# Date 2008-01-16 Time 04:26:59 PST -0800 (1200486419.40 s)
#phil __OFF__

Command line arguments: "../322.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2271
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 322

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.3993, 85.5261, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8205 1.97059
Completeness in resolution range: 0.958178
Completeness with d_max=infinity: 0.955188

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8205
                             d_min =   1.9706

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8205 1.97059
Completeness in resolution range: 0.958178
Completeness with d_max=infinity: 0.955188

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8210 -  4.2160 [2152/2180]  1936   216  10.0%
  bin  2:  4.2160 -  3.3592 [2044/2067]  1842   202   9.9%
  bin  3:  3.3592 -  2.9383 [2045/2067]  1839   206  10.1%
  bin  4:  2.9383 -  2.6714 [2013/2032]  1815   198   9.8%
  bin  5:  2.6714 -  2.4808 [2010/2039]  1801   209  10.4%
  bin  6:  2.4808 -  2.3352 [1977/2019]  1788   189   9.6%
  bin  7:  2.3352 -  2.2186 [1982/2018]  1785   197   9.9%
  bin  8:  2.2186 -  2.1223 [1980/2017]  1776   204  10.3%
  bin  9:  2.1223 -  2.0409 [1950/1982]  1754   196  10.1%
  bin 10:  2.0409 -  1.9706 [1436/2023]  1294   142   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_322/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 19
        2.26 -     2.92: 1488
        2.92 -     3.58: 4534
        3.58 -     4.24: 9265
        4.24 -     4.90: 13200
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.597 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.710 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.868 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.903 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28501 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_322/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_322/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.3993 85.5261 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: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3630   r_free= 0.3570   ksol= 0.00   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.117324                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8210 -  4.7020 0.99   1392  156 0.3011 0.3142      6.3922      6.4362|
|  2:  4.7020 -  3.7521 0.99   1344  149 0.2900 0.2700      6.5182      6.5045|
|  3:  3.7521 -  3.2836 0.99   1316  150 0.3112 0.2985       6.417      6.4443|
|  4:  3.2836 -  2.9861 0.99   1309  133 0.3338 0.3382      6.2918       6.247|
|  5:  2.9861 -  2.7736 0.98   1285  147 0.3676 0.3218      6.1762      6.1233|
|  6:  2.7736 -  2.6110 0.98   1293  143 0.3894 0.3788      6.1183      6.0015|
|  7:  2.6110 -  2.4808 0.99   1294  153 0.3870 0.3503      6.1037      5.9878|
|  8:  2.4808 -  2.3733 0.99   1286  133 0.3933 0.4381      6.0304      6.0828|
|  9:  2.3733 -  2.2823 0.98   1283  147 0.4284 0.4211      6.0099      6.0372|
| 10:  2.2823 -  2.2038 0.97   1255  142 0.4094 0.4667      5.9937      6.0388|
| 11:  2.2038 -  2.1351 0.98   1271  141 0.4195 0.4241      5.9159       5.991|
| 12:  2.1351 -  2.0742 0.99   1275  141 0.4303 0.4192      5.8873      5.9039|
| 13:  2.0742 -  2.0198 0.97   1264  133 0.4400 0.4265      5.8202      5.7815|
| 14:  2.0198 -  1.9706 0.60    763   91 0.4396 0.4077      5.7586      5.6417|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8210 -  4.7020  1392   156  0.76  28.91   0.86     0.76      50395.89|
|  2:  4.7020 -  3.7521  1344   149  0.81  24.96   0.97     0.90      55852.64|
|  3:  3.7521 -  3.2836  1316   150  0.78  28.48   0.99     0.94      53639.04|
|  4:  3.2836 -  2.9861  1309   133  0.75  31.09   0.99     0.94      45610.95|
|  5:  2.9861 -  2.7736  1285   147  0.71  34.98   0.97     0.91      36829.46|
|  6:  2.7736 -  2.6110  1293   143  0.69  36.27   0.98     0.90      32005.66|
|  7:  2.6110 -  2.4808  1294   153  0.70  35.43   0.98     0.90      29653.26|
|  8:  2.4808 -  2.3733  1286   133  0.66  39.41   1.00     0.87      30956.45|
|  9:  2.3733 -  2.2823  1283   147  0.61  43.52   1.00     0.83      31226.11|
| 10:  2.2823 -  2.2038  1255   142  0.59  45.03   1.03     0.80      31299.87|
| 11:  2.2038 -  2.1351  1271   141  0.57  46.53   1.02     0.81      29297.19|
| 12:  2.1351 -  2.0742  1275   141  0.58  46.09   1.03     0.84      26777.09|
| 13:  2.0742 -  2.0198  1264   133  0.59  45.32   1.01     0.84      22411.95|
| 14:  2.0198 -  1.9706   763    91  0.61  43.19   1.00     0.80      17350.85|
|alpha:            min =        0.76 max =            0.94 mean =         0.86|
|beta:             min =    17350.85 max =        55852.64 mean =     36000.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.96 mean =        37.48|
|phase err.(test): min =        0.00 max =           89.77 mean =        37.41|
|-----------------------------------------------------------------------------|

============================== 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 = 3.391559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.761   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.871030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.385   (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 |  1.597 -  1.927:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.927 -  2.257:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.257 -  2.588:       45 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.588 -  2.918:     1443 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.918 -  3.248:     1932 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.248 -  3.579:     2602 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.579 -  3.909:     4737 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.909 -  4.239:     4528 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.239 -  4.570:     6013 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.570 -  4.900:     7187 |
|-----------------------------------------------------------------------------|
|-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 |        0.174 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.597 |       0.361 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    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: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3630   r_free= 0.3570   ksol= 0.00   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.117324                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3527   r_free= 0.3455   ksol= 0.31   Bsol= 29.35   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,0.22,-0.54,0.00,-0.00,-0.00); trace/3= -0.53                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.101855                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.044291              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.598   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.470486              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.142   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3527      final r-factor (work) = 0.2199          |
| start r-factor (free) = 0.3455      final r-factor (free) = 0.2369          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4733 = 3.04 * 0.50 * 6.1094 + 1.00 * 0.1739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9768 = 3.04 * 0.50 * 5.8504 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2199      final r-factor (work) = 0.1999          |
| start r-factor (free) = 0.2369      final r-factor (free) = 0.2453          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7586 = 0.47 * 1.00 * 5.8504 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6561 = 0.47 * 1.00 * 5.6231 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.58   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    76.58   17.52    None  None   None       |
|    Sol.    : 438    0      5.95    76.58   38.94    None  None   None       |
|    Mac.    : 2385   0      0.00    76.15   13.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.658:  544   |   5:    38.291 -  45.949:  102        |
|      1:     7.658 -  15.316: 1209   |   6:    45.949 -  53.607:   73        |
