH Z 163 " =    1.761
peak=    3.092 closest distance to " O   HOH Z 116 " =    1.733
peak=    3.086 closest distance to " CA  ALA A 154 " =    0.983
peak=    3.083 closest distance to " O   HOH Z  88 " =    2.539
peak=    3.068 closest distance to " O   GLY A  75 " =    1.429
peak=    3.068 closest distance to " O   HOH Z 369 " =    1.693
peak=    3.062 closest distance to " ND1 HIS A  81 " =    1.639
peak=    3.058 closest distance to " CA  THR A  82 " =    1.443
peak=    3.057 closest distance to " CA  SER A 146 " =    1.696
peak=    3.046 closest distance to " CA  ARG A 102 " =    1.028
peak=    3.046 closest distance to " CB  VAL A 126 " =    1.042
peak=    3.001 closest distance to " O   GLN A 278 " =    1.506
peak=    3.001 closest distance to " O   HOH Z 361 " =    3.165

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.792 - 5.988
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 193
   mapped sites are within: 0.792 - 5.988

peak=   -4.543 closest distance to " O   HOH Z 266 " =    5.164
peak=   -4.518 closest distance to " CD  ARG A 156 " =    2.013
peak=   -4.454 closest distance to " CG  GLN A 223 " =    1.928
peak=   -4.453 closest distance to " CB  PRO A 243 " =    2.632
peak=   -4.389 closest distance to " O   VAL A  67 " =    2.695
peak=   -4.337 closest distance to " O   HOH Z 377 " =    2.089
peak=   -4.330 closest distance to " SG  CYS A 254 " =    3.501
peak=   -4.319 closest distance to " CD  GLN A  58 " =    1.019
peak=   -4.257 closest distance to " CG1 VAL A 112 " =    2.641
peak=   -4.247 closest distance to " C   HIS A 108 " =    1.063
peak=   -4.221 closest distance to " O   HOH Z 231 " =    2.266
peak=   -4.219 closest distance to " O   HOH Z 389 " =    1.966
peak=   -4.211 closest distance to " OG BSER A 134 " =    1.244
peak=   -4.204 closest distance to " ND2 ASN A  45 " =    1.794
peak=   -4.179 closest distance to " CG1 VAL A 112 " =    2.863
peak=   -4.115 closest distance to " CE  MET A 105 " =    2.405
peak=   -4.107 closest distance to " CZ3 TRP A 179 " =    1.176
peak=   -4.089 closest distance to " CD2 PHE A 192 " =    2.028
peak=   -4.019 closest distance to " CA  VAL A  67 " =    2.941
peak=   -4.018 closest distance to " O   HOH Z 372 " =    2.343
peak=   -3.991 closest distance to " O   HOH Z 435 " =    2.826
peak=   -3.912 closest distance to " O   HOH Z 198 " =    1.959
peak=   -3.892 closest distance to " O   PRO A 198 " =    1.280
peak=   -3.878 closest distance to " O   HOH Z 114 " =    3.010
peak=   -3.866 closest distance to " CB  ALA A 291 " =    2.243
peak=   -3.852 closest distance to " O   HOH Z 313 " =    1.895
peak=   -3.824 closest distance to " CB  ALA A  43 " =    2.533
peak=   -3.816 closest distance to " O   ILE A 109 " =    2.561
peak=   -3.816 closest distance to " CG2 ILE A 263 " =    2.317
peak=   -3.809 closest distance to " N   ALA A  43 " =    2.599
peak=   -3.808 closest distance to " CB  ALA A 291 " =    2.486
peak=   -3.792 closest distance to " CE2 TYR A  30 " =    2.740
peak=   -3.777 closest distance to " O   HOH Z  10 " =    1.497
peak=   -3.762 closest distance to " CD  ARG A 139 " =    1.505
peak=   -3.756 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.755 closest distance to " CB  ASN A  39 " =    2.347
peak=   -3.745 closest distance to " O   HOH Z 185 " =    2.242
peak=   -3.733 closest distance to " OG  SER A  97 " =    2.204
peak=   -3.732 closest distance to " CG  PHE A 283 " =    2.654
