# Date 2008-01-16 Time 04:57:38 PST -0800 (1200488258.40 s)
#phil __OFF__

Command line arguments: "../535.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11869
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 535

-------------------------------------------------------------------------------
  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: (69.8988, 46.6953, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


================================== 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: (69.8988, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99025
Completeness in resolution range: 0.971918
Completeness with d_max=infinity: 0.968889

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9790
                             d_min =   1.9903

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: (69.8988, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99025
Completeness in resolution range: 0.971918
Completeness with d_max=infinity: 0.968889

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9794 -  4.2581 [2124/2148]  1909   215  10.1%
  bin  2:  4.2581 -  3.3927 [2032/2052]  1833   199   9.8%
  bin  3:  3.3927 -  2.9676 [2010/2029]  1809   201  10.0%
  bin  4:  2.9676 -  2.6980 [1968/1998]  1767   201  10.2%
  bin  5:  2.6980 -  2.5056 [1992/2011]  1793   199  10.0%
  bin  6:  2.5056 -  2.3585 [1967/1992]  1772   195   9.9%
  bin  7:  2.3585 -  2.2408 [1946/1974]  1751   195  10.0%
  bin  8:  2.2408 -  2.1435 [1960/1996]  1765   195   9.9%
  bin  9:  2.1435 -  2.0612 [1929/1971]  1734   195  10.1%
  bin 10:  2.0612 -  1.9903 [1661/1984]  1497   164   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_535/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: 0.12 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: 19
        2.42 -     3.04: 2192
        3.04 -     3.66: 4677
        3.66 -     4.28: 9042
        4.28 -     4.90: 12362
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.873 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.042 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.165 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28287 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_535/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_535/model_refine_001.geo

CPU time processing inputs: 8.17


============================ 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 = 69.89875 46.69535 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2687   r_free= 0.2652   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.873272                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7490 0.99   1382  152 0.2580 0.2491      6.2794      6.2011|
|  2:  4.7490 -  3.7895 0.99   1312  151 0.1990 0.2020         6.2      6.2167|
|  3:  3.7895 -  3.3164 0.99   1299  141 0.2249 0.2215      6.1483      6.2003|
|  4:  3.3164 -  3.0159 0.99   1296  141 0.2406 0.2631      6.0444      6.0932|
|  5:  3.0159 -  2.8012 0.99   1269  144 0.2706 0.2288      5.9165      5.7821|
|  6:  2.8012 -  2.6370 0.99   1286  144 0.2659 0.2922      5.8296      5.8126|
|  7:  2.6370 -  2.5056 0.99   1267  142 0.2694 0.2530      5.7923      5.7665|
|  8:  2.5056 -  2.3970 0.98   1271  137 0.2967 0.2764      5.8252      5.7851|
|  9:  2.3970 -  2.3051 0.98   1248  142 0.2935 0.2981      5.7579      5.7318|
| 10:  2.3051 -  2.2258 1.00   1275  139 0.3061 0.2793      5.7753       5.681|
| 11:  2.2258 -  2.1564 0.97   1248  138 0.3096 0.3175      5.7165      5.7534|
| 12:  2.1564 -  2.0949 0.98   1252  139 0.3156 0.3000      5.6736      5.7407|
| 13:  2.0949 -  2.0399 0.99   1250  139 0.3187 0.3036      5.5829      5.5424|
| 14:  2.0399 -  1.9903 0.77    975  110 0.3122 0.3220      5.5382      5.4875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7490  1382   152  0.82  22.96   0.87     0.84      33908.07|
|  2:  4.7490 -  3.7895  1312   151  0.88  17.96   0.99     0.94      31899.40|
|  3:  3.7895 -  3.3164  1299   141  0.87  19.76   1.01     0.99      28016.60|
|  4:  3.3164 -  3.0159  1296   141  0.86  20.71   1.01     0.98      23233.79|
|  5:  3.0159 -  2.8012  1269   144  0.82  24.71   1.03     0.96      18338.19|
|  6:  2.8012 -  2.6370  1286   144  0.82  24.52   1.02     0.96      15992.83|
|  7:  2.6370 -  2.5056  1267   142  0.81  26.00   1.04     0.97      15130.15|
|  8:  2.5056 -  2.3970  1271   137  0.81  26.23   1.03     0.98      14895.11|
|  9:  2.3970 -  2.3051  1248   142  0.81  26.47   1.06     0.99      14126.60|
| 10:  2.3051 -  2.2258  1275   139  0.79  28.04   1.08     1.00      13586.82|
| 11:  2.2258 -  2.1564  1248   138  0.78  28.46   1.06     1.02      13465.02|
| 12:  2.1564 -  2.0949  1252   139  0.77  30.09   1.09     1.03      13260.15|
| 13:  2.0949 -  2.0399  1250   139  0.76  30.89   1.07     1.00      11791.32|
| 14:  2.0399 -  1.9903   975   110  0.77  30.00   1.09     0.95       9400.92|
|alpha:            min =        0.84 max =            1.03 mean =         0.97|
|beta:             min =     9400.92 max =        33908.07 mean =     18685.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.96 mean =        25.34|
|phase err.(test): min =        0.00 max =           89.74 mean =        25.10|
|-----------------------------------------------------------------------------|