|      2:    15.316 -  22.975:  457   |   7:    53.607 -  61.265:   69        |
|      3:    22.975 -  30.633:  183   |   8:    61.265 -  68.924:   33        |
|      4:    30.633 -  38.291:  141   |   9:    68.924 -  76.582:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1999 r_free = 0.2453             target_work(ml) = 5.636         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1995 r_free = 0.2453             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1995   r_free= 0.2453   ksol= 0.31   Bsol= 29.35   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,0.22,-0.54,0.00,-0.00,-0.00); trace/3= -0.53                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.635402                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1979   r_free= 0.2442   ksol= 0.31   Bsol= 36.28   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.24,-1.42,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.632398                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.831064              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.746   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.178145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.445  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1979      final r-factor (work) = 0.1409          |
| start r-factor (free) = 0.2442      final r-factor (free) = 0.1850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0421 = 2.83 * 0.50 * 5.6308 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8270 = 2.83 * 0.50 * 5.4910 + 1.00 * 0.0544                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1409      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.1850      final r-factor (free) = 0.1728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9886 = 0.18 * 1.00 * 5.4910 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9519 = 0.18 * 1.00 * 5.3016 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.03    78.67   16.99    None  None   None       |
|    all(noH): 2823   0      2.03    78.67   16.99    None  None   None       |
|    Sol.    : 438    0      4.99    71.97   38.06    None  None   None       |
|    Mac.    : 2385   0      2.03    78.67   13.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.035 -   9.698:  908   |   5:    40.353 -  48.017:  109        |
|      1:     9.698 -  17.362: 1130   |   6:    48.017 -  55.680:   80        |
|      2:    17.362 -  25.026:  282   |   7:    55.680 -  63.344:   39        |
|      3:    25.026 -  32.689:  118   |   8:    63.344 -  71.007:   16        |
|      4:    32.689 -  40.353:  136   |   9:    71.007 -  78.671:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1330 r_free = 0.1728             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1328 r_free = 0.1727             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1727   ksol= 0.31   Bsol= 36.28   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.24,-1.42,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.267709                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1332   r_free= 0.1719   ksol= 0.32   Bsol= 41.71   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-1.71,-1.57,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.267438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.668680              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.860  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.587979              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.779  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1332      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1303 = 2.67 * 0.50 * 5.3030 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9985 = 2.67 * 0.50 * 5.1992 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0644 = 0.59 * 1.00 * 5.1992 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0297 = 0.59 * 1.00 * 5.1381 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    85.72   17.08    None  None   None       |
|    all(noH): 2823   0      0.81    85.72   17.08    None  None   None       |
|    Sol.    : 438    0      0.81    73.06   39.47    None  None   None       |
|    Mac.    : 2385   0      1.53    85.72   12.97    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:     0.810 -   9.302:  839   |   5:    43.266 -  51.757:  127        |
|      1:     9.302 -  17.793: 1229   |   6:    51.757 -  60.249:   84        |
|      2:    17.793 -  26.284:  274   |   7:    60.249 -  68.740:   22        |
|      3:    26.284 -  34.775:  126   |   8:    68.740 -  77.231:   11        |
|      4:    34.775 -  43.266:  105   |   9:    77.231 -  85.722:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1553             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1552             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1552   ksol= 0.32   Bsol= 41.71   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-1.71,-1.57,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132477                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1552   ksol= 0.32   Bsol= 41.71   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.76,-1.45,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132517                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.487449              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.035  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662651              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.659  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8823 = 1.49 * 0.50 * 5.1380 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8689 = 1.49 * 0.50 * 5.1347 + 1.00 * 0.0501                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4111 = 0.66 * 1.00 * 5.1347 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4093 = 0.66 * 1.00 * 5.1313 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    91.69   17.00    None  None   None       |
|    all(noH): 2823   0      0.91    91.69   17.00    None  None   None       |
|    Sol.    : 438    0      1.62    81.71   39.45    None  None   None       |
|    Mac.    : 2385   0      0.91    91.69   12.87    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:     0.914 -   9.991: 1054   |   5:    46.302 -  55.380:  102        |
|      1:     9.991 -  19.069: 1102   |   6:    55.380 -  64.458:   66        |
|      2:    19.069 -  28.147:  217   |   7:    64.458 -  73.535:   14        |
|      3:    28.147 -  37.225:  133   |   8:    73.535 -  82.613:    7        |
|      4:    37.225 -  46.302:  122   |   9:    82.613 -  91.691:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1554             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1554             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1554   ksol= 0.32   Bsol= 41.71   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.76,-1.45,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1555   ksol= 0.32   Bsol= 44.05   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-1.68,-1.32,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135691                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.582920              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.610  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.684372              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.658  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6780 = 2.58 * 0.50 * 5.1321 + 1.00 * 0.0501                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6711 = 2.58 * 0.50 * 5.1159 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1058      final r-factor (work) = 0.1056          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5102 = 0.68 * 1.00 * 5.1159 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5056 = 0.68 * 1.00 * 5.1091 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    93.42   16.80    None  None   None       |
|    all(noH): 2823   0      0.79    93.42   16.80    None  None   None       |
|    Sol.    : 438    0      2.99    83.34   39.19    None  None   None       |