peak=   -3.722 closest distance to " O   PRO A 163 " =    2.035
peak=   -3.707 closest distance to " CD1 PHE A  59 " =    1.930
peak=   -3.701 closest distance to " O   HOH Z 193 " =    1.962
peak=   -3.694 closest distance to " O   HOH Z 407 " =    3.057
peak=   -3.687 closest distance to " O   HOH Z 353 " =    2.143
peak=   -3.686 closest distance to " O   HOH Z 351 " =    1.522
peak=   -3.684 closest distance to " O   HOH Z 290 " =    1.273
peak=   -3.680 closest distance to " OD2 ASP A 191 " =    1.428
peak=   -3.667 closest distance to " O   HOH Z 196 " =    2.127
peak=   -3.662 closest distance to " OD1 ASN A 187 " =    1.548
peak=   -3.660 closest distance to " CA  GLY A 203 " =    2.374
peak=   -3.653 closest distance to " OXT GLY A 302 " =    2.822
peak=   -3.649 closest distance to " N   ALA A 248 " =    1.711
peak=   -3.636 closest distance to " O   HOH Z 211 " =    1.652
peak=   -3.633 closest distance to " CZ  PHE A  59 " =    1.530
peak=   -3.582 closest distance to " O   HOH Z 126 " =    1.923
peak=   -3.580 closest distance to " O   HOH Z  73 " =    2.222
peak=   -3.580 closest distance to " CE2 PHE A 218 " =    2.440
peak=   -3.578 closest distance to " NH2AARG A 275 " =    5.281
peak=   -3.568 closest distance to " CG  ARG A 269 " =    2.398
peak=   -3.564 closest distance to " O   HOH Z  44 " =    2.286
peak=   -3.563 closest distance to " CB  ASP A 132 " =    2.285
peak=   -3.560 closest distance to " O   ALA A 161 " =    1.701
peak=   -3.554 closest distance to " CD1 LEU A 101 " =    2.301
peak=   -3.543 closest distance to " CB  TYR A  15 " =    2.145
peak=   -3.513 closest distance to " NH2BARG A 275 " =    1.883
peak=   -3.503 closest distance to " OD1 ASN A 148 " =    1.523
peak=   -3.501 closest distance to " CB  ALA A 248 " =    2.373
peak=   -3.497 closest distance to " ND2 ASN A 249 " =    2.328
peak=   -3.493 closest distance to " O   HOH Z 298 " =    1.246
peak=   -3.487 closest distance to " NE2 GLN A 278 " =    1.747
peak=   -3.483 closest distance to " NE2 GLN A 194 " =    1.737
peak=   -3.482 closest distance to " O   HOH Z  43 " =    1.705
peak=   -3.479 closest distance to " N   ASP A 286 " =    2.360
peak=   -3.478 closest distance to " CB  PRO A 163 " =    2.461
peak=   -3.478 closest distance to " CA  GLY A 133 " =    2.010
peak=   -3.475 closest distance to " OD1 ASP A 191 " =    1.539
peak=   -3.475 closest distance to " O   HOH Z  51 " =    1.646
peak=   -3.472 closest distance to " O   VAL A 189 " =    2.590
peak=   -3.469 closest distance to " CG  ASP A 231 " =    0.792
peak=   -3.465 closest distance to " CZ  TYR A 169 " =    1.700
peak=   -3.464 closest distance to " CB  ALA A 248 " =    2.150
peak=   -3.461 closest distance to " O   PHE A 218 " =    1.590
peak=   -3.457 closest distance to " O   HOH Z 253 " =    3.930
peak=   -3.451 closest distance to " CG1 VAL A 250 " =    2.644
peak=   -3.449 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.445 closest distance to " N   SER A 212 " =    1.998
peak=   -3.440 closest distance to " CD2 PHE A  61 " =    2.587
peak=   -3.413 closest distance to " O   HOH Z 198 " =    1.498
peak=   -3.405 closest distance to " O   HOH Z 310 " =    1.706
peak=   -3.399 closest distance to " O   HOH Z  13 " =    1.584
peak=   -3.399 closest distance to " O   ALA A  10 " =    1.650
peak=   -3.397 closest distance to " N   GLN A  58 " =    1.711
