# Date 2008-01-16 Time 05:34:09 PST -0800 (1200490449.36 s)
#phil __OFF__

Command line arguments: "../786.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24796
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 786

-------------------------------------------------------------------------------
  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: (70.6012, 46.93, 86.39, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00038
Completeness in resolution range: 0.981216
Completeness with d_max=infinity: 0.97813

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   2.0004

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: (70.6012, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00038
Completeness in resolution range: 0.981216
Completeness with d_max=infinity: 0.97813

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2797 [2095/2119]  1886   209  10.0%
  bin  2:  4.2797 -  3.4100 [2023/2043]  1820   203  10.0%
  bin  3:  3.4100 -  2.9827 [1982/2001]  1783   199  10.0%
  bin  4:  2.9827 -  2.7117 [1954/1984]  1759   195  10.0%
  bin  5:  2.7117 -  2.5183 [1963/1982]  1769   194   9.9%
  bin  6:  2.5183 -  2.3705 [1956/1981]  1760   196  10.0%
  bin  7:  2.3705 -  2.2522 [1948/1976]  1750   198  10.2%
  bin  8:  2.2522 -  2.1544 [1919/1955]  1728   191  10.0%
  bin  9:  2.1544 -  2.0717 [1915/1957]  1726   189   9.9%
  bin 10:  2.0717 -  2.0004 [1834/1966]  1649   185  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_786/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: 7
        2.42 -     3.04: 2201
        3.04 -     3.66: 4617
        3.66 -     4.28: 9037
        4.28 -     4.90: 12308
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.205 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28165 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_786/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_786/model_refine_001.geo

CPU time processing inputs: 8.95


============================ 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 = 70.60125 46.93 86.39 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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1752   r_free= 0.1739   ksol= 0.00   Bsol= 0.00   scale= 1.015    |
|                                                                             |
| 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:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.422210                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7731 0.99   1367  152 0.2397 0.2304       6.214      6.1445|
|  2:  4.7731 -  3.8088 0.99   1310  145 0.1389 0.1303      5.8761       5.841|
|  3:  3.8088 -  3.3333 0.99   1273  143 0.1398 0.1431      5.6926      5.8216|
|  4:  3.3333 -  3.0312 0.99   1281  144 0.1449 0.1518      5.5668      5.5919|
|  5:  3.0312 -  2.8155 0.99   1262  138 0.1631 0.1402      5.4754      5.4436|
|  6:  2.8155 -  2.6504 0.99   1266  141 0.1611 0.1726      5.3858      5.3705|
|  7:  2.6504 -  2.5183 0.99   1258  137 0.1697 0.1720      5.3773      5.4071|
|  8:  2.5183 -  2.4092 0.98   1259  140 0.1651 0.1521      5.3093      5.2736|
|  9:  2.4092 -  2.3168 0.98   1240  136 0.1644 0.1672      5.2461      5.2815|
| 10:  2.3168 -  2.2371 1.00   1241  139 0.1656 0.1777      5.2322      5.1778|
| 11:  2.2371 -  2.1674 0.97   1249  142 0.1669 0.1657      5.1528      5.2216|
| 12:  2.1674 -  2.1056 0.97   1231  134 0.1700 0.1725      5.1417      5.2154|
| 13:  2.1056 -  2.0503 0.99   1227  141 0.1726 0.1720      5.0735      5.0571|
| 14:  2.0503 -  2.0004 0.91   1166  127 0.1699 0.1548      5.0234       4.833|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7731  1367   152  0.83  22.16   0.88     0.83      31138.30|
|  2:  4.7731 -  3.8088  1310   145  0.92  13.60   1.00     0.95      19093.16|
|  3:  3.8088 -  3.3333  1273   143  0.93  11.91   1.03     1.02      11818.16|
|  4:  3.3333 -  3.0312  1281   144  0.93  12.38   1.04     1.02       9044.47|
|  5:  3.0312 -  2.8155  1262   138  0.91  14.28   1.04     1.02       7349.54|
|  6:  2.8155 -  2.6504  1266   141  0.92  14.00   1.06     1.03       6042.50|
|  7:  2.6504 -  2.5183  1258   137  0.92  14.21   1.06     1.04       5470.03|
|  8:  2.5183 -  2.4092  1259   140  0.91  14.53   1.08     1.06       5044.55|
|  9:  2.4092 -  2.3168  1240   136  0.92  14.46   1.10     1.07       4707.06|
| 10:  2.3168 -  2.2371  1241   139  0.91  14.62   1.12     1.09       4408.96|
| 11:  2.2371 -  2.1674  1249   142  0.91  15.37   1.13     1.10       4141.31|
| 12:  2.1674 -  2.1056  1231   134  0.92  13.97   1.12     1.13       3691.12|
| 13:  2.1056 -  2.0503  1227   141  0.92  13.91   1.13     1.13       2986.20|
| 14:  2.0503 -  2.0004  1166   127  0.93  12.56   1.12     1.11       2116.14|
|alpha:            min =        0.83 max =            1.13 mean =         1.04|
|beta:             min =     2116.14 max =        31138.30 mean =      8594.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.48|
|phase err.(test): min =        0.00 max =           88.74 mean =        14.42|
|-----------------------------------------------------------------------------|