|    Mac.    : 2385   0      0.79    93.42   12.69    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:     0.785 -  10.049: 1104   |   5:    47.104 -  56.368:   99        |
|      1:    10.049 -  19.313: 1077   |   6:    56.368 -  65.632:   56        |
|      2:    19.313 -  28.577:  205   |   7:    65.632 -  74.896:   12        |
|      3:    28.577 -  37.841:  132   |   8:    74.896 -  84.160:    6        |
|      4:    37.841 -  47.104:  126   |   9:    84.160 -  93.423:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1056 r_free = 0.1549             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1056 r_free = 0.1549             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1549   ksol= 0.32   Bsol= 44.05   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-1.68,-1.32,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108893                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8210 -  4.7020 0.99   1392  156 0.0940 0.1273      5.3399      5.5135|
|  2:  4.7020 -  3.7521 0.99   1344  149 0.0808 0.1081      5.3946       5.608|
|  3:  3.7521 -  3.2836 0.99   1316  150 0.0991 0.1494      5.4239        5.81|
|  4:  3.2836 -  2.9861 0.99   1309  133 0.1149 0.1529      5.4115       5.587|
|  5:  2.9861 -  2.7736 0.98   1285  147 0.1212 0.1645       5.277      5.4959|
|  6:  2.7736 -  2.6110 0.98   1293  143 0.1200 0.1890      5.1996      5.4323|
|  7:  2.6110 -  2.4808 0.99   1294  153 0.1114 0.1599      5.1014      5.3484|
|  8:  2.4808 -  2.3733 0.99   1286  133 0.1108 0.1756      5.0463      5.3156|
|  9:  2.3733 -  2.2823 0.98   1283  147 0.1117 0.1803       4.986      5.3068|
| 10:  2.2823 -  2.2038 0.97   1255  142 0.1062 0.1699      4.9469      5.1592|
| 11:  2.2038 -  2.1351 0.98   1271  141 0.1085 0.1733      4.9032      5.2448|
| 12:  2.1351 -  2.0742 0.99   1275  141 0.1043 0.1658       4.826      5.1275|
| 13:  2.0742 -  2.0198 0.97   1264  133 0.1054 0.1642       4.755      4.9952|
| 14:  2.0198 -  1.9706 0.60    763   91 0.1044 0.1763      4.6778      4.9486|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8210 -  4.7020  1392   156  0.94   8.73   0.98     0.95       6638.78|
|  2:  4.7020 -  3.7521  1344   149  0.95   7.73   1.02     1.00       8524.87|
|  3:  3.7521 -  3.2836  1316   150  0.94  10.71   1.03     1.02       9601.01|
|  4:  3.2836 -  2.9861  1309   133  0.93  12.98   1.01     1.00       9701.40|
|  5:  2.9861 -  2.7736  1285   147  0.91  15.25   1.00     0.97       7810.31|
|  6:  2.7736 -  2.6110  1293   143  0.90  16.04   0.98     0.95       6923.28|
|  7:  2.6110 -  2.4808  1294   153  0.91  14.64   0.99     0.96       5633.53|
|  8:  2.4808 -  2.3733  1286   133  0.91  14.62   0.99     0.97       5233.95|
|  9:  2.3733 -  2.2823  1283   147  0.91  15.12   1.00     0.97       4646.52|
| 10:  2.2823 -  2.2038  1255   142  0.90  15.48   0.99     0.95       4420.02|
| 11:  2.2038 -  2.1351  1271   141  0.91  15.57   1.00     0.97       4165.96|
| 12:  2.1351 -  2.0742  1275   141  0.92  14.67   1.00     0.99       3611.68|
| 13:  2.0742 -  2.0198  1264   133  0.91  15.33   0.99     0.99       3173.04|
| 14:  2.0198 -  1.9706   763    91  0.91  14.91   0.97     0.93       2628.47|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2628.47 max =         9701.40 mean =      6038.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.60|
|phase err.(test): min =        0.00 max =           89.79 mean =        13.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1549   ksol= 0.32   Bsol= 44.38   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-1.48,-1.08,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109131                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1549   ksol= 0.32   Bsol= 44.38   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-1.48,-1.08,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109131                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8210 -  4.7020 0.99   1392  156 0.0941 0.1275      5.3424      5.5164|
|  2:  4.7020 -  3.7521 0.99   1344  149 0.0808 0.1080      5.3954      5.6077|
|  3:  3.7521 -  3.2836 0.99   1316  150 0.0991 0.1494      5.4239      5.8102|
|  4:  3.2836 -  2.9861 0.99   1309  133 0.1148 0.1529      5.4114       5.587|
|  5:  2.9861 -  2.7736 0.98   1285  147 0.1212 0.1645      5.2769      5.4957|
|  6:  2.7736 -  2.6110 0.98   1293  143 0.1200 0.1889      5.1994      5.4317|
|  7:  2.6110 -  2.4808 0.99   1294  153 0.1114 0.1599      5.1013      5.3485|
|  8:  2.4808 -  2.3733 0.99   1286  133 0.1108 0.1756      5.0463      5.3154|
|  9:  2.3733 -  2.2823 0.98   1283  147 0.1116 0.1803      4.9861      5.3068|
| 10:  2.2823 -  2.2038 0.97   1255  142 0.1062 0.1700      4.9471      5.1598|
| 11:  2.2038 -  2.1351 0.98   1271  141 0.1085 0.1732      4.9033      5.2449|
| 12:  2.1351 -  2.0742 0.99   1275  141 0.1043 0.1659       4.826      5.1278|
| 13:  2.0742 -  2.0198 0.97   1264  133 0.1055 0.1641       4.755      4.9949|
| 14:  2.0198 -  1.9706 0.60    763   91 0.1044 0.1762      4.6777      4.9484|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8210 -  4.7020  1392   156  0.94   8.76   0.98     0.96       6683.31|
|  2:  4.7020 -  3.7521  1344   149  0.95   7.75   1.02     1.01       8547.75|
|  3:  3.7521 -  3.2836  1316   150  0.94  10.72   1.03     1.03       9599.49|
|  4:  3.2836 -  2.9861  1309   133  0.93  12.99   1.02     1.01       9701.07|
|  5:  2.9861 -  2.7736  1285   147  0.91  15.25   1.00     0.98       7806.23|
|  6:  2.7736 -  2.6110  1293   143  0.90  16.03   0.99     0.95       6919.95|
|  7:  2.6110 -  2.4808  1294   153  0.91  14.64   0.99     0.97       5631.27|
|  8:  2.4808 -  2.3733  1286   133  0.91  14.62   1.00     0.98       5233.65|
|  9:  2.3733 -  2.2823  1283   147  0.91  15.12   1.01     0.98       4647.69|
| 10:  2.2823 -  2.2038  1255   142  0.90  15.49   1.00     0.96       4421.53|
| 11:  2.2038 -  2.1351  1271   141  0.91  15.57   1.01     0.98       4167.00|
| 12:  2.1351 -  2.0742  1275   141  0.92  14.68   1.01     1.00       3611.80|
| 13:  2.0742 -  2.0198  1264   133  0.91  15.33   1.00     1.00       3172.08|
| 14:  2.0198 -  1.9706   763    91  0.91  14.90   0.98     0.94       2626.92|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2626.92 max =         9701.07 mean =      6043.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.61|
|phase err.(test): min =        0.00 max =           89.78 mean =        13.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    93.40   16.77    None  None   None       |
|    all(noH): 2823   0      0.76    93.40   16.77    None  None   None       |
|    Sol.    : 438    0      2.96    83.32   39.17    None  None   None       |
|    Mac.    : 2385   0      0.76    93.40   12.66    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:     0.759 -  10.023: 1104   |   5:    47.078 -  56.342:   99        |
|      1:    10.023 -  19.286: 1077   |   6:    56.342 -  65.605:   56        |
|      2:    19.286 -  28.550:  205   |   7:    65.605 -  74.869:   12        |
|      3:    28.550 -  37.814:  132   |   8:    74.869 -  84.133:    6        |
|      4:    37.814 -  47.078:  126   |   9:    84.133 -  93.397:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 292         
Filter by distance & map next to the model:
   mapped sites are within: 0.542 - 4.479
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 292
   mapped sites are within: 0.749 - 4.479

peak=    5.606 closest distance to " CB  ARG A 275 " =    0.958
peak=    5.594 closest distance to " NH2 ARG A  56 " =    2.262
peak=    5.212 closest distance to " CB  SER A  63 " =    1.121
peak=    5.158 closest distance to " CG  PRO A  54 " =    1.230
peak=    5.050 closest distance to " CB  GLN A 223 " =    1.425
peak=    5.047 closest distance to " O   HOH Z 142 " =    1.653
peak=    4.970 closest distance to " CB  GLN A 183 " =    1.304
peak=    4.791 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.775 closest distance to " O   HOH Z 403 " =    1.823
peak=    4.733 closest distance to " O   HOH Z 298 " =    1.851
peak=    4.668 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.633 closest distance to " O   HOH Z 126 " =    1.837
peak=    4.631 closest distance to " O   HOH Z 232 " =    2.369
