# Date 2008-01-16 Time 05:30:35 PST -0800 (1200490235.25 s)
#phil __OFF__

Command line arguments: "../763.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6792
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 763

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.4607, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.98157
Completeness in resolution range: 0.96865
Completeness with d_max=infinity: 0.965689

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9816

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.98157
Completeness in resolution range: 0.96865
Completeness with d_max=infinity: 0.965689

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2402 [2115/2140]  1905   210   9.9%
  bin  2:  4.2402 -  3.3781 [2042/2062]  1836   206  10.1%
  bin  3:  3.3781 -  2.9548 [2018/2037]  1815   203  10.1%
  bin  4:  2.9548 -  2.6863 [2003/2033]  1810   193   9.6%
  bin  5:  2.6863 -  2.4947 [1984/2003]  1785   199  10.0%
  bin  6:  2.4947 -  2.3482 [1968/1993]  1763   205  10.4%
  bin  7:  2.3482 -  2.2310 [1947/1975]  1752   195  10.0%
  bin  8:  2.2310 -  2.1342 [1975/2011]  1778   197  10.0%
  bin  9:  2.1342 -  2.0522 [1953/1995]  1762   191   9.8%
  bin 10:  2.0522 -  1.9816 [1584/1974]  1424   160  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_763/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 16
        2.42 -     3.04: 2202
        3.04 -     3.66: 4714
        3.66 -     4.28: 9117
        4.28 -     4.90: 12360
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.273 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.313 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28404 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_763/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_763/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.4607 85.95805 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: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2922   r_free= 0.2891   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.964132                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7293 0.99   1386  154 0.2740 0.2677      6.3184      6.2598|
|  2:  4.7293 -  3.7734 0.99   1324  146 0.2303 0.2225      6.3475      6.2919|
|  3:  3.7734 -  3.3022 0.99   1300  143 0.2399 0.2301      6.2187      6.3313|
|  4:  3.3022 -  3.0029 0.99   1285  148 0.2602 0.2886      6.1395      6.1787|
|  5:  3.0029 -  2.7891 0.99   1292  141 0.2941 0.2674      6.0123       5.963|
|  6:  2.7891 -  2.6256 0.99   1281  141 0.2960 0.3023      5.9457      5.8895|
|  7:  2.6256 -  2.4947 0.99   1283  138 0.3087 0.2806      5.9181      5.8864|
|  8:  2.4947 -  2.3866 0.98   1253  147 0.3156 0.3193      5.8893      5.9088|
|  9:  2.3866 -  2.2950 0.98   1269  138 0.3144 0.3149      5.8315      5.7947|
| 10:  2.2950 -  2.2161 1.00   1266  142 0.3272 0.3100      5.8309      5.7521|
| 11:  2.2161 -  2.1470 0.97   1249  137 0.3367 0.3339      5.8093      5.8203|
| 12:  2.1470 -  2.0858 0.98   1256  141 0.3377 0.3368      5.7564      5.7836|
| 13:  2.0858 -  2.0310 0.99   1283  140 0.3395 0.3616      5.6544       5.633|
| 14:  2.0310 -  1.9816 0.72    903  103 0.3642 0.3548       5.685       5.579|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0283 -  4.7293  1386   154  0.81  24.46   0.87     0.83      37955.52|
|  2:  4.7293 -  3.7734  1324   146  0.86  19.91   0.98     0.94      38413.55|
|  3:  3.7734 -  3.3022  1300   143  0.83  22.97   1.02     0.99      36549.81|
|  4:  3.3022 -  3.0029  1285   148  0.82  24.79   1.01     0.98      31613.51|
|  5:  3.0029 -  2.7891  1292   141  0.78  28.25   1.00     0.96      25614.76|
|  6:  2.7891 -  2.6256  1281   141  0.79  28.04   1.01     0.96      21486.32|
|  7:  2.6256 -  2.4947  1283   138  0.78  29.01   1.03     0.97      19806.11|
|  8:  2.4947 -  2.3866  1253   147  0.77  29.55   1.03     0.97      18636.71|
|  9:  2.3866 -  2.2950  1269   138  0.77  29.56   1.04     0.98      17557.16|
| 10:  2.2950 -  2.2161  1266   142  0.76  30.78   1.06     1.00      16797.54|
| 11:  2.2161 -  2.1470  1249   137  0.74  32.77   1.07     1.00      16888.30|
| 12:  2.1470 -  2.0858  1256   141  0.73  33.36   1.08     0.98      16207.21|
| 13:  2.0858 -  2.0310  1283   140  0.70  36.15   1.07     0.95      14607.86|
| 14:  2.0310 -  1.9816   903   103  0.72  34.52   1.06     0.93      12043.31|
|alpha:            min =        0.83 max =            1.00 mean =         0.96|
|beta:             min =    12043.31 max =        38413.55 mean =     23573.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.78|
|phase err.(work): min =        0.00 max =           89.95 mean =        28.67|
|phase err.(test): min =        0.00 max =           89.97 mean =        28.45|
|-----------------------------------------------------------------------------|

============================== 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 = 3.491743              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.165   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.577322              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.797   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      208 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1994 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1874 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2840 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4667 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4450 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5618 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6742 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.159 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    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: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2922   r_free= 0.2891   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.964132                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2766   r_free= 0.2747   ksol= 0.33   Bsol= 44.44   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,0.11,-1.54,0.00,-0.00,-0.00); trace/3= -1.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.940079                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.104394              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.353   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284225              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.709   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2766      final r-factor (work) = 0.1619          |
| start r-factor (free) = 0.2747      final r-factor (free) = 0.1839          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4073 = 3.10 * 0.50 * 5.9571 + 1.00 * 0.1607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7841 = 3.10 * 0.50 * 5.6213 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1619      final r-factor (work) = 0.1501          |
| start r-factor (free) = 0.1839      final r-factor (free) = 0.1890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6038 = 0.28 * 1.00 * 5.6213 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5463 = 0.28 * 1.00 * 5.3643 + 1.00 * 0.0216                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.36   16.48    None  None   None       |
|    all(noH): 2823   0      0.00    62.36   16.48    None  None   None       |
|    Sol.    : 438    0      7.19    62.36   37.41    None  None   None       |
|    Mac.    : 2385   0      0.00    52.18   12.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.236:  188   |   5:    31.179 -  37.415:  104        |
|      1:     6.236 -  12.472: 1267   |   6:    37.415 -  43.651:  100        |
|      2:    12.472 -  18.708:  680   |   7:    43.651 -  49.887:   73        |
|      3:    18.708 -  24.944:  217   |   8:    49.887 -  56.123:   54        |