============================== 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 = 2.414301              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.681   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261203              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.915   (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:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      178 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2023 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1824 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2793 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4666 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4371 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5602 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6706 |
|-----------------------------------------------------------------------------|
|-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 |       0.130 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1752   r_free= 0.1739   ksol= 0.00   Bsol= 0.00   scale= 1.015    |
|                                                                             |
| 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:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.422210                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1528   r_free= 0.1528   ksol= 0.33   Bsol= 54.53   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.84,-1.73,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.368376                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.267351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.910   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.137770              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.795   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1528      final r-factor (work) = 0.1231          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1460          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4336 = 2.27 * 0.50 * 5.5341 + 1.00 * 0.1597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9492 = 2.27 * 0.50 * 5.1834 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1460      final r-factor (free) = 0.1458          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7203 = 0.14 * 1.00 * 5.1834 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7262 = 0.14 * 1.00 * 5.1078 + 1.00 * 0.0225                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.51   16.32    None  None   None       |
|    all(noH): 2823   0      0.00    62.51   16.32    None  None   None       |
|    Sol.    : 438    0      3.74    62.51   36.73    None  None   None       |
|    Mac.    : 2385   0      0.00    57.29   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:     0.000 -   6.251:  118   |   5:    31.255 -  37.506:   94        |
|      1:     6.251 -  12.502: 1400   |   6:    37.506 -  43.758:  104        |
|      2:    12.502 -  18.753:  649   |   7:    43.758 -  50.009:   74        |
|      3:    18.753 -  25.004:  195   |   8:    50.009 -  56.260:   51        |
|      4:    25.004 -  31.255:  113   |   9:    56.260 -  62.511:   25        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1458             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1454             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1454   ksol= 0.33   Bsol= 54.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.84,-1.73,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.107689                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1449   ksol= 0.33   Bsol= 54.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.71,-1.61,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.108630                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.728897              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.640  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.156722              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.876   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1449      final r-factor (free) = 0.1477          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4876 = 1.73 * 0.50 * 5.1070 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4739 = 1.73 * 0.50 * 5.1035 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1477      final r-factor (free) = 0.1486          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8381 = 0.16 * 1.00 * 5.1035 + 1.00 * 0.0382                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8056 = 0.16 * 1.00 * 5.0982 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.95    67.70   16.44    None  None   None       |
|    all(noH): 2823   0      1.95    67.70   16.44    None  None   None       |
|    Sol.    : 438    0      5.05    64.77   36.47    None  None   None       |
|    Mac.    : 2385   0      1.95    67.70   12.77    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:     1.950 -   8.524:  579   |   5:    34.822 -  41.397:  122        |
|      1:     8.524 -  15.099: 1308   |   6:    41.397 -  47.971:   89        |
|      2:    15.099 -  21.673:  383   |   7:    47.971 -  54.546:   79        |
|      3:    21.673 -  28.248:  132   |   8:    54.546 -  61.121:   25        |
|      4:    28.248 -  34.822:  101   |   9:    61.121 -  67.695:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1486             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1487             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1487   ksol= 0.33   Bsol= 54.53   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.71,-1.61,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104168                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1487   ksol= 0.33   Bsol= 54.53   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.48,-1.40,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104265                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.438499              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.665  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.305896              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.783  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1487      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7297 = 1.44 * 0.50 * 5.0992 + 1.00 * 0.0622                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7296 = 1.44 * 0.50 * 5.1096 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5696 = 0.31 * 1.00 * 5.1096 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5716 = 0.31 * 1.00 * 5.1125 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.11    74.91   16.59    None  None   None       |
|    all(noH): 2823   0      1.11    74.91   16.59    None  None   None       |
|    Sol.    : 438    0      6.55    66.33   37.61    None  None   None       |
|    Mac.    : 2385   0      1.11    74.91   12.73    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:     1.108 -   8.488:  637   |   5:    38.011 -  45.391:  118        |
|      1:     8.488 -  15.869: 1304   |   6:    45.391 -  52.772:   89        |
|      2:    15.869 -  23.250:  362   |   7:    52.772 -  60.152:   56        |
|      3:    23.250 -  30.630:  126   |   8:    60.152 -  67.533:   20        |
|      4:    30.630 -  38.011:  108   |   9:    67.533 -  74.913:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1517             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1517             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1517   ksol= 0.33   Bsol= 54.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.48,-1.40,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115895                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1518   ksol= 0.33   Bsol= 54.53   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.28,-1.21,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.168232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.965  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218535              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.032  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5982 = 2.17 * 0.50 * 5.1136 + 1.00 * 0.0545                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5976 = 2.17 * 0.50 * 5.1051 + 1.00 * 0.0631                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1233 = 0.22 * 1.00 * 5.1051 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1230 = 0.22 * 1.00 * 5.1045 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    75.22   16.39    None  None   None       |
|    all(noH): 2823   0      1.23    75.22   16.39    None  None   None       |
|    Sol.    : 438    0      6.43    66.63   37.24    None  None   None       |
|    Mac.    : 2385   0      1.23    75.22   12.56    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:     1.232 -   8.631:  722   |   5:    38.226 -  45.625:  114        |
|      1:     8.631 -  16.030: 1246   |   6:    45.625 -  53.023:   87        |