peak=    4.599 closest distance to " CB  GLU A 152 " =    1.189
peak=    4.596 closest distance to " C   PRO A 198 " =    1.449
peak=    4.593 closest distance to " O   HOH Z 272 " =    1.836
peak=    4.552 closest distance to " O   HOH Z  15 " =    2.111
peak=    4.538 closest distance to " NE2 GLN A  11 " =    1.014
peak=    4.534 closest distance to " CB  ARG A  79 " =    1.381
peak=    4.522 closest distance to " O   HOH Z 209 " =    2.253
peak=    4.497 closest distance to " O   HOH Z 234 " =    3.658
peak=    4.494 closest distance to " O   HOH Z 193 " =    1.748
peak=    4.470 closest distance to " O   HOH Z  97 " =    1.906
peak=    4.449 closest distance to " O   SER A  87 " =    2.152
peak=    4.399 closest distance to " O   HOH Z 402 " =    1.457
peak=    4.348 closest distance to " CB  TYR A 169 " =    0.830
peak=    4.309 closest distance to " O   HOH Z 369 " =    2.231
peak=    4.299 closest distance to " O   HOH Z  78 " =    1.660
peak=    4.271 closest distance to " O   HOH Z 203 " =    1.771
peak=    4.269 closest distance to " O   HOH Z  43 " =    2.008
peak=    4.264 closest distance to " O   HOH Z 287 " =    2.070
peak=    4.233 closest distance to " CD2 TRP A 179 " =    1.396
peak=    4.232 closest distance to " NZ  LYS A 117 " =    3.083
peak=    4.207 closest distance to " O   HOH Z 368 " =    2.013
peak=    4.181 closest distance to " CA  ALA A  21 " =    1.202
peak=    4.169 closest distance to " CG1 ILE A  33 " =    1.251
peak=    4.160 closest distance to " CB  ASN A 148 " =    1.423
peak=    4.133 closest distance to " O   HOH Z  40 " =    1.810
peak=    4.132 closest distance to " ND2 ASN A 187 " =    1.508
peak=    4.124 closest distance to " O   HOH Z  44 " =    1.967
peak=    4.117 closest distance to " CB  ARG A 190 " =    1.698
peak=    4.110 closest distance to " CG  ARG A  66 " =    2.668
peak=    4.109 closest distance to " O   HOH Z 346 " =    1.574
peak=    4.034 closest distance to " NH2BARG A 145 " =    2.055
peak=    4.022 closest distance to " O   HOH Z 327 " =    1.662
peak=    4.012 closest distance to " O   HOH Z  54 " =    1.698
peak=    4.009 closest distance to " O   HOH Z 128 " =    1.912
peak=    4.009 closest distance to " CB  GLU A 277 " =    3.519
peak=    3.995 closest distance to " O   HOH Z  63 " =    1.958
peak=    3.990 closest distance to " CG  PRO A  90 " =    1.180
peak=    3.982 closest distance to " OD1 ASN A  69 " =    2.559
peak=    3.979 closest distance to " O   HOH Z 284 " =    2.899
peak=    3.978 closest distance to " O   HOH Z 316 " =    2.956
peak=    3.971 closest distance to " O   HOH Z 144 " =    2.151
peak=    3.960 closest distance to " CB  PRO A  54 " =    0.852
peak=    3.947 closest distance to " CG2 ILE A  20 " =    1.378
peak=    3.941 closest distance to " O   HOH Z 427 " =    2.797
peak=    3.926 closest distance to " O   HOH Z 345 " =    2.880
peak=    3.925 closest distance to " CA  ASN A 176 " =    1.129
peak=    3.922 closest distance to " CB  SER A   3 " =    1.213
peak=    3.917 closest distance to " O   HOH Z 158 " =    2.948
peak=    3.896 closest distance to " CD  ARG A 269 " =    0.972
peak=    3.895 closest distance to " O   HOH Z 250 " =    1.434
peak=    3.884 closest distance to " O   HOH Z 303 " =    2.108
peak=    3.874 closest distance to " O   HOH Z 147 " =    1.752
peak=    3.867 closest distance to " OD2 ASP A 298 " =    3.927
peak=    3.865 closest distance to " OE1 GLU A   2 " =    2.241
peak=    3.862 closest distance to " O   HOH Z  61 " =    1.589
peak=    3.862 closest distance to " CB  VAL A 265 " =    1.284
peak=    3.860 closest distance to " O   HOH Z 421 " =    1.637
peak=    3.853 closest distance to " O   HOH Z  59 " =    2.271
peak=    3.851 closest distance to " O   HOH Z 128 " =    2.122
peak=    3.838 closest distance to " OD2 ASP A 286 " =    2.805
peak=    3.815 closest distance to " CB  GLU A 128 " =    1.197
peak=    3.811 closest distance to " O   HOH Z 261 " =    1.613
peak=    3.807 closest distance to " CB  TRP A 179 " =    1.223
peak=    3.801 closest distance to " OG BSER A 164 " =    2.314
peak=    3.795 closest distance to " O   HOH Z 227 " =    1.592
peak=    3.791 closest distance to " CB  ARG A 139 " =    0.957
peak=    3.791 closest distance to " O   HOH Z 426 " =    1.494
peak=    3.790 closest distance to " O   HOH Z 189 " =    2.043
peak=    3.782 closest distance to " O   HOH Z 389 " =    1.881
peak=    3.781 closest distance to " O   HOH Z 423 " =    1.989
peak=    3.767 closest distance to " CA  ALA A  84 " =    1.217
peak=    3.764 closest distance to " CB  SER A  26 " =    1.644
peak=    3.763 closest distance to " O   HOH Z 126 " =    1.876
peak=    3.750 closest distance to " O   HOH Z 344 " =    3.037
peak=    3.724 closest distance to " O   HOH Z 371 " =    3.379
peak=    3.719 closest distance to " CB  LEU A 228 " =    1.162
peak=    3.713 closest distance to " O   HOH Z 214 " =    2.220
peak=    3.712 closest distance to " O   HOH Z 245 " =    1.358
peak=    3.707 closest distance to " O   HOH Z 416 " =    2.760
peak=    3.693 closest distance to " O   HOH Z  97 " =    2.524
peak=    3.693 closest distance to " CG  GLN A  58 " =    2.608
peak=    3.691 closest distance to " O   HOH Z 411 " =    3.622
peak=    3.691 closest distance to " CG1BVAL A  72 " =    1.643
peak=    3.686 closest distance to " CG  ARG A  66 " =    0.976
peak=    3.685 closest distance to " CB  TRP A 266 " =    0.966
peak=    3.681 closest distance to " CG  PRO A 198 " =    1.211
peak=    3.677 closest distance to " O   HOH Z 425 " =    2.055
peak=    3.673 closest distance to " O   HOH Z  80 " =    1.656
peak=    3.672 closest distance to " CD2 LEU A 297 " =    0.956
peak=    3.671 closest distance to " C   ILE A 106 " =    1.905
peak=    3.664 closest distance to " CB  ASP A 140 " =    0.994
peak=    3.660 closest distance to " CG AARG A 275 " =    1.083
peak=    3.657 closest distance to " O   HOH Z 197 " =    2.847
peak=    3.650 closest distance to " N   ASN A  39 " =    1.290
peak=    3.646 closest distance to " CA  ALA A 291 " =    0.838
peak=    3.641 closest distance to " O   HOH Z 102 " =    1.257
peak=    3.638 closest distance to " NH2AARG A 275 " =    3.651
peak=    3.638 closest distance to " O   HOH Z 132 " =    2.560
peak=    3.635 closest distance to " CB  ASN A  39 " =    0.825
peak=    3.633 closest distance to " CG2 ILE A 120 " =    1.098
peak=    3.633 closest distance to " O   HOH Z 406 " =    1.572
peak=    3.627 closest distance to " O   HOH Z 108 " =    2.584
peak=    3.620 closest distance to " CA  LYS A 117 " =    1.256
peak=    3.614 closest distance to " CA  ARG A 195 " =    1.256
peak=    3.607 closest distance to " O   HOH Z  68 " =    2.100
peak=    3.605 closest distance to " O   HOH Z 357 " =    1.863
peak=    3.604 closest distance to " O   HOH Z 279 " =    2.117
peak=    3.597 closest distance to " CG  PRO A 243 " =    1.145
peak=    3.578 closest distance to " CA  ALA A  51 " =    0.976
peak=    3.575 closest distance to " O   HOH Z 298 " =    2.323
peak=    3.574 closest distance to " CZ  PHE A 218 " =    1.080
peak=    3.562 closest distance to " CA  THR A 221 " =    0.963
peak=    3.559 closest distance to " O   HOH Z 417 " =    3.095
peak=    3.559 closest distance to " O   HOH Z  19 " =    1.864
peak=    3.548 closest distance to " O   HOH Z 124 " =    1.300
peak=    3.545 closest distance to " O   HOH Z 361 " =    3.680
peak=    3.545 closest distance to " O   HOH Z   1 " =    2.148
peak=    3.543 closest distance to " O   HOH Z 365 " =    2.781
peak=    3.541 closest distance to " CB  TYR A 169 " =    0.939
peak=    3.539 closest distance to " O   HOH Z  49 " =    2.094
peak=    3.535 closest distance to " O   HOH Z 291 " =    1.411
peak=    3.535 closest distance to " O   HOH Z 132 " =    2.570
peak=    3.532 closest distance to " CA  ARG A  36 " =    1.028
peak=    3.529 closest distance to " O   HOH Z  21 " =    1.771
peak=    3.525 closest distance to " ND2 ASN A 110 " =    1.614
peak=    3.523 closest distance to " CE  LYS A 119 " =    1.140
peak=    3.521 closest distance to " O   HOH Z 299 " =    4.327
peak=    3.518 closest distance to " O   HOH Z 427 " =    3.062
peak=    3.515 closest distance to " O   HOH Z 185 " =    1.696