|      4:    24.944 -  31.179:  108   |   9:    56.123 -  62.359:   32        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1501 r_free = 0.1890             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1496 r_free = 0.1889             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1496   r_free= 0.1889   ksol= 0.33   Bsol= 44.44   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,0.11,-1.54,0.00,-0.00,-0.00); trace/3= -1.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.375171                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.1870   ksol= 0.33   Bsol= 48.21   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.13,-1.80,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.369699                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.576682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.526  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.176030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.157   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1490      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.1870      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2941 = 1.58 * 0.50 * 5.3724 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2138 = 1.58 * 0.50 * 5.2827 + 1.00 * 0.0492                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1238      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1087 = 0.18 * 1.00 * 5.2827 + 1.00 * 0.1788                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9199 = 0.18 * 1.00 * 5.1871 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    65.01   16.58    None  None   None       |
|    all(noH): 2823   0      1.75    65.01   16.58    None  None   None       |
|    Sol.    : 438    0      4.52    65.01   37.38    None  None   None       |
|    Mac.    : 2385   0      1.75    57.23   12.76    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:     1.754 -   8.080:  479   |   5:    33.384 -  39.710:  102        |
|      1:     8.080 -  14.406: 1303   |   6:    39.710 -  46.036:   89        |
|      2:    14.406 -  20.732:  444   |   7:    46.036 -  52.362:   82        |
|      3:    20.732 -  27.058:  151   |   8:    52.362 -  58.688:   61        |
|      4:    27.058 -  33.384:  105   |   9:    58.688 -  65.014:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1195 r_free = 0.1565             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1566             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1566   ksol= 0.33   Bsol= 48.21   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.13,-1.80,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1565   ksol= 0.33   Bsol= 48.21   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.44,-1.51,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.171947                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.627865              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.647  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.668391              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.102  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8638 = 2.63 * 0.50 * 5.1864 + 1.00 * 0.0492                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8071 = 2.63 * 0.50 * 5.1324 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1514      final r-factor (free) = 0.1519          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5696 = 1.67 * 1.00 * 5.1324 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5212 = 1.67 * 1.00 * 5.1020 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    78.45   17.08    None  None   None       |
|    all(noH): 2823   0      0.70    78.45   17.08    None  None   None       |
|    Sol.    : 438    0      3.35    75.99   39.80    None  None   None       |
|    Mac.    : 2385   0      0.70    78.45   12.91    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:     0.700 -   8.476:  654   |   5:    39.578 -  47.353:  111        |
|      1:     8.476 -  16.251: 1305   |   6:    47.353 -  55.129:   72        |
|      2:    16.251 -  24.027:  350   |   7:    55.129 -  62.904:   69        |
|      3:    24.027 -  31.802:  127   |   8:    62.904 -  70.679:   26        |
|      4:    31.802 -  39.578:  100   |   9:    70.679 -  78.455:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1519             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1520             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1520   ksol= 0.33   Bsol= 48.21   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.44,-1.51,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104780                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1517   ksol= 0.32   Bsol= 48.46   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.41,-1.36,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104345                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.526134              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.145  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.095124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.553  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9566 = 1.53 * 0.50 * 5.1020 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9515 = 1.53 * 0.50 * 5.1118 + 1.00 * 0.0509                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1512          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4952 = 0.10 * 1.00 * 5.1118 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5282 = 0.10 * 1.00 * 5.1210 + 1.00 * 0.0410                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.18   16.99    None  None   None       |
|    all(noH): 2823   0      0.00    78.18   16.99    None  None   None       |
|    Sol.    : 438    0      5.24    75.98   39.30    None  None   None       |
|    Mac.    : 2385   0      0.00    78.18   12.89    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 -   7.818:  464   |   5:    39.088 -  46.905:  115        |
|      1:     7.818 -  15.635: 1469   |   6:    46.905 -  54.723:   72        |
|      2:    15.635 -  23.453:  375   |   7:    54.723 -  62.540:   69        |
|      3:    23.453 -  31.270:  123   |   8:    62.540 -  70.358:   25        |
|      4:    31.270 -  39.088:  102   |   9:    70.358 -  78.176:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1512             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1511             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1511   ksol= 0.32   Bsol= 48.46   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.41,-1.36,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113073                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1511   ksol= 0.32   Bsol= 48.46   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.45,-1.33,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112994                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.627047              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.930  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.677567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.387   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1511      final r-factor (free) = 0.1508          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2166 = 1.63 * 0.50 * 5.1206 + 1.00 * 0.0509                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2078 = 1.63 * 0.50 * 5.1061 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1508      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4899 = 0.68 * 1.00 * 5.1061 + 1.00 * 0.0302                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4644 = 0.68 * 1.00 * 5.1001 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    85.01   16.87    None  None   None       |
|    all(noH): 2823   0      0.96    85.01   16.87    None  None   None       |
|    Sol.    : 438    0      6.32    79.12   39.13    None  None   None       |
|    Mac.    : 2385   0      0.96    85.01   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:     0.959 -   9.364:  904   |   5:    42.986 -  51.392:   95        |