|      2:    16.030 -  23.429:  346   |   7:    53.023 -  60.422:   48        |
|      3:    23.429 -  30.827:  128   |   8:    60.422 -  67.821:   19        |
|      4:    30.827 -  38.226:  110   |   9:    67.821 -  75.219:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1522             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1071 r_free = 0.1521             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1521   ksol= 0.33   Bsol= 54.53   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.28,-1.21,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104318                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1521   ksol= 0.33   Bsol= 54.53   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.10,-1.01,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.360522              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.927  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.754225              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.628  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0888 = 2.36 * 0.50 * 5.1056 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0861 = 2.36 * 0.50 * 5.1026 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1067      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.2665 = 4.75 * 1.00 * 5.1026 + 1.00 * 0.0075                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.2681 = 4.75 * 1.00 * 5.1025 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.87   16.68    None  None   None       |
|    all(noH): 2823   0      0.00    84.87   16.68    None  None   None       |
|    Sol.    : 438    0      6.00    73.28   39.15    None  None   None       |
|    Mac.    : 2385   0      0.00    84.87   12.56    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 -   8.487:  750   |   5:    42.436 -  50.923:  102        |
|      1:     8.487 -  16.974: 1301   |   6:    50.923 -  59.410:   79        |
|      2:    16.974 -  25.461:  292   |   7:    59.410 -  67.897:   44        |
|      3:    25.461 -  33.948:  130   |   8:    67.897 -  76.384:   10        |
|      4:    33.948 -  42.436:  111   |   9:    76.384 -  84.871:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1061 r_free = 0.1553             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1060 r_free = 0.1554             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1554   ksol= 0.33   Bsol= 54.53   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.10,-1.01,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110002                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7731 0.99   1367  152 0.0986 0.1314      5.3899      5.5279|
|  2:  4.7731 -  3.8088 0.99   1310  145 0.0831 0.1121      5.4251      5.6301|
|  3:  3.8088 -  3.3333 0.99   1273  143 0.1013 0.1480      5.4552      5.8365|
|  4:  3.3333 -  3.0312 0.99   1281  144 0.1156 0.1522      5.4278       5.581|
|  5:  3.0312 -  2.8155 0.99   1262  138 0.1249 0.1722      5.3009      5.5361|
|  6:  2.8155 -  2.6504 0.99   1266  141 0.1138 0.1791      5.1866      5.4233|
|  7:  2.6504 -  2.5183 0.99   1258  137 0.1198 0.1655      5.1276      5.3743|
|  8:  2.5183 -  2.4092 0.98   1259  140 0.1076 0.1663      5.0228      5.3234|
|  9:  2.4092 -  2.3168 0.98   1240  136 0.1084 0.1596      4.9865       5.211|
| 10:  2.3168 -  2.2371 1.00   1241  139 0.1023 0.1896       4.931      5.2904|
| 11:  2.2371 -  2.1674 0.97   1249  142 0.1089 0.1572      4.9214      5.1827|
| 12:  2.1674 -  2.1056 0.97   1231  134 0.1061 0.1788      4.8579      5.2676|
| 13:  2.1056 -  2.0503 0.99   1227  141 0.1018 0.1577      4.7695      5.0157|
| 14:  2.0503 -  2.0004 0.91   1166  127 0.0980 0.1809      4.6355      4.9591|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7731  1367   152  0.94   9.50   0.98     0.95       7474.25|
|  2:  4.7731 -  3.8088  1310   145  0.95   7.94   1.01     0.99       9107.59|
|  3:  3.8088 -  3.3333  1273   143  0.94  10.73   1.02     1.01      10036.62|
|  4:  3.3333 -  3.0312  1281   144  0.92  13.06   1.00     0.99       9929.77|
|  5:  3.0312 -  2.8155  1262   138  0.90  15.34   0.99     0.96       8083.68|
|  6:  2.8155 -  2.6504  1266   141  0.91  15.42   0.98     0.96       6897.18|
|  7:  2.6504 -  2.5183  1258   137  0.91  15.21   0.98     0.96       5873.28|
|  8:  2.5183 -  2.4092  1259   140  0.92  14.00   0.98     0.96       4862.95|
|  9:  2.4092 -  2.3168  1240   136  0.92  14.47   0.99     0.96       4638.60|
| 10:  2.3168 -  2.2371  1241   139  0.91  14.59   0.99     0.94       4131.39|
| 11:  2.2371 -  2.1674  1249   142  0.90  16.01   0.99     0.95       4324.66|
| 12:  2.1674 -  2.1056  1231   134  0.92  14.71   0.99     0.97       3803.71|
| 13:  2.1056 -  2.0503  1227   141  0.91  15.01   0.99     0.98       3306.59|
| 14:  2.0503 -  2.0004  1166   127  0.92  14.35   0.96     0.92       2475.28|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2475.28 max =        10036.62 mean =      6125.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.54|
|phase err.(test): min =        0.00 max =           89.17 mean =        13.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1553   ksol= 0.33   Bsol= 54.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.86,-0.79,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109811                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1553   ksol= 0.33   Bsol= 54.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.86,-0.79,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109811                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7731 0.99   1367  152 0.0984 0.1315      5.3875       5.526|
|  2:  4.7731 -  3.8088 0.99   1310  145 0.0832 0.1121      5.4256      5.6306|
|  3:  3.8088 -  3.3333 0.99   1273  143 0.1013 0.1480      5.4554      5.8367|
|  4:  3.3333 -  3.0312 0.99   1281  144 0.1155 0.1523      5.4276      5.5809|
|  5:  3.0312 -  2.8155 0.99   1262  138 0.1248 0.1721      5.3005      5.5356|
|  6:  2.8155 -  2.6504 0.99   1266  141 0.1138 0.1791      5.1864      5.4232|
|  7:  2.6504 -  2.5183 0.99   1258  137 0.1199 0.1655      5.1276      5.3743|
|  8:  2.5183 -  2.4092 0.98   1259  140 0.1077 0.1662      5.0228      5.3231|
|  9:  2.4092 -  2.3168 0.98   1240  136 0.1084 0.1596      4.9865      5.2111|
| 10:  2.3168 -  2.2371 1.00   1241  139 0.1022 0.1897      4.9311      5.2903|
| 11:  2.2371 -  2.1674 0.97   1249  142 0.1089 0.1571      4.9213      5.1824|
| 12:  2.1674 -  2.1056 0.97   1231  134 0.1061 0.1788      4.8578      5.2674|
| 13:  2.1056 -  2.0503 0.99   1227  141 0.1018 0.1576      4.7694      5.0156|
| 14:  2.0503 -  2.0004 0.91   1166  127 0.0980 0.1809      4.6357      4.9592|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7731  1367   152  0.94   9.48   0.98     0.95       7429.63|
|  2:  4.7731 -  3.8088  1310   145  0.95   7.93   1.01     1.00       9093.81|
|  3:  3.8088 -  3.3333  1273   143  0.94  10.73   1.02     1.02      10039.76|
|  4:  3.3333 -  3.0312  1281   144  0.92  13.06   1.01     1.00       9924.02|
|  5:  3.0312 -  2.8155  1262   138  0.90  15.33   1.00     0.97       8079.86|
|  6:  2.8155 -  2.6504  1266   141  0.91  15.42   0.99     0.96       6893.84|
|  7:  2.6504 -  2.5183  1258   137  0.91  15.21   0.99     0.97       5872.29|
|  8:  2.5183 -  2.4092  1259   140  0.92  14.00   0.99     0.97       4862.24|
|  9:  2.4092 -  2.3168  1240   136  0.92  14.47   1.00     0.97       4639.26|
| 10:  2.3168 -  2.2371  1241   139  0.91  14.59   1.00     0.96       4130.93|
| 11:  2.2371 -  2.1674  1249   142  0.90  16.01   1.00     0.96       4323.43|
| 12:  2.1674 -  2.1056  1231   134  0.92  14.71   1.00     0.98       3802.07|
| 13:  2.1056 -  2.0503  1227   141  0.91  15.01   1.00     0.99       3306.05|
| 14:  2.0503 -  2.0004  1166   127  0.92  14.36   0.97     0.94       2476.39|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2476.39 max =        10039.76 mean =      6120.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.54|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.87   16.68    None  None   None       |
|    all(noH): 2823   0      0.00    84.87   16.68    None  None   None       |
|    Sol.    : 438    0      6.00    73.28   39.15    None  None   None       |
|    Mac.    : 2385   0      0.00    84.87   12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.490:  750   |   5:    42.438 -  50.926:  102        |
|      1:     8.490 -  16.977: 1301   |   6:    50.926 -  59.413:   79        |
|      2:    16.977 -  25.464:  292   |   7:    59.413 -  67.900:   44        |
|      3:    25.464 -  33.951:  130   |   8:    67.900 -  76.387:   10        |
|      4:    33.951 -  42.438:  111   |   9:    76.387 -  84.874:    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)= 278         
Filter by distance & map next to the model:
   mapped sites are within: 0.476 - 4.742
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 274 from: 278
   mapped sites are within: 0.731 - 4.742