============================== 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 = 3.113601              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.377   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.393241              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.864   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      202 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1990 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2836 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4636 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4406 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5655 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6707 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| 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 |       0.169 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2687   r_free= 0.2652   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.873272                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2519   r_free= 0.2485   ksol= 0.33   Bsol= 50.00   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.05,0.57,-0.00,0.00,0.00); trace/3= -1.46                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.838914                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.722831              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.224   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222757              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.787   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2519      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2485      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1397 = 2.72 * 0.50 * 5.8600 + 1.00 * 0.1619                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5706 = 2.72 * 0.50 * 5.5177 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1475      final r-factor (work) = 0.1360          |
| start r-factor (free) = 0.1684      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2353 = 0.22 * 1.00 * 5.5177 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2122 = 0.22 * 1.00 * 5.2671 + 1.00 * 0.0389                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.49   16.46    None  None   None       |
|    all(noH): 2823   0      0.00    71.49   16.46    None  None   None       |
|    Sol.    : 438    0      7.28    62.79   37.22    None  None   None       |
|    Mac.    : 2385   0      0.00    71.49   12.65    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 -   7.150:  289   |   5:    35.747 -  42.897:  118        |
|      1:     7.150 -  14.299: 1473   |   6:    42.897 -  50.046:   79        |
|      2:    14.299 -  21.448:  501   |   7:    50.046 -  57.196:   64        |
|      3:    21.448 -  28.598:  152   |   8:    57.196 -  64.345:   21        |
|      4:    28.598 -  35.747:  125   |   9:    64.345 -  71.495:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1360 r_free = 0.1716             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1356 r_free = 0.1714             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1714   ksol= 0.33   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.05,0.57,-0.00,0.00,0.00); trace/3= -1.46                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1353   r_free= 0.1707   ksol= 0.33   Bsol= 52.94   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,-2.62,-0.81,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.295737              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.047  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222260              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.582   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1353      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1707      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4768 = 1.30 * 0.50 * 5.2758 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4314 = 1.30 * 0.50 * 5.2196 + 1.00 * 0.0497                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8805 = 0.22 * 1.00 * 5.2196 + 1.00 * 0.7203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1540 = 0.22 * 1.00 * 5.1588 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    65.30   16.65    None  None   None       |
|    all(noH): 2823   0      1.53    65.30   16.65    None  None   None       |
|    Sol.    : 438    0      5.95    65.30   37.64    None  None   None       |
|    Mac.    : 2385   0      1.53    59.54   12.79    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:     1.525 -   7.902:  476   |   5:    33.412 -  39.789:  108        |
|      1:     7.902 -  14.280: 1291   |   6:    39.789 -  46.166:   87        |
|      2:    14.280 -  20.657:  447   |   7:    46.166 -  52.544:   93        |
|      3:    20.657 -  27.034:  155   |   8:    52.544 -  58.921:   54        |
|      4:    27.034 -  33.412:  101   |   9:    58.921 -  65.298:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1544             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1544             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1544   ksol= 0.33   Bsol= 52.94   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,-2.62,-0.81,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157636                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1543   ksol= 0.33   Bsol= 52.94   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.49,-0.88,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157349                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.654880              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.604  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.824415              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.482  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3180 = 1.65 * 0.50 * 5.1588 + 1.00 * 0.0495                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3041 = 1.65 * 0.50 * 5.1352 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.7815 = 4.82 * 1.00 * 5.1352 + 1.00 * 0.0074                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.7117 = 4.82 * 1.00 * 5.1202 + 1.00 * 0.0099                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.56    82.34   17.20    None  None   None       |
|    all(noH): 2823   0      0.56    82.34   17.20    None  None   None       |
|    Sol.    : 438    0      4.89    75.94   40.36    None  None   None       |
|    Mac.    : 2385   0      0.56    82.34   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.559 -   8.737:  743   |   5:    41.449 -  49.627:   96        |
|      1:     8.737 -  16.915: 1270   |   6:    49.627 -  57.805:   76        |
|      2:    16.915 -  25.093:  307   |   7:    57.805 -  65.982:   57        |
|      3:    25.093 -  33.271:  130   |   8:    65.982 -  74.160:   27        |
|      4:    33.271 -  41.449:  110   |   9:    74.160 -  82.338:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1537             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1537             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1537   ksol= 0.33   Bsol= 52.94   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.49,-0.88,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123959                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1535   ksol= 0.32   Bsol= 52.94   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.22,-0.69,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123786                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.046733              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.668  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.085675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.838  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2961 = 2.05 * 0.50 * 5.1214 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2938 = 2.05 * 0.50 * 5.1165 + 1.00 * 0.0577                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4483 = 0.09 * 1.00 * 5.1165 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4552 = 0.09 * 1.00 * 5.1299 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.72   17.05    None  None   None       |
|    all(noH): 2823   0      0.00    81.72   17.05    None  None   None       |
|    Sol.    : 438    0      6.39    74.58   39.49    None  None   None       |
|    Mac.    : 2385   0      0.00    81.72   12.93    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 -   8.172:  566   |   5:    40.860 -  49.032:   98        |
|      1:     8.172 -  16.344: 1434   |   6:    49.032 -  57.204:   76        |
|      2:    16.344 -  24.516:  320   |   7:    57.204 -  65.376:   55        |