peak=   -3.381 closest distance to " O   HOH Z 359 " =    3.190
peak=   -3.380 closest distance to " O   HOH Z 295 " =    1.522
peak=   -3.374 closest distance to " O   HOH Z 123 " =    2.359
peak=   -3.370 closest distance to " OD2 ASP A 171 " =    2.354
peak=   -3.369 closest distance to " C   ALA A 158 " =    1.336
peak=   -3.356 closest distance to " O   HOH Z  38 " =    1.513
peak=   -3.355 closest distance to " CA  GLY A 241 " =    3.093
peak=   -3.352 closest distance to " CB  PHE A 208 " =    2.233
peak=   -3.350 closest distance to " O   HOH Z 311 " =    3.691
peak=   -3.350 closest distance to " O   ALA A 180 " =    1.235
peak=   -3.349 closest distance to " NH2 ARG A  79 " =    1.563
peak=   -3.348 closest distance to " O   HOH Z 166 " =    2.066
peak=   -3.345 closest distance to " O   MET A  40 " =    2.793
peak=   -3.344 closest distance to " C   LEU A 143 " =    1.056
peak=   -3.343 closest distance to " O   ARG A 145 " =    1.525
peak=   -3.339 closest distance to " CZ  PHE A 155 " =    1.279
peak=   -3.338 closest distance to " CD1 ILE A 239 " =    2.382
peak=   -3.331 closest distance to " O   HOH Z 394 " =    1.439
peak=   -3.331 closest distance to " O   HOH Z 322 " =    1.668
peak=   -3.322 closest distance to " O   HOH Z  60 " =    2.239
peak=   -3.322 closest distance to " CD1 LEU A 297 " =    2.422
peak=   -3.321 closest distance to " CB  TRP A  85 " =    2.446
peak=   -3.321 closest distance to " NH1 ARG A  36 " =    2.059
peak=   -3.318 closest distance to " C   MET A 188 " =    1.322
peak=   -3.314 closest distance to " CD1 LEU A 228 " =    2.198
peak=   -3.314 closest distance to " CG  GLU A 277 " =    1.198
peak=   -3.305 closest distance to " O   SER A 135 " =    1.459
peak=   -3.297 closest distance to " O   HOH Z 165 " =    2.012
peak=   -3.292 closest distance to " O   GLY A 211 " =    1.319
peak=   -3.285 closest distance to " NH1 ARG A 195 " =    2.599
peak=   -3.284 closest distance to " CD  ARG A 195 " =    5.237
peak=   -3.280 closest distance to " CB  GLN A  11 " =    1.778
peak=   -3.276 closest distance to " CD  GLU A 236 " =    1.065
peak=   -3.270 closest distance to " CA  ASP A 298 " =    1.064
peak=   -3.269 closest distance to " CD2 LEU A 237 " =    2.706
peak=   -3.265 closest distance to " CA  GLY A  98 " =    1.918
peak=   -3.263 closest distance to " O   HOH Z 292 " =    4.578
peak=   -3.260 closest distance to " N   THR A 157 " =    1.486
peak=   -3.257 closest distance to " O   ALA A  51 " =    1.335
peak=   -3.252 closest distance to " CB  ASN A 252 " =    1.712
peak=   -3.249 closest distance to " CB  ASP A 286 " =    1.746
peak=   -3.248 closest distance to " O   HOH Z 362 " =    5.988
peak=   -3.245 closest distance to " O   HOH Z  11 " =    1.724
peak=   -3.244 closest distance to " O   HOH Z 191 " =    5.589
peak=   -3.243 closest distance to " CB  ASP A 286 " =    2.160
peak=   -3.238 closest distance to " O   HOH Z 426 " =    1.544
peak=   -3.236 closest distance to " C   GLY A  17 " =    1.097
peak=   -3.235 closest distance to " O   VAL A 189 " =    1.606
peak=   -3.231 closest distance to " CD1 LEU A   5 " =    2.596
peak=   -3.228 closest distance to " O   ALA A  34 " =    2.545
peak=   -3.225 closest distance to " NE2 GLN A  88 " =    1.832
peak=   -3.225 closest distance to " O   SER A  95 " =    1.551
peak=   -3.223 closest distance to " CZ  PHE A 192 " =    2.894
peak=   -3.223 closest distance to " OE2 GLU A 152 " =    1.205