peak=    3.500 closest distance to " O   HOH Z 173 " =    2.017
peak=    3.500 closest distance to " CG  LYS A  76 " =    1.040
peak=    3.494 closest distance to " CA  ASN A 215 " =    1.127
peak=    3.492 closest distance to " O   HOH Z 305 " =    3.600
peak=    3.492 closest distance to " CB  SER A 141 " =    1.040
peak=    3.487 closest distance to " CB  VAL A 202 " =    1.514
peak=    3.479 closest distance to " NH2 ARG A 156 " =    1.141
peak=    3.476 closest distance to " O   HOH Z  61 " =    1.525
peak=    3.473 closest distance to " O   HOH Z 286 " =    2.197
peak=    3.470 closest distance to " O   HOH Z 134 " =    1.224
peak=    3.468 closest distance to " CA  ASP A 162 " =    1.119
peak=    3.463 closest distance to " O   HOH Z 180 " =    2.307
peak=    3.463 closest distance to " O   HOH Z 374 " =    2.550
peak=    3.461 closest distance to " O   HOH Z 250 " =    1.643
peak=    3.460 closest distance to " OG1 THR A 294 " =    2.352
peak=    3.457 closest distance to " CB  ALA A 291 " =    1.348
peak=    3.457 closest distance to " CB  SER A  62 " =    0.867
peak=    3.434 closest distance to " O   HOH Z 265 " =    2.271
peak=    3.433 closest distance to " CB  ALA A 248 " =    1.371
peak=    3.431 closest distance to " O   HOH Z  66 " =    2.154
peak=    3.427 closest distance to " CA  ASP A 140 " =    1.137
peak=    3.427 closest distance to " O   HOH Z  35 " =    2.384
peak=    3.418 closest distance to " O   HOH Z 380 " =    1.971
peak=    3.410 closest distance to " CG2 THR A 221 " =    1.268
peak=    3.408 closest distance to " O   HOH Z 281 " =    4.479
peak=    3.397 closest distance to " CB  GLN A  89 " =    1.307
peak=    3.394 closest distance to " NH2 ARG A  79 " =    1.330
peak=    3.388 closest distance to " CB  THR A  31 " =    1.767
peak=    3.385 closest distance to " O   HOH Z 183 " =    1.460
peak=    3.369 closest distance to " OG  SER A  62 " =    2.799
peak=    3.365 closest distance to " O   HOH Z  89 " =    2.137
peak=    3.365 closest distance to " O   HOH Z 193 " =    2.175
peak=    3.365 closest distance to " O   HOH Z 258 " =    2.308
peak=    3.362 closest distance to " O   HOH Z 273 " =    2.754
peak=    3.360 closest distance to " O   HOH Z 359 " =    1.411
peak=    3.358 closest distance to " CD  ARG A 159 " =    0.749
peak=    3.354 closest distance to " ND1 HIS A  81 " =    1.568
peak=    3.353 closest distance to " O   HOH Z 163 " =    1.460
peak=    3.344 closest distance to " O   HOH Z 345 " =    1.577
peak=    3.343 closest distance to " CZ2 TRP A 179 " =    1.700
peak=    3.334 closest distance to " NH2 ARG A 219 " =    1.897
peak=    3.327 closest distance to " O   HOH Z 148 " =    3.145
peak=    3.325 closest distance to " O   HOH Z 217 " =    2.316
peak=    3.325 closest distance to " CD1 ILE A 106 " =    0.938
peak=    3.324 closest distance to " O   HOH Z 423 " =    3.418
peak=    3.323 closest distance to " O   HOH Z  85 " =    1.283
peak=    3.318 closest distance to " CE  LYS A  76 " =    0.777
peak=    3.318 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.312 closest distance to " O   HOH Z 247 " =    1.325
peak=    3.309 closest distance to " O   HOH Z  68 " =    1.677
peak=    3.306 closest distance to " CB  ILE A 120 " =    1.303
peak=    3.303 closest distance to " O   HOH Z  30 " =    2.089
peak=    3.303 closest distance to " O   HOH Z 126 " =    1.588
peak=    3.302 closest distance to " O  BHOH Z  74 " =    1.344
peak=    3.297 closest distance to " O   ALA A 165 " =    1.379
peak=    3.297 closest distance to " CG2BVAL A  41 " =    0.805
peak=    3.292 closest distance to " O   HOH Z 166 " =    3.900
peak=    3.291 closest distance to " NZ  LYS A 119 " =    1.538
peak=    3.290 closest distance to " CD1 LEU A 228 " =    1.628
peak=    3.290 closest distance to " CD1 LEU A 300 " =    1.286
peak=    3.290 closest distance to " O   HOH Z 189 " =    2.568
peak=    3.289 closest distance to " CD1 LEU A  96 " =    0.758
peak=    3.289 closest distance to " CB  ALA A   9 " =    1.572
peak=    3.282 closest distance to " O   HOH Z 353 " =    2.736
peak=    3.279 closest distance to " CG  MET A 185 " =    1.114
peak=    3.274 closest distance to " NH1AARG A 145 " =    1.204
peak=    3.273 closest distance to " O   HOH Z 334 " =    1.427
peak=    3.268 closest distance to " O   HOH Z 325 " =    2.278
peak=    3.267 closest distance to " CA  ASN A 217 " =    1.249
peak=    3.266 closest distance to " O   HOH Z 422 " =    2.638
peak=    3.266 closest distance to " CA  MET A 105 " =    1.067
peak=    3.255 closest distance to " O   HOH Z 261 " =    1.403
peak=    3.254 closest distance to " O   HOH Z  64 " =    2.327
peak=    3.252 closest distance to " O   HOH Z 336 " =    1.717
peak=    3.251 closest distance to " O   HOH Z 313 " =    1.646
peak=    3.250 closest distance to " O   HOH Z 380 " =    1.978
peak=    3.249 closest distance to " CB  TYR A 116 " =    0.833
peak=    3.248 closest distance to " CA  GLY A  80 " =    0.861
peak=    3.247 closest distance to " CD BLYS A 290 " =    1.218
peak=    3.241 closest distance to " O   HOH Z  47 " =    1.460
peak=    3.240 closest distance to " O   HOH Z 267 " =    1.954
peak=    3.238 closest distance to " O   SER A  26 " =    1.712
peak=    3.237 closest distance to " CA  MET A  40 " =    1.075
peak=    3.231 closest distance to " O   HOH Z  88 " =    3.205
peak=    3.228 closest distance to " CE1 TYR A 186 " =    1.235
peak=    3.220 closest distance to " CA  ALA A 160 " =    0.844
peak=    3.219 closest distance to " CG  GLN A  77 " =    2.013
peak=    3.219 closest distance to " CB  ASN A 285 " =    0.970
peak=    3.218 closest distance to " O   HOH Z 419 " =    1.500
peak=    3.213 closest distance to " O   HOH Z 437 " =    1.415
peak=    3.209 closest distance to " CD2 HIS A  81 " =    1.112
peak=    3.208 closest distance to " O   TRP A 274 " =    1.921
peak=    3.205 closest distance to " N   ARG A 156 " =    1.361
peak=    3.204 closest distance to " O   HOH Z  10 " =    1.761
peak=    3.203 closest distance to " CA  SER A 146 " =    1.741
peak=    3.203 closest distance to " CG BARG A 102 " =    1.783
peak=    3.203 closest distance to " CB  GLN A 205 " =    1.166
peak=    3.200 closest distance to " O   HOH Z 214 " =    2.291
peak=    3.198 closest distance to " CA  VAL A 125 " =    1.181
peak=    3.190 closest distance to " O   HOH Z 417 " =    2.272
peak=    3.188 closest distance to " CG2 VAL A 257 " =    0.771
peak=    3.185 closest distance to " O   HOH Z 368 " =    2.711
peak=    3.183 closest distance to " O   HOH Z  64 " =    2.190
peak=    3.180 closest distance to " CB  ALA A  34 " =    1.020
peak=    3.180 closest distance to " CB  ALA A  71 " =    1.276
peak=    3.179 closest distance to " CD  LYS A  76 " =    1.933
peak=    3.167 closest distance to " O   HOH Z 234 " =    1.783
peak=    3.165 closest distance to " CA  SER A  32 " =    1.583
peak=    3.164 closest distance to " CB  ASN A 215 " =    1.111
peak=    3.164 closest distance to " O   HOH Z 152 " =    1.936
peak=    3.164 closest distance to " N   TYR A 116 " =    1.611
peak=    3.163 closest distance to " O   HOH Z 255 " =    1.554
peak=    3.163 closest distance to " CB  ASN A 110 " =    1.089
peak=    3.163 closest distance to " N   TRP A 150 " =    1.092
peak=    3.162 closest distance to " CG2 VAL A 197 " =    1.135
peak=    3.161 closest distance to " CD  ARG A 139 " =    1.786
peak=    3.161 closest distance to " O   HOH Z 435 " =    1.856
peak=    3.160 closest distance to " O   HOH Z 251 " =    1.612
peak=    3.150 closest distance to " CB  THR A 157 " =    1.025
peak=    3.140 closest distance to " O   HOH Z 341 " =    1.812
peak=    3.137 closest distance to " OG BSER A 134 " =    2.860
peak=    3.136 closest distance to " CA  ALA A 233 " =    1.357
peak=    3.135 closest distance to " CG  MET A 113 " =    1.198
peak=    3.133 closest distance to " N   ASP A 162 " =    1.205
peak=    3.130 closest distance to " O   ILE A  33 " =    1.344
peak=    3.127 closest distance to " O   HOH Z 248 " =    1.649
peak=    3.127 closest distance to " O   HOH Z 438 " =    1.848
peak=    3.119 closest distance to " CB  GLN A 278 " =    0.867