peak=    5.908 closest distance to " NH2 ARG A  56 " =    2.226
peak=    5.524 closest distance to " CG  PRO A  54 " =    1.272
peak=    5.230 closest distance to " CB  GLN A 223 " =    1.419
peak=    5.203 closest distance to " O   HOH Z 126 " =    1.874
peak=    5.184 closest distance to " CB  SER A  63 " =    1.200
peak=    5.017 closest distance to " CB  ARG A 275 " =    0.912
peak=    4.869 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.805 closest distance to " NE2 GLN A  11 " =    1.053
peak=    4.797 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.738 closest distance to " CA  TYR A  30 " =    0.940
peak=    4.669 closest distance to " C   PRO A 198 " =    1.463
peak=    4.624 closest distance to " O   HOH Z 142 " =    1.689
peak=    4.563 closest distance to " CB  PRO A  54 " =    0.929
peak=    4.562 closest distance to " O   HOH Z  15 " =    2.184
peak=    4.536 closest distance to " CB  ARG A  79 " =    1.317
peak=    4.496 closest distance to " O   HOH Z 298 " =    1.924
peak=    4.476 closest distance to " O   HOH Z  78 " =    1.704
peak=    4.443 closest distance to " O   HOH Z 236 " =    1.957
peak=    4.422 closest distance to " CB  GLU A 152 " =    1.188
peak=    4.382 closest distance to " O   HOH Z 427 " =    2.936
peak=    4.357 closest distance to " OD1 ASN A  69 " =    2.576
peak=    4.343 closest distance to " CB  TYR A 169 " =    0.731
peak=    4.328 closest distance to " O   HOH Z 250 " =    1.486
peak=    4.314 closest distance to " O   HOH Z 303 " =    2.071
peak=    4.292 closest distance to " CB  ASN A 148 " =    1.405
peak=    4.274 closest distance to " O   HOH Z 369 " =    2.236
peak=    4.263 closest distance to " O   HOH Z 234 " =    3.690
peak=    4.261 closest distance to " CB  ARG A 190 " =    1.636
peak=    4.235 closest distance to " CG  PRO A 198 " =    1.284
peak=    4.214 closest distance to " O   HOH Z 158 " =    3.014
peak=    4.211 closest distance to " CB  ASP A 140 " =    0.952
peak=    4.208 closest distance to " CG2 VAL A 257 " =    0.910
peak=    4.196 closest distance to " O   HOH Z 203 " =    1.758
peak=    4.174 closest distance to " CB  LEU A 228 " =    1.089
peak=    4.138 closest distance to " O   HOH Z 197 " =    3.160
peak=    4.109 closest distance to " CZ  PHE A 218 " =    1.032
peak=    4.079 closest distance to " O   HOH Z 193 " =    1.888
peak=    4.079 closest distance to " O   HOH Z 209 " =    2.314
peak=    4.058 closest distance to " O   HOH Z 346 " =    1.718
peak=    4.056 closest distance to " O   HOH Z  61 " =    1.604
peak=    4.041 closest distance to " CA  ASN A 215 " =    1.181
peak=    4.030 closest distance to " ND2 ASN A 187 " =    1.393
peak=    4.021 closest distance to " O   HOH Z 189 " =    2.438
peak=    4.009 closest distance to " CG  PRO A 243 " =    1.053
peak=    4.007 closest distance to " O   HOH Z 261 " =    2.196
peak=    3.992 closest distance to " NZ  LYS A 117 " =    3.293
peak=    3.975 closest distance to " O   HOH Z 316 " =    3.154
peak=    3.960 closest distance to " O   HOH Z 423 " =    1.869
peak=    3.951 closest distance to " O   HOH Z  40 " =    1.724
peak=    3.909 closest distance to " CB  VAL A 265 " =    1.235
peak=    3.909 closest distance to " O   HOH Z  66 " =    2.147
peak=    3.909 closest distance to " CB  TRP A 266 " =    0.981
peak=    3.881 closest distance to " O   HOH Z 389 " =    1.936
peak=    3.877 closest distance to " O   HOH Z 403 " =    1.647
peak=    3.867 closest distance to " CB  GLU A 128 " =    1.042
peak=    3.866 closest distance to " CD  ARG A 159 " =    0.753
peak=    3.863 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.861 closest distance to " CB  GLU A 277 " =    3.597
peak=    3.860 closest distance to " O   HOH Z  19 " =    2.505
peak=    3.822 closest distance to " CB  SER A   3 " =    1.311
peak=    3.815 closest distance to " O   HOH Z  43 " =    1.900
peak=    3.804 closest distance to " O   HOH Z  10 " =    1.811
peak=    3.781 closest distance to " O   HOH Z 344 " =    3.206
peak=    3.776 closest distance to " CB  VAL A 202 " =    1.540
peak=    3.776 closest distance to " O   HOH Z 214 " =    2.071
peak=    3.773 closest distance to " CD  ARG A  66 " =    2.541
peak=    3.770 closest distance to " O   HOH Z 245 " =    1.273
peak=    3.763 closest distance to " O   HOH Z 272 " =    1.819
peak=    3.758 closest distance to " CB  TYR A 169 " =    0.763
peak=    3.751 closest distance to " O   HOH Z   1 " =    1.967
peak=    3.738 closest distance to " CA  ARG A  36 " =    1.039
peak=    3.738 closest distance to " O   HOH Z 280 " =    2.980
peak=    3.724 closest distance to " CD2 TRP A 179 " =    1.370
peak=    3.721 closest distance to " O   HOH Z 368 " =    2.078
peak=    3.719 closest distance to " O   HOH Z 305 " =    3.583
peak=    3.701 closest distance to " O   HOH Z 425 " =    1.986
peak=    3.695 closest distance to " OD2 ASP A 286 " =    2.840
peak=    3.691 closest distance to " CD1 LEU A 300 " =    1.246
peak=    3.685 closest distance to " O   HOH Z 371 " =    3.176
peak=    3.685 closest distance to " NH1AARG A 145 " =    1.227
peak=    3.684 closest distance to " O   HOH Z  54 " =    2.466
peak=    3.681 closest distance to " O   SER A  87 " =    2.307
peak=    3.672 closest distance to " O   HOH Z 291 " =    1.632
peak=    3.664 closest distance to " CA  MET A  40 " =    1.126
peak=    3.657 closest distance to " CA  THR A 221 " =    0.988
peak=    3.654 closest distance to " CB  ALA A 291 " =    1.393
peak=    3.651 closest distance to " CB  MET A  47 " =    0.971
peak=    3.651 closest distance to " O   HOH Z 426 " =    1.643
peak=    3.647 closest distance to " CB  TRP A 179 " =    1.359
peak=    3.643 closest distance to " O   MET A 105 " =    1.877
peak=    3.641 closest distance to " O   HOH Z 180 " =    2.201
peak=    3.639 closest distance to " CA  ARG A 195 " =    1.181
peak=    3.638 closest distance to " O   HOH Z 172 " =    3.376
peak=    3.636 closest distance to " N   ARG A 156 " =    1.322
peak=    3.623 closest distance to " CD BLYS A 290 " =    1.058
peak=    3.611 closest distance to " O   HOH Z 213 " =    1.814
peak=    3.606 closest distance to " CG1BVAL A  72 " =    1.641
peak=    3.600 closest distance to " O   HOH Z   9 " =    2.085
peak=    3.594 closest distance to " CA  ALA A  51 " =    0.910
peak=    3.593 closest distance to " NH2 ARG A 156 " =    1.165
peak=    3.591 closest distance to " O   HOH Z 193 " =    1.661
peak=    3.586 closest distance to " CG1 ILE A  33 " =    1.211
peak=    3.581 closest distance to " O   HOH Z 147 " =    1.799
peak=    3.575 closest distance to " CD1 ILE A 106 " =    0.782
peak=    3.569 closest distance to " OG BSER A 164 " =    2.299
peak=    3.561 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.554 closest distance to " NH2BARG A 145 " =    2.103
peak=    3.553 closest distance to " CB  ARG A 139 " =    0.964
peak=    3.552 closest distance to " CA  THR A 264 " =    0.903
peak=    3.549 closest distance to " O   HOH Z 403 " =    1.353
peak=    3.543 closest distance to " O   HOH Z 248 " =    1.611
peak=    3.542 closest distance to " CD2 LEU A 297 " =    0.849
peak=    3.536 closest distance to " O   HOH Z 368 " =    3.624
peak=    3.528 closest distance to " O   HOH Z 417 " =    3.060
peak=    3.524 closest distance to " O   HOH Z 132 " =    2.464
peak=    3.524 closest distance to " CG2 ILE A 120 " =    1.139
peak=    3.510 closest distance to " O   HOH Z  61 " =    1.497
peak=    3.507 closest distance to " CG2 THR A 221 " =    1.149
peak=    3.505 closest distance to " CB  ASN A 142 " =    1.067
peak=    3.502 closest distance to " CB  SER A 212 " =    1.143
peak=    3.493 closest distance to " O   HOH Z 313 " =    1.966
peak=    3.491 closest distance to " CA  ALA A  21 " =    1.188
peak=    3.488 closest distance to " CB  TYR A 116 " =    0.786
peak=    3.487 closest distance to " CB  ILE A 120 " =    1.266
peak=    3.487 closest distance to " O   HOH Z 402 " =    1.407
peak=    3.476 closest distance to " CA  ALA A  43 " =    1.257
peak=    3.472 closest distance to " CD  LYS A 119 " =    1.310
peak=    3.463 closest distance to " CG  LEU A 167 " =    1.263
peak=    3.455 closest distance to " O   HOH Z  59 " =    1.975
peak=    3.444 closest distance to " CB  ALA A  34 " =    1.004
peak=    3.442 closest distance to " O   HOH Z 148 " =    3.321
peak=    3.440 closest distance to " CB  ASN A 110 " =    1.173
peak=    3.440 closest distance to " CD1 LEU A  96 " =    0.760
peak=    3.434 closest distance to " CD2 LEU A 255 " =    1.429
peak=    3.434 closest distance to " O   HOH Z 359 " =    1.459
peak=    3.434 closest distance to " CB  THR A 157 " =    1.104
peak=    3.426 closest distance to " CB  GLU A  46 " =    1.006