peak=   -3.222 closest distance to " OG  SER A  62 " =    1.712
peak=   -3.218 closest distance to " C   PHE A  59 " =    1.393
peak=   -3.215 closest distance to " O   HOH Z 357 " =    2.041
peak=   -3.210 closest distance to " O   VAL A 174 " =    2.094
peak=   -3.206 closest distance to " O   LYS A 117 " =    1.722
peak=   -3.203 closest distance to " ND2 ASN A 187 " =    1.553
peak=   -3.202 closest distance to " O   HOH Z  37 " =    1.804
peak=   -3.198 closest distance to " O   ALA A 180 " =    1.029
peak=   -3.196 closest distance to " CG1 VAL A 197 " =    2.297
peak=   -3.194 closest distance to " CA  GLY A 241 " =    2.281
peak=   -3.194 closest distance to " OXT GLY A 302 " =    3.411
peak=   -3.193 closest distance to " OG BSER A 134 " =    1.706
peak=   -3.192 closest distance to " OD2 ASP A 171 " =    1.816
peak=   -3.191 closest distance to " O   GLN A 240 " =    2.070
peak=   -3.182 closest distance to " O   HOH Z   6 " =    1.452
peak=   -3.175 closest distance to " CG  GLU A 152 " =    1.326
peak=   -3.171 closest distance to " CA  TRP A 274 " =    1.477
peak=   -3.171 closest distance to " O   HOH Z 134 " =    3.068
peak=   -3.169 closest distance to " CE3 TRP A 150 " =    2.152
peak=   -3.169 closest distance to " CD2 TYR A 293 " =    1.986
peak=   -3.165 closest distance to " OD1AASN A 224 " =    1.799
peak=   -3.165 closest distance to " CG  TRP A 266 " =    1.919
peak=   -3.160 closest distance to " O   GLY A  80 " =    2.448
peak=   -3.158 closest distance to " CG1 VAL A 125 " =    1.948
peak=   -3.153 closest distance to " O   TRP A  70 " =    1.433
peak=   -3.148 closest distance to " NH2 ARG A  79 " =    2.031
peak=   -3.137 closest distance to " CD2 HIS A 207 " =    2.405
peak=   -3.136 closest distance to " CD1 TRP A  70 " =    1.104
peak=   -3.134 closest distance to " O   ILE A 106 " =    2.043
peak=   -3.119 closest distance to " CA  GLY A 241 " =    2.819
peak=   -3.116 closest distance to " OG  SER A 206 " =    1.787
peak=   -3.113 closest distance to " O   HOH Z 266 " =    4.940
peak=   -3.111 closest distance to " CG  GLU A   2 " =    1.963
peak=   -3.111 closest distance to " OD2 ASP A  50 " =    1.602
peak=   -3.111 closest distance to " CB  LEU A  83 " =    2.392
peak=   -3.108 closest distance to " SG ACYS A 201 " =    1.847
peak=   -3.105 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.102 closest distance to " CG1AVAL A  41 " =    2.924
peak=   -3.101 closest distance to " O   HOH Z 414 " =    1.658
peak=   -3.099 closest distance to " O   HOH Z 421 " =    3.014
peak=   -3.093 closest distance to " CB  ASP A 132 " =    2.370
peak=   -3.086 closest distance to " O   PRO A  90 " =    1.731
peak=   -3.076 closest distance to " O   HOH Z 111 " =    1.964
peak=   -3.057 closest distance to " N   SER A 276 " =    1.232
peak=   -3.052 closest distance to " CB  ALA A 100 " =    2.177
peak=   -3.048 closest distance to " CG  ARG A 269 " =    2.039
peak=   -3.020 closest distance to " CD1 ILE A 199 " =    2.491

================= 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    :  0.2177 0.2165   5.670899e+00   5.651516e+00
   1_bss:  0.1980 0.1977   5.626878e+00   5.599971e+00
   1_xyz:  0.1301 0.1513   5.216134e+00   5.338997e+00
   1_adp:  0.1202 0.1523   5.165150e+00   5.354825e+00
   1_occ:  0.1197 0.1524   5.163378e+00   5.354918e+00
   2_bss:  0.1200 0.1521   5.164862e+00   5.354499e+00