peak=    3.117 closest distance to " O   HOH Z 425 " =    1.254
peak=    3.111 closest distance to " O   HOH Z  40 " =    2.897
peak=    3.108 closest distance to " OE1 GLN A  11 " =    1.896
peak=    3.105 closest distance to " CG  GLU A 277 " =    2.163
peak=    3.105 closest distance to " O   ALA A   1 " =    1.665
peak=    3.103 closest distance to " CA  TYR A 116 " =    1.421
peak=    3.097 closest distance to " O   HOH Z 222 " =    2.480
peak=    3.095 closest distance to " O   HOH Z 123 " =    2.229
peak=    3.091 closest distance to " CB  MET A 113 " =    1.744
peak=    3.088 closest distance to " O   HOH Z 433 " =    1.904
peak=    3.083 closest distance to " O   HOH Z 263 " =    1.775
peak=    3.070 closest distance to " CG2 THR A 294 " =    1.557
peak=    3.070 closest distance to " CG  MET A 185 " =    0.992
peak=    3.069 closest distance to " O   HOH Z 329 " =    3.782
peak=    3.067 closest distance to " OE2 GLU A  53 " =    2.129
peak=    3.065 closest distance to " O   HOH Z  85 " =    2.201
peak=    3.062 closest distance to " O   HOH Z  88 " =    2.636
peak=    3.053 closest distance to " O   HOH Z 271 " =    2.174
peak=    3.050 closest distance to " CB  VAL A 126 " =    1.231
peak=    3.012 closest distance to " O   HOH Z 163 " =    1.670

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.869 - 5.885
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 199
   mapped sites are within: 0.869 - 5.885

peak=   -5.079 closest distance to " O   HOH Z 266 " =    4.605
peak=   -4.493 closest distance to " C   HIS A 108 " =    1.117
peak=   -4.283 closest distance to " SG  CYS A 254 " =    3.320
peak=   -4.222 closest distance to " OXT GLY A 302 " =    2.807
peak=   -4.208 closest distance to " CD  ARG A 156 " =    2.035
peak=   -4.191 closest distance to " CD1 PHE A 130 " =    2.347
peak=   -4.182 closest distance to " O   HOH Z  13 " =    1.635
peak=   -4.174 closest distance to " O   PRO A 163 " =    2.074
peak=   -4.174 closest distance to " O   HOH Z 377 " =    2.169
peak=   -4.163 closest distance to " OG BSER A 134 " =    1.257
peak=   -4.152 closest distance to " CB  PRO A 243 " =    2.626
peak=   -4.129 closest distance to " CG  GLN A 223 " =    2.057
peak=   -4.093 closest distance to " O   VAL A  67 " =    2.882
peak=   -4.084 closest distance to " N   ALA A 248 " =    1.771
peak=   -4.076 closest distance to " O   VAL A  67 " =    2.717
peak=   -4.068 closest distance to " CD  GLN A  58 " =    1.168
peak=   -4.030 closest distance to " O   HOH Z 198 " =    1.923
peak=   -3.993 closest distance to " O   HOH Z 353 " =    2.204
peak=   -3.987 closest distance to " O   HOH Z 165 " =    1.923
peak=   -3.975 closest distance to " OG  SER A  97 " =    2.133
peak=   -3.971 closest distance to " O   HOH Z 290 " =    1.048
peak=   -3.949 closest distance to " CD1 LEU A 101 " =    2.411
peak=   -3.932 closest distance to " CB  ALA A 161 " =    2.574
peak=   -3.882 closest distance to " CG  ASP A 132 " =    2.333
peak=   -3.852 closest distance to " CB  PHE A 192 " =    1.921
peak=   -3.849 closest distance to " N   GLN A  58 " =    1.637
peak=   -3.844 closest distance to " CD1 LEU A  25 " =    2.479
peak=   -3.825 closest distance to " O   SER A 210 " =    1.901
peak=   -3.813 closest distance to " O   HOH Z 196 " =    1.970
peak=   -3.801 closest distance to " O   HOH Z 407 " =    2.878
peak=   -3.797 closest distance to " CB  ALA A 291 " =    2.335
peak=   -3.787 closest distance to " CA  ASP A 298 " =    1.042
peak=   -3.783 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -3.774 closest distance to " OD1 ASN A  39 " =    2.205
peak=   -3.756 closest distance to " CG1 VAL A 112 " =    2.763
peak=   -3.753 closest distance to " ND2 ASN A 187 " =    1.495
peak=   -3.734 closest distance to " O   PHE A 218 " =    1.568
peak=   -3.730 closest distance to " O   HOH Z 234 " =    4.061
peak=   -3.723 closest distance to " O   HOH Z 292 " =    4.489
peak=   -3.720 closest distance to " CD1 PHE A  59 " =    1.993
peak=   -3.718 closest distance to " O   HOH Z 114 " =    3.280
peak=   -3.694 closest distance to " CD  ARG A 139 " =    1.600
peak=   -3.689 closest distance to " OG  SER A   3 " =    1.641
peak=   -3.681 closest distance to " CB  ASN A  39 " =    2.311
peak=   -3.678 closest distance to " O   HOH Z 351 " =    1.507
peak=   -3.677 closest distance to " O   HOH Z 166 " =    1.532
peak=   -3.675 closest distance to " O   HOH Z  11 " =    2.062
peak=   -3.671 closest distance to " CZ  TYR A 169 " =    1.818
peak=   -3.670 closest distance to " OD2 ASP A 171 " =    2.381
peak=   -3.665 closest distance to " C   GLY A  80 " =    2.431
peak=   -3.653 closest distance to " O   HOH Z  10 " =    1.502
peak=   -3.647 closest distance to " O   HOH Z 394 " =    1.514
peak=   -3.641 closest distance to " O   VAL A 174 " =    2.083
peak=   -3.630 closest distance to " OG BSER A 134 " =    1.695
peak=   -3.611 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.594 closest distance to " O   HOH Z 166 " =    1.847
peak=   -3.593 closest distance to " CG2 ILE A 263 " =    2.199
peak=   -3.572 closest distance to " O   HOH Z 126 " =    1.878
peak=   -3.570 closest distance to " O   HOH Z 372 " =    2.224
peak=   -3.569 closest distance to " ND2 ASN A  45 " =    1.039
peak=   -3.567 closest distance to " O   LEU A 167 " =    1.545
peak=   -3.566 closest distance to " CE  MET A 105 " =    2.222
peak=   -3.566 closest distance to " CG  ASP A 231 " =    0.869
peak=   -3.565 closest distance to " O   MET A  40 " =    2.646
peak=   -3.558 closest distance to " CD1 LEU A 228 " =    2.083
peak=   -3.554 closest distance to " OD2 ASP A 191 " =    1.505
peak=   -3.544 closest distance to " N   ALA A  43 " =    2.635
peak=   -3.543 closest distance to " CB  ALA A 248 " =    2.255
peak=   -3.527 closest distance to " CZ3 TRP A 179 " =    1.319
peak=   -3.525 closest distance to " CB  ASP A 286 " =    1.896
peak=   -3.523 closest distance to " NH1 ARG A 195 " =    2.558
peak=   -3.519 closest distance to " CB  PHE A 208 " =    2.245
peak=   -3.514 closest distance to " CZ  PHE A  59 " =    1.635
peak=   -3.509 closest distance to " NE2 GLN A  88 " =    1.732
peak=   -3.507 closest distance to " OD1 ASN A 148 " =    1.563
peak=   -3.504 closest distance to " O   HOH Z 389 " =    1.743
peak=   -3.497 closest distance to " CG  PHE A 283 " =    2.501
peak=   -3.492 closest distance to " CG2 THR A 178 " =    2.177
peak=   -3.490 closest distance to " CD2 LEU A 300 " =    2.818
peak=   -3.485 closest distance to " O   TRP A  92 " =    1.839
peak=   -3.484 closest distance to " CD1 TYR A 247 " =    2.595
peak=   -3.483 closest distance to " CG  GLU A  53 " =    1.449
peak=   -3.477 closest distance to " O   HOH Z 102 " =    1.683
peak=   -3.474 closest distance to " CG1 VAL A 125 " =    2.306
peak=   -3.473 closest distance to " O   HOH Z 435 " =    2.710
peak=   -3.469 closest distance to " CD  ARG A 195 " =    5.132
peak=   -3.461 closest distance to " O   HOH Z 414 " =    1.537
peak=   -3.457 closest distance to " O   HOH Z 185 " =    2.344
peak=   -3.457 closest distance to " OD1 ASP A 171 " =    1.573
peak=   -3.443 closest distance to " ND2 ASN A  45 " =    1.638
peak=   -3.437 closest distance to " O   ALA A  34 " =    2.192
peak=   -3.430 closest distance to " NH2 ARG A  79 " =    2.018
peak=   -3.429 closest distance to " O   HOH Z 362 " =    5.885
peak=   -3.420 closest distance to " NH2 ARG A  66 " =    5.152
peak=   -3.417 closest distance to " O   HOH Z 311 " =    3.600
peak=   -3.413 closest distance to " O   HOH Z  38 " =    1.605
peak=   -3.410 closest distance to " O   HOH Z 111 " =    2.153
peak=   -3.406 closest distance to " C   LEU A 143 " =    1.026
peak=   -3.396 closest distance to " C   ILE A 234 " =    1.383
peak=   -3.392 closest distance to " CD2 LEU A 237 " =    2.392
peak=   -3.392 closest distance to " CB  ALA A 248 " =    2.022
peak=   -3.391 closest distance to " N   THR A  52 " =    1.717
peak=   -3.387 closest distance to " O   GLY A  75 " =    1.749
peak=   -3.386 closest distance to " O   PRO A 198 " =    1.287
peak=   -3.385 closest distance to " OG  SER A  62 " =    1.496
peak=   -3.371 closest distance to " O   SER A 135 " =    1.558