peak=    3.425 closest distance to " O   HOH Z 185 " =    1.777
peak=    3.424 closest distance to " O   HOH Z  97 " =    2.700
peak=    3.424 closest distance to " OG1 THR A 294 " =    2.413
peak=    3.422 closest distance to " CB  SER A 216 " =    0.854
peak=    3.419 closest distance to " CD  ARG A  66 " =    2.388
peak=    3.418 closest distance to " O   HOH Z 173 " =    1.839
peak=    3.415 closest distance to " CB  MET A  40 " =    0.836
peak=    3.415 closest distance to " CA  SER A  87 " =    1.047
peak=    3.412 closest distance to " CB  HIS A 108 " =    0.820
peak=    3.409 closest distance to " NE2 GLN A  73 " =    3.887
peak=    3.407 closest distance to " O   HOH Z  49 " =    2.209
peak=    3.401 closest distance to " ND2 ASN A 110 " =    1.709
peak=    3.401 closest distance to " ND1 HIS A  86 " =    1.762
peak=    3.399 closest distance to " CG1 VAL A 153 " =    0.965
peak=    3.398 closest distance to " O  BHOH Z 338 " =    2.339
peak=    3.394 closest distance to " CA  ALA A 158 " =    1.272
peak=    3.390 closest distance to " CD  LYS A 166 " =    1.210
peak=    3.390 closest distance to " O   HOH Z 133 " =    1.558
peak=    3.388 closest distance to " O   THR A 220 " =    1.268
peak=    3.388 closest distance to " OE1 GLU A   2 " =    2.176
peak=    3.387 closest distance to " O   HOH Z 133 " =    2.437
peak=    3.385 closest distance to " O   HOH Z  88 " =    3.137
peak=    3.385 closest distance to " O   HOH Z 407 " =    2.517
peak=    3.381 closest distance to " CA  ALA A 291 " =    0.840
peak=    3.380 closest distance to " O   ALA A 165 " =    1.518
peak=    3.378 closest distance to " CG  GLN A  77 " =    2.192
peak=    3.376 closest distance to " O   HOH Z 128 " =    2.123
peak=    3.376 closest distance to " O   HOH Z  54 " =    1.688
peak=    3.374 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.364 closest distance to " O   HOH Z  44 " =    1.719
peak=    3.363 closest distance to " O   HOH Z 219 " =    1.992
peak=    3.360 closest distance to " CB  LEU A 143 " =    1.120
peak=    3.356 closest distance to " O   HOH Z 128 " =    2.355
peak=    3.352 closest distance to " O   HOH Z 435 " =    1.886
peak=    3.352 closest distance to " O   HOH Z 298 " =    2.584
peak=    3.349 closest distance to " O   HOH Z 383 " =    1.830
peak=    3.344 closest distance to " CA  MET A 105 " =    1.012
peak=    3.343 closest distance to " NH2AARG A 275 " =    3.682
peak=    3.334 closest distance to " CZ2 TRP A 179 " =    1.719
peak=    3.331 closest distance to " CB  THR A  31 " =    1.678
peak=    3.331 closest distance to " O   HOH Z 421 " =    1.802
peak=    3.325 closest distance to " CA  LYS A 117 " =    1.206
peak=    3.324 closest distance to " CD  ARG A 269 " =    0.883
peak=    3.324 closest distance to " CG2 ILE A  20 " =    1.377
peak=    3.323 closest distance to " O   HOH Z 175 " =    2.200
peak=    3.317 closest distance to " O   HOH Z 345 " =    3.413
peak=    3.317 closest distance to " O   HOH Z 193 " =    2.060
peak=    3.316 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.315 closest distance to " CB  ASN A 224 " =    0.982
peak=    3.313 closest distance to " NE2 GLN A  77 " =    3.222
peak=    3.308 closest distance to " O   HOH Z 285 " =    2.857
peak=    3.304 closest distance to " CB  GLN A  89 " =    1.352
peak=    3.302 closest distance to " O   HOH Z  97 " =    1.957
peak=    3.294 closest distance to " CB  SER A 141 " =    1.018
peak=    3.286 closest distance to " CD2 HIS A  81 " =    1.072
peak=    3.286 closest distance to " N   VAL A 126 " =    1.332
peak=    3.285 closest distance to " O   HOH Z  64 " =    2.136
peak=    3.279 closest distance to " CB  SER A  26 " =    1.657
peak=    3.279 closest distance to " OG  SER A  22 " =    2.702
peak=    3.277 closest distance to " O   HOH Z 273 " =    2.777
peak=    3.277 closest distance to " ND1 HIS A  81 " =    1.644
peak=    3.268 closest distance to " CB  ALA A 242 " =    0.896
peak=    3.267 closest distance to " O   HOH Z 261 " =    1.482
peak=    3.266 closest distance to " CB  LEU A 255 " =    0.769
peak=    3.264 closest distance to " O   HOH Z 108 " =    2.721
peak=    3.263 closest distance to " CB  ALA A 248 " =    1.357
peak=    3.262 closest distance to " O   HOH Z 411 " =    1.742
peak=    3.255 closest distance to " O   TRP A 274 " =    1.848
peak=    3.255 closest distance to " O   HOH Z  49 " =    2.735
peak=    3.251 closest distance to " O   HOH Z  44 " =    3.164
peak=    3.248 closest distance to " CA  ALA A  84 " =    1.303
peak=    3.246 closest distance to " O   HOH Z 419 " =    1.969
peak=    3.243 closest distance to " CB  ALA A   9 " =    1.528
peak=    3.243 closest distance to " CB  GLN A  88 " =    1.220
peak=    3.241 closest distance to " CB  SER A 273 " =    0.862
peak=    3.241 closest distance to " CA  ILE A  33 " =    1.514
peak=    3.234 closest distance to " CB  ALA A 248 " =    0.870
peak=    3.230 closest distance to " N   ASN A 127 " =    1.223
peak=    3.227 closest distance to " O   HOH Z 411 " =    3.868
peak=    3.225 closest distance to " O   HOH Z 163 " =    1.781
peak=    3.221 closest distance to " O   THR A 251 " =    1.246
peak=    3.218 closest distance to " CG2 VAL A 197 " =    1.071
peak=    3.218 closest distance to " CG  GLN A  11 " =    1.608
peak=    3.218 closest distance to " N   ASN A  39 " =    1.311
peak=    3.217 closest distance to " O   HOH Z 295 " =    1.520
peak=    3.216 closest distance to " CB  LYS A 290 " =    1.042
peak=    3.214 closest distance to " CA  TYR A 116 " =    1.334
peak=    3.212 closest distance to " O   HOH Z 391 " =    2.916
peak=    3.211 closest distance to " O   ALA A 158 " =    1.276
peak=    3.209 closest distance to " CG  LYS A  76 " =    0.970
peak=    3.207 closest distance to " O   HOH Z 409 " =    3.087
peak=    3.199 closest distance to " O   HOH Z 353 " =    2.694
peak=    3.198 closest distance to " CA  ALA A 233 " =    1.320
peak=    3.195 closest distance to " CA  ASN A 252 " =    1.900
peak=    3.192 closest distance to " O   HOH Z 171 " =    2.093
peak=    3.192 closest distance to " O   HOH Z 329 " =    3.932
peak=    3.191 closest distance to " CA  ALA A 248 " =    1.193
peak=    3.182 closest distance to " CA  GLY A 267 " =    1.187
peak=    3.178 closest distance to " O   HOH Z 365 " =    3.012
peak=    3.177 closest distance to " CG1 ILE A  49 " =    1.474
peak=    3.175 closest distance to " CB  ALA A   1 " =    4.742
peak=    3.169 closest distance to " O   HOH Z 271 " =    2.473
peak=    3.165 closest distance to " CB  ASN A 215 " =    1.145
peak=    3.164 closest distance to " O   HOH Z 433 " =    1.757
peak=    3.162 closest distance to " CB  LYS A 117 " =    1.174
peak=    3.162 closest distance to " O   HOH Z 327 " =    1.683
peak=    3.155 closest distance to " CE  LYS A  48 " =    1.043
peak=    3.152 closest distance to " CD  ARG A  36 " =    0.989
peak=    3.150 closest distance to " CA  SER A 146 " =    1.716
peak=    3.147 closest distance to " CA  MET A 188 " =    1.010
peak=    3.145 closest distance to " O   HOH Z 188 " =    2.102
peak=    3.142 closest distance to " O   HOH Z 423 " =    3.005
peak=    3.141 closest distance to " NZ  LYS A  76 " =    1.591
peak=    3.140 closest distance to " OG  SER A 206 " =    1.281
peak=    3.139 closest distance to " CA  ASP A 140 " =    1.153
peak=    3.139 closest distance to " CB  VAL A 126 " =    1.101
peak=    3.136 closest distance to " O   ALA A   1 " =    1.707
peak=    3.134 closest distance to " O   HOH Z 437 " =    1.220
peak=    3.134 closest distance to " CB  VAL A 265 " =    1.962
peak=    3.133 closest distance to " CB  THR A 235 " =    1.054
peak=    3.130 closest distance to " CG2 ILE A 234 " =    0.794
peak=    3.126 closest distance to " O   HOH Z 299 " =    4.541
peak=    3.125 closest distance to " CG  PRO A 213 " =    0.973
peak=    3.124 closest distance to " CA  ASN A 217 " =    1.181
peak=    3.119 closest distance to " CD1AILE A 234 " =    0.916
peak=    3.114 closest distance to " CA  VAL A 125 " =    1.098
peak=    3.102 closest distance to " O   HOH Z 374 " =    2.671
peak=    3.100 closest distance to " O   HOH Z 116 " =    1.756
peak=    3.098 closest distance to " O   HOH Z 371 " =    1.751
peak=    3.091 closest distance to " CD  ARG A 219 " =    1.123
peak=    3.084 closest distance to " CA  ARG A 102 " =    1.049
peak=    3.083 closest distance to " O   HOH Z 357 " =    1.903
peak=    3.079 closest distance to " CB  ARG A 138 " =    0.942
peak=    3.078 closest distance to " O   HOH Z 258 " =    1.892
peak=    3.074 closest distance to " CD1 ILE A 263 " =    1.269
peak=    3.060 closest distance to " CA  ALA A 154 " =    0.988
peak=    3.047 closest distance to " O   HOH Z 302 " =    1.887

