# Date 2008-01-16 Time 05:01:34 PST -0800 (1200488494.87 s)
#phil __OFF__

Command line arguments: "../561.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22585
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 561

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.3993, 84.2302, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95143
Completeness in resolution range: 0.935929
Completeness with d_max=infinity: 0.933076

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8359
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95143
Completeness in resolution range: 0.935929
Completeness with d_max=infinity: 0.933076

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8363 -  4.1759 [2203/2231]  1984   219   9.9%
  bin  2:  4.1759 -  3.3268 [2100/2123]  1891   209  10.0%
  bin  3:  3.3268 -  2.9099 [2085/2110]  1871   214  10.3%
  bin  4:  2.9099 -  2.6455 [2063/2079]  1863   200   9.7%
  bin  5:  2.6455 -  2.4568 [2049/2093]  1841   208  10.2%
  bin  6:  2.4568 -  2.3125 [2051/2079]  1849   202   9.8%
  bin  7:  2.3125 -  2.1971 [2008/2044]  1807   201  10.0%
  bin  8:  2.1971 -  2.1017 [2019/2061]  1817   202  10.0%
  bin  9:  2.1017 -  2.0210 [2017/2063]  1813   204  10.1%
  bin 10:  2.0210 -  1.9514 [ 994/2047]   894   100  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_561/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:
        1.49 -     2.18: 25
        2.18 -     2.86: 1164
        2.86 -     3.54: 4477
        3.54 -     4.22: 9317
        4.22 -     4.90: 13632
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.494 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.595 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.603 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.630 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28610 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_561/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_561/model_refine_001.geo

CPU time processing inputs: 9.28


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.3993 84.23025 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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4092   r_free= 0.4053   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.211215                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6577 0.99   1426  161 0.3295 0.3370      6.4692      6.4865|
|  2:  4.6577 -  3.7161 0.99   1370  148 0.3409 0.3251      6.6752      6.6268|
|  3:  3.7161 -  3.2520 0.99   1346  154 0.3616 0.3657      6.5439      6.6641|
|  4:  3.2520 -  2.9572 0.99   1341  146 0.3847 0.3817      6.4104      6.4016|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.4198 0.3744      6.2764      6.2242|
|  6:  2.7467 -  2.5857 0.99   1320  146 0.4299 0.4200      6.1964       6.113|
|  7:  2.5857 -  2.4568 0.98   1315  147 0.4351 0.3877      6.1773      6.1158|
|  8:  2.4568 -  2.3503 0.99   1307  147 0.4479 0.4957      6.1085      6.1627|
|  9:  2.3503 -  2.2601 0.99   1315  144 0.4699 0.4629      6.0888      6.0952|
| 10:  2.2601 -  2.1824 0.98   1306  145 0.4693 0.4930      6.0604      6.1305|
| 11:  2.1824 -  2.1143 0.97   1278  139 0.4783 0.5213      6.0014      6.0015|
| 12:  2.1143 -  2.0541 0.99   1302  153 0.4671 0.4983      5.9188       5.973|
| 13:  2.0541 -  2.0001 0.93   1242  136 0.4858 0.4513       5.857      5.8229|
| 14:  2.0001 -  1.9514 0.33    430   45 0.5458 0.5011      5.8387       5.727|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6577  1426   161  0.73  31.35   0.85     0.75      58308.05|
|  2:  4.6577 -  3.7161  1370   148  0.76  29.74   0.95     0.86      76658.33|
|  3:  3.7161 -  3.2520  1346   154  0.70  35.49   0.96     0.88      79054.41|
|  4:  3.2520 -  2.9572  1341   146  0.64  40.65   0.97     0.86      69457.40|
|  5:  2.9572 -  2.7467  1332   148  0.60  44.13   0.93     0.82      54931.03|
|  6:  2.7467 -  2.5857  1320   146  0.58  45.91   0.95     0.79      47718.48|
|  7:  2.5857 -  2.4568  1315   147  0.57  46.45   0.97     0.76      44928.89|
|  8:  2.4568 -  2.3503  1307   147  0.50  51.91   0.94     0.71      45671.88|
|  9:  2.3503 -  2.2601  1315   144  0.45  55.70   0.97     0.65      44663.46|
| 10:  2.2601 -  2.1824  1306   145  0.41  58.82   1.01     0.59      45201.41|
| 11:  2.1824 -  2.1143  1278   139  0.37  62.12   0.98     0.56      43504.78|
| 12:  2.1143 -  2.0541  1302   153  0.35  63.58   0.99     0.57      41688.94|
| 13:  2.0541 -  2.0001  1242   136  0.37  62.61   0.98     0.58      34425.63|
| 14:  2.0001 -  1.9514   430    45  0.41  58.71   0.91     0.62      26570.41|
|alpha:            min =        0.56 max =            0.88 mean =         0.72|
|beta:             min =    26570.41 max =        79054.41 mean =     52437.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.29|
|phase err.(test): min =        0.00 max =           89.97 mean =        48.18|
|-----------------------------------------------------------------------------|