|      1:     9.364 -  17.770: 1184   |   6:    51.392 -  59.797:   78        |
|      2:    17.770 -  26.175:  260   |   7:    59.797 -  68.203:   27        |
|      3:    26.175 -  34.581:  132   |   8:    68.203 -  76.608:   17        |
|      4:    34.581 -  42.986:  122   |   9:    76.608 -  85.014:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1524             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1523             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1523   ksol= 0.32   Bsol= 48.46   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.45,-1.33,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108438                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7293 0.99   1386  154 0.0978 0.1242      5.3692      5.5009|
|  2:  4.7293 -  3.7734 0.99   1324  146 0.0842 0.1085      5.4219      5.5918|
|  3:  3.7734 -  3.3022 0.99   1300  143 0.1036 0.1481      5.4548      5.8454|
|  4:  3.3022 -  3.0029 0.99   1285  148 0.1174 0.1521      5.4263      5.5564|
|  5:  3.0029 -  2.7891 0.99   1292  141 0.1262 0.1709      5.2924      5.5393|
|  6:  2.7891 -  2.6256 0.99   1281  141 0.1135 0.1745      5.1748      5.4089|
|  7:  2.6256 -  2.4947 0.99   1283  138 0.1232 0.1477       5.139      5.3174|
|  8:  2.4947 -  2.3866 0.98   1253  147 0.1098 0.1731      5.0113      5.3243|
|  9:  2.3866 -  2.2950 0.98   1269  138 0.1097 0.1627      4.9856      5.2233|
| 10:  2.2950 -  2.2161 1.00   1266  142 0.1054 0.1717      4.9141      5.2499|
| 11:  2.2161 -  2.1470 0.97   1249  137 0.1083 0.1598      4.9162      5.1784|
| 12:  2.1470 -  2.0858 0.98   1256  141 0.1054 0.1655      4.8409       5.184|
| 13:  2.0858 -  2.0310 0.99   1283  140 0.1051 0.1722      4.7471      5.0577|
| 14:  2.0310 -  1.9816 0.72    903  103 0.0988 0.1624      4.6282      4.8709|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0283 -  4.7293  1386   154  0.94   8.88   0.98     0.95       6749.44|
|  2:  4.7293 -  3.7734  1324   146  0.96   7.56   1.02     1.01       8600.87|
|  3:  3.7734 -  3.3022  1300   143  0.94  10.77   1.03     1.02       9751.22|
|  4:  3.3022 -  3.0029  1285   148  0.92  13.08   1.01     0.99       9729.36|
|  5:  3.0029 -  2.7891  1292   141  0.91  15.23   0.99     0.96       7778.70|
|  6:  2.7891 -  2.6256  1281   141  0.91  15.10   0.99     0.96       6689.14|
|  7:  2.6256 -  2.4947  1283   138  0.91  15.06   0.99     0.96       5842.60|
|  8:  2.4947 -  2.3866  1253   147  0.92  14.06   0.99     0.97       4663.01|
|  9:  2.3866 -  2.2950  1269   138  0.92  14.25   1.00     0.97       4530.63|
| 10:  2.2950 -  2.2161  1266   142  0.91  14.37   1.00     0.96       3980.58|
| 11:  2.2161 -  2.1470  1249   137  0.90  16.11   0.99     0.96       4230.08|
| 12:  2.1470 -  2.0858  1256   141  0.92  14.15   1.00     0.98       3668.54|
| 13:  2.0858 -  2.0310  1283   140  0.91  15.22   1.00     0.98       3116.45|
| 14:  2.0310 -  1.9816   903   103  0.92  13.72   0.98     0.94       2380.68|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2380.68 max =         9751.22 mean =      5939.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.34|
|phase err.(test): min =        0.00 max =           88.91 mean =        12.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1524   ksol= 0.32   Bsol= 48.42   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.30,-1.16,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1524   ksol= 0.32   Bsol= 48.42   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.30,-1.16,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108489                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7293 0.99   1386  154 0.0979 0.1244        5.37      5.5019|
|  2:  4.7293 -  3.7734 0.99   1324  146 0.0842 0.1085      5.4223      5.5917|
|  3:  3.7734 -  3.3022 0.99   1300  143 0.1036 0.1481      5.4548      5.8456|
|  4:  3.3022 -  3.0029 0.99   1285  148 0.1174 0.1522      5.4263      5.5565|
|  5:  3.0029 -  2.7891 0.99   1292  141 0.1262 0.1709      5.2923      5.5391|
|  6:  2.7891 -  2.6256 0.99   1281  141 0.1135 0.1745      5.1746      5.4088|
|  7:  2.6256 -  2.4947 0.99   1283  138 0.1232 0.1477      5.1391      5.3177|
|  8:  2.4947 -  2.3866 0.98   1253  147 0.1098 0.1731      5.0113      5.3241|
|  9:  2.3866 -  2.2950 0.98   1269  138 0.1097 0.1627      4.9856      5.2233|
| 10:  2.2950 -  2.2161 1.00   1266  142 0.1054 0.1718      4.9142      5.2502|
| 11:  2.2161 -  2.1470 0.97   1249  137 0.1083 0.1597      4.9162      5.1782|
| 12:  2.1470 -  2.0858 0.98   1256  141 0.1054 0.1655      4.8407      5.1841|
| 13:  2.0858 -  2.0310 0.99   1283  140 0.1051 0.1721       4.747      5.0572|
| 14:  2.0310 -  1.9816 0.72    903  103 0.0988 0.1624       4.628      4.8706|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0283 -  4.7293  1386   154  0.94   8.89   0.98     0.95       6762.48|
|  2:  4.7293 -  3.7734  1324   146  0.96   7.56   1.02     1.01       8609.42|
|  3:  3.7734 -  3.3022  1300   143  0.94  10.77   1.03     1.02       9752.65|
|  4:  3.3022 -  3.0029  1285   148  0.92  13.08   1.01     1.00       9728.39|
|  5:  3.0029 -  2.7891  1292   141  0.91  15.23   1.00     0.97       7777.03|
|  6:  2.7891 -  2.6256  1281   141  0.91  15.10   0.99     0.97       6687.87|
|  7:  2.6256 -  2.4947  1283   138  0.91  15.06   1.00     0.96       5842.89|
|  8:  2.4947 -  2.3866  1253   147  0.92  14.06   0.99     0.97       4662.20|
|  9:  2.3866 -  2.2950  1269   138  0.92  14.25   1.01     0.98       4531.17|
| 10:  2.2950 -  2.2161  1266   142  0.91  14.37   1.00     0.97       3980.32|
| 11:  2.2161 -  2.1470  1249   137  0.90  16.11   1.00     0.97       4230.56|
| 12:  2.1470 -  2.0858  1256   141  0.92  14.15   1.01     0.99       3667.43|
| 13:  2.0858 -  2.0310  1283   140  0.91  15.22   1.00     0.99       3115.20|
| 14:  2.0310 -  1.9816   903   103  0.92  13.71   0.99     0.95       2379.09|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2379.09 max =         9752.65 mean =      5940.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.34|
|phase err.(test): min =        0.00 max =           88.91 mean =        12.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    84.98   16.84    None  None   None       |
|    all(noH): 2823   0      0.93    84.98   16.84    None  None   None       |
|    Sol.    : 438    0      6.29    79.09   39.10    None  None   None       |
|    Mac.    : 2385   0      0.93    84.98   12.75    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:     0.926 -   9.331:  904   |   5:    42.953 -  51.359:   95        |
|      1:     9.331 -  17.737: 1184   |   6:    51.359 -  59.764:   78        |
|      2:    17.737 -  26.142:  260   |   7:    59.764 -  68.170:   27        |
|      3:    26.142 -  34.548:  132   |   8:    68.170 -  76.575:   17        |
|      4:    34.548 -  42.953:  122   |   9:    76.575 -  84.981:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 286         
Filter by distance & map next to the model:
   mapped sites are within: 0.496 - 4.675
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 282 from: 286
   mapped sites are within: 0.717 - 4.675

peak=    5.778 closest distance to " NE2 GLN A  11 " =    1.165
peak=    5.658 closest distance to " NH2 ARG A  56 " =    2.157
peak=    5.655 closest distance to " CG  PRO A  54 " =    1.280
peak=    5.451 closest distance to " O   HOH Z 126 " =    1.968
peak=    5.181 closest distance to " CB  GLN A 223 " =    1.446
peak=    5.123 closest distance to " O   HOH Z 144 " =    1.771
peak=    5.046 closest distance to " CB  SER A  63 " =    1.219
peak=    4.970 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.868 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.844 closest distance to " CB  PRO A  54 " =    0.970
peak=    4.802 closest distance to " O   HOH Z 232 " =    2.359
peak=    4.617 closest distance to " O   HOH Z  78 " =    1.768
peak=    4.593 closest distance to " O   HOH Z 369 " =    2.156
peak=    4.508 closest distance to " C   PRO A 198 " =    1.478