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.801 - 5.611
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 191
   mapped sites are within: 0.801 - 5.611

peak=   -4.679 closest distance to " O   HOH Z 266 " =    5.040
peak=   -4.576 closest distance to " CD  ARG A 156 " =    2.014
peak=   -4.483 closest distance to " CB  PRO A 243 " =    2.633
peak=   -4.424 closest distance to " CG  GLN A 223 " =    1.993
peak=   -4.388 closest distance to " SG  CYS A 254 " =    3.520
peak=   -4.378 closest distance to " O   VAL A  67 " =    2.763
peak=   -4.291 closest distance to " O   HOH Z 231 " =    2.261
peak=   -4.287 closest distance to " C   HIS A 108 " =    1.055
peak=   -4.262 closest distance to " O   HOH Z 377 " =    2.131
peak=   -4.184 closest distance to " OG BSER A 134 " =    1.225
peak=   -4.180 closest distance to " CD  GLN A  58 " =    1.015
peak=   -4.078 closest distance to " O   HOH Z 198 " =    2.033
peak=   -4.062 closest distance to " CZ3 TRP A 179 " =    1.148
peak=   -4.056 closest distance to " O   HOH Z 389 " =    1.901
peak=   -4.040 closest distance to " O   HOH Z 372 " =    2.337
peak=   -4.020 closest distance to " O   HOH Z  10 " =    1.540
peak=   -4.018 closest distance to " O   ILE A 109 " =    2.562
peak=   -3.954 closest distance to " CE  MET A 105 " =    2.354
peak=   -3.934 closest distance to " CG1 VAL A 112 " =    2.847
peak=   -3.909 closest distance to " O   HOH Z 196 " =    1.996
peak=   -3.901 closest distance to " CD  ARG A 139 " =    1.564
peak=   -3.875 closest distance to " CG2 ILE A 263 " =    2.321
peak=   -3.862 closest distance to " CE2 TYR A  30 " =    2.729
peak=   -3.850 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.846 closest distance to " O   HOH Z 114 " =    3.125
peak=   -3.819 closest distance to " O   HOH Z 126 " =    1.879
peak=   -3.810 closest distance to " N   ALA A  43 " =    2.689
peak=   -3.798 closest distance to " O   VAL A  67 " =    2.904
peak=   -3.798 closest distance to " O   PRO A 198 " =    1.315
peak=   -3.791 closest distance to " ND2 ASN A  45 " =    1.696
peak=   -3.768 closest distance to " CB  ASN A  39 " =    2.321
peak=   -3.765 closest distance to " O   HOH Z 311 " =    3.649
peak=   -3.756 closest distance to " O   HOH Z 313 " =    1.906
peak=   -3.754 closest distance to " O   HOH Z 435 " =    2.807
peak=   -3.749 closest distance to " O   HOH Z  43 " =    1.612
peak=   -3.748 closest distance to " CD2 PHE A 192 " =    2.012
peak=   -3.737 closest distance to " CG1 VAL A 112 " =    2.615
peak=   -3.719 closest distance to " OG  SER A  97 " =    2.201
peak=   -3.718 closest distance to " CZ  PHE A  59 " =    1.565
peak=   -3.717 closest distance to " CB  ALA A  43 " =    2.593
peak=   -3.711 closest distance to " CB  ALA A 291 " =    2.384
peak=   -3.706 closest distance to " OXT GLY A 302 " =    2.851
peak=   -3.696 closest distance to " O   HOH Z 407 " =    3.083
peak=   -3.692 closest distance to " O   HOH Z 185 " =    2.263
peak=   -3.687 closest distance to " CD1 PHE A  59 " =    1.864
peak=   -3.659 closest distance to " O   HOH Z 290 " =    1.314
peak=   -3.654 closest distance to " O   PRO A 163 " =    2.028
peak=   -3.641 closest distance to " CE2 PHE A 218 " =    2.410
peak=   -3.634 closest distance to " O   HOH Z 198 " =    1.416
peak=   -3.632 closest distance to " CG  PHE A 283 " =    2.562
peak=   -3.626 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.605 closest distance to " O   HOH Z 353 " =    2.111
peak=   -3.600 closest distance to " ND2 ASN A  45 " =    1.052
peak=   -3.590 closest distance to " NH2AARG A 275 " =    5.324
peak=   -3.589 closest distance to " O   HOH Z 211 " =    1.673
peak=   -3.583 closest distance to " CA  GLY A 203 " =    2.350
peak=   -3.572 closest distance to " OD1 ASN A 187 " =    1.560
peak=   -3.568 closest distance to " O   HOH Z  73 " =    2.161
peak=   -3.564 closest distance to " CB  ASP A 132 " =    2.311
peak=   -3.559 closest distance to " CG1 VAL A 250 " =    2.623
peak=   -3.554 closest distance to " CA  GLY A 241 " =    3.087
peak=   -3.553 closest distance to " CG  ARG A 269 " =    2.465
peak=   -3.553 closest distance to " OD1 ASP A 171 " =    1.601
peak=   -3.543 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.539 closest distance to " C   LEU A 143 " =    1.070
peak=   -3.526 closest distance to " O   PHE A 218 " =    1.590
peak=   -3.521 closest distance to " NE2 GLN A  88 " =    1.906
peak=   -3.519 closest distance to " OD2 ASP A 191 " =    1.499
peak=   -3.517 closest distance to " O   HOH Z 292 " =    4.626
peak=   -3.515 closest distance to " O   HOH Z  60 " =    2.387
peak=   -3.511 closest distance to " CZ  TYR A 169 " =    1.727
peak=   -3.502 closest distance to " CB  TYR A  15 " =    2.151
peak=   -3.487 closest distance to " C   ALA A 158 " =    1.266
peak=   -3.486 closest distance to " CA  GLY A 133 " =    2.008
peak=   -3.479 closest distance to " NH2 ARG A  79 " =    1.551
peak=   -3.476 closest distance to " CD1 LEU A 228 " =    2.257
peak=   -3.469 closest distance to " O   HOH Z  51 " =    1.692
peak=   -3.469 closest distance to " O   HOH Z 394 " =    1.474
peak=   -3.467 closest distance to " SG ACYS A 201 " =    1.944
peak=   -3.460 closest distance to " CD1 LEU A 297 " =    2.420
peak=   -3.451 closest distance to " O   HOH Z  11 " =    1.708
peak=   -3.448 closest distance to " OD1 ASN A 148 " =    1.548
peak=   -3.448 closest distance to " CB  PHE A 208 " =    2.232
peak=   -3.446 closest distance to " O   HOH Z 102 " =    1.596
peak=   -3.435 closest distance to " N   SER A 212 " =    2.048
peak=   -3.415 closest distance to " N   ALA A 248 " =    1.596
peak=   -3.415 closest distance to " O   HOH Z 166 " =    1.966
peak=   -3.413 closest distance to " ND2 ASN A 249 " =    2.103
peak=   -3.405 closest distance to " OG  SER A  62 " =    1.689
peak=   -3.397 closest distance to " CB  ALA A 248 " =    2.097
peak=   -3.394 closest distance to " CG  ARG A  66 " =    2.422
peak=   -3.392 closest distance to " CD  ARG A 195 " =    5.184
peak=   -3.389 closest distance to " CD1 LEU A 101 " =    2.351
peak=   -3.384 closest distance to " CG  GLU A 277 " =    1.122