   2_xyz:  0.1156 0.1498   5.136989e+00   5.339531e+00
   2_adp:  0.1132 0.1494   5.125940e+00   5.340092e+00
   2_occ:  0.1131 0.1494   5.125732e+00   5.340278e+00
   3_bss:  0.1131 0.1493   5.125249e+00   5.339954e+00
   3_xyz:  0.1066 0.1506   5.097498e+00   5.345043e+00
   3_adp:  0.1050 0.1513   5.093171e+00   5.348721e+00
   3_occ:  0.1049 0.1513   5.093430e+00   5.349214e+00
   4_bss:  0.1048 0.1513   5.093328e+00   5.349151e+00
   4_xyz:  0.1084 0.1529   5.115861e+00   5.361752e+00
   4_adp:  0.1100 0.1517   5.118737e+00   5.355323e+00
   4_occ:  0.1099 0.1517   5.118744e+00   5.355477e+00
   5_bss:  0.1099 0.1518   5.118823e+00   5.355574e+00
   5_xyz:  0.1080 0.1518   5.108733e+00   5.354174e+00
   5_adp:  0.1067 0.1536   5.109279e+00   5.364446e+00
   5_occ:  0.1067 0.1536   5.109261e+00   5.364498e+00
   5_bss:  0.1066 0.1535   5.109220e+00   5.364427e+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:  0.333  50.000  -3.104  -1.997  -0.961  -0.000  -0.000  -0.000
   1_xyz:  0.333  50.000  -3.104  -1.997  -0.961  -0.000  -0.000  -0.000
   1_adp:  0.333  50.000  -3.104  -1.997  -0.961  -0.000  -0.000  -0.000
   1_occ:  0.333  50.000  -3.104  -1.997  -0.961  -0.000  -0.000  -0.000
   2_bss:  0.333  50.000  -3.082  -2.572  -1.301  -0.000  -0.000  -0.000
   2_xyz:  0.333  50.000  -3.082  -2.572  -1.301  -0.000  -0.000  -0.000
   2_adp:  0.333  50.000  -3.082  -2.572  -1.301  -0.000  -0.000  -0.000
   2_occ:  0.333  50.000  -3.082  -2.572  -1.301  -0.000  -0.000  -0.000
   3_bss:  0.326  50.000  -2.839  -2.534  -1.197  -0.000  -0.000  -0.000
   3_xyz:  0.326  50.000  -2.839  -2.534  -1.197  -0.000  -0.000  -0.000
   3_adp:  0.326  50.000  -2.839  -2.534  -1.197  -0.000  -0.000  -0.000
   3_occ:  0.326  50.000  -2.839  -2.534  -1.197  -0.000  -0.000  -0.000
   4_bss:  0.322  50.000  -2.527  -2.308  -0.961  -0.000  -0.000  -0.000
   4_xyz:  0.322  50.000  -2.527  -2.308  -0.961  -0.000  -0.000  -0.000
   4_adp:  0.322  50.000  -2.527  -2.308  -0.961  -0.000  -0.000  -0.000
   4_occ:  0.322  50.000  -2.527  -2.308  -0.961  -0.000  -0.000  -0.000
   5_bss:  0.324  50.000  -2.452  -2.247  -0.888  -0.000  -0.000  -0.000
   5_xyz:  0.324  50.000  -2.452  -2.247  -0.888  -0.000  -0.000  -0.000
   5_adp:  0.324  50.000  -2.452  -2.247  -0.888  -0.000  -0.000  -0.000
   5_occ:  0.324  50.000  -2.452  -2.247  -0.888  -0.000  -0.000  -0.000
   5_bss:  0.320  49.995  -2.187  -2.005  -0.663  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  19.339 0.8720  1.0171    12443.812
   1_bss:  17.820 0.8846  0.9610     9611.530
   1_xyz:  13.027 0.9229  0.9860     5831.713
   1_adp:  13.376 0.9199  0.9856     5976.891
   1_occ:  13.363 0.9200  0.9853     5957.221
   2_bss:  13.342 0.9202  0.9750     5951.221
   2_xyz:  12.928 0.9237  0.9745     5753.003
   2_adp:  12.940 0.9235  0.9703     5718.730
   2_occ:  12.949 0.9235  0.9702     5720.159
   3_bss:  12.941 0.9235  0.9748     5713.405
   3_xyz:  13.008 0.9230  0.9756     5817.840
   3_adp:  13.126 0.9220  0.9690     5829.772
   3_occ:  13.135 0.9220  0.9689     5835.633
   4_bss:  13.133 0.9220  0.9781     5833.940
   4_xyz:  13.329 0.9207  0.9768     5986.250
   4_adp:  13.183 0.9217  0.9722     5942.428
   4_occ:  13.189 0.9217  0.9721     5943.447
   5_bss:  13.191 0.9217  0.9746     5945.572
   5_xyz:  13.175 0.9218  0.9750     5941.973
   5_adp:  13.406 0.9200  0.9673     6019.651
   5_occ:  13.407 0.9200  0.9672     6021.735