|      3:    24.516 -  32.688:  133   |   8:    65.376 -  73.548:   25        |
|      4:    32.688 -  40.860:  111   |   9:    73.548 -  81.720:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1523             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1523             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1523   ksol= 0.32   Bsol= 52.94   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.22,-0.69,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1517   ksol= 0.32   Bsol= 52.94   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.22,-0.69,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.306227              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.150794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.666   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9723 = 2.31 * 0.50 * 5.1293 + 1.00 * 0.0577                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9528 = 2.31 * 0.50 * 5.1085 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8945 = 0.15 * 1.00 * 5.1085 + 1.00 * 0.1242                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7771 = 0.15 * 1.00 * 5.1067 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.86    79.64   16.45    None  None   None       |
|    all(noH): 2823   0      1.86    79.64   16.45    None  None   None       |
|    Sol.    : 438    0      6.44    73.33   37.13    None  None   None       |
|    Mac.    : 2385   0      1.86    79.64   12.65    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:     1.858 -   9.636:  962   |   5:    40.749 -  48.527:   91        |
|      1:     9.636 -  17.414: 1121   |   6:    48.527 -  56.305:   74        |
|      2:    17.414 -  25.192:  264   |   7:    56.305 -  64.083:   28        |
|      3:    25.192 -  32.970:  130   |   8:    64.083 -  71.861:   19        |
|      4:    32.970 -  40.749:  131   |   9:    71.861 -  79.639:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1522             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1080 r_free = 0.1521             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1521   ksol= 0.32   Bsol= 52.94   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.22,-0.69,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110116                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7490 0.99   1382  152 0.1003 0.1258      5.3885      5.5083|
|  2:  4.7490 -  3.7895 0.99   1312  151 0.0863 0.1138      5.4433      5.6426|
|  3:  3.7895 -  3.3164 0.99   1299  141 0.1032 0.1472      5.4595      5.8324|
|  4:  3.3164 -  3.0159 0.99   1296  141 0.1164 0.1503      5.4151      5.5436|
|  5:  3.0159 -  2.8012 0.99   1269  144 0.1260 0.1643      5.2885      5.5216|
|  6:  2.8012 -  2.6370 0.99   1286  144 0.1157 0.1933        5.18      5.4742|
|  7:  2.6370 -  2.5056 0.99   1267  142 0.1226 0.1540      5.1393      5.3085|
|  8:  2.5056 -  2.3970 0.98   1271  137 0.1118 0.1625      5.0394      5.2933|
|  9:  2.3970 -  2.3051 0.98   1248  142 0.1101 0.1693      4.9829      5.2453|
| 10:  2.3051 -  2.2258 1.00   1275  139 0.1095 0.1634      4.9261      5.1938|
| 11:  2.2258 -  2.1564 0.97   1248  138 0.1080 0.1631      4.9003      5.1578|
| 12:  2.1564 -  2.0949 0.98   1252  139 0.1090 0.1646      4.8358      5.2183|
| 13:  2.0949 -  2.0399 0.99   1250  139 0.1032 0.1680      4.7426      5.0128|
| 14:  2.0399 -  1.9903 0.77    975  110 0.0977 0.1577      4.6217      4.8638|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7490  1382   152  0.94   9.12   0.98     0.95       7100.78|
|  2:  4.7490 -  3.7895  1312   151  0.95   7.86   1.01     1.00       8985.67|
|  3:  3.7895 -  3.3164  1299   141  0.94  10.81   1.02     1.01       9897.70|
|  4:  3.3164 -  3.0159  1296   141  0.93  12.66   1.00     0.98       9412.46|
|  5:  3.0159 -  2.8012  1269   144  0.91  14.86   1.00     0.97       7612.54|
|  6:  2.8012 -  2.6370  1286   144  0.90  15.38   0.99     0.96       6618.61|
|  7:  2.6370 -  2.5056  1267   142  0.91  15.13   0.99     0.96       5849.78|
|  8:  2.5056 -  2.3970  1271   137  0.92  14.01   0.99     0.98       4869.62|
|  9:  2.3970 -  2.3051  1248   142  0.92  14.39   1.01     0.98       4574.91|
| 10:  2.3051 -  2.2258  1275   139  0.91  14.73   1.00     0.96       3953.70|
| 11:  2.2258 -  2.1564  1248   138  0.91  15.14   1.00     0.97       4054.91|
| 12:  2.1564 -  2.0949  1252   139  0.91  14.75   1.01     1.00       3587.29|
| 13:  2.0949 -  2.0399  1250   139  0.92  14.52   1.00     0.99       3026.26|
| 14:  2.0399 -  1.9903   975   110  0.93  13.10   0.98     0.95       2304.98|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2304.98 max =         9897.70 mean =      5942.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.27|
|phase err.(test): min =        0.00 max =           89.31 mean =        12.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1522   ksol= 0.32   Bsol= 52.88   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.15,-0.62,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110198                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1522   ksol= 0.32   Bsol= 52.88   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.15,-0.62,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110198                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7490 0.99   1382  152 0.1004 0.1257      5.3896      5.5095|
|  2:  4.7490 -  3.7895 0.99   1312  151 0.0863 0.1138      5.4429       5.642|
|  3:  3.7895 -  3.3164 0.99   1299  141 0.1032 0.1472      5.4593      5.8324|
|  4:  3.3164 -  3.0159 0.99   1296  141 0.1164 0.1503      5.4151      5.5438|
|  5:  3.0159 -  2.8012 0.99   1269  144 0.1260 0.1643      5.2886      5.5217|
|  6:  2.8012 -  2.6370 0.99   1286  144 0.1157 0.1934      5.1801      5.4744|
|  7:  2.6370 -  2.5056 0.99   1267  142 0.1226 0.1540      5.1394      5.3085|
|  8:  2.5056 -  2.3970 0.98   1271  137 0.1118 0.1625      5.0394      5.2934|
|  9:  2.3970 -  2.3051 0.98   1248  142 0.1101 0.1693       4.983      5.2453|
| 10:  2.3051 -  2.2258 1.00   1275  139 0.1095 0.1634      4.9261      5.1938|
| 11:  2.2258 -  2.1564 0.97   1248  138 0.1080 0.1631      4.9003      5.1579|
| 12:  2.1564 -  2.0949 0.98   1252  139 0.1090 0.1646      4.8358      5.2184|
| 13:  2.0949 -  2.0399 0.99   1250  139 0.1032 0.1680      4.7426      5.0129|
| 14:  2.0399 -  1.9903 0.77    975  110 0.0977 0.1578      4.6217      4.8638|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7490  1382   152  0.94   9.14   0.98     0.95       7121.20|
|  2:  4.7490 -  3.7895  1312   151  0.95   7.86   1.01     1.00       8990.65|
|  3:  3.7895 -  3.3164  1299   141  0.94  10.81   1.02     1.01       9892.87|
|  4:  3.3164 -  3.0159  1296   141  0.93  12.66   1.00     0.98       9413.59|
|  5:  3.0159 -  2.8012  1269   144  0.91  14.86   1.00     0.97       7614.40|
|  6:  2.8012 -  2.6370  1286   144  0.90  15.38   0.99     0.96       6620.08|
|  7:  2.6370 -  2.5056  1267   142  0.91  15.13   0.99     0.96       5851.19|
|  8:  2.5056 -  2.3970  1271   137  0.92  14.01   0.99     0.98       4870.23|
|  9:  2.3970 -  2.3051  1248   142  0.92  14.39   1.01     0.98       4575.27|
| 10:  2.3051 -  2.2258  1275   139  0.91  14.73   1.00     0.96       3953.82|
| 11:  2.2258 -  2.1564  1248   138  0.91  15.14   1.00     0.97       4055.16|
| 12:  2.1564 -  2.0949  1252   139  0.91  14.76   1.01     1.00       3587.45|
| 13:  2.0949 -  2.0399  1250   139  0.92  14.52   1.00     0.99       3026.41|
| 14:  2.0399 -  1.9903   975   110  0.93  13.10   0.98     0.95       2305.15|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2305.15 max =         9892.87 mean =      5944.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.28|
|phase err.(test): min =        0.00 max =           89.32 mean =        12.83|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.79    79.57   16.38    None  None   None       |
|    all(noH): 2823   0      1.79    79.57   16.38    None  None   None       |
|    Sol.    : 438    0      6.37    73.26   37.07    None  None   None       |
|    Mac.    : 2385   0      1.79    79.57   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.791 -   9.569:  962   |   5:    40.682 -  48.460:   91        |
|      1:     9.569 -  17.347: 1121   |   6:    48.460 -  56.238:   74        |
|      2:    17.347 -  25.126:  264   |   7:    56.238 -  64.016:   28        |
|      3:    25.126 -  32.904:  130   |   8:    64.016 -  71.794:   19        |
|      4:    32.904 -  40.682:  131   |   9:    71.794 -  79.573:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 289         
Filter by distance & map next to the model:
   mapped sites are within: 0.430 - 4.765
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 289
   mapped sites are within: 0.702 - 4.765