============================== 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 = 7.476897              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.896   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.691032              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.903   (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 |  1.494 -  1.835:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.835 -  2.175:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.175 -  2.516:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.516 -  2.856:     1133 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.856 -  3.197:     1974 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.197 -  3.538:     2503 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.538 -  3.878:     4660 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.878 -  4.219:     4657 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.219 -  4.559:     6185 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7447 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.494 |       0.557 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4092   r_free= 0.4053   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.211215                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3970   r_free= 0.3922   ksol= 0.32   Bsol= 24.70   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,0.01,3.05,0.00,0.00,0.00); trace/3= -0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.199572                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.219750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.731   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.798927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.830   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3970      final r-factor (work) = 0.2755          |
| start r-factor (free) = 0.3922      final r-factor (free) = 0.3018          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4645 = 6.22 * 0.50 * 6.1989 + 1.00 * 0.1867                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8174 = 6.22 * 0.50 * 6.0175 + 1.00 * 0.1037                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2755      final r-factor (work) = 0.2506          |
| start r-factor (free) = 0.3018      final r-factor (free) = 0.3113          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8138 = 0.80 * 1.00 * 6.0175 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6768 = 0.80 * 1.00 * 5.8314 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.71   18.21    None  None   None       |
|    all(noH): 2823   0      0.00    92.71   18.21    None  None   None       |
|    Sol.    : 438    0      3.94    92.71   40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    88.93   14.18    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 -   9.271:  857   |   5:    46.355 -  55.626:   93        |
|      1:     9.271 -  18.542: 1038   |   6:    55.626 -  64.897:   54        |
|      2:    18.542 -  27.813:  390   |   7:    64.897 -  74.168:   35        |
|      3:    27.813 -  37.084:  192   |   8:    74.168 -  83.439:    6        |
|      4:    37.084 -  46.355:  154   |   9:    83.439 -  92.710:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2506 r_free = 0.3113             target_work(ml) = 5.842         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2501 r_free = 0.3117             target_work(ml) = 5.841         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2501   r_free= 0.3117   ksol= 0.32   Bsol= 24.70   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,0.01,3.05,0.00,0.00,0.00); trace/3= -0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.840870                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2471   r_free= 0.3080   ksol= 0.32   Bsol= 45.73   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.10,0.13,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.834495                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.386069              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.493   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340096              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.643  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2471      final r-factor (work) = 0.1810          |
| start r-factor (free) = 0.3080      final r-factor (free) = 0.2363          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9745 = 3.39 * 0.50 * 5.8302 + 1.00 * 0.1037                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7323 = 3.39 * 0.50 * 5.7120 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1810      final r-factor (work) = 0.1668          |
| start r-factor (free) = 0.2363      final r-factor (free) = 0.2189          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9613 = 0.34 * 1.00 * 5.7120 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8886 = 0.34 * 1.00 * 5.5267 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.88   17.66    None  None   None       |
|    all(noH): 2823   0      0.00    83.88   17.66    None  None   None       |
|    Sol.    : 438    0      6.01    82.27   40.28    None  None   None       |
|    Mac.    : 2385   0      0.00    83.88   13.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.388:  664   |   5:    41.940 -  50.328:  116        |
|      1:     8.388 -  16.776: 1247   |   6:    50.328 -  58.715:   81        |
|      2:    16.776 -  25.164:  359   |   7:    58.715 -  67.103:   36        |
|      3:    25.164 -  33.552:  156   |   8:    67.103 -  75.491:   16        |