peak=   -3.370 closest distance to " O   HOH Z  71 " =    1.740
peak=   -3.362 closest distance to " C   GLN A 205 " =    1.858
peak=   -3.356 closest distance to " O   HOH Z  52 " =    1.469
peak=   -3.351 closest distance to " N   SER A 276 " =    1.362
peak=   -3.347 closest distance to " ND2 ASN A  39 " =    1.194
peak=   -3.335 closest distance to " N   ASP A 286 " =    2.346
peak=   -3.334 closest distance to " O   HOH Z  15 " =    1.539
peak=   -3.329 closest distance to " O   HOH Z 250 " =    1.412
peak=   -3.327 closest distance to " NH1 ARG A  66 " =    1.153
peak=   -3.327 closest distance to " O   HOH Z 422 " =    1.551
peak=   -3.326 closest distance to " CG1AVAL A  41 " =    2.742
peak=   -3.325 closest distance to " SG ACYS A 201 " =    1.944
peak=   -3.318 closest distance to " OG ASER A 134 " =    1.255
peak=   -3.316 closest distance to " O   ALA A  10 " =    1.813
peak=   -3.313 closest distance to " O   GLY A 196 " =    0.959
peak=   -3.310 closest distance to " O   HOH Z 198 " =    1.497
peak=   -3.309 closest distance to " NE2 GLN A 194 " =    1.703
peak=   -3.305 closest distance to " CA  TYR A  68 " =    3.014
peak=   -3.301 closest distance to " CG2 VAL A 189 " =    2.186
peak=   -3.300 closest distance to " C   ALA A 158 " =    1.265
peak=   -3.299 closest distance to " O   HOH Z 251 " =    1.543
peak=   -3.298 closest distance to " NH2AARG A 275 " =    5.062
peak=   -3.293 closest distance to " O   HOH Z  61 " =    1.638
peak=   -3.291 closest distance to " O   HOH Z 369 " =    2.238
peak=   -3.289 closest distance to " O   ALA A  51 " =    1.370
peak=   -3.288 closest distance to " O   SER A   3 " =    1.073
peak=   -3.285 closest distance to " O   HOH Z 283 " =    2.021
peak=   -3.284 closest distance to " O   HOH Z 361 " =    3.437
peak=   -3.284 closest distance to " CA  GLY A 133 " =    1.943
peak=   -3.284 closest distance to " O   HOH Z 243 " =    2.053
peak=   -3.284 closest distance to " OD1 ASP A 191 " =    1.753
peak=   -3.284 closest distance to " CA  GLY A 203 " =    2.266
peak=   -3.282 closest distance to " O   ALA A 292 " =    1.868
peak=   -3.281 closest distance to " OG  SER A  26 " =    1.288
peak=   -3.280 closest distance to " NE2 GLN A 103 " =    1.660
peak=   -3.277 closest distance to " O   VAL A 189 " =    2.571
peak=   -3.277 closest distance to " N   ALA A 226 " =    1.943
peak=   -3.270 closest distance to " O   HOH Z 377 " =    1.711
peak=   -3.267 closest distance to " ND2 ASN A 209 " =    1.757
peak=   -3.266 closest distance to " O   HOH Z  41 " =    2.209
peak=   -3.266 closest distance to " O   ALA A 161 " =    1.652
peak=   -3.266 closest distance to " OE1 GLN A 223 " =    1.931
peak=   -3.262 closest distance to " O   ASN A  45 " =    1.829
peak=   -3.256 closest distance to " O   HOH Z   6 " =    1.722
peak=   -3.255 closest distance to " O   HOH Z 326 " =    1.716
peak=   -3.253 closest distance to " O   HOH Z 191 " =    5.799
peak=   -3.252 closest distance to " O   HOH Z 252 " =    3.494
peak=   -3.252 closest distance to " O   HOH Z  43 " =    1.609
peak=   -3.248 closest distance to " O   HOH Z 265 " =    2.137
peak=   -3.245 closest distance to " CD2 LEU A 237 " =    2.507
peak=   -3.244 closest distance to " CB  GLN A  11 " =    1.905
peak=   -3.242 closest distance to " CE3 TRP A 150 " =    2.249
peak=   -3.241 closest distance to " CG  GLU A 277 " =    1.183
peak=   -3.241 closest distance to " O   HOH Z 211 " =    1.586
peak=   -3.240 closest distance to " O   HOH Z 263 " =    2.889
peak=   -3.233 closest distance to " O   HOH Z  11 " =    1.812
peak=   -3.226 closest distance to " O   HOH Z 233 " =    2.403
peak=   -3.223 closest distance to " CG  PRO A 243 " =    1.720
peak=   -3.222 closest distance to " CD2 TYR A 247 " =    2.417
peak=   -3.221 closest distance to " O   HOH Z 427 " =    1.344
peak=   -3.219 closest distance to " CG  GLU A   2 " =    1.777
peak=   -3.218 closest distance to " CA  SER A  12 " =    1.384
peak=   -3.217 closest distance to " OE1 GLN A 183 " =    1.486
peak=   -3.217 closest distance to " CB  ALA A 291 " =    2.262
peak=   -3.215 closest distance to " O   HOH Z 385 " =    1.986
peak=   -3.214 closest distance to " O   HOH Z 193 " =    1.783
peak=   -3.199 closest distance to " CD1 LEU A  83 " =    2.330
peak=   -3.194 closest distance to " O   GLY A 111 " =    1.218
peak=   -3.193 closest distance to " O   HOH Z 123 " =    2.288
peak=   -3.185 closest distance to " O   HOH Z  60 " =    2.297
peak=   -3.182 closest distance to " C   PRO A  90 " =    1.472
peak=   -3.179 closest distance to " OD2 ASP A  50 " =    2.321
peak=   -3.178 closest distance to " N   VAL A 189 " =    1.607
peak=   -3.176 closest distance to " NH2 ARG A  66 " =    5.001
peak=   -3.175 closest distance to " O   HOH Z 281 " =    2.593
peak=   -3.172 closest distance to " O   ILE A 234 " =    1.260
peak=   -3.169 closest distance to " O   ALA A 160 " =    1.452
peak=   -3.164 closest distance to " OG BSER A 210 " =    2.089
peak=   -3.164 closest distance to " O   HOH Z 171 " =    2.006
peak=   -3.158 closest distance to " O   HOH Z 417 " =    2.463
peak=   -3.136 closest distance to " O   HOH Z 193 " =    1.881
peak=   -3.135 closest distance to " CZ3 TRP A 274 " =    2.410
peak=   -3.132 closest distance to " O   HOH Z 351 " =    1.340
peak=   -3.129 closest distance to " O   HOH Z 148 " =    3.789
peak=   -3.128 closest distance to " O   GLU A 152 " =    1.499
peak=   -3.125 closest distance to " CD2 PHE A 225 " =    1.321
peak=   -3.122 closest distance to " O   ASP A 171 " =    2.009
peak=   -3.117 closest distance to " CG  PRO A 163 " =    2.661
peak=   -3.111 closest distance to " CE  MET A  93 " =    1.192
peak=   -3.106 closest distance to " CG  GLU A 152 " =    1.161
peak=   -3.099 closest distance to " O   HOH Z 134 " =    2.789
peak=   -3.096 closest distance to " OD1 ASN A 301 " =    1.986
peak=   -3.091 closest distance to " O   GLY A  80 " =    2.555

================= 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    :  0.3630 0.3570   6.117324e+00   6.104499e+00
   1_bss:  0.3527 0.3455   6.101855e+00   6.080250e+00
   1_xyz:  0.2199 0.2369   5.693221e+00   5.765191e+00
   1_adp:  0.1999 0.2453   5.636020e+00   5.800033e+00
   1_occ:  0.1995 0.2453   5.635402e+00   5.800391e+00
   2_bss:  0.1979 0.2442   5.632398e+00   5.796887e+00
   2_xyz:  0.1409 0.1850   5.329829e+00   5.532402e+00
   2_adp:  0.1330 0.1728   5.268358e+00   5.464496e+00
   2_occ:  0.1328 0.1727   5.267709e+00   5.463892e+00
   3_bss:  0.1332 0.1719   5.267438e+00   5.460001e+00
   3_xyz:  0.1144 0.1564   5.153171e+00   5.378179e+00
   3_adp:  0.1112 0.1553   5.132756e+00   5.367582e+00
   3_occ:  0.1111 0.1552   5.132477e+00   5.367361e+00
   4_bss:  0.1111 0.1552   5.132517e+00   5.367455e+00
   4_xyz:  0.1111 0.1545   5.134415e+00   5.367464e+00
   4_adp:  0.1107 0.1554   5.134862e+00   5.372486e+00
   4_occ:  0.1106 0.1554   5.134894e+00   5.372736e+00
   5_bss:  0.1107 0.1555   5.135691e+00   5.372617e+00
   5_xyz:  0.1058 0.1551   5.110807e+00   5.365773e+00
   5_adp:  0.1056 0.1549   5.108895e+00   5.364929e+00
   5_occ:  0.1056 0.1549   5.108893e+00   5.365071e+00
   5_bss:  0.1055 0.1549   5.109131e+00   5.365268e+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:  0.308  29.349  -1.277   0.216  -0.538   0.000  -0.000  -0.000
   1_xyz:  0.308  29.349  -1.277   0.216  -0.538   0.000  -0.000  -0.000
   1_adp:  0.308  29.349  -1.277   0.216  -0.538   0.000  -0.000  -0.000
   1_occ:  0.308  29.349  -1.277   0.216  -0.538   0.000  -0.000  -0.000
   2_bss:  0.309  36.284  -2.684  -1.236  -1.416  -0.000  -0.000  -0.000
   2_xyz:  0.309  36.284  -2.684  -1.236  -1.416  -0.000  -0.000  -0.000
   2_adp:  0.309  36.284  -2.684  -1.236  -1.416  -0.000  -0.000  -0.000
   2_occ:  0.309  36.284  -2.684  -1.236  -1.416  -0.000  -0.000  -0.000
   3_bss:  0.320  41.709  -2.954  -1.713  -1.574  -0.000  -0.000  -0.000
   3_xyz:  0.320  41.709  -2.954  -1.713  -1.574  -0.000  -0.000  -0.000
   3_adp:  0.320  41.709  -2.954  -1.713  -1.574  -0.000  -0.000  -0.000
   3_occ:  0.320  41.709  -2.954  -1.713  -1.574  -0.000  -0.000  -0.000
   4_bss:  0.320  41.709  -2.836  -1.758  -1.446  -0.000  -0.000  -0.000