peak=    5.976 closest distance to " NH2 ARG A  56 " =    2.194
peak=    5.487 closest distance to " CG  PRO A  54 " =    1.340
peak=    5.388 closest distance to " CB  ARG A 275 " =    0.910
peak=    5.301 closest distance to " O   HOH Z 232 " =    2.373
peak=    5.237 closest distance to " O   HOH Z 126 " =    1.838
peak=    5.195 closest distance to " NE2 GLN A  11 " =    1.148
peak=    5.146 closest distance to " O   HOH Z 142 " =    1.799
peak=    4.932 closest distance to " CB  GLN A 223 " =    1.455
peak=    4.783 closest distance to " CB  GLN A 183 " =    1.161
peak=    4.774 closest distance to " ND2 ASN A 187 " =    1.576
peak=    4.714 closest distance to " CB  ARG A  79 " =    1.340
peak=    4.714 closest distance to " CB  GLU A 152 " =    1.204
peak=    4.703 closest distance to " CB  SER A  63 " =    1.172
peak=    4.620 closest distance to " CG  PRO A 213 " =    1.235
peak=    4.442 closest distance to " O   HOH Z 236 " =    2.049
peak=    4.416 closest distance to " O   HOH Z 303 " =    2.076
peak=    4.397 closest distance to " O   HOH Z 250 " =    1.515
peak=    4.392 closest distance to " CB  ASN A 148 " =    1.524
peak=    4.384 closest distance to " CG2 VAL A 257 " =    0.906
peak=    4.360 closest distance to " O   HOH Z 369 " =    2.183
peak=    4.357 closest distance to " O   HOH Z 189 " =    2.497
peak=    4.341 closest distance to " CB  VAL A 265 " =    1.295
peak=    4.335 closest distance to " O   HOH Z 209 " =    2.292
peak=    4.320 closest distance to " O   HOH Z 427 " =    2.899
peak=    4.313 closest distance to " O   HOH Z  40 " =    1.677
peak=    4.299 closest distance to " CB  PRO A  54 " =    0.964
peak=    4.265 closest distance to " O   HOH Z  15 " =    2.170
peak=    4.248 closest distance to " O   HOH Z 158 " =    3.133
peak=    4.224 closest distance to " O   HOH Z 298 " =    1.872
peak=    4.218 closest distance to " O   HOH Z  61 " =    1.658
peak=    4.216 closest distance to " O   HOH Z 346 " =    1.670
peak=    4.212 closest distance to " C   PRO A 198 " =    1.442
peak=    4.209 closest distance to " O   SER A  87 " =    2.141
peak=    4.180 closest distance to " CZ  PHE A 218 " =    1.051
peak=    4.143 closest distance to " CB  ARG A 190 " =    1.632
peak=    4.142 closest distance to " CD2 TRP A 179 " =    1.287
peak=    4.127 closest distance to " O   HOH Z  78 " =    1.659
peak=    4.126 closest distance to " CA  TYR A  30 " =    0.908
peak=    4.104 closest distance to " O   HOH Z 272 " =    1.825
peak=    4.103 closest distance to " O   HOH Z 234 " =    3.686
peak=    4.067 closest distance to " CA  ASN A 215 " =    1.049
peak=    4.042 closest distance to " O   HOH Z 193 " =    1.921
peak=    4.040 closest distance to " O   HOH Z  66 " =    2.257
peak=    4.037 closest distance to " CB  SER A   3 " =    1.294
peak=    4.015 closest distance to " O   HOH Z 423 " =    1.936
peak=    4.011 closest distance to " CB  LEU A 228 " =    1.053
peak=    3.991 closest distance to " OD1 ASN A  69 " =    2.611
peak=    3.960 closest distance to " O   HOH Z 248 " =    1.592
peak=    3.954 closest distance to " O   HOH Z 368 " =    2.010
peak=    3.952 closest distance to " CB  GLU A  46 " =    0.972
peak=    3.932 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.930 closest distance to " O   HOH Z 406 " =    1.607
peak=    3.925 closest distance to " O   HOH Z 203 " =    1.695
peak=    3.922 closest distance to " CG  PRO A 198 " =    1.330
peak=    3.918 closest distance to " CG  PRO A 243 " =    1.103
peak=    3.913 closest distance to " OG ASER A 258 " =    3.115
peak=    3.901 closest distance to " O   HOH Z 392 " =    3.068
peak=    3.898 closest distance to " CB  VAL A 202 " =    1.533
peak=    3.894 closest distance to " NZ  LYS A 117 " =    3.163
peak=    3.886 closest distance to " CB  TYR A 169 " =    0.710
peak=    3.868 closest distance to " O   HOH Z 353 " =    2.578
peak=    3.867 closest distance to " O   HOH Z 313 " =    1.999
peak=    3.847 closest distance to " CB  ASP A 140 " =    0.909
peak=    3.838 closest distance to " O   HOH Z 261 " =    2.108
peak=    3.835 closest distance to " CB  TRP A 266 " =    1.010
peak=    3.823 closest distance to " CB  ASN A  39 " =    0.849
peak=    3.819 closest distance to " O   HOH Z 419 " =    2.080
peak=    3.816 closest distance to " CB  ASN A 142 " =    1.014
peak=    3.804 closest distance to " O   HOH Z  21 " =    1.814
peak=    3.770 closest distance to " O   HOH Z  43 " =    1.888
peak=    3.767 closest distance to " O   HOH Z  10 " =    1.831
peak=    3.753 closest distance to " O   HOH Z 128 " =    2.120
peak=    3.737 closest distance to " CB  GLU A 128 " =    0.905
peak=    3.725 closest distance to " O   HOH Z 132 " =    2.507
peak=    3.707 closest distance to " CD  ARG A 159 " =    0.702
peak=    3.704 closest distance to " CA  SER A  87 " =    0.970
peak=    3.702 closest distance to " CG2 ILE A 120 " =    1.170
peak=    3.681 closest distance to " O   HOH Z 291 " =    1.609
peak=    3.671 closest distance to " O   HOH Z 213 " =    1.980
peak=    3.670 closest distance to " O   HOH Z 234 " =    1.898
peak=    3.666 closest distance to " O   HOH Z  97 " =    2.566
peak=    3.660 closest distance to " O   HOH Z 402 " =    1.428
peak=    3.655 closest distance to " NH1AARG A 145 " =    1.230
peak=    3.651 closest distance to " O  BHOH Z 338 " =    2.376
peak=    3.646 closest distance to " O   HOH Z 214 " =    2.078
peak=    3.637 closest distance to " O   HOH Z   1 " =    1.998
peak=    3.614 closest distance to " O   HOH Z  59 " =    1.853
peak=    3.611 closest distance to " O   HOH Z 128 " =    2.134
peak=    3.611 closest distance to " OG BSER A 164 " =    2.372
peak=    3.600 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.596 closest distance to " CB  SER A 212 " =    1.141
peak=    3.590 closest distance to " CG2AVAL A  72 " =    1.631
peak=    3.590 closest distance to " O   HOH Z 389 " =    1.840
peak=    3.582 closest distance to " O   HOH Z 180 " =    2.151
peak=    3.582 closest distance to " CB  TYR A 169 " =    0.768
peak=    3.577 closest distance to " O   HOH Z  92 " =    2.517
peak=    3.573 closest distance to " O   HOH Z  44 " =    1.695
peak=    3.566 closest distance to " CB  GLN A  88 " =    1.154
peak=    3.552 closest distance to " O   HOH Z 417 " =    3.274
peak=    3.543 closest distance to " O   HOH Z 172 " =    3.186
peak=    3.541 closest distance to " O   HOH Z 403 " =    1.579
peak=    3.541 closest distance to " O   HOH Z   1 " =    1.663
peak=    3.537 closest distance to " O   HOH Z 294 " =    1.441
peak=    3.536 closest distance to " O   HOH Z 368 " =    3.534
peak=    3.535 closest distance to " O   HOH Z 273 " =    2.738
peak=    3.533 closest distance to " CG1 VAL A 153 " =    0.936
peak=    3.532 closest distance to " CD  LYS A 166 " =    1.208
peak=    3.530 closest distance to " CD1 LEU A 300 " =    1.260
peak=    3.524 closest distance to " CA  ASP A 162 " =    0.999
peak=    3.522 closest distance to " CA  THR A 264 " =    0.941
peak=    3.520 closest distance to " O   HOH Z 133 " =    2.625
peak=    3.513 closest distance to " CA  ALA A 233 " =    1.224
peak=    3.511 closest distance to " O   ASN A  74 " =    1.523
peak=    3.509 closest distance to " O   HOH Z  61 " =    1.498
peak=    3.509 closest distance to " CD  ARG A  66 " =    2.558
peak=    3.508 closest distance to " O   HOH Z 371 " =    2.900
peak=    3.506 closest distance to " O   HOH Z 325 " =    3.955
peak=    3.503 closest distance to " CB  GLU A 277 " =    3.560
peak=    3.503 closest distance to " CB  ASN A 110 " =    1.067
peak=    3.497 closest distance to " CB  ARG A 139 " =    1.004
peak=    3.496 closest distance to " N   PHE A 130 " =    1.316
peak=    3.495 closest distance to " O   HOH Z 305 " =    3.626
peak=    3.493 closest distance to " O   HOH Z 425 " =    1.995
peak=    3.491 closest distance to " O   HOH Z 193 " =    1.673
peak=    3.491 closest distance to " CD1 ILE A 106 " =    0.914
peak=    3.491 closest distance to " O   HOH Z 265 " =    2.363
peak=    3.490 closest distance to " CB  PRO A  90 " =    1.119
peak=    3.487 closest distance to " O   HOH Z 147 " =    1.791
peak=    3.480 closest distance to " O   HOH Z   9 " =    2.090
peak=    3.479 closest distance to " NE2 GLN A  73 " =    3.845
peak=    3.479 closest distance to " O   HOH Z 261 " =    1.644
peak=    3.476 closest distance to " CG2 ILE A  20 " =    1.471
peak=    3.470 closest distance to " O   HOH Z   3 " =    1.889
peak=    3.464 closest distance to " ND2 ASN A 110 " =    1.664
peak=    3.457 closest distance to " O   HOH Z 344 " =    3.207
peak=    3.453 closest distance to " N   ASN A  39 " =    1.228
peak=    3.443 closest distance to " CB  MET A  47 " =    1.100
peak=    3.441 closest distance to " CB  ILE A 120 " =    1.186
peak=    3.439 closest distance to " CA  ARG A  36 " =    0.978
peak=    3.437 closest distance to " CB  ALA A   9 " =    1.561
peak=    3.431 closest distance to " CD  ARG A 269 " =    0.907