|      4:    33.552 -  41.940:  136   |   9:    75.491 -  83.879:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1668 r_free = 0.2189             target_work(ml) = 5.490         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1665 r_free = 0.2188             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1665   r_free= 0.2188   ksol= 0.32   Bsol= 45.73   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.10,0.13,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.489113                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1664   r_free= 0.2171   ksol= 0.32   Bsol= 40.79   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.56,-1.20,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.484918                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.180068              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.949  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.142  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1664      final r-factor (work) = 0.1293          |
| start r-factor (free) = 0.2171      final r-factor (free) = 0.1741          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6119 = 4.18 * 0.50 * 5.5264 + 1.00 * 0.0615                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3075 = 4.18 * 0.50 * 5.3784 + 1.00 * 0.0666                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1293      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1741      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1175 = 0.21 * 1.00 * 5.3784 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0860 = 0.21 * 1.00 * 5.2322 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.20    85.75   17.22    None  None   None       |
|    all(noH): 2823   0      2.20    85.75   17.22    None  None   None       |
|    Sol.    : 438    0      4.87    78.47   39.67    None  None   None       |
|    Mac.    : 2385   0      2.20    85.75   13.10    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:     2.205 -  10.559: 1103   |   5:    43.976 -  52.330:  107        |
|      1:    10.559 -  18.913: 1024   |   6:    52.330 -  60.684:   64        |
|      2:    18.913 -  27.267:  232   |   7:    60.684 -  69.038:   24        |
|      3:    27.267 -  35.621:  120   |   8:    69.038 -  77.392:   16        |
|      4:    35.621 -  43.976:  127   |   9:    77.392 -  85.746:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1215 r_free = 0.1651             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1213 r_free = 0.1649             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1649   ksol= 0.32   Bsol= 40.79   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.56,-1.20,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.202071                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1653   ksol= 0.32   Bsol= 42.46   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.97,-1.87,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.205733                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.301405              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.468  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.316606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.526  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0914 = 2.30 * 0.50 * 5.2358 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0213 = 2.30 * 0.50 * 5.1815 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6481 = 0.32 * 1.00 * 5.1815 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6380 = 0.32 * 1.00 * 5.1483 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.11    90.38   17.09    None  None   None       |
|    all(noH): 2823   0      2.11    90.38   17.09    None  None   None       |
|    Sol.    : 438    0      5.28    81.36   39.54    None  None   None       |
|    Mac.    : 2385   0      2.11    90.38   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:     2.109 -  10.936: 1217   |   5:    46.243 -  55.069:  104        |
|      1:    10.936 -  19.762:  961   |   6:    55.069 -  63.896:   57        |
|      2:    19.762 -  28.589:  211   |   7:    63.896 -  72.723:   19        |
|      3:    28.589 -  37.416:  122   |   8:    72.723 -  81.549:    9        |
|      4:    37.416 -  46.243:  119   |   9:    81.549 -  90.376:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1582             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1581             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1581   ksol= 0.32   Bsol= 42.46   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.97,-1.87,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148337                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1581   ksol= 0.32   Bsol= 43.68   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.97,-1.96,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148139                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.053206              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.266  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.517544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.850  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9178 = 3.05 * 0.50 * 5.1480 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9006 = 3.05 * 0.50 * 5.1294 + 1.00 * 0.0700                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6627 = 0.52 * 1.00 * 5.1294 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6579 = 0.52 * 1.00 * 5.1191 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    94.32   16.99    None  None   None       |