   4_xyz:  0.320  41.709  -2.836  -1.758  -1.446  -0.000  -0.000  -0.000
   4_adp:  0.320  41.709  -2.836  -1.758  -1.446  -0.000  -0.000  -0.000
   4_occ:  0.320  41.709  -2.836  -1.758  -1.446  -0.000  -0.000  -0.000
   5_bss:  0.319  44.053  -2.734  -1.677  -1.320  -0.000  -0.000  -0.000
   5_xyz:  0.319  44.053  -2.734  -1.677  -1.320  -0.000  -0.000  -0.000
   5_adp:  0.319  44.053  -2.734  -1.677  -1.320  -0.000  -0.000  -0.000
   5_occ:  0.319  44.053  -2.734  -1.677  -1.320  -0.000  -0.000  -0.000
   5_bss:  0.321  44.378  -2.509  -1.482  -1.083  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.477 0.6753  0.8636    35996.345
   1_bss:  36.272 0.6875  0.8649    32630.306
   1_xyz:  22.878 0.8347  0.9939    14258.131
   1_adp:  24.104 0.8211  0.9826    15313.184
   1_occ:  24.128 0.8209  0.9821    15342.682
   2_bss:  23.973 0.8224  0.9407    15137.524
   2_xyz:  17.369 0.8855  0.9845     8427.543
   2_adp:  15.759 0.9002  0.9873     7387.996
   2_occ:  15.754 0.9003  0.9871     7374.112
   3_bss:  15.648 0.9011  0.9773     7280.879
   3_xyz:  14.012 0.9145  0.9840     6218.629
   3_adp:  13.743 0.9169  0.9804     6108.723
   3_occ:  13.737 0.9169  0.9803     6102.387
   4_bss:  13.738 0.9169  0.9829     6103.604
   4_xyz:  13.640 0.9180  0.9822     6057.972
   4_adp:  13.720 0.9174  0.9764     6122.663
   4_occ:  13.721 0.9174  0.9763     6123.630
   5_bss:  13.722 0.9174  0.9801     6129.350
   5_xyz:  13.588 0.9184  0.9806     6051.317
   5_adp:  13.560 0.9186  0.9749     6037.090
   5_occ:  13.564 0.9185  0.9748     6037.421
   5_bss:  13.568 0.9185  0.9817     6041.957
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7392e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7392e-01
   1_xyz:   1.130  0.008  0.069 15.103  0.004  4.108   7.1553e-02
   1_adp:   1.130  0.008  0.069 15.103  0.004  4.108   7.1553e-02
   1_occ:   1.130  0.008  0.069 15.103  0.004  4.108   7.1553e-02
   2_bss:   1.130  0.008  0.069 15.103  0.004  4.108   7.1553e-02
   2_xyz:   0.979  0.006  0.065 14.436  0.004  4.115   5.4419e-02
   2_adp:   0.979  0.006  0.065 14.436  0.004  4.115   5.4419e-02
   2_occ:   0.979  0.006  0.065 14.436  0.004  4.115   5.4419e-02
   3_bss:   0.979  0.006  0.065 14.436  0.004  4.115   5.4419e-02
   3_xyz:   1.023  0.007  0.073 14.768  0.004  4.113   6.1000e-02
   3_adp:   1.023  0.007  0.073 14.768  0.004  4.113   6.1000e-02
   3_occ:   1.023  0.007  0.073 14.768  0.004  4.113   6.1000e-02
   4_bss:   1.023  0.007  0.073 14.768  0.004  4.113   6.1000e-02
   4_xyz:   0.907  0.005  0.068 14.453  0.004  4.114   5.0104e-02
   4_adp:   0.907  0.005  0.068 14.453  0.004  4.114   5.0104e-02
   4_occ:   0.907  0.005  0.068 14.453  0.004  4.114   5.0104e-02
   5_bss:   0.907  0.005  0.068 14.453  0.004  4.114   5.0104e-02
   5_xyz:   1.052  0.008  0.078 14.783  0.004  4.115   6.4106e-02
   5_adp:   1.052  0.008  0.078 14.783  0.004  4.115   6.4106e-02
   5_occ:   1.052  0.008  0.078 14.783  0.004  4.115   6.4106e-02
   5_bss:   1.052  0.008  0.078 14.783  0.004  4.115   6.4106e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.597   2.4009e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.597   2.4009e-01
   1_xyz:   8.518  0.041  0.293 85.493  0.032  2.150   7.2669e-02
   1_adp:   8.518  0.041  0.293 85.493  0.032  2.150   7.2669e-02
   1_occ:   8.518  0.041  0.293 85.493  0.032  2.150   7.2669e-02
   2_bss:   8.518  0.041  0.293 85.493  0.032  2.150   7.2669e-02
   2_xyz:   7.083  0.037  0.193 81.027  0.040  2.309   4.3749e-02
   2_adp:   7.083  0.037  0.193 81.027  0.040  2.309   4.3749e-02
   2_occ:   7.083  0.037  0.193 81.027  0.040  2.309   4.3749e-02
   3_bss:   7.083  0.037  0.193 81.027  0.040  2.309   4.3749e-02
   3_xyz:   7.298  0.046  0.239 83.552  0.040  2.330   4.9106e-02
   3_adp:   7.298  0.046  0.239 83.552  0.040  2.330   4.9106e-02
   3_occ:   7.298  0.046  0.239 83.552  0.040  2.330   4.9106e-02
   4_bss:   7.298  0.046  0.239 83.552  0.040  2.330   4.9106e-02
   4_xyz:   6.516  0.042  0.219 81.485  0.036  2.373   3.2990e-02
   4_adp:   6.516  0.042  0.219 81.485  0.036  2.373   3.2990e-02
   4_occ:   6.516  0.042  0.219 81.485  0.036  2.373   3.2990e-02
   5_bss:   6.516  0.042  0.219 81.485  0.036  2.373   3.2990e-02
   5_xyz:   7.544  0.049  0.260 82.497  0.038  2.285   4.7774e-02
   5_adp:   7.544  0.049  0.260 82.497  0.038  2.285   4.7774e-02
   5_occ:   7.544  0.049  0.260 82.497  0.038  2.285   4.7774e-02
   5_bss:   7.544  0.049  0.260 82.497  0.038  2.285   4.7774e-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:  76.58   0.00  17.52  76.15   0.00  13.59  76.58   5.95  38.94
   1_occ:  76.58   0.00  17.52  76.15   0.00  13.59  76.58   5.95  38.94
   2_bss:  76.58   0.00  17.52  76.15   0.00  13.59  76.58   5.95  38.94
   2_xyz:  76.58   0.00  17.52  76.15   0.00  13.59  76.58   5.95  38.94
   2_adp:  78.67   2.03  16.99  78.67   2.03  13.12  71.97   4.99  38.06
   2_occ:  78.67   2.03  16.99  78.67   2.03  13.12  71.97   4.99  38.06
   3_bss:  78.67   2.03  16.99  78.67   2.03  13.12  71.97   4.99  38.06
   3_xyz:  78.67   2.03  16.99  78.67   2.03  13.12  71.97   4.99  38.06
   3_adp:  85.72   0.81  17.08  85.72   1.53  12.97  73.06   0.81  39.47
   3_occ:  85.72   0.81  17.08  85.72   1.53  12.97  73.06   0.81  39.47
   4_bss:  85.72   0.81  17.08  85.72   1.53  12.97  73.06   0.81  39.47
   4_xyz:  85.72   0.81  17.08  85.72   1.53  12.97  73.06   0.81  39.47
   4_adp:  91.69   0.91  17.00  91.69   0.91  12.87  81.71   1.62  39.45
   4_occ:  91.69   0.91  17.00  91.69   0.91  12.87  81.71   1.62  39.45
   5_bss:  91.69   0.91  17.00  91.69   0.91  12.87  81.71   1.62  39.45
   5_xyz:  91.69   0.91  17.00  91.69   0.91  12.87  81.71   1.62  39.45
   5_adp:  93.42   0.79  16.80  93.42   0.79  12.69  83.34   2.99  39.19
   5_occ:  93.42   0.79  16.80  93.42   0.79  12.69  83.34   2.99  39.19
   5_bss:  93.40   0.76  16.77  93.40   0.76  12.66  83.32   2.96  39.17
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.656    0.016    0.285
   1_adp:    1.656    0.016    0.285
   1_occ:    1.656    0.016    0.285
   2_bss:    1.656    0.016    0.285
   2_xyz:    1.004    0.022    0.397
   2_adp:    1.004    0.022    0.397
   2_occ:    1.004    0.022    0.397
   3_bss:    1.004    0.022    0.397
   3_xyz:    1.143    0.040    0.452
   3_adp:    1.143    0.040    0.452
   3_occ:    1.143    0.040    0.452
   4_bss:    1.143    0.040    0.452
   4_xyz:    1.238    0.044    0.462
   4_adp:    1.238    0.044    0.462
   4_occ:    1.238    0.044    0.462
   5_bss:    1.238    0.044    0.462
   5_xyz:    1.188    0.040    0.475
   5_adp:    1.188    0.040    0.475
   5_occ:    1.188    0.040    0.475
   5_bss:    1.188    0.040    0.475
------------------------------------------------------------------------

CPU time actual refinement: 352.94


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_322/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_322/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_322/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_322/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_322/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.79 
  Macro-tasks:
    bulk solvent and scale       = 35.88  
    individual site refinement   = 156.26 
    weights calculation          = 30.49  
    collect and process          = 6.71   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 229.45 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 115.98 
    alpha_beta                      = 8.18   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 126.47 
    fmodel                         = 6.92   
    r_factors                      = 0.24   
    phase_errors                   = 11.27  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 272.26 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.856 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    673 calls, 115.54 s
gradients_fft:          618 calls, 111.72 s

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

# Date 2008-01-16 Time 04:33:06 PST -0800 (1200486786.25 s)
Start R-work = 0.3630, R-free = 0.3570 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.3527, R-free = 0.3455
Final R-work = 0.1055, R-free = 0.1549