peak=    3.431 closest distance to " O   HOH Z 175 " =    2.197
peak=    3.430 closest distance to " ND2 ASN A 249 " =    0.886
peak=    3.425 closest distance to " CB  TRP A 179 " =    1.410
peak=    3.425 closest distance to " O   HOH Z 148 " =    3.362
peak=    3.421 closest distance to " O   HOH Z 407 " =    2.311
peak=    3.417 closest distance to " CB  THR A  31 " =    1.612
peak=    3.413 closest distance to " O   HOH Z  85 " =    2.343
peak=    3.407 closest distance to " CA  ALA A  51 " =    0.903
peak=    3.403 closest distance to " O   HOH Z 433 " =    1.815
peak=    3.395 closest distance to " O   HOH Z  44 " =    2.996
peak=    3.393 closest distance to " O   HOH Z 193 " =    1.902
peak=    3.393 closest distance to " O   HOH Z 188 " =    1.992
peak=    3.392 closest distance to " CG AARG A 275 " =    1.129
peak=    3.392 closest distance to " O   HOH Z 173 " =    1.852
peak=    3.388 closest distance to " CB  ALA A 291 " =    1.262
peak=    3.382 closest distance to " CB  LEU A  83 " =    0.734
peak=    3.381 closest distance to " N   ARG A 156 " =    1.327
peak=    3.377 closest distance to " NE2 HIS A 207 " =    1.287
peak=    3.377 closest distance to " CB  SER A  62 " =    1.127
peak=    3.368 closest distance to " CA  TYR A 116 " =    1.339
peak=    3.367 closest distance to " N   TYR A 116 " =    1.550
peak=    3.362 closest distance to " O   HOH Z 245 " =    1.370
peak=    3.361 closest distance to " CA  ARG A 195 " =    1.150
peak=    3.356 closest distance to " O   HOH Z 371 " =    1.683
peak=    3.356 closest distance to " CA  ALA A  84 " =    1.252
peak=    3.354 closest distance to " O   HOH Z 337 " =    3.610
peak=    3.351 closest distance to " O   HOH Z 280 " =    3.032
peak=    3.347 closest distance to " CA  THR A 221 " =    1.000
peak=    3.345 closest distance to " CZ2 TRP A 179 " =    1.781
peak=    3.342 closest distance to " O   HOH Z  97 " =    1.922
peak=    3.342 closest distance to " O   HOH Z 285 " =    2.570
peak=    3.342 closest distance to " O   HOH Z 286 " =    2.293
peak=    3.341 closest distance to " O   HOH Z 365 " =    2.861
peak=    3.333 closest distance to " O   HOH Z  54 " =    1.593
peak=    3.333 closest distance to " CB  GLN A 103 " =    0.826
peak=    3.332 closest distance to " CB  GLN A  89 " =    1.368
peak=    3.326 closest distance to " NH2BARG A 145 " =    2.001
peak=    3.324 closest distance to " O   HOH Z  88 " =    2.635
peak=    3.323 closest distance to " CB  PHE A 204 " =    0.711
peak=    3.318 closest distance to " ND1 HIS A  86 " =    1.642
peak=    3.317 closest distance to " CG  MET A 185 " =    1.169
peak=    3.315 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.314 closest distance to " CD BLYS A 290 " =    1.064
peak=    3.307 closest distance to " NZ  LYS A  48 " =    1.231
peak=    3.298 closest distance to " NE2 GLN A  77 " =    3.194
peak=    3.295 closest distance to " CA  PHE A  59 " =    0.996
peak=    3.292 closest distance to " N   ASN A 127 " =    1.229
peak=    3.291 closest distance to " CB  ALA A  34 " =    1.092
peak=    3.290 closest distance to " O   HOH Z 116 " =    3.021
peak=    3.290 closest distance to " CB  LYS A 290 " =    0.961
peak=    3.288 closest distance to " O   ALA A 165 " =    1.560
peak=    3.288 closest distance to " OG1 THR A 294 " =    2.443
peak=    3.288 closest distance to " O   ALA A   1 " =    1.689
peak=    3.286 closest distance to " CG  LYS A  76 " =    0.934
peak=    3.285 closest distance to " O   HOH Z 359 " =    1.517
peak=    3.280 closest distance to " OH  TYR A 116 " =    1.060
peak=    3.275 closest distance to " CB  SER A  26 " =    1.643
peak=    3.265 closest distance to " O   HOH Z  88 " =    1.872
peak=    3.265 closest distance to " O   HOH Z 422 " =    2.613
peak=    3.261 closest distance to " O   SER A 164 " =    1.214
peak=    3.257 closest distance to " O   HOH Z  88 " =    2.505
peak=    3.257 closest distance to " O   HOH Z 435 " =    1.881
peak=    3.256 closest distance to " CA  ALA A  21 " =    1.099
peak=    3.250 closest distance to " CA  ALA A 291 " =    0.822
peak=    3.249 closest distance to " O   HOH Z   6 " =    2.132
peak=    3.248 closest distance to " NH1 ARG A 138 " =    1.208
peak=    3.245 closest distance to " O   HOH Z  66 " =    2.115
peak=    3.244 closest distance to " CB  GLN A 278 " =    0.833
peak=    3.243 closest distance to " CD1 ILE A 263 " =    1.298
peak=    3.242 closest distance to " O   HOH Z  96 " =    2.162
peak=    3.240 closest distance to " CB  TYR A 116 " =    0.805
peak=    3.238 closest distance to " O   HOH Z 257 " =    2.207
peak=    3.226 closest distance to " O   HOH Z  40 " =    1.813
peak=    3.224 closest distance to " CZ  PHE A  38 " =    1.297
peak=    3.223 closest distance to " CB  LEU A 300 " =    0.924
peak=    3.221 closest distance to " O   HOH Z 345 " =    3.336
peak=    3.219 closest distance to " N   GLN A 278 " =    1.180
peak=    3.218 closest distance to " NH2 ARG A 156 " =    1.148
peak=    3.217 closest distance to " O   HOH Z 162 " =    2.078
peak=    3.216 closest distance to " OE1 GLN A  11 " =    2.100
peak=    3.212 closest distance to " CB  ASN A 215 " =    1.097
peak=    3.211 closest distance to " CA  ASN A 217 " =    1.246
peak=    3.210 closest distance to " O   HOH Z 152 " =    2.111
peak=    3.209 closest distance to " CB  ALA A 248 " =    0.874
peak=    3.204 closest distance to " CE1 TYR A 186 " =    1.334
peak=    3.203 closest distance to " O   HOH Z 299 " =    4.431
peak=    3.201 closest distance to " CB  ALA A   1 " =    4.765
peak=    3.197 closest distance to " CB  ASP A 298 " =    1.169
peak=    3.197 closest distance to " O   ASN A 209 " =    1.253
peak=    3.194 closest distance to " O   HOH Z 185 " =    1.808
peak=    3.192 closest distance to " CB  HIS A 108 " =    0.762
peak=    3.186 closest distance to " CB  PRO A 243 " =    1.679
peak=    3.185 closest distance to " CB  THR A 157 " =    1.126
peak=    3.183 closest distance to " O   HOH Z 327 " =    1.647
peak=    3.181 closest distance to " CD2 TYR A 186 " =    1.007
peak=    3.178 closest distance to " N   ASP A 162 " =    1.219
peak=    3.170 closest distance to " CG2 THR A 221 " =    1.038
peak=    3.166 closest distance to " O   HOH Z 411 " =    3.783
peak=    3.166 closest distance to " O   HOH Z  85 " =    2.015
peak=    3.165 closest distance to " O   HOH Z 329 " =    3.967
peak=    3.164 closest distance to " O   HOH Z 261 " =    2.355
peak=    3.160 closest distance to " O   HOH Z  99 " =    1.850
peak=    3.158 closest distance to " O   PHE A 192 " =    1.374
peak=    3.157 closest distance to " CB  ALA A 291 " =    0.814
peak=    3.156 closest distance to " O   HOH Z 219 " =    1.830
peak=    3.152 closest distance to " O   HOH Z 371 " =    3.262
peak=    3.149 closest distance to " N   SER A 135 " =    1.268
peak=    3.144 closest distance to " O   HOH Z 187 " =    2.292
peak=    3.142 closest distance to " NH1BARG A 145 " =    1.209
peak=    3.139 closest distance to " O   HOH Z 233 " =    1.838
peak=    3.137 closest distance to " O   HOH Z 271 " =    2.150
peak=    3.135 closest distance to " OE2 GLU A  53 " =    2.120
peak=    3.132 closest distance to " CB  SER A  62 " =    0.836
peak=    3.129 closest distance to " CG  MET A 113 " =    1.164
peak=    3.128 closest distance to " CA  GLU A  46 " =    1.045
peak=    3.126 closest distance to " CG  GLN A 278 " =    1.258
peak=    3.126 closest distance to " CG  GLN A  77 " =    1.892
peak=    3.124 closest distance to " O   HOH Z 357 " =    1.886
peak=    3.122 closest distance to " O   HOH Z 426 " =    1.902
peak=    3.114 closest distance to " CG2 VAL A 197 " =    1.064
peak=    3.113 closest distance to " OD1BASN A 224 " =    2.382
peak=    3.111 closest distance to " CB  ARG A 138 " =    0.965
peak=    3.108 closest distance to " CA  ILE A 106 " =    0.789
peak=    3.107 closest distance to " CB  ALA A 114 " =    1.136
peak=    3.106 closest distance to " O   HOH Z 188 " =    2.428
peak=    3.105 closest distance to " OG1 THR A 294 " =    1.676
peak=    3.104 closest distance to " O   HOH Z  28 " =    1.796
peak=    3.104 closest distance to " O   HOH Z 336 " =    1.805
peak=    3.103 closest distance to " CG1 VAL A 189 " =    1.866
peak=    3.093 closest distance to " CG BARG A 102 " =    1.696
peak=    3.090 closest distance to " O   GLY A  75 " =    1.461
peak=    3.090 closest distance to " O   HOH Z 171 " =    2.017
peak=    3.086 closest distance to " O   HOH Z 141 " =    1.636
peak=    3.085 closest distance to " CB  SER A 216 " =    0.761
peak=    3.081 closest distance to " O   ALA A 292 " =    1.742
peak=    3.080 closest distance to " CD1 LEU A  96 " =    0.757
peak=    3.077 closest distance to " CA  SER A 146 " =    1.738
peak=    3.060 closest distance to " O   HOH Z 291 " =    1.901
peak=    3.046 closest distance to " CA  ALA A 299 " =    0.908
peak=    3.028 closest distance to " CB  ALA A 114 " =    1.187