peak=    4.502 closest distance to " CB  GLU A 152 " =    1.255
peak=    4.490 closest distance to " O   HOH Z  15 " =    2.323
peak=    4.474 closest distance to " CG2 VAL A 257 " =    0.911
peak=    4.452 closest distance to " CG  PRO A  90 " =    1.072
peak=    4.448 closest distance to " O   HOH Z 298 " =    1.941
peak=    4.433 closest distance to " CB  ASN A 148 " =    1.379
peak=    4.418 closest distance to " O   HOH Z 427 " =    2.873
peak=    4.406 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.398 closest distance to " O   HOH Z 236 " =    2.165
peak=    4.320 closest distance to " CG  PRO A 198 " =    1.249
peak=    4.311 closest distance to " OD1 ASN A  69 " =    2.597
peak=    4.286 closest distance to " O   HOH Z 193 " =    1.819
peak=    4.277 closest distance to " O   HOH Z  61 " =    1.638
peak=    4.273 closest distance to " O   HOH Z 303 " =    2.112
peak=    4.249 closest distance to " CB  TYR A 169 " =    0.717
peak=    4.244 closest distance to " CB  LEU A 228 " =    1.077
peak=    4.239 closest distance to " ND2 ASN A 187 " =    1.430
peak=    4.233 closest distance to " CB  SER A   3 " =    1.316
peak=    4.226 closest distance to " CB  ARG A  79 " =    1.364
peak=    4.211 closest distance to " O   HOH Z 203 " =    1.818
peak=    4.208 closest distance to " CG  PRO A 243 " =    1.110
peak=    4.197 closest distance to " CB  GLU A 128 " =    1.036
peak=    4.193 closest distance to " O   HOH Z 158 " =    3.013
peak=    4.139 closest distance to " OG ASER A 258 " =    3.128
peak=    4.137 closest distance to " CB  VAL A 265 " =    1.277
peak=    4.137 closest distance to " O   HOH Z 234 " =    3.693
peak=    4.095 closest distance to " O   HOH Z 419 " =    2.079
peak=    4.060 closest distance to " CA  ASN A 215 " =    1.156
peak=    4.050 closest distance to " O   HOH Z  78 " =    2.116
peak=    4.037 closest distance to " CB  TRP A 266 " =    1.009
peak=    4.022 closest distance to " CB  ARG A 190 " =    1.625
peak=    4.012 closest distance to " O   HOH Z 346 " =    1.681
peak=    3.983 closest distance to " CB  SER A 216 " =    0.840
peak=    3.966 closest distance to " O   HOH Z 132 " =    2.386
peak=    3.964 closest distance to " CG1 ILE A  33 " =    1.225
peak=    3.951 closest distance to " NZ  LYS A 117 " =    3.194
peak=    3.947 closest distance to " O   HOH Z 250 " =    1.527
peak=    3.945 closest distance to " O   HOH Z 144 " =    2.228
peak=    3.944 closest distance to " O   HOH Z 189 " =    2.296
peak=    3.936 closest distance to " O   HOH Z 193 " =    1.682
peak=    3.931 closest distance to " O   HOH Z  66 " =    2.188
peak=    3.871 closest distance to " O   HOH Z 272 " =    1.812
peak=    3.865 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.859 closest distance to " O   HOH Z 344 " =    3.135
peak=    3.857 closest distance to " O   HOH Z  44 " =    1.732
peak=    3.851 closest distance to " O   HOH Z   1 " =    1.938
peak=    3.841 closest distance to " CD  ARG A 159 " =    0.746
peak=    3.813 closest distance to " OD2 ASP A 286 " =    2.798
peak=    3.812 closest distance to " CD BLYS A 290 " =    1.194
peak=    3.795 closest distance to " CD  ARG A  66 " =    2.415
peak=    3.784 closest distance to " O   HOH Z 368 " =    3.614
peak=    3.768 closest distance to " O   SER A  87 " =    2.195
peak=    3.765 closest distance to " O   HOH Z  61 " =    1.516
peak=    3.752 closest distance to " O   HOH Z   9 " =    1.993
peak=    3.743 closest distance to " CD2 TRP A 179 " =    1.342
peak=    3.742 closest distance to " O   HOH Z 209 " =    2.233
peak=    3.739 closest distance to " O   HOH Z 425 " =    2.095
peak=    3.735 closest distance to " O   HOH Z  21 " =    1.740
peak=    3.732 closest distance to " O   HOH Z 386 " =    3.213
peak=    3.715 closest distance to " CB  TRP A 179 " =    1.364
peak=    3.710 closest distance to " CG  LEU A 167 " =    1.232
peak=    3.708 closest distance to " NH1AARG A 145 " =    1.162
peak=    3.696 closest distance to " O   HOH Z 368 " =    1.983
peak=    3.687 closest distance to " O   HOH Z  40 " =    1.772
peak=    3.687 closest distance to " CZ  PHE A 218 " =    1.017
peak=    3.683 closest distance to " O   HOH Z 214 " =    2.098
peak=    3.682 closest distance to " ND1 HIS A  86 " =    1.717
peak=    3.673 closest distance to " O   HOH Z 265 " =    2.465
peak=    3.668 closest distance to " O   HOH Z 180 " =    2.195
peak=    3.667 closest distance to " CB  ALA A  34 " =    1.124
peak=    3.657 closest distance to " CA  THR A 264 " =    0.861
peak=    3.653 closest distance to " O   HOH Z 327 " =    1.723
peak=    3.650 closest distance to " CB  ARG A 139 " =    0.934
peak=    3.648 closest distance to " CB  ASP A 140 " =    0.872
peak=    3.647 closest distance to " CB  SER A 212 " =    1.080
peak=    3.646 closest distance to " O   HOH Z  10 " =    1.817
peak=    3.641 closest distance to " O   HOH Z 128 " =    2.226
peak=    3.635 closest distance to " CD2 LEU A 255 " =    1.494
peak=    3.633 closest distance to " O   HOH Z 423 " =    1.471
peak=    3.626 closest distance to " CB  VAL A 202 " =    1.611
peak=    3.625 closest distance to " O   HOH Z 437 " =    1.500
peak=    3.625 closest distance to " O   HOH Z   1 " =    1.742
peak=    3.625 closest distance to " O   HOH Z 133 " =    2.386
peak=    3.622 closest distance to " O   HOH Z 207 " =    1.809
peak=    3.613 closest distance to " O   HOH Z 305 " =    3.540
peak=    3.612 closest distance to " CB  THR A 157 " =    1.135
peak=    3.610 closest distance to " O   HOH Z  64 " =    2.195
peak=    3.604 closest distance to " O   HOH Z 135 " =    1.687
peak=    3.601 closest distance to " O   HOH Z 403 " =    1.673
peak=    3.587 closest distance to " O   HOH Z  43 " =    1.825
peak=    3.579 closest distance to " O   HOH Z 371 " =    3.003
peak=    3.576 closest distance to " OD1BASN A 224 " =    2.310
peak=    3.570 closest distance to " O   HOH Z 133 " =    1.600
peak=    3.569 closest distance to " O   HOH Z 411 " =    3.820
peak=    3.567 closest distance to " CA  ALA A  21 " =    1.107
peak=    3.567 closest distance to " O   HOH Z 280 " =    3.003
peak=    3.559 closest distance to " CG2 THR A 221 " =    1.082
peak=    3.558 closest distance to " CB  ASN A  39 " =    0.890
peak=    3.549 closest distance to " OG BSER A 164 " =    2.364
peak=    3.535 closest distance to " O   HOH Z  59 " =    1.710
peak=    3.525 closest distance to " NH2AARG A 190 " =    1.964
peak=    3.525 closest distance to " CB  SER A  62 " =    1.202
peak=    3.524 closest distance to " CB  GLU A 277 " =    3.547
peak=    3.524 closest distance to " O   HOH Z 245 " =    1.288
peak=    3.524 closest distance to " O   HOH Z 128 " =    2.106
peak=    3.521 closest distance to " O   HOH Z 389 " =    1.848
peak=    3.517 closest distance to " O   HOH Z 426 " =    1.842
peak=    3.515 closest distance to " NH2BARG A 145 " =    2.068
peak=    3.514 closest distance to " N   PHE A 130 " =    1.279
peak=    3.510 closest distance to " O   HOH Z 371 " =    1.733
peak=    3.504 closest distance to " CA  ALA A 158 " =    1.185
peak=    3.503 closest distance to " CA  MET A  40 " =    1.132
peak=    3.502 closest distance to " CB  ALA A 291 " =    1.366
peak=    3.497 closest distance to " N   ARG A 156 " =    1.273
peak=    3.496 closest distance to " CA  ARG A 195 " =    1.197
peak=    3.491 closest distance to " O   HOH Z 402 " =    1.408
peak=    3.489 closest distance to " CA  THR A 221 " =    0.979
peak=    3.483 closest distance to " CB  HIS A 108 " =    0.809
peak=    3.482 closest distance to " CD1 LEU A 300 " =    1.241
peak=    3.480 closest distance to " NZ  LYS A  76 " =    1.549
peak=    3.480 closest distance to " CB  TYR A 116 " =    0.794
peak=    3.477 closest distance to " O   HOH Z 172 " =    3.159
peak=    3.475 closest distance to " O   HOH Z 407 " =    2.329
peak=    3.473 closest distance to " O  BHOH Z  74 " =    1.303
peak=    3.472 closest distance to " O   HOH Z 425 " =    1.248