peak=   -3.381 closest distance to " O   HOH Z 322 " =    1.625
peak=   -3.377 closest distance to " O   HOH Z 298 " =    1.273
peak=   -3.376 closest distance to " OG BSER A 134 " =    1.758
peak=   -3.374 closest distance to " O   SER A 135 " =    1.471
peak=   -3.374 closest distance to " O   HOH Z 123 " =    2.330
peak=   -3.373 closest distance to " CB  ALA A 248 " =    2.384
peak=   -3.370 closest distance to " NE2 GLN A 278 " =    1.717
peak=   -3.366 closest distance to " NH1 ARG A  36 " =    2.096
peak=   -3.363 closest distance to " O   HOH Z 243 " =    2.064
peak=   -3.358 closest distance to " O   HOH Z  52 " =    1.306
peak=   -3.358 closest distance to " N   ASP A 286 " =    2.435
peak=   -3.345 closest distance to " O   HOH Z 295 " =    1.595
peak=   -3.340 closest distance to " O   ALA A 161 " =    1.689
peak=   -3.338 closest distance to " O   HOH Z 165 " =    1.996
peak=   -3.336 closest distance to " O   HOH Z  13 " =    1.581
peak=   -3.336 closest distance to " O   GLY A 211 " =    1.395
peak=   -3.333 closest distance to " NH2BARG A 275 " =    1.878
peak=   -3.332 closest distance to " O   VAL A 189 " =    2.614
peak=   -3.325 closest distance to " CD2 TYR A 247 " =    2.366
peak=   -3.314 closest distance to " CG  TRP A 266 " =    1.892
peak=   -3.314 closest distance to " CA  ASP A 298 " =    1.039
peak=   -3.314 closest distance to " O   HOH Z 253 " =    3.944
peak=   -3.301 closest distance to " NE2 GLN A 194 " =    1.724
peak=   -3.301 closest distance to " O   HOH Z  44 " =    2.207
peak=   -3.301 closest distance to " NH1 ARG A 195 " =    2.570
peak=   -3.298 closest distance to " O   LYS A 117 " =    1.708
peak=   -3.295 closest distance to " O   SER A  95 " =    1.595
peak=   -3.281 closest distance to " O   ALA A  10 " =    1.645
peak=   -3.280 closest distance to " CB  PRO A 163 " =    2.471
peak=   -3.278 closest distance to " O   HOH Z   6 " =    1.437
peak=   -3.277 closest distance to " CD  LYS A 289 " =    2.448
peak=   -3.277 closest distance to " O   HOH Z  38 " =    1.485
peak=   -3.271 closest distance to " OD2 ASP A 171 " =    1.792
peak=   -3.263 closest distance to " CA  GLY A 241 " =    2.807
peak=   -3.258 closest distance to " O   ARG A 145 " =    1.542
peak=   -3.251 closest distance to " CD2 PHE A  61 " =    2.536
peak=   -3.248 closest distance to " OD1 ASP A 191 " =    1.535
peak=   -3.246 closest distance to " O   HOH Z 426 " =    1.567
peak=   -3.245 closest distance to " NH2 ARG A  79 " =    2.019
peak=   -3.239 closest distance to " O   HOH Z 234 " =    4.134
peak=   -3.230 closest distance to " O   HOH Z  11 " =    2.120
peak=   -3.230 closest distance to " CG  GLU A 152 " =    1.273
peak=   -3.229 closest distance to " CD2 LEU A 237 " =    2.736
peak=   -3.228 closest distance to " OE1 GLN A  88 " =    1.120
peak=   -3.221 closest distance to " O   VAL A 174 " =    2.061
peak=   -3.219 closest distance to " O   HOH Z 322 " =    1.231
peak=   -3.218 closest distance to " O   HOH Z  37 " =    1.798
peak=   -3.217 closest distance to " N   MET A 105 " =    2.646
peak=   -3.217 closest distance to " CE3 TRP A 150 " =    2.174
peak=   -3.212 closest distance to " CG  GLU A   2 " =    1.891
peak=   -3.210 closest distance to " O   HOH Z 385 " =    1.855
peak=   -3.207 closest distance to " ND2 ASN A 187 " =    1.569
peak=   -3.202 closest distance to " O   HOH Z 359 " =    3.149
peak=   -3.202 closest distance to " CB  ASP A 286 " =    1.793
peak=   -3.201 closest distance to " CB  ASP A 286 " =    2.174
peak=   -3.200 closest distance to " C   GLY A  17 " =    1.184
peak=   -3.199 closest distance to " CD2 TYR A 293 " =    2.071
peak=   -3.193 closest distance to " CG2 THR A 221 " =    2.261
peak=   -3.188 closest distance to " CD  GLU A 236 " =    1.053
peak=   -3.184 closest distance to " CZ  PHE A 155 " =    1.280
peak=   -3.183 closest distance to " O   HOH Z 414 " =    1.585
peak=   -3.180 closest distance to " O   VAL A 189 " =    1.581
peak=   -3.173 closest distance to " CG  GLN A  11 " =    1.729
peak=   -3.172 closest distance to " OD2 ASP A  50 " =    1.575
peak=   -3.169 closest distance to " CZ  PHE A 192 " =    2.922
peak=   -3.168 closest distance to " CG  MET A 105 " =    0.947
peak=   -3.167 closest distance to " OD2 ASP A 171 " =    2.404
peak=   -3.167 closest distance to " OG  SER A  26 " =    1.303
peak=   -3.165 closest distance to " N   ALA A 226 " =    2.038
peak=   -3.163 closest distance to " O   HOH Z 111 " =    2.044
peak=   -3.159 closest distance to " CG  PRO A 163 " =    2.485
peak=   -3.158 closest distance to " C   MET A 188 " =    1.360
peak=   -3.154 closest distance to " O   ALA A 292 " =    2.088
peak=   -3.150 closest distance to " CG1 VAL A 125 " =    1.985
peak=   -3.143 closest distance to " O   HOH Z 421 " =    3.047
peak=   -3.117 closest distance to " CG2 VAL A 189 " =    2.102
peak=   -3.108 closest distance to " O   HOH Z 377 " =    1.651
peak=   -3.104 closest distance to " O   ALA A  51 " =    1.374
peak=   -3.100 closest distance to " CG1 VAL A 197 " =    2.330
peak=   -3.097 closest distance to " O   HOH Z  93 " =    2.325
peak=   -3.095 closest distance to " O   HOH Z 191 " =    5.611
peak=   -3.092 closest distance to " CB  TRP A  85 " =    2.401
peak=   -3.091 closest distance to " OD1 ASP A 200 " =    1.409
peak=   -3.091 closest distance to " O   HOH Z 263 " =    3.218
peak=   -3.083 closest distance to " O   GLU A 152 " =    1.385
peak=   -3.078 closest distance to " N   TYR A  68 " =    3.183
peak=   -3.076 closest distance to " O   HOH Z 361 " =    3.420
peak=   -3.075 closest distance to " O   HOH Z 324 " =    2.161
peak=   -3.074 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.072 closest distance to " OD1AASN A 224 " =    1.771
peak=   -3.063 closest distance to " O   GLN A 240 " =    2.440
peak=   -3.051 closest distance to " O   TRP A  70 " =    1.477
peak=   -3.037 closest distance to " OE2 GLU A 152 " =    1.194
peak=   -3.034 closest distance to " O   HOH Z 357 " =    2.062
peak=   -3.028 closest distance to " O   HOH Z 193 " =    1.732
peak=   -3.014 closest distance to " N   GLN A  58 " =    2.049