   5_bss:  13.406 0.9200  0.9756     6019.874
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5998e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5998e-01
   1_xyz:   0.998  0.007  0.076 15.323  0.004  4.112   6.1585e-02
   1_adp:   0.998  0.007  0.076 15.323  0.004  4.112   6.1585e-02
   1_occ:   0.998  0.007  0.076 15.323  0.004  4.112   6.1585e-02
   2_bss:   0.998  0.007  0.076 15.323  0.004  4.112   6.1585e-02
   2_xyz:   0.904  0.006  0.072 15.058  0.003  4.113   5.2216e-02
   2_adp:   0.904  0.006  0.072 15.058  0.003  4.113   5.2216e-02
   2_occ:   0.904  0.006  0.072 15.058  0.003  4.113   5.2216e-02
   3_bss:   0.904  0.006  0.072 15.058  0.003  4.113   5.2216e-02
   3_xyz:   1.088  0.010  0.085 15.379  0.004  4.115   7.3820e-02
   3_adp:   1.088  0.010  0.085 15.379  0.004  4.115   7.3820e-02
   3_occ:   1.088  0.010  0.085 15.379  0.004  4.115   7.3820e-02
   4_bss:   1.088  0.010  0.085 15.379  0.004  4.115   7.3820e-02
   4_xyz:   0.914  0.006  0.072 15.066  0.003  4.115   5.4117e-02
   4_adp:   0.914  0.006  0.072 15.066  0.003  4.115   5.4117e-02
   4_occ:   0.914  0.006  0.072 15.066  0.003  4.115   5.4117e-02
   5_bss:   0.914  0.006  0.072 15.066  0.003  4.115   5.4117e-02
   5_xyz:   0.980  0.007  0.077 15.112  0.004  4.116   6.0545e-02
   5_adp:   0.980  0.007  0.077 15.112  0.004  4.116   6.0545e-02
   5_occ:   0.980  0.007  0.077 15.112  0.004  4.116   6.0545e-02
   5_bss:   0.980  0.007  0.077 15.112  0.004  4.116   6.0545e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4103e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4103e-01
   1_xyz:   6.920  0.037  0.220 84.271  0.040  2.311   6.7374e-02
   1_adp:   6.920  0.037  0.220 84.271  0.040  2.311   6.7374e-02
   1_occ:   6.920  0.037  0.220 84.271  0.040  2.311   6.7374e-02
   2_bss:   6.920  0.037  0.220 84.271  0.040  2.311   6.7374e-02
   2_xyz:   6.726  0.037  0.216 83.155  0.033  2.372   3.2497e-02
   2_adp:   6.726  0.037  0.216 83.155  0.033  2.372   3.2497e-02
   2_occ:   6.726  0.037  0.216 83.155  0.033  2.372   3.2497e-02
   3_bss:   6.726  0.037  0.216 83.155  0.033  2.372   3.2497e-02
   3_xyz:   6.850  0.047  0.291 83.683  0.036  2.243   6.1241e-02
   3_adp:   6.850  0.047  0.291 83.683  0.036  2.243   6.1241e-02
   3_occ:   6.850  0.047  0.291 83.683  0.036  2.243   6.1241e-02
   4_bss:   6.850  0.047  0.291 83.683  0.036  2.243   6.1241e-02
   4_xyz:   6.560  0.042  0.225 83.088  0.034  2.374   3.6644e-02
   4_adp:   6.560  0.042  0.225 83.088  0.034  2.374   3.6644e-02
   4_occ:   6.560  0.042  0.225 83.088  0.034  2.374   3.6644e-02
   5_bss:   6.560  0.042  0.225 83.088  0.034  2.374   3.6644e-02
   5_xyz:   6.534  0.044  0.251 83.375  0.035  2.293   4.1516e-02
   5_adp:   6.534  0.044  0.251 83.375  0.035  2.293   4.1516e-02
   5_occ:   6.534  0.044  0.251 83.375  0.035  2.293   4.1516e-02
   5_bss:   6.534  0.044  0.251 83.375  0.035  2.293   4.1516e-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:  62.81   0.00  16.40  60.32   0.00  12.64  62.81   6.96  36.92
   1_occ:  62.81   0.00  16.40  60.32   0.00  12.64  62.81   6.96  36.92
   2_bss:  62.81   0.00  16.40  60.32   0.00  12.64  62.81   6.96  36.92
   2_xyz:  62.81   0.00  16.40  60.32   0.00  12.64  62.81   6.96  36.92
   2_adp:  66.02   1.84  16.54  62.91   1.84  12.82  66.02   5.93  36.79
   2_occ:  66.02   1.84  16.54  62.91   1.84  12.82  66.02   5.93  36.79
   3_bss:  66.02   1.84  16.54  62.91   1.84  12.82  66.02   5.93  36.79