peak=    3.469 closest distance to " CB  ASN A 142 " =    0.956
peak=    3.467 closest distance to " O   HOH Z 248 " =    1.640
peak=    3.453 closest distance to " O   HOH Z  97 " =    2.005
peak=    3.443 closest distance to " O   HOH Z 353 " =    2.689
peak=    3.438 closest distance to " O   HOH Z  93 " =    2.461
peak=    3.436 closest distance to " O   HOH Z 345 " =    3.443
peak=    3.435 closest distance to " O   HOH Z  44 " =    3.041
peak=    3.434 closest distance to " O   HOH Z 147 " =    1.730
peak=    3.433 closest distance to " CD1 ILE A 106 " =    0.822
peak=    3.423 closest distance to " CB  MET A  47 " =    1.113
peak=    3.422 closest distance to " CD  PRO A 243 " =    1.542
peak=    3.418 closest distance to " CG1 VAL A 153 " =    0.906
peak=    3.418 closest distance to " O   HOH Z  40 " =    1.945
peak=    3.417 closest distance to " CA  SER A  87 " =    1.044
peak=    3.412 closest distance to " O   HOH Z  88 " =    3.044
peak=    3.412 closest distance to " CA  ALA A 291 " =    0.877
peak=    3.406 closest distance to " O   HOH Z 291 " =    1.569
peak=    3.405 closest distance to " CA  ILE A 234 " =    0.976
peak=    3.403 closest distance to " O   HOH Z 409 " =    2.635
peak=    3.403 closest distance to " O   HOH Z 271 " =    2.410
peak=    3.400 closest distance to " NE2 GLN A  73 " =    3.711
peak=    3.399 closest distance to " O   HOH Z 391 " =    2.880
peak=    3.397 closest distance to " O   HOH Z   3 " =    1.892
peak=    3.392 closest distance to " N   GLN A 278 " =    1.191
peak=    3.386 closest distance to " CB  LYS A 117 " =    1.183
peak=    3.382 closest distance to " N   ASN A 127 " =    1.258
peak=    3.381 closest distance to " CA  ALA A 233 " =    1.226
peak=    3.380 closest distance to " CG1BVAL A  72 " =    1.509
peak=    3.377 closest distance to " CA  ALA A  51 " =    0.941
peak=    3.376 closest distance to " O   HOH Z 417 " =    3.281
peak=    3.375 closest distance to " O   HOH Z  53 " =    2.545
peak=    3.368 closest distance to " CB  ILE A 120 " =    1.290
peak=    3.364 closest distance to " OG  SER A  22 " =    2.745
peak=    3.361 closest distance to " NH1BARG A 145 " =    1.192
peak=    3.358 closest distance to " CB  ALA A   1 " =    4.675
peak=    3.346 closest distance to " O   HOH Z   6 " =    2.055
peak=    3.336 closest distance to " O   HOH Z 175 " =    2.101
peak=    3.334 closest distance to " O   MET A 105 " =    1.796
peak=    3.332 closest distance to " CG2 ILE A 120 " =    1.121
peak=    3.328 closest distance to " O   HOH Z 193 " =    1.941
peak=    3.327 closest distance to " O   HOH Z 213 " =    2.561
peak=    3.325 closest distance to " O   HOH Z 261 " =    2.265
peak=    3.325 closest distance to " O   HOH Z 219 " =    2.172
peak=    3.320 closest distance to " O   HOH Z 357 " =    1.867
peak=    3.318 closest distance to " O  BHOH Z 338 " =    2.379
peak=    3.316 closest distance to " NE2 HIS A 207 " =    1.385
peak=    3.315 closest distance to " O   ALA A 165 " =    1.464
peak=    3.315 closest distance to " O   HOH Z 433 " =    1.763
peak=    3.313 closest distance to " CB  MET A  40 " =    0.825
peak=    3.310 closest distance to " O   HOH Z  96 " =    2.144
peak=    3.304 closest distance to " O   HOH Z 213 " =    1.964
peak=    3.301 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.298 closest distance to " CB  GLN A  89 " =    1.378
peak=    3.295 closest distance to " CA  ALA A  84 " =    1.370
peak=    3.292 closest distance to " CB  GLN A  88 " =    1.225
peak=    3.289 closest distance to " O   HOH Z 234 " =    1.823
peak=    3.285 closest distance to " CB  SER A 273 " =    0.862
peak=    3.285 closest distance to " CG  LYS A  76 " =    1.019
peak=    3.284 closest distance to " CB  LEU A 143 " =    1.128
peak=    3.282 closest distance to " CG  ARG A 159 " =    0.834
peak=    3.280 closest distance to " CG  PRO A 213 " =    0.982
peak=    3.279 closest distance to " CA  ARG A  36 " =    1.018
peak=    3.275 closest distance to " CA  ASN A 127 " =    1.068
peak=    3.273 closest distance to " O   HOH Z 435 " =    1.943
peak=    3.263 closest distance to " CG  MET A 113 " =    1.204
peak=    3.260 closest distance to " O   HOH Z 273 " =    2.808
peak=    3.258 closest distance to " CB  ASN A 224 " =    1.004
peak=    3.258 closest distance to " O   HOH Z 188 " =    1.976
peak=    3.254 closest distance to " CG  GLN A  89 " =    1.495
peak=    3.244 closest distance to " O   HOH Z 128 " =    2.035
peak=    3.244 closest distance to " O   HOH Z 411 " =    1.758
peak=    3.243 closest distance to " CB  THR A  31 " =    1.667
peak=    3.241 closest distance to " CG1 VAL A 189 " =    2.021
peak=    3.238 closest distance to " CA  GLY A 267 " =    1.199
peak=    3.238 closest distance to " NH2 ARG A 156 " =    1.177
peak=    3.236 closest distance to " CB  VAL A 126 " =    1.020
peak=    3.233 closest distance to " O   HOH Z 163 " =    1.858
peak=    3.231 closest distance to " O   HOH Z 163 " =    1.799
peak=    3.231 closest distance to " O   HOH Z 406 " =    1.557
peak=    3.221 closest distance to " O   HOH Z 286 " =    2.323
peak=    3.220 closest distance to " O   HOH Z 227 " =    2.105
peak=    3.218 closest distance to " O   HOH Z 173 " =    1.767
peak=    3.218 closest distance to " O   HOH Z 295 " =    1.565
peak=    3.217 closest distance to " CE1 TYR A 186 " =    1.342
peak=    3.216 closest distance to " O   HOH Z 148 " =    3.372
peak=    3.213 closest distance to " O   HOH Z  85 " =    2.198
peak=    3.211 closest distance to " O   HOH Z  66 " =    2.090
peak=    3.210 closest distance to " O   HOH Z  88 " =    2.548
peak=    3.209 closest distance to " OG  SER A  97 " =    3.545
peak=    3.206 closest distance to " CA  VAL A 125 " =    1.094
peak=    3.205 closest distance to " CB  THR A 235 " =    1.066
peak=    3.204 closest distance to " CB  VAL A 268 " =    0.849
peak=    3.203 closest distance to " O   HOH Z 211 " =    2.848
peak=    3.203 closest distance to " N   SER A 135 " =    1.244
peak=    3.202 closest distance to " O   HOH Z 329 " =    3.760
peak=    3.200 closest distance to " CA  MET A 105 " =    0.972
peak=    3.200 closest distance to " CA  ARG A 102 " =    1.066
peak=    3.198 closest distance to " N   TYR A  15 " =    0.763
peak=    3.195 closest distance to " CD1 LEU A  96 " =    0.798
peak=    3.195 closest distance to " O   HOH Z 236 " =    1.479
peak=    3.186 closest distance to " O   HOH Z 365 " =    2.917
peak=    3.183 closest distance to " CD2 LEU A 297 " =    0.879
peak=    3.183 closest distance to " NH1 ARG A 138 " =    1.107
peak=    3.182 closest distance to " O   HOH Z 290 " =    0.994
peak=    3.181 closest distance to " OD1 ASN A 217 " =    1.699
peak=    3.179 closest distance to " CA  LYS A 290 " =    1.283
peak=    3.179 closest distance to " O   HOH Z 285 " =    2.789
peak=    3.173 closest distance to " CB  ASN A 110 " =    1.119
peak=    3.172 closest distance to " CB  ARG A 138 " =    0.943
peak=    3.172 closest distance to " O   HOH Z 336 " =    1.922
peak=    3.169 closest distance to " O   HOH Z 303 " =    1.662
peak=    3.168 closest distance to " CG2 VAL A 197 " =    1.099
peak=    3.165 closest distance to " CG BARG A 102 " =    1.787
peak=    3.163 closest distance to " ND1 HIS A  81 " =    1.628
peak=    3.162 closest distance to " O   HOH Z 359 " =    1.386
peak=    3.160 closest distance to " O   HOH Z 108 " =    2.291
peak=    3.157 closest distance to " CG1 ILE A 151 " =    0.960
peak=    3.148 closest distance to " CD  LYS A 166 " =    1.234
peak=    3.147 closest distance to " N   ALA A 154 " =    0.902
peak=    3.146 closest distance to " CD  LYS A 119 " =    1.254
peak=    3.142 closest distance to " O   HOH Z 423 " =    2.675
peak=    3.139 closest distance to " O   HOH Z 298 " =    2.563
peak=    3.136 closest distance to " CA  SER A 146 " =    1.755
peak=    3.134 closest distance to " CB  TRP A 150 " =    1.268
peak=    3.133 closest distance to " CB  GLN A 278 " =    0.833
peak=    3.131 closest distance to " CB  LEU A 255 " =    0.823