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.675 - 5.959
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 185
   mapped sites are within: 0.708 - 5.959

peak=   -4.561 closest distance to " CB  PRO A 243 " =    2.683
peak=   -4.545 closest distance to " CD  ARG A 156 " =    2.052
peak=   -4.413 closest distance to " O   VAL A  67 " =    2.657
peak=   -4.408 closest distance to " O   HOH Z 266 " =    5.209
peak=   -4.400 closest distance to " SG  CYS A 254 " =    3.495
peak=   -4.372 closest distance to " CD  GLN A  58 " =    0.978
peak=   -4.357 closest distance to " O   HOH Z 290 " =    1.132
peak=   -4.291 closest distance to " CG  GLN A 223 " =    1.838
peak=   -4.269 closest distance to " OG BSER A 134 " =    1.277
peak=   -4.214 closest distance to " C   HIS A 108 " =    1.174
peak=   -4.098 closest distance to " O   HOH Z 377 " =    2.052
peak=   -4.052 closest distance to " CD2 PHE A 192 " =    2.021
peak=   -4.021 closest distance to " CZ3 TRP A 179 " =    1.177
peak=   -4.018 closest distance to " ND2 ASN A  45 " =    1.762
peak=   -4.011 closest distance to " O   PRO A 198 " =    1.235
peak=   -4.003 closest distance to " O   HOH Z 313 " =    1.908
peak=   -3.997 closest distance to " CG1 VAL A  67 " =    2.861
peak=   -3.984 closest distance to " O   HOH Z 231 " =    2.323
peak=   -3.876 closest distance to " CB  ALA A 161 " =    2.571
peak=   -3.860 closest distance to " CD1 PHE A  59 " =    2.007
peak=   -3.859 closest distance to " OG  SER A  97 " =    2.235
peak=   -3.848 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.840 closest distance to " CG1 VAL A 112 " =    2.826
peak=   -3.838 closest distance to " OD1 ASP A 171 " =    1.698
peak=   -3.826 closest distance to " N   ALA A  43 " =    2.554
peak=   -3.821 closest distance to " O   HOH Z 211 " =    1.680
peak=   -3.802 closest distance to " CB  ALA A 291 " =    2.160
peak=   -3.786 closest distance to " CB  ALA A 248 " =    2.399
peak=   -3.769 closest distance to " O   HOH Z 407 " =    3.043
peak=   -3.761 closest distance to " CB  ASN A  39 " =    2.262
peak=   -3.758 closest distance to " O   HOH Z 372 " =    2.377
peak=   -3.721 closest distance to " CD1 LEU A 101 " =    2.276
peak=   -3.707 closest distance to " O   HOH Z 389 " =    1.996
peak=   -3.699 closest distance to " O   HOH Z 198 " =    1.864
peak=   -3.695 closest distance to " O   HOH Z 185 " =    2.325
peak=   -3.695 closest distance to " CE2 TYR A  30 " =    2.792
peak=   -3.689 closest distance to " N   GLN A  58 " =    1.656
peak=   -3.678 closest distance to " N   ALA A 248 " =    1.697
peak=   -3.677 closest distance to " CG2 ILE A 263 " =    2.265
peak=   -3.675 closest distance to " CG  ASP A 231 " =    0.750
peak=   -3.664 closest distance to " CE  MET A 105 " =    2.383
peak=   -3.642 closest distance to " CD  ARG A 139 " =    1.647
peak=   -3.631 closest distance to " NE2 GLN A 278 " =    1.712
peak=   -3.624 closest distance to " OXT GLY A 302 " =    2.787
peak=   -3.617 closest distance to " CD1 LEU A 255 " =    2.870
peak=   -3.614 closest distance to " O   HOH Z 114 " =    3.073
peak=   -3.607 closest distance to " O   VAL A 189 " =    2.576
peak=   -3.605 closest distance to " CB  ALA A 248 " =    2.172
peak=   -3.597 closest distance to " CB  ALA A 291 " =    2.221
peak=   -3.595 closest distance to " CB  ALA A  43 " =    2.493
peak=   -3.577 closest distance to " O   PRO A 163 " =    2.060
peak=   -3.575 closest distance to " O   HOH Z  10 " =    1.436
peak=   -3.575 closest distance to " O   HOH Z 394 " =    1.413
peak=   -3.539 closest distance to " CB  PRO A 163 " =    2.503
peak=   -3.528 closest distance to " CZ  TYR A 169 " =    1.759
peak=   -3.527 closest distance to " N   SER A 212 " =    2.052
peak=   -3.526 closest distance to " NH2 ARG A  79 " =    1.564
peak=   -3.526 closest distance to " ND2 ASN A 187 " =    1.395
peak=   -3.522 closest distance to " O   SER A  95 " =    1.538
peak=   -3.509 closest distance to " O   HOH Z  60 " =    2.188
peak=   -3.501 closest distance to " ND2 ASN A 249 " =    2.186
peak=   -3.497 closest distance to " O   GLN A 240 " =    2.108
peak=   -3.493 closest distance to " CG1 VAL A 112 " =    2.611
peak=   -3.492 closest distance to " O   HOH Z  38 " =    1.538
peak=   -3.477 closest distance to " OD2 ASP A 171 " =    2.346
peak=   -3.467 closest distance to " CG  PHE A 283 " =    2.607
peak=   -3.465 closest distance to " CB  PHE A 208 " =    2.262
peak=   -3.447 closest distance to " O   HOH Z 196 " =    2.082
peak=   -3.446 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.445 closest distance to " OD1 ASN A 148 " =    1.546
peak=   -3.445 closest distance to " CB  ASP A 132 " =    2.266
peak=   -3.445 closest distance to " NH2 ARG A 159 " =    2.409
peak=   -3.444 closest distance to " O   ALA A 161 " =    1.714
peak=   -3.443 closest distance to " C   MET A 188 " =    1.391
peak=   -3.442 closest distance to " NH2AARG A 275 " =    5.236
peak=   -3.437 closest distance to " O   TYR A 247 " =    2.851
peak=   -3.435 closest distance to " O   HOH Z  63 " =    1.671
peak=   -3.433 closest distance to " O   VAL A 189 " =    1.604
peak=   -3.432 closest distance to " CE2 PHE A 218 " =    2.420
peak=   -3.430 closest distance to " C   ALA A 158 " =    1.439
peak=   -3.415 closest distance to " CG  GLU A 277 " =    1.266
peak=   -3.410 closest distance to " CE BMET A  47 " =    1.401
peak=   -3.408 closest distance to " OG BSER A 134 " =    1.781
peak=   -3.404 closest distance to " CG2 THR A 178 " =    2.274
peak=   -3.402 closest distance to " CD1 ILE A 239 " =    2.361
peak=   -3.402 closest distance to " CE3 TRP A 274 " =    1.103
peak=   -3.400 closest distance to " O   HOH Z  13 " =    1.608
peak=   -3.389 closest distance to " N   GLY A  23 " =    2.435
peak=   -3.388 closest distance to " CE2 PHE A  61 " =    2.621
peak=   -3.387 closest distance to " NE2 GLN A 194 " =    1.824
peak=   -3.387 closest distance to " O   HOH Z 353 " =    2.220