   3_xyz:  66.02   1.84  16.54  62.91   1.84  12.82  66.02   5.93  36.79
   3_adp:  77.59   0.98  16.92  77.59   0.98  12.86  71.03   6.19  39.05
   3_occ:  77.59   0.98  16.92  77.59   0.98  12.86  71.03   6.19  39.05
   4_bss:  77.59   0.98  16.92  77.59   0.98  12.86  71.03   6.19  39.05
   4_xyz:  77.59   0.98  16.92  77.59   0.98  12.86  71.03   6.19  39.05
   4_adp:  76.10   2.26  16.38  76.10   2.26  12.62  70.92   6.50  36.89
   4_occ:  76.10   2.26  16.38  76.10   2.26  12.62  70.92   6.50  36.89
   5_bss:  76.10   2.26  16.38  76.10   2.26  12.62  70.92   6.50  36.89
   5_xyz:  76.10   2.26  16.38  76.10   2.26  12.62  70.92   6.50  36.89
   5_adp:  83.65   0.22  16.68  83.65   0.22  12.57  72.74   6.10  39.04
   5_occ:  83.65   0.22  16.68  83.65   0.22  12.57  72.74   6.10  39.04
   5_bss:  83.64   0.22  16.67  83.64   0.22  12.57  72.73   6.10  39.04
------------------------------------------------------------------------
 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:    0.501    0.002    0.182
   1_adp:    0.501    0.002    0.182
   1_occ:    0.501    0.002    0.182
   2_bss:    0.501    0.002    0.182
   2_xyz:    0.698    0.011    0.187
   2_adp:    0.698    0.011    0.187
   2_occ:    0.698    0.011    0.187
   3_bss:    0.698    0.011    0.187
   3_xyz:    0.894    0.028    0.206
   3_adp:    0.894    0.028    0.206
   3_occ:    0.894    0.028    0.206
   4_bss:    0.894    0.028    0.206
   4_xyz:    0.977    0.026    0.208
   4_adp:    0.977    0.026    0.208
   4_occ:    0.977    0.026    0.208
   5_bss:    0.977    0.026    0.208
   5_xyz:    1.056    0.024    0.211
   5_adp:    1.056    0.024    0.211
   5_occ:    1.056    0.024    0.211
   5_bss:    1.056    0.024    0.211
------------------------------------------------------------------------

CPU time actual refinement: 306.94


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_655/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_655/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_655/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_655/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_655/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 306.79 
  Macro-tasks:
    bulk solvent and scale       = 35.26  
    individual site refinement   = 123.73 
    weights calculation          = 29.21  
    collect and process          = 6.65   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 194.96 
  Micro-tasks:
    mask                            = 0.59   
    f_calc                          = 97.18  
    alpha_beta                      = 8.05   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 105.55 
    fmodel                         = 6.32   
    r_factors                      = 0.16   
    phase_errors                   = 11.33  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 230.61 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.432 micro seconds
Total CPU time: 5.34 minutes
from_scatterers_fft:    623 calls, 96.94 s
gradients_fft:          568 calls, 92.61 s

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

# Date 2008-01-16 Time 05:19:47 PST -0800 (1200489587.96 s)
Start R-work = 0.2177, R-free = 0.2165 (no bulk solvent and anisotropic scale)
Final R-work = 0.1303, R-free = 0.1723 (no bulk solvent and anisotropic scale)

Start R-work = 0.1980, R-free = 0.1977
Final R-work = 0.1066, R-free = 0.1535