peak=    3.120 closest distance to " CA  ALA A 248 " =    1.236
peak=    3.107 closest distance to " CB  THR A 294 " =    1.680
peak=    3.104 closest distance to " O   HOH Z  88 " =    2.347
peak=    3.099 closest distance to " O   THR A 220 " =    1.316
peak=    3.099 closest distance to " O   ALA A   1 " =    1.707
peak=    3.096 closest distance to " CD  ARG A  36 " =    1.043
peak=    3.086 closest distance to " CD1AILE A 234 " =    0.903
peak=    3.083 closest distance to " CB  ALA A   9 " =    1.539
peak=    3.076 closest distance to " CA  ALA A 299 " =    0.910
peak=    3.075 closest distance to " OG  SER A 206 " =    1.231
peak=    3.072 closest distance to " CB  ALA A 114 " =    1.397
peak=    3.056 closest distance to " OG BSER A  99 " =    2.157
peak=    3.030 closest distance to " O   ASN A 209 " =    1.334
peak=    3.029 closest distance to " O   HOH Z 383 " =    1.699
peak=    3.018 closest distance to " CB  GLU A  46 " =    1.100
peak=    3.012 closest distance to " NH2AARG A 190 " =    1.039
peak=    3.000 closest distance to " O   GLN A 278 " =    1.513

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.700 - 5.583
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 193
   mapped sites are within: 0.771 - 5.583

peak=   -4.703 closest distance to " CB  PRO A 243 " =    2.603
peak=   -4.615 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.503 closest distance to " CG  GLN A 223 " =    1.765
peak=   -4.501 closest distance to " O   HOH Z 266 " =    4.924
peak=   -4.381 closest distance to " O   HOH Z 377 " =    2.010
peak=   -4.340 closest distance to " OG BSER A 134 " =    1.218
peak=   -4.240 closest distance to " O   VAL A  67 " =    2.627
peak=   -4.188 closest distance to " SG  CYS A 254 " =    3.425
peak=   -4.147 closest distance to " C   HIS A 108 " =    1.048
peak=   -4.143 closest distance to " ND2 ASN A  45 " =    1.673
peak=   -4.110 closest distance to " O   HOH Z 435 " =    2.848
peak=   -4.083 closest distance to " O   HOH Z 372 " =    2.430
peak=   -4.065 closest distance to " O   HOH Z 389 " =    1.961
peak=   -4.048 closest distance to " O   HOH Z 231 " =    2.173
peak=   -4.041 closest distance to " O   HOH Z 290 " =    1.179
peak=   -4.033 closest distance to " CE  MET A 105 " =    2.304
peak=   -4.023 closest distance to " O   PRO A 198 " =    1.269
peak=   -3.993 closest distance to " CG1 VAL A 112 " =    2.891
peak=   -3.967 closest distance to " CB  ALA A 291 " =    2.191
peak=   -3.948 closest distance to " O   HOH Z 313 " =    1.872
peak=   -3.943 closest distance to " O   HOH Z 198 " =    1.951
peak=   -3.939 closest distance to " O   VAL A  67 " =    2.810
peak=   -3.873 closest distance to " CZ3 TRP A 179 " =    1.151
peak=   -3.872 closest distance to " CD  GLN A  58 " =    1.048
peak=   -3.856 closest distance to " O   HOH Z 351 " =    1.533
peak=   -3.846 closest distance to " CG  PHE A 283 " =    2.641
peak=   -3.829 closest distance to " CZ  PHE A  59 " =    1.512
peak=   -3.818 closest distance to " N   ALA A  43 " =    2.543
peak=   -3.815 closest distance to " CE2 TYR A  30 " =    2.796
peak=   -3.794 closest distance to " CD2 PHE A 192 " =    2.008
peak=   -3.771 closest distance to " CE2 PHE A 218 " =    2.442
peak=   -3.764 closest distance to " CB  ALA A  43 " =    2.501
peak=   -3.758 closest distance to " O   HOH Z 407 " =    3.140
peak=   -3.756 closest distance to " OD1 ASN A 187 " =    1.541
peak=   -3.752 closest distance to " OD1 ASP A 171 " =    1.617
peak=   -3.739 closest distance to " CB  ALA A 161 " =    2.528
peak=   -3.735 closest distance to " CG  ASP A 231 " =    0.771
peak=   -3.727 closest distance to " CA  GLY A 203 " =    2.225
peak=   -3.719 closest distance to " O   HOH Z  43 " =    1.722
peak=   -3.716 closest distance to " C   ALA A 158 " =    1.367
peak=   -3.711 closest distance to " CB  ALA A 291 " =    2.339
peak=   -3.696 closest distance to " O   PRO A 163 " =    1.982
peak=   -3.690 closest distance to " CD  ARG A 139 " =    1.522
peak=   -3.688 closest distance to " N   ASP A 286 " =    2.431
peak=   -3.686 closest distance to " O   HOH Z 185 " =    2.224
peak=   -3.662 closest distance to " CB  TYR A  15 " =    2.150
peak=   -3.658 closest distance to " O   HOH Z 353 " =    2.129
peak=   -3.636 closest distance to " CZ  TYR A 169 " =    1.664
peak=   -3.635 closest distance to " O   HOH Z 114 " =    3.028
peak=   -3.620 closest distance to " CD1 LEU A 101 " =    2.291
peak=   -3.619 closest distance to " O   HOH Z 102 " =    1.603
peak=   -3.619 closest distance to " CB  ASN A  39 " =    2.282
peak=   -3.616 closest distance to " CB  ALA A 248 " =    2.024
peak=   -3.616 closest distance to " NH2BARG A 275 " =    1.795
peak=   -3.610 closest distance to " O   HOH Z 298 " =    1.251
peak=   -3.608 closest distance to " CG2 ILE A 263 " =    2.323
peak=   -3.603 closest distance to " O   HOH Z 395 " =    5.187
peak=   -3.599 closest distance to " O   HOH Z 211 " =    1.632
peak=   -3.595 closest distance to " O   SER A 135 " =    1.465
peak=   -3.584 closest distance to " O   VAL A 189 " =    2.548
peak=   -3.582 closest distance to " CA  GLY A  98 " =    1.882
peak=   -3.581 closest distance to " N   GLN A  58 " =    1.806
peak=   -3.580 closest distance to " O   HOH Z 126 " =    1.891
peak=   -3.579 closest distance to " O   HOH Z  10 " =    1.481
peak=   -3.571 closest distance to " CD1 PHE A  59 " =    1.871
peak=   -3.558 closest distance to " O   HOH Z 193 " =    1.880
peak=   -3.555 closest distance to " O   ARG A 145 " =    1.537
peak=   -3.544 closest distance to " OXT GLY A 302 " =    2.863
peak=   -3.542 closest distance to " O   HOH Z 198 " =    1.526
peak=   -3.521 closest distance to " O   HOH Z  13 " =    1.561
peak=   -3.515 closest distance to " O   HOH Z  44 " =    2.237
peak=   -3.515 closest distance to " OD2 ASP A 191 " =    1.431
peak=   -3.504 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.502 closest distance to " NH1 ARG A 195 " =    2.619
peak=   -3.498 closest distance to " C   LEU A 143 " =    1.169
peak=   -3.497 closest distance to " NH2AARG A 275 " =    5.332
peak=   -3.493 closest distance to " CD1 LEU A 228 " =    2.213
peak=   -3.475 closest distance to " O   HOH Z  60 " =    2.467
peak=   -3.472 closest distance to " CB  PRO A 163 " =    2.489
peak=   -3.470 closest distance to " O   PRO A 243 " =    2.583
peak=   -3.467 closest distance to " CB  PHE A 208 " =    2.244
peak=   -3.466 closest distance to " O   ALA A 161 " =    1.600
peak=   -3.457 closest distance to " O   PRO A 198 " =    1.265
peak=   -3.451 closest distance to " O   GLY A 211 " =    1.232
peak=   -3.447 closest distance to " NH1 ARG A  36 " =    2.114
peak=   -3.434 closest distance to " OD2 ASP A 171 " =    2.277
peak=   -3.420 closest distance to " CA  GLY A 133 " =    1.975
peak=   -3.417 closest distance to " CB  TRP A  85 " =    2.488
peak=   -3.414 closest distance to " O   HOH Z 322 " =    1.597
peak=   -3.409 closest distance to " N   ALA A 248 " =    1.558
peak=   -3.406 closest distance to " CB  CYS A 254 " =    2.306
peak=   -3.403 closest distance to " O   HOH Z  38 " =    1.560
peak=   -3.392 closest distance to " O   HOH Z 385 " =    1.953
peak=   -3.376 closest distance to " CB  ASP A 286 " =    2.200
peak=   -3.370 closest distance to " CB  ALA A 131 " =    2.053
peak=   -3.368 closest distance to " O   PHE A 218 " =    1.569
peak=   -3.366 closest distance to " O   HOH Z 351 " =    1.668
peak=   -3.356 closest distance to " O   GLY A  17 " =    1.164
peak=   -3.355 closest distance to " O   HOH Z  24 " =    1.380
peak=   -3.346 closest distance to " OD1 ASN A 148 " =    1.582
peak=   -3.343 closest distance to " O   HOH Z  11 " =    1.808
peak=   -3.335 closest distance to " O   GLN A 240 " =    2.051
peak=   -3.331 closest distance to " O   HOH Z 311 " =    3.595
peak=   -3.329 closest distance to " O   ALA A 180 " =    1.161
peak=   -3.328 closest distance to " O   HOH Z 316 " =    1.705