peak=   -3.379 closest distance to " O   ALA A  10 " =    1.629
peak=   -3.377 closest distance to " N   THR A 157 " =    1.512
peak=   -3.375 closest distance to " O   HOH Z  11 " =    1.706
peak=   -3.372 closest distance to " CD  GLN A  88 " =    0.823
peak=   -3.371 closest distance to " O   HOH Z 243 " =    1.919
peak=   -3.371 closest distance to " CA  GLY A 241 " =    3.273
peak=   -3.366 closest distance to " CA  GLY A 203 " =    2.396
peak=   -3.363 closest distance to " O   HOH Z  73 " =    2.361
peak=   -3.355 closest distance to " CD2 TYR A 293 " =    2.039
peak=   -3.347 closest distance to " C   LEU A 143 " =    1.011
peak=   -3.342 closest distance to " CA  ASP A 298 " =    1.124
peak=   -3.338 closest distance to " O   PRO A 198 " =    1.256
peak=   -3.337 closest distance to " CB  ASP A 286 " =    1.780
peak=   -3.330 closest distance to " O   HOH Z 359 " =    3.172
peak=   -3.328 closest distance to " CD1 ILE A 199 " =    2.503
peak=   -3.323 closest distance to " N   MET A 188 " =    1.926
peak=   -3.315 closest distance to " OD2 ASP A 191 " =    1.379
peak=   -3.312 closest distance to " O   PRO A 198 " =    1.590
peak=   -3.310 closest distance to " CA  GLY A 133 " =    2.039
peak=   -3.309 closest distance to " N   THR A  52 " =    1.703
peak=   -3.308 closest distance to " N   ASP A 286 " =    2.372
peak=   -3.306 closest distance to " O   HOH Z 298 " =    1.304
peak=   -3.302 closest distance to " O   PHE A 218 " =    1.659
peak=   -3.299 closest distance to " O   HOH Z 421 " =    3.078
peak=   -3.298 closest distance to " NE2 GLN A 103 " =    1.640
peak=   -3.298 closest distance to " CG2 VAL A 189 " =    1.977
peak=   -3.297 closest distance to " O   HOH Z 362 " =    5.959
peak=   -3.295 closest distance to " O   HOH Z 174 " =    4.208
peak=   -3.295 closest distance to " O   ALA A 292 " =    2.054
peak=   -3.294 closest distance to " CG  GLU A 152 " =    0.791
peak=   -3.292 closest distance to " O   HOH Z 395 " =    5.233
peak=   -3.287 closest distance to " O   HOH Z 253 " =    3.862
peak=   -3.275 closest distance to " OE1 GLN A  88 " =    1.213
peak=   -3.274 closest distance to " O   HOH Z 102 " =    1.537
peak=   -3.268 closest distance to " CD  GLN A 223 " =    0.708
peak=   -3.266 closest distance to " CB  TYR A  15 " =    2.189
peak=   -3.264 closest distance to " O   HOH Z 311 " =    3.700
peak=   -3.257 closest distance to " CG1 VAL A  67 " =    3.179
peak=   -3.257 closest distance to " O   LEU A 101 " =    2.710
peak=   -3.254 closest distance to " O   ARG A 145 " =    1.530
peak=   -3.251 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -3.251 closest distance to " C   GLY A 262 " =    1.869
peak=   -3.250 closest distance to " O   HOH Z 357 " =    2.023
peak=   -3.250 closest distance to " CG  TRP A 266 " =    1.925
peak=   -3.248 closest distance to " O   HOH Z 377 " =    0.980
peak=   -3.232 closest distance to " CG  LEU A  83 " =    1.903
peak=   -3.220 closest distance to " CB  ALA A 114 " =    2.592
peak=   -3.215 closest distance to " NH2 ARG A  79 " =    2.050
peak=   -3.212 closest distance to " CD1 LEU A 297 " =    2.388
peak=   -3.211 closest distance to " CG  ARG A  66 " =    2.296
peak=   -3.210 closest distance to " ND2 ASN A  60 " =    1.276
peak=   -3.205 closest distance to " CG1 VAL A 197 " =    2.286
peak=   -3.205 closest distance to " O   ALA A 248 " =    1.774
peak=   -3.204 closest distance to " CB  ASP A 132 " =    2.416
peak=   -3.199 closest distance to " O   VAL A 174 " =    2.127
peak=   -3.198 closest distance to " CE  LYS A  76 " =    2.792
peak=   -3.197 closest distance to " CG  ARG A 269 " =    2.586
peak=   -3.196 closest distance to " CE3 TRP A 150 " =    2.100
peak=   -3.195 closest distance to " CA  TRP A 274 " =    1.300
peak=   -3.194 closest distance to " CG2 ILE A  20 " =    2.799
peak=   -3.190 closest distance to " O   ALA A  51 " =    1.340
peak=   -3.187 closest distance to " O   HOH Z 266 " =    4.984
peak=   -3.176 closest distance to " NH2BARG A 275 " =    1.925
peak=   -3.174 closest distance to " O   SER A 135 " =    1.452
peak=   -3.171 closest distance to " O   HOH Z 371 " =    1.604
peak=   -3.169 closest distance to " CA  ILE A 263 " =    1.048
peak=   -3.167 closest distance to " O   SER A 276 " =    1.719
peak=   -3.166 closest distance to " CB  GLN A  11 " =    1.774
peak=   -3.155 closest distance to " O   HOH Z 281 " =    2.751
peak=   -3.150 closest distance to " O   HOH Z  89 " =    2.912
peak=   -3.144 closest distance to " O   GLY A  80 " =    2.487
peak=   -3.138 closest distance to " C   ALA A 114 " =    2.379
peak=   -3.136 closest distance to " O   HOH Z  43 " =    1.746
peak=   -3.135 closest distance to " CG1 VAL A 125 " =    1.860
peak=   -3.131 closest distance to " O   LYS A 289 " =    2.935
peak=   -3.130 closest distance to " SD  MET A 105 " =    1.008
peak=   -3.121 closest distance to " O   HOH Z 166 " =    2.082
peak=   -3.121 closest distance to " O   HOH Z  52 " =    1.285
peak=   -3.116 closest distance to " O   HOH Z  51 " =    1.269
peak=   -3.108 closest distance to " O   HOH Z 134 " =    3.198
peak=   -3.102 closest distance to " OE2 GLU A 152 " =    1.216
peak=   -3.097 closest distance to " CD1 TRP A  70 " =    1.076
peak=   -3.096 closest distance to " OD1 ASN A 187 " =    1.547
peak=   -3.094 closest distance to " CG2 THR A 221 " =    2.245
peak=   -3.094 closest distance to " CD1 LEU A 228 " =    2.165
peak=   -3.091 closest distance to " CB  TRP A  85 " =    2.565
peak=   -3.086 closest distance to " O   HOH Z 111 " =    1.907
peak=   -3.076 closest distance to " N   SER A 276 " =    1.253
peak=   -3.062 closest distance to " O   HOH Z 288 " =    1.385
peak=   -3.058 closest distance to " OD1AASN A 224 " =    1.787
peak=   -3.042 closest distance to " SG ACYS A 201 " =    1.728
peak=   -3.028 closest distance to " CA  GLY A 241 " =    2.835
peak=   -3.023 closest distance to " CE  LYS A  76 " =    2.852