================= 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    :  0.1752 0.1739   5.422210e+00   5.416708e+00
   1_bss:  0.1528 0.1528   5.368376e+00   5.359046e+00
   1_xyz:  0.1231 0.1460   5.163467e+00   5.308218e+00
   1_adp:  0.1135 0.1458   5.110269e+00   5.311839e+00
   1_occ:  0.1130 0.1454   5.107689e+00   5.310301e+00
   2_bss:  0.1132 0.1449   5.108630e+00   5.308550e+00
   2_xyz:  0.1120 0.1477   5.111175e+00   5.325257e+00
   2_adp:  0.1096 0.1486   5.104059e+00   5.334368e+00
   2_occ:  0.1095 0.1487   5.104168e+00   5.335098e+00
   3_bss:  0.1094 0.1487   5.104265e+00   5.335089e+00
   3_xyz:  0.1107 0.1513   5.118924e+00   5.352519e+00
   3_adp:  0.1096 0.1517   5.115568e+00   5.355646e+00
   3_occ:  0.1095 0.1517   5.115895e+00   5.356267e+00
   4_bss:  0.1095 0.1518   5.115988e+00   5.356322e+00
   4_xyz:  0.1070 0.1523   5.104871e+00   5.357581e+00
   4_adp:  0.1072 0.1522   5.104346e+00   5.356107e+00
   4_occ:  0.1071 0.1521   5.104318e+00   5.356101e+00
   5_bss:  0.1071 0.1521   5.104399e+00   5.356147e+00
   5_xyz:  0.1067 0.1535   5.107235e+00   5.364899e+00
   5_adp:  0.1061 0.1553   5.109853e+00   5.373805e+00
   5_occ:  0.1060 0.1554   5.110002e+00   5.374176e+00
   5_bss:  0.1059 0.1553   5.109811e+00   5.373969e+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:  0.330  54.527  -2.617  -2.835  -1.729  -0.000  -0.000  -0.000
   1_xyz:  0.330  54.527  -2.617  -2.835  -1.729  -0.000  -0.000  -0.000
   1_adp:  0.330  54.527  -2.617  -2.835  -1.729  -0.000  -0.000  -0.000
   1_occ:  0.330  54.527  -2.617  -2.835  -1.729  -0.000  -0.000  -0.000
   2_bss:  0.332  54.527  -2.788  -2.709  -1.606  -0.000  -0.000  -0.000
   2_xyz:  0.332  54.527  -2.788  -2.709  -1.606  -0.000  -0.000  -0.000
   2_adp:  0.332  54.527  -2.788  -2.709  -1.606  -0.000  -0.000  -0.000
   2_occ:  0.332  54.527  -2.788  -2.709  -1.606  -0.000  -0.000  -0.000
   3_bss:  0.332  54.527  -2.637  -2.480  -1.395  -0.000  -0.000  -0.000
   3_xyz:  0.332  54.527  -2.637  -2.480  -1.395  -0.000  -0.000  -0.000
   3_adp:  0.332  54.527  -2.637  -2.480  -1.395  -0.000  -0.000  -0.000
   3_occ:  0.332  54.527  -2.637  -2.480  -1.395  -0.000  -0.000  -0.000
   4_bss:  0.332  54.527  -2.448  -2.284  -1.205  -0.000  -0.000  -0.000
   4_xyz:  0.332  54.527  -2.448  -2.284  -1.205  -0.000  -0.000  -0.000
   4_adp:  0.332  54.527  -2.448  -2.284  -1.205  -0.000  -0.000  -0.000
   4_occ:  0.332  54.527  -2.448  -2.284  -1.205  -0.000  -0.000  -0.000
   5_bss:  0.332  54.527  -2.260  -2.099  -1.013  -0.000  -0.000  -0.000
   5_xyz:  0.332  54.527  -2.260  -2.099  -1.013  -0.000  -0.000  -0.000
   5_adp:  0.332  54.527  -2.260  -2.099  -1.013  -0.000  -0.000  -0.000
   5_occ:  0.332  54.527  -2.260  -2.099  -1.013  -0.000  -0.000  -0.000
   5_bss:  0.327  54.530  -2.008  -1.862  -0.795  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  14.471 0.9128  1.0407     8594.782
   1_bss:  13.034 0.9243  0.9686     5993.064
   1_xyz:  12.173 0.9299  0.9737     5464.428
   1_adp:  12.326 0.9283  0.9721     5466.774
   1_occ:  12.298 0.9285  0.9719     5424.805
   2_bss:  12.279 0.9286  0.9725     5394.682
   2_xyz:  12.542 0.9268  0.9707     5619.133
   2_adp:  12.717 0.9254  0.9660     5657.314
   2_occ:  12.732 0.9253  0.9658     5664.417
   3_bss:  12.734 0.9253  0.9727     5665.079
   3_xyz:  13.061 0.9229  0.9716     5886.853
   3_adp:  13.145 0.9222  0.9658     5900.096
   3_occ:  13.156 0.9221  0.9657     5907.071
   4_bss:  13.159 0.9221  0.9724     5908.515
   4_xyz:  13.180 0.9218  0.9727     5938.034
   4_adp:  13.148 0.9220  0.9671     5921.197
   4_occ:  13.150 0.9220  0.9670     5921.086
   5_bss:  13.152 0.9220  0.9736     5922.259
   5_xyz:  13.294 0.9209  0.9734     6046.913
   5_adp:  13.497 0.9194  0.9654     6120.817
   5_occ:  13.502 0.9193  0.9654     6125.904
   5_bss:  13.499 0.9194  0.9737     6120.443
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5972e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5972e-01
   1_xyz:   1.064  0.010  0.084 15.587  0.004  4.116   7.2893e-02
   1_adp:   1.064  0.010  0.084 15.587  0.004  4.116   7.2893e-02
   1_occ:   1.064  0.010  0.084 15.587  0.004  4.116   7.2893e-02
   2_bss:   1.064  0.010  0.084 15.587  0.004  4.116   7.2893e-02
   2_xyz:   0.991  0.008  0.078 15.177  0.004  4.117   6.2172e-02
   2_adp:   0.991  0.008  0.078 15.177  0.004  4.117   6.2172e-02
   2_occ:   0.991  0.008  0.078 15.177  0.004  4.117   6.2172e-02
   3_bss:   0.991  0.008  0.078 15.177  0.004  4.117   6.2172e-02
   3_xyz:   0.922  0.006  0.073 15.016  0.003  4.117   5.4548e-02
   3_adp:   0.922  0.006  0.073 15.016  0.003  4.117   5.4548e-02
   3_occ:   0.922  0.006  0.073 15.016  0.003  4.117   5.4548e-02
   4_bss:   0.922  0.006  0.073 15.016  0.003  4.117   5.4548e-02
   4_xyz:   0.998  0.008  0.078 15.146  0.004  4.119   6.3104e-02
   4_adp:   0.998  0.008  0.078 15.146  0.004  4.119   6.3104e-02
   4_occ:   0.998  0.008  0.078 15.146  0.004  4.119   6.3104e-02
   5_bss:   0.998  0.008  0.078 15.146  0.004  4.119   6.3104e-02
   5_xyz:   1.004  0.008  0.079 15.131  0.004  4.120   6.3667e-02
   5_adp:   1.004  0.008  0.079 15.131  0.004  4.120   6.3667e-02
   5_occ:   1.004  0.008  0.079 15.131  0.004  4.120   6.3667e-02
   5_bss:   1.004  0.008  0.079 15.131  0.004  4.120   6.3667e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4172e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4172e-01
   1_xyz:   7.639  0.048  0.251 83.723  0.038  2.339   6.6455e-02
   1_adp:   7.639  0.048  0.251 83.723  0.038  2.339   6.6455e-02
   1_occ:   7.639  0.048  0.251 83.723  0.038  2.339   6.6455e-02
   2_bss:   7.639  0.048  0.251 83.723  0.038  2.339   6.6455e-02
   2_xyz:   6.947  0.042  0.249 83.956  0.034  2.323   4.2386e-02
   2_adp:   6.947  0.042  0.249 83.956  0.034  2.323   4.2386e-02
   2_occ:   6.947  0.042  0.249 83.956  0.034  2.323   4.2386e-02
   3_bss:   6.947  0.042  0.249 83.956  0.034  2.323   4.2386e-02
   3_xyz:   6.947  0.040  0.226 83.564  0.033  2.381   3.3941e-02
   3_adp:   6.947  0.040  0.226 83.564  0.033  2.381   3.3941e-02
   3_occ:   6.947  0.040  0.226 83.564  0.033  2.381   3.3941e-02
   4_bss:   6.947  0.040  0.226 83.564  0.033  2.381   3.3941e-02
   4_xyz:   6.689  0.044  0.252 83.456  0.035  2.319   4.5885e-02
   4_adp:   6.689  0.044  0.252 83.456  0.035  2.319   4.5885e-02
   4_occ:   6.689  0.044  0.252 83.456  0.035  2.319   4.5885e-02
   5_bss:   6.689  0.044  0.252 83.456  0.035  2.319   4.5885e-02
   5_xyz:   6.738  0.043  0.257 83.305  0.035  2.312   4.6036e-02
   5_adp:   6.738  0.043  0.257 83.305  0.035  2.312   4.6036e-02
   5_occ:   6.738  0.043  0.257 83.305  0.035  2.312   4.6036e-02
   5_bss:   6.738  0.043  0.257 83.305  0.035  2.312   4.6036e-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:  62.51   0.00  16.32  57.29   0.00  12.57  62.51   3.74  36.73
   1_occ:  62.51   0.00  16.32  57.29   0.00  12.57  62.51   3.74  36.73
   2_bss:  62.51   0.00  16.32  57.29   0.00  12.57  62.51   3.74  36.73
   2_xyz:  62.51   0.00  16.32  57.29   0.00  12.57  62.51   3.74  36.73
   2_adp:  67.70   1.95  16.44  67.70   1.95  12.77  64.77   5.05  36.47
   2_occ:  67.70   1.95  16.44  67.70   1.95  12.77  64.77   5.05  36.47
   3_bss:  67.70   1.95  16.44  67.70   1.95  12.77  64.77   5.05  36.47
   3_xyz:  67.70   1.95  16.44  67.70   1.95  12.77  64.77   5.05  36.47
   3_adp:  74.91   1.11  16.59  74.91   1.11  12.73  66.33   6.55  37.61
   3_occ:  74.91   1.11  16.59  74.91   1.11  12.73  66.33   6.55  37.61
   4_bss:  74.91   1.11  16.59  74.91   1.11  12.73  66.33   6.55  37.61
   4_xyz:  74.91   1.11  16.59  74.91   1.11  12.73  66.33   6.55  37.61
   4_adp:  75.22   1.23  16.39  75.22   1.23  12.56  66.63   6.43  37.24
   4_occ:  75.22   1.23  16.39  75.22   1.23  12.56  66.63   6.43  37.24
   5_bss:  75.22   1.23  16.39  75.22   1.23  12.56  66.63   6.43  37.24
   5_xyz:  75.22   1.23  16.39  75.22   1.23  12.56  66.63   6.43  37.24
   5_adp:  84.87   0.00  16.68  84.87   0.00  12.56  73.28   6.00  39.15
   5_occ:  84.87   0.00  16.68  84.87   0.00  12.56  73.28   6.00  39.15
   5_bss:  84.87   0.00  16.68  84.87   0.00  12.56  73.28   6.00  39.15
------------------------------------------------------------------------
 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:    0.430    0.007    0.105
   1_adp:    0.430    0.007    0.105
   1_occ:    0.430    0.007    0.105
   2_bss:    0.430    0.007    0.105
   2_xyz:    0.678    0.009    0.116
   2_adp:    0.678    0.009    0.116
   2_occ:    0.678    0.009    0.116
   3_bss:    0.678    0.009    0.116
   3_xyz:    0.820    0.007    0.123
   3_adp:    0.820    0.007    0.123
   3_occ:    0.820    0.007    0.123
   4_bss:    0.820    0.007    0.123
   4_xyz:    0.895    0.006    0.127
   4_adp:    0.895    0.006    0.127
   4_occ:    0.895    0.006    0.127
   5_bss:    0.895    0.006    0.127
   5_xyz:    1.001    0.006    0.132
   5_adp:    1.001    0.006    0.132
   5_occ:    1.001    0.006    0.132
   5_bss:    1.001    0.006    0.132
------------------------------------------------------------------------

CPU time actual refinement: 332.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_786/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_786/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_786/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_786/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_786/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.69 
  Macro-tasks:
    bulk solvent and scale       = 38.63  
    individual site refinement   = 141.07 
    weights calculation          = 29.19  
    collect and process          = 6.70   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 215.67 
  Micro-tasks:
    mask                            = 0.55   
    f_calc                          = 107.86 
    alpha_beta                      = 8.40   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 113.46 
    fmodel                         = 6.92   
    r_factors                      = 0.14   
    phase_errors                   = 12.03  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 250.85 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.624 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    668 calls, 107.42 s
gradients_fft:          613 calls, 100.91 s

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

# Date 2008-01-16 Time 05:39:55 PST -0800 (1200490795.28 s)
Start R-work = 0.1752, R-free = 0.1739 (no bulk solvent and anisotropic scale)
Final R-work = 0.1290, R-free = 0.1732 (no bulk solvent and anisotropic scale)

Start R-work = 0.1528, R-free = 0.1528
Final R-work = 0.1059, R-free = 0.1553