peak=   -3.314 closest distance to " O   HOH Z 253 " =    3.952
peak=   -3.304 closest distance to " OH  TYR A 214 " =    1.198
peak=   -3.296 closest distance to " ND2 ASN A 187 " =    1.580
peak=   -3.296 closest distance to " OD1 ASP A 191 " =    1.568
peak=   -3.295 closest distance to " CE3 TRP A 274 " =    2.346
peak=   -3.294 closest distance to " O   HOH Z 196 " =    2.204
peak=   -3.293 closest distance to " OD2 ASP A  50 " =    1.620
peak=   -3.292 closest distance to " CD2 LEU A 237 " =    2.767
peak=   -3.287 closest distance to " N   SER A 212 " =    1.965
peak=   -3.285 closest distance to " O   SER A  95 " =    1.473
peak=   -3.284 closest distance to " OXT GLY A 302 " =    3.392
peak=   -3.284 closest distance to " CG  GLU A 277 " =    1.243
peak=   -3.278 closest distance to " NH2 ARG A  79 " =    1.984
peak=   -3.277 closest distance to " O   HOH Z 165 " =    2.080
peak=   -3.272 closest distance to " ND2 ASN A 249 " =    2.253
peak=   -3.269 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.269 closest distance to " CB  ALA A 248 " =    2.410
peak=   -3.267 closest distance to " O   ALA A  10 " =    1.620
peak=   -3.267 closest distance to " O   HOH Z  51 " =    1.236
peak=   -3.266 closest distance to " OG BSER A 134 " =    1.636
peak=   -3.265 closest distance to " O   HOH Z 266 " =    4.679
peak=   -3.264 closest distance to " N   THR A 235 " =    1.271
peak=   -3.260 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.257 closest distance to " O   HOH Z 359 " =    3.257
peak=   -3.257 closest distance to " O   SER A  22 " =    2.430
peak=   -3.254 closest distance to " CD  GLU A 236 " =    1.042
peak=   -3.252 closest distance to " CB  CYS A 201 " =    2.501
peak=   -3.250 closest distance to " O   HOH Z 417 " =    2.474
peak=   -3.247 closest distance to " CG  TRP A 266 " =    1.844
peak=   -3.246 closest distance to " O   HOH Z  63 " =    1.672
peak=   -3.246 closest distance to " CG1 VAL A 250 " =    2.647
peak=   -3.242 closest distance to " CA  TRP A 274 " =    1.453
peak=   -3.241 closest distance to " CD1 LEU A 297 " =    2.466
peak=   -3.237 closest distance to " O   HOH Z 426 " =    1.576
peak=   -3.233 closest distance to " CA  GLY A 241 " =    2.216
peak=   -3.230 closest distance to " NE  ARG A  36 " =    1.948
peak=   -3.227 closest distance to " CB  ILE A  33 " =    2.861
peak=   -3.224 closest distance to " O   HOH Z 282 " =    1.226
peak=   -3.223 closest distance to " OD1AASN A 224 " =    1.809
peak=   -3.222 closest distance to " O   HOH Z 140 " =    1.684
peak=   -3.211 closest distance to " O   HOH Z  93 " =    2.285
peak=   -3.211 closest distance to " O   VAL A 174 " =    2.128
peak=   -3.211 closest distance to " CG  LEU A  83 " =    1.860
peak=   -3.210 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.204 closest distance to " O   TRP A  70 " =    1.447
peak=   -3.202 closest distance to " CA  GLY A 241 " =    3.121
peak=   -3.198 closest distance to " O   GLY A  80 " =    2.424
peak=   -3.197 closest distance to " CB  ASP A 286 " =    1.763
peak=   -3.195 closest distance to " SG ACYS A 201 " =    1.842
peak=   -3.191 closest distance to " OG  SER A  26 " =    1.221
peak=   -3.180 closest distance to " CD2 PHE A  61 " =    2.543
peak=   -3.176 closest distance to " CD2 PHE A 225 " =    1.083
peak=   -3.173 closest distance to " O   HOH Z 191 " =    5.583
peak=   -3.171 closest distance to " CZ  PHE A 155 " =    1.299
peak=   -3.171 closest distance to " OE1 GLN A  88 " =    1.262
peak=   -3.168 closest distance to " O   ALA A  51 " =    1.402
peak=   -3.167 closest distance to " CG  ARG A 269 " =    2.532
peak=   -3.159 closest distance to " CG1 VAL A 197 " =    2.216
peak=   -3.158 closest distance to " CG  GLN A  88 " =    0.858
peak=   -3.153 closest distance to " CD1 ILE A 151 " =    2.186
peak=   -3.153 closest distance to " O   LYS A 289 " =    3.072
peak=   -3.151 closest distance to " CB  ASP A 132 " =    2.256
peak=   -3.149 closest distance to " O   HOH Z 394 " =    1.407
peak=   -3.140 closest distance to " CE1 TYR A 169 " =    2.515
peak=   -3.135 closest distance to " O   HOH Z 137 " =    1.491
peak=   -3.135 closest distance to " O   HOH Z 388 " =    2.099
peak=   -3.135 closest distance to " O   HOH Z 111 " =    2.189
peak=   -3.132 closest distance to " O   HOH Z 377 " =    0.936
peak=   -3.132 closest distance to " O   HOH Z 414 " =    1.844
peak=   -3.131 closest distance to " CG  GLU A 152 " =    1.184
peak=   -3.128 closest distance to " O   HOH Z 281 " =    2.695
peak=   -3.127 closest distance to " O   ASN A 249 " =    1.426
peak=   -3.123 closest distance to " O   HOH Z 263 " =    3.050
peak=   -3.121 closest distance to " O   HOH Z  73 " =    2.191
peak=   -3.119 closest distance to " OD2 ASP A 171 " =    1.729
peak=   -3.117 closest distance to " NH2 ARG A  79 " =    1.585
peak=   -3.116 closest distance to " O   HOH Z 423 " =    1.199
peak=   -3.115 closest distance to " CE  LYS A  76 " =    2.815
peak=   -3.109 closest distance to " CD2 TYR A 293 " =    1.977
peak=   -3.106 closest distance to " O   HOH Z 298 " =    2.413
peak=   -3.097 closest distance to " CG2 VAL A 189 " =    1.948
peak=   -3.088 closest distance to " O   HOH Z 250 " =    1.392
peak=   -3.084 closest distance to " CE3 TRP A 123 " =    1.277
peak=   -3.064 closest distance to " CB  ASP A 132 " =    2.347
peak=   -3.054 closest distance to " O   HOH Z 184 " =    1.758
peak=   -3.030 closest distance to " C   LYS A  76 " =    1.657

================= 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    :  0.2922 0.2891   5.964132e+00   5.945464e+00
   1_bss:  0.2766 0.2747   5.940079e+00   5.911297e+00
   1_xyz:  0.1619 0.1839   5.423816e+00   5.531775e+00
   1_adp:  0.1501 0.1890   5.377165e+00   5.562635e+00
   1_occ:  0.1496 0.1889   5.375171e+00   5.561548e+00
   2_bss:  0.1490 0.1870   5.369699e+00   5.553000e+00
   2_xyz:  0.1238 0.1612   5.204246e+00   5.413406e+00
   2_adp:  0.1195 0.1565   5.173395e+00   5.386360e+00
   2_occ:  0.1194 0.1566   5.173204e+00   5.386442e+00
   3_bss:  0.1193 0.1565   5.171947e+00   5.385378e+00
   3_xyz:  0.1098 0.1514   5.113752e+00   5.351855e+00
   3_adp:  0.1073 0.1519   5.104657e+00   5.352901e+00
   3_occ:  0.1072 0.1520   5.104780e+00   5.353294e+00
   4_bss:  0.1073 0.1517   5.104345e+00   5.351143e+00
   4_xyz:  0.1090 0.1531   5.117494e+00   5.361354e+00
   4_adp:  0.1096 0.1512   5.113625e+00   5.349789e+00
   4_occ:  0.1095 0.1511   5.113073e+00   5.349675e+00
   5_bss:  0.1095 0.1511   5.112994e+00   5.349611e+00
   5_xyz:  0.1080 0.1508   5.104326e+00   5.347252e+00
   5_adp:  0.1073 0.1524   5.108521e+00   5.359166e+00
   5_occ:  0.1073 0.1523   5.108438e+00   5.359070e+00
   5_bss:  0.1073 0.1524   5.108489e+00   5.359114e+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  44.445  -2.604   0.113  -1.539   0.000  -0.000  -0.000
   1_xyz:  0.333  44.445  -2.604   0.113  -1.539   0.000  -0.000  -0.000
   1_adp:  0.333  44.445  -2.604   0.113  -1.539   0.000  -0.000  -0.000
   1_occ:  0.333  44.445  -2.604   0.113  -1.539   0.000  -0.000  -0.000
   2_bss:  0.328  48.212  -2.826  -2.132  -1.795  -0.000  -0.000  -0.000
   2_xyz:  0.328  48.212  -2.826  -2.132  -1.795  -0.000  -0.000  -0.000
   2_adp:  0.328  48.212  -2.826  -2.132  -1.795  -0.000  -0.000  -0.000
   2_occ:  0.328  48.212  -2.826  -2.132  -1.795  -0.000  -0.000  -0.000
   3_bss:  0.328  48.212  -2.624  -2.438  -1.512  -0.000  -0.000  -0.000
   3_xyz:  0.328  48.212  -2.624  -2.438  -1.512  -0.000  -0.000  -0.000
   3_adp:  0.328  48.212  -2.624  -2.438  -1.512  -0.000  -0.000  -0.000
   3_occ:  0.328  48.212  -2.624  -2.438  -1.512  -0.000  -0.000  -0.000
   4_bss:  0.323  48.458  -2.432  -2.410  -1.363  -0.000  -0.000  -0.000
   4_xyz:  0.323  48.458  -2.432  -2.410  -1.363  -0.000  -0.000  -0.000
   4_adp:  0.323  48.458  -2.432  -2.410  -1.363  -0.000  -0.000  -0.000
   4_occ:  0.323  48.458  -2.432  -2.410  -1.363  -0.000  -0.000  -0.000
   5_bss:  0.323  48.458  -2.418  -2.455  -1.331  -0.000  -0.000  -0.000