================= 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    :  0.2687 0.2652   5.873272e+00   5.852590e+00
   1_bss:  0.2519 0.2485   5.838914e+00   5.809677e+00
   1_xyz:  0.1475 0.1684   5.326680e+00   5.432410e+00
   1_adp:  0.1360 0.1716   5.277504e+00   5.460523e+00
   1_occ:  0.1356 0.1714   5.275756e+00   5.459629e+00
   2_bss:  0.1353 0.1707   5.275669e+00   5.457084e+00
   2_xyz:  0.1205 0.1550   5.175996e+00   5.371827e+00
   2_adp:  0.1170 0.1544   5.158058e+00   5.367335e+00
   2_occ:  0.1169 0.1544   5.157636e+00   5.367126e+00
   3_bss:  0.1168 0.1543   5.157349e+00   5.367032e+00
   3_xyz:  0.1117 0.1527   5.129783e+00   5.361040e+00
   3_adp:  0.1100 0.1537   5.123950e+00   5.364853e+00
   3_occ:  0.1099 0.1537   5.123959e+00   5.365073e+00
   4_bss:  0.1098 0.1535   5.123786e+00   5.364894e+00
   4_xyz:  0.1081 0.1549   5.120761e+00   5.372861e+00
   4_adp:  0.1098 0.1523   5.118207e+00   5.354614e+00
   4_occ:  0.1097 0.1523   5.118116e+00   5.355154e+00
   5_bss:  0.1098 0.1517   5.116595e+00   5.351281e+00
   5_xyz:  0.1079 0.1516   5.106478e+00   5.349436e+00
   5_adp:  0.1081 0.1522   5.110192e+00   5.355468e+00
   5_occ:  0.1080 0.1521   5.110116e+00   5.355498e+00
   5_bss:  0.1080 0.1522   5.110198e+00   5.355592e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.333  50.000  -2.900  -2.055   0.572  -0.000   0.000   0.000
   1_xyz:  0.333  50.000  -2.900  -2.055   0.572  -0.000   0.000   0.000
   1_adp:  0.333  50.000  -2.900  -2.055   0.572  -0.000   0.000   0.000
   1_occ:  0.333  50.000  -2.900  -2.055   0.572  -0.000   0.000   0.000
   2_bss:  0.329  52.943  -3.156  -2.624  -0.808  -0.000  -0.000  -0.000
   2_xyz:  0.329  52.943  -3.156  -2.624  -0.808  -0.000  -0.000  -0.000
   2_adp:  0.329  52.943  -3.156  -2.624  -0.808  -0.000  -0.000  -0.000
   2_occ:  0.329  52.943  -3.156  -2.624  -0.808  -0.000  -0.000  -0.000
   3_bss:  0.329  52.943  -2.901  -2.492  -0.875  -0.000  -0.000  -0.000
   3_xyz:  0.329  52.943  -2.901  -2.492  -0.875  -0.000  -0.000  -0.000
   3_adp:  0.329  52.943  -2.901  -2.492  -0.875  -0.000  -0.000  -0.000
   3_occ:  0.329  52.943  -2.901  -2.492  -0.875  -0.000  -0.000  -0.000
   4_bss:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   4_xyz:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   4_adp:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   4_occ:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   5_bss:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   5_xyz:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   5_adp:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   5_occ:  0.322  52.943  -2.581  -2.216  -0.690  -0.000  -0.000  -0.000
   5_bss:  0.325  52.877  -2.514  -2.149  -0.623  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  25.319 0.8123  0.9716    18684.988
   1_bss:  23.802 0.8258  0.9392    15595.296
   1_xyz:  14.944 0.9077  0.9989     7056.435
   1_adp:  15.519 0.9025  0.9962     7387.199
   1_occ:  15.496 0.9027  0.9960     7360.494
   2_bss:  15.410 0.9035  0.9709     7350.122
   2_xyz:  13.634 0.9180  0.9749     6111.941
   2_adp:  13.565 0.9186  0.9699     6044.684
   2_occ:  13.566 0.9186  0.9697     6038.432
   3_bss:  13.560 0.9187  0.9737     6039.409
   3_xyz:  13.367 0.9203  0.9756     5990.700
   3_adp:  13.458 0.9196  0.9688     6006.397
   3_occ:  13.462 0.9196  0.9687     6008.766
   4_bss:  13.459 0.9196  0.9779     6005.498
   4_xyz:  13.603 0.9185  0.9771     6134.262
   4_adp:  13.243 0.9212  0.9808     5944.937
   4_occ:  13.250 0.9211  0.9807     5951.325
   5_bss:  13.205 0.9214  0.9806     5873.961
   5_xyz:  13.143 0.9219  0.9815     5873.076
   5_adp:  13.228 0.9213  0.9765     5943.885
   5_occ:  13.229 0.9213  0.9764     5942.161
   5_bss:  13.231 0.9213  0.9764     5944.329
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6187e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6187e-01
   1_xyz:   0.982  0.007  0.070 15.343  0.004  4.113   5.8736e-02
   1_adp:   0.982  0.007  0.070 15.343  0.004  4.113   5.8736e-02
   1_occ:   0.982  0.007  0.070 15.343  0.004  4.113   5.8736e-02
   2_bss:   0.982  0.007  0.070 15.343  0.004  4.113   5.8736e-02
   2_xyz:   0.885  0.005  0.069 14.797  0.003  4.115   4.9728e-02
   2_adp:   0.885  0.005  0.069 14.797  0.003  4.115   4.9728e-02
   2_occ:   0.885  0.005  0.069 14.797  0.003  4.115   4.9728e-02
   3_bss:   0.885  0.005  0.069 14.797  0.003  4.115   4.9728e-02
   3_xyz:   0.940  0.007  0.074 14.856  0.003  4.121   5.5029e-02
   3_adp:   0.940  0.007  0.074 14.856  0.003  4.121   5.5029e-02
   3_occ:   0.940  0.007  0.074 14.856  0.003  4.121   5.5029e-02
   4_bss:   0.940  0.007  0.074 14.856  0.003  4.121   5.5029e-02
   4_xyz:   0.961  0.007  0.076 14.818  0.004  4.122   5.7662e-02
   4_adp:   0.961  0.007  0.076 14.818  0.004  4.122   5.7662e-02
   4_occ:   0.961  0.007  0.076 14.818  0.004  4.122   5.7662e-02
   5_bss:   0.961  0.007  0.076 14.818  0.004  4.122   5.7662e-02
   5_xyz:   1.007  0.008  0.079 14.867  0.004  4.124   6.2058e-02
   5_adp:   1.007  0.008  0.079 14.867  0.004  4.124   6.2058e-02
   5_occ:   1.007  0.008  0.079 14.867  0.004  4.124   6.2058e-02
   5_bss:   1.007  0.008  0.079 14.867  0.004  4.124   6.2058e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4092e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4092e-01
   1_xyz:   6.817  0.038  0.236 83.522  0.037  2.250   4.5668e-02
   1_adp:   6.817  0.038  0.236 83.522  0.037  2.250   4.5668e-02
   1_occ:   6.817  0.038  0.236 83.522  0.037  2.250   4.5668e-02
   2_bss:   6.817  0.038  0.236 83.522  0.037  2.250   4.5668e-02
   2_xyz:   6.540  0.039  0.213 81.737  0.031  2.394   3.3517e-02
   2_adp:   6.540  0.039  0.213 81.737  0.031  2.394   3.3517e-02
   2_occ:   6.540  0.039  0.213 81.737  0.031  2.394   3.3517e-02
   3_bss:   6.540  0.039  0.213 81.737  0.031  2.394   3.3517e-02
   3_xyz:   6.380  0.041  0.245 83.771  0.033  2.356   3.5179e-02
   3_adp:   6.380  0.041  0.245 83.771  0.033  2.356   3.5179e-02
   3_occ:   6.380  0.041  0.245 83.771  0.033  2.356   3.5179e-02
   4_bss:   6.380  0.041  0.245 83.771  0.033  2.356   3.5179e-02
   4_xyz:   6.226  0.048  0.245 82.452  0.035  2.365   4.2225e-02
   4_adp:   6.226  0.048  0.245 82.452  0.035  2.365   4.2225e-02
   4_occ:   6.226  0.048  0.245 82.452  0.035  2.365   4.2225e-02
   5_bss:   6.226  0.048  0.245 82.452  0.035  2.365   4.2225e-02
   5_xyz:   6.754  0.049  0.256 83.902  0.035  2.313   4.5694e-02
   5_adp:   6.754  0.049  0.256 83.902  0.035  2.313   4.5694e-02
   5_occ:   6.754  0.049  0.256 83.902  0.035  2.313   4.5694e-02
   5_bss:   6.754  0.049  0.256 83.902  0.035  2.313   4.5694e-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:  71.49   0.00  16.46  71.49   0.00  12.65  62.79   7.28  37.22
   1_occ:  71.49   0.00  16.46  71.49   0.00  12.65  62.79   7.28  37.22
   2_bss:  71.49   0.00  16.46  71.49   0.00  12.65  62.79   7.28  37.22
   2_xyz:  71.49   0.00  16.46  71.49   0.00  12.65  62.79   7.28  37.22
   2_adp:  65.30   1.53  16.65  59.54   1.53  12.79  65.30   5.95  37.64
   2_occ:  65.30   1.53  16.65  59.54   1.53  12.79  65.30   5.95  37.64
   3_bss:  65.30   1.53  16.65  59.54   1.53  12.79  65.30   5.95  37.64
   3_xyz:  65.30   1.53  16.65  59.54   1.53  12.79  65.30   5.95  37.64
   3_adp:  82.34   0.56  17.20  82.34   0.56  12.95  75.94   4.89  40.36
   3_occ:  82.34   0.56  17.20  82.34   0.56  12.95  75.94   4.89  40.36
   4_bss:  82.34   0.56  17.20  82.34   0.56  12.95  75.94   4.89  40.36
   4_xyz:  82.34   0.56  17.20  82.34   0.56  12.95  75.94   4.89  40.36
   4_adp:  81.72   0.00  17.05  81.72   0.00  12.93  74.58   6.39  39.49
   4_occ:  81.72   0.00  17.05  81.72   0.00  12.93  74.58   6.39  39.49
   5_bss:  81.72   0.00  17.05  81.72   0.00  12.93  74.58   6.39  39.49
   5_xyz:  81.72   0.00  17.05  81.72   0.00  12.93  74.58   6.39  39.49
   5_adp:  79.64   1.86  16.45  79.64   1.86  12.65  73.33   6.44  37.13
   5_occ:  79.64   1.86  16.45  79.64   1.86  12.65  73.33   6.44  37.13
   5_bss:  79.57   1.79  16.38  79.57   1.79  12.59  73.26   6.37  37.07
------------------------------------------------------------------------
 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:    0.677    0.009    0.233
   1_adp:    0.677    0.009    0.233
   1_occ:    0.677    0.009    0.233
   2_bss:    0.677    0.009    0.233
   2_xyz:    0.730    0.015    0.258
   2_adp:    0.730    0.015    0.258
   2_occ:    0.730    0.015    0.258
   3_bss:    0.730    0.015    0.258
   3_xyz:    1.093    0.020    0.282
   3_adp:    1.093    0.020    0.282
   3_occ:    1.093    0.020    0.282
   4_bss:    1.093    0.020    0.282
   4_xyz:    1.180    0.033    0.288
   4_adp:    1.180    0.033    0.288
   4_occ:    1.180    0.033    0.288
   5_bss:    1.180    0.033    0.288
   5_xyz:    1.223    0.016    0.294
   5_adp:    1.223    0.016    0.294
   5_occ:    1.223    0.016    0.294
   5_bss:    1.223    0.016    0.294
------------------------------------------------------------------------

CPU time actual refinement: 259.81


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_535/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_535/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_535/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_535/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_535/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 259.69 
  Macro-tasks:
    bulk solvent and scale       = 30.06  
    individual site refinement   = 102.40 
    weights calculation          = 24.43  
    collect and process          = 5.44   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 162.41 
  Micro-tasks:
    mask                            = 0.98   
    f_calc                          = 82.40  
    alpha_beta                      = 7.01   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 89.44  
    fmodel                         = 5.22   
    r_factors                      = 0.22   
    phase_errors                   = 9.10   
    foms                           = 0.16   
    TOTAL for micro-tasks          = 195.52 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.778 micro seconds
Total CPU time: 4.52 minutes
from_scatterers_fft:    625 calls, 82.12 s
gradients_fft:          570 calls, 78.43 s

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

# Date 2008-01-16 Time 05:02:08 PST -0800 (1200488528.56 s)
Start R-work = 0.2687, R-free = 0.2652 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1730 (no bulk solvent and anisotropic scale)

Start R-work = 0.2519, R-free = 0.2485
Final R-work = 0.1080, R-free = 0.1522