   5_xyz:  0.323  48.458  -2.418  -2.455  -1.331  -0.000  -0.000  -0.000
   5_adp:  0.323  48.458  -2.418  -2.455  -1.331  -0.000  -0.000  -0.000
   5_occ:  0.323  48.458  -2.418  -2.455  -1.331  -0.000  -0.000  -0.000
   5_bss:  0.323  48.425  -2.227  -2.298  -1.160  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.650 0.7769  0.9596    23572.587
   1_bss:  27.337 0.7888  0.9277    20417.667
   1_xyz:  16.835 0.8923  0.9985     8674.729
   1_adp:  17.600 0.8851  0.9936     9173.805
   1_occ:  17.582 0.8852  0.9933     9129.624
   2_bss:  17.346 0.8872  0.9641     8951.956
   2_xyz:  14.397 0.9118  0.9781     6618.773
   2_adp:  13.837 0.9164  0.9779     6311.502
   2_occ:  13.844 0.9164  0.9777     6311.563
   3_bss:  13.815 0.9166  0.9803     6298.177
   3_xyz:  13.184 0.9214  0.9818     5893.153
   3_adp:  13.219 0.9212  0.9760     5866.614
   3_occ:  13.225 0.9211  0.9760     5872.484
   4_bss:  13.206 0.9212  0.9804     5835.071
   4_xyz:  13.357 0.9203  0.9791     5971.317
   4_adp:  13.122 0.9221  0.9802     5851.269
   4_occ:  13.118 0.9221  0.9803     5850.179
   5_bss:  13.115 0.9221  0.9804     5849.440
   5_xyz:  13.071 0.9224  0.9807     5819.243
   5_adp:  13.301 0.9207  0.9744     5939.286
   5_occ:  13.302 0.9207  0.9743     5938.882
   5_bss:  13.303 0.9207  0.9793     5940.134
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6068e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6068e-01
   1_xyz:   0.975  0.007  0.068 15.104  0.004  4.111   5.8832e-02
   1_adp:   0.975  0.007  0.068 15.104  0.004  4.111   5.8832e-02
   1_occ:   0.975  0.007  0.068 15.104  0.004  4.111   5.8832e-02
   2_bss:   0.975  0.007  0.068 15.104  0.004  4.111   5.8832e-02
   2_xyz:   0.894  0.005  0.068 14.726  0.004  4.116   4.9229e-02
   2_adp:   0.894  0.005  0.068 14.726  0.004  4.116   4.9229e-02
   2_occ:   0.894  0.005  0.068 14.726  0.004  4.116   4.9229e-02
   3_bss:   0.894  0.005  0.068 14.726  0.004  4.116   4.9229e-02
   3_xyz:   1.012  0.008  0.079 15.102  0.004  4.117   6.3472e-02
   3_adp:   1.012  0.008  0.079 15.102  0.004  4.117   6.3472e-02
   3_occ:   1.012  0.008  0.079 15.102  0.004  4.117   6.3472e-02
   4_bss:   1.012  0.008  0.079 15.102  0.004  4.117   6.3472e-02
   4_xyz:   0.887  0.006  0.069 14.764  0.004  4.117   5.0854e-02
   4_adp:   0.887  0.006  0.069 14.764  0.004  4.117   5.0854e-02
   4_occ:   0.887  0.006  0.069 14.764  0.004  4.117   5.0854e-02
   5_bss:   0.887  0.006  0.069 14.764  0.004  4.117   5.0854e-02
   5_xyz:   0.926  0.006  0.072 14.802  0.004  4.118   5.3949e-02
   5_adp:   0.926  0.006  0.072 14.802  0.004  4.118   5.3949e-02
   5_occ:   0.926  0.006  0.072 14.802  0.004  4.118   5.3949e-02
   5_bss:   0.926  0.006  0.072 14.802  0.004  4.118   5.3949e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_xyz:   7.813  0.045  0.291 85.176  0.040  2.309   5.4474e-02
   1_adp:   7.813  0.045  0.291 85.176  0.040  2.309   5.4474e-02
   1_occ:   7.813  0.045  0.291 85.176  0.040  2.309   5.4474e-02
   2_bss:   7.813  0.045  0.291 85.176  0.040  2.309   5.4474e-02
   2_xyz:   7.421  0.039  0.210 83.516  0.040  2.370   3.3154e-02
   2_adp:   7.421  0.039  0.210 83.516  0.040  2.370   3.3154e-02
   2_occ:   7.421  0.039  0.210 83.516  0.040  2.370   3.3154e-02
   3_bss:   7.421  0.039  0.210 83.516  0.040  2.370   3.3154e-02
   3_xyz:   7.081  0.046  0.261 85.143  0.035  2.261   5.1105e-02
   3_adp:   7.081  0.046  0.261 85.143  0.035  2.261   5.1105e-02
   3_occ:   7.081  0.046  0.261 85.143  0.035  2.261   5.1105e-02
   4_bss:   7.081  0.046  0.261 85.143  0.035  2.261   5.1105e-02
   4_xyz:   6.818  0.041  0.211 84.024  0.040  2.372   3.5840e-02
   4_adp:   6.818  0.041  0.211 84.024  0.040  2.372   3.5840e-02
   4_occ:   6.818  0.041  0.211 84.024  0.040  2.372   3.5840e-02
   5_bss:   6.818  0.041  0.211 84.024  0.040  2.372   3.5840e-02
   5_xyz:   6.999  0.042  0.225 84.527  0.036  2.320   3.5444e-02
   5_adp:   6.999  0.042  0.225 84.527  0.036  2.320   3.5444e-02
   5_occ:   6.999  0.042  0.225 84.527  0.036  2.320   3.5444e-02
   5_bss:   6.999  0.042  0.225 84.527  0.036  2.320   3.5444e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  62.36   0.00  16.48  52.18   0.00  12.63  62.36   7.19  37.41
   1_occ:  62.36   0.00  16.48  52.18   0.00  12.63  62.36   7.19  37.41
   2_bss:  62.36   0.00  16.48  52.18   0.00  12.63  62.36   7.19  37.41
   2_xyz:  62.36   0.00  16.48  52.18   0.00  12.63  62.36   7.19  37.41
   2_adp:  65.01   1.75  16.58  57.23   1.75  12.76  65.01   4.52  37.38
   2_occ:  65.01   1.75  16.58  57.23   1.75  12.76  65.01   4.52  37.38
   3_bss:  65.01   1.75  16.58  57.23   1.75  12.76  65.01   4.52  37.38
   3_xyz:  65.01   1.75  16.58  57.23   1.75  12.76  65.01   4.52  37.38
   3_adp:  78.45   0.70  17.08  78.45   0.70  12.91  75.99   3.35  39.80
   3_occ:  78.45   0.70  17.08  78.45   0.70  12.91  75.99   3.35  39.80
   4_bss:  78.45   0.70  17.08  78.45   0.70  12.91  75.99   3.35  39.80
   4_xyz:  78.45   0.70  17.08  78.45   0.70  12.91  75.99   3.35  39.80
   4_adp:  78.18   0.00  16.99  78.18   0.00  12.89  75.98   5.24  39.30
   4_occ:  78.18   0.00  16.99  78.18   0.00  12.89  75.98   5.24  39.30
   5_bss:  78.18   0.00  16.99  78.18   0.00  12.89  75.98   5.24  39.30
   5_xyz:  78.18   0.00  16.99  78.18   0.00  12.89  75.98   5.24  39.30
   5_adp:  85.01   0.96  16.87  85.01   0.96  12.79  79.12   6.32  39.13
   5_occ:  85.01   0.96  16.87  85.01   0.96  12.79  79.12   6.32  39.13
   5_bss:  84.98   0.93  16.84  84.98   0.93  12.75  79.09   6.29  39.10
------------------------------------------------------------------------
 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:    0.959    0.029    0.271
   1_adp:    0.959    0.029    0.271
   1_occ:    0.959    0.029    0.271
   2_bss:    0.959    0.029    0.271
   2_xyz:    0.632    0.025    0.305
   2_adp:    0.632    0.025    0.305
   2_occ:    0.632    0.025    0.305
   3_bss:    0.632    0.025    0.305
   3_xyz:    0.731    0.016    0.339
   3_adp:    0.731    0.016    0.339
   3_occ:    0.731    0.016    0.339
   4_bss:    0.731    0.016    0.339
   4_xyz:    0.836    0.028    0.345
   4_adp:    0.836    0.028    0.345
   4_occ:    0.836    0.028    0.345
   5_bss:    0.836    0.028    0.345
   5_xyz:    0.930    0.033    0.351
   5_adp:    0.930    0.033    0.351
   5_occ:    0.930    0.033    0.351
   5_bss:    0.930    0.033    0.351
------------------------------------------------------------------------

CPU time actual refinement: 312.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_763/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_763/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_763/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_763/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_763/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 312.71 
  Macro-tasks:
    bulk solvent and scale       = 37.77  
    individual site refinement   = 125.38 
    weights calculation          = 28.57  
    collect and process          = 6.55   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 198.37 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 98.97  
    alpha_beta                      = 7.88   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 106.85 
    fmodel                         = 6.20   
    r_factors                      = 0.22   
    phase_errors                   = 11.35  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 234.05 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.495 micro seconds
Total CPU time: 5.43 minutes
from_scatterers_fft:    631 calls, 98.69 s
gradients_fft:          576 calls, 93.87 s

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

# Date 2008-01-16 Time 05:35:59 PST -0800 (1200490559.89 s)
Start R-work = 0.2922, R-free = 0.2891 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1728 (no bulk solvent and anisotropic scale)

Start R-work = 0.2766, R-free = 0.2747
Final R-work = 0.1073, R-free = 0.1524