|    all(noH): 2823   0      1.47    94.32   16.99    None  None   None       |
|    Sol.    : 438    0      5.50    82.32   39.50    None  None   None       |
|    Mac.    : 2385   0      1.47    94.32   12.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.474 -  10.758: 1198   |   5:    47.894 -  57.179:  104        |
|      1:    10.758 -  20.042:  995   |   6:    57.179 -  66.463:   42        |
|      2:    20.042 -  29.326:  212   |   7:    66.463 -  75.747:   16        |
|      3:    29.326 -  38.610:  125   |   8:    75.747 -  85.031:    6        |
|      4:    38.610 -  47.894:  122   |   9:    85.031 -  94.315:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1064 r_free = 0.1568             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1064 r_free = 0.1568             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1568   ksol= 0.32   Bsol= 43.68   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.97,-1.96,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121858                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6577 0.99   1426  161 0.0942 0.1250       5.349      5.5296|
|  2:  4.6577 -  3.7161 0.99   1370  148 0.0801 0.1090      5.3897      5.6175|
|  3:  3.7161 -  3.2520 0.99   1346  154 0.1002 0.1541      5.4236      5.8332|
|  4:  3.2520 -  2.9572 0.99   1341  146 0.1192 0.1505      5.4328        5.59|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.1223 0.1776      5.2789      5.4852|
|  6:  2.7467 -  2.5857 0.99   1320  146 0.1170 0.1865      5.1856      5.4188|
|  7:  2.5857 -  2.4568 0.98   1315  147 0.1162 0.1675      5.1166      5.3652|
|  8:  2.4568 -  2.3503 0.99   1307  147 0.1122 0.1703      5.0478      5.2669|
|  9:  2.3503 -  2.2601 0.99   1315  144 0.1145 0.1847      5.0054      5.3111|
| 10:  2.2601 -  2.1824 0.98   1306  145 0.1056 0.1688      4.9453      5.2201|
| 11:  2.1824 -  2.1143 0.97   1278  139 0.1082 0.1852      4.9006      5.2488|
| 12:  2.1143 -  2.0541 0.99   1302  153 0.1042 0.1598      4.8277      5.0348|
| 13:  2.0541 -  2.0001 0.93   1242  136 0.1078 0.1825       4.758      5.0397|
| 14:  2.0001 -  1.9514 0.33    430   45 0.1080 0.1579      4.6517       4.886|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6577  1426   161  0.94   8.73   0.98     0.96       6844.77|
|  2:  4.6577 -  3.7161  1370   148  0.95   7.73   1.02     1.01       8519.47|
|  3:  3.7161 -  3.2520  1346   154  0.94  10.92   1.03     1.02       9724.78|
|  4:  3.2520 -  2.9572  1341   146  0.92  13.92   1.01     0.99      10234.36|
|  5:  2.9572 -  2.7467  1332   148  0.90  15.71   0.99     0.97       7878.75|
|  6:  2.7467 -  2.5857  1320   146  0.90  15.76   0.99     0.96       6868.48|
|  7:  2.5857 -  2.4568  1315   147  0.91  14.97   0.99     0.95       5789.74|
|  8:  2.4568 -  2.3503  1307   147  0.91  15.43   1.00     0.97       5397.36|
|  9:  2.3503 -  2.2601  1315   144  0.90  16.28   1.00     0.96       4899.52|
| 10:  2.2601 -  2.1824  1306   145  0.91  14.83   0.99     0.96       4397.02|
| 11:  2.1824 -  2.1143  1278   139  0.90  16.21   1.00     0.96       4212.91|
| 12:  2.1143 -  2.0541  1302   153  0.92  14.72   1.00     0.99       3695.70|
| 13:  2.0541 -  2.0001  1242   136  0.90  16.09   1.00     0.99       3229.24|
| 14:  2.0001 -  1.9514   430    45  0.90  15.80   0.98     0.95       2570.71|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2570.71 max =        10234.36 mean =      6237.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.92|
|phase err.(test): min =        0.00 max =           89.27 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1568   ksol= 0.32   Bsol= 44.46   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-1.77,-1.76,-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: 5.121907                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1568   ksol= 0.32   Bsol= 44.46   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-1.77,-1.76,-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: 5.121907                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6577 0.99   1426  161 0.0943 0.1253      5.3503      5.5315|
|  2:  4.6577 -  3.7161 0.99   1370  148 0.0802 0.1090      5.3907      5.6176|
|  3:  3.7161 -  3.2520 0.99   1346  154 0.1002 0.1542      5.4239      5.8337|
|  4:  3.2520 -  2.9572 0.99   1341  146 0.1192 0.1506      5.4328        5.59|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.1222 0.1775      5.2785      5.4847|
|  6:  2.7467 -  2.5857 0.99   1320  146 0.1170 0.1865      5.1852      5.4185|
|  7:  2.5857 -  2.4568 0.98   1315  147 0.1162 0.1675      5.1165      5.3653|
|  8:  2.4568 -  2.3503 0.99   1307  147 0.1122 0.1702      5.0476      5.2663|
|  9:  2.3503 -  2.2601 0.99   1315  144 0.1144 0.1848      5.0053      5.3113|
| 10:  2.2601 -  2.1824 0.98   1306  145 0.1056 0.1687      4.9453      5.2198|
| 11:  2.1824 -  2.1143 0.97   1278  139 0.1082 0.1851      4.9004      5.2486|
| 12:  2.1143 -  2.0541 0.99   1302  153 0.1042 0.1598      4.8274      5.0345|
| 13:  2.0541 -  2.0001 0.93   1242  136 0.1078 0.1824      4.7576      5.0389|
| 14:  2.0001 -  1.9514 0.33    430   45 0.1079 0.1579      4.6514       4.886|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6577  1426   161  0.94   8.75   0.98     0.96       6864.83|
|  2:  4.6577 -  3.7161  1370   148  0.95   7.74   1.02     1.01       8535.10|
|  3:  3.7161 -  3.2520  1346   154  0.94  10.93   1.03     1.03       9732.41|
|  4:  3.2520 -  2.9572  1341   146  0.92  13.92   1.01     0.99      10233.98|
|  5:  2.9572 -  2.7467  1332   148  0.90  15.71   1.00     0.97       7873.72|
|  6:  2.7467 -  2.5857  1320   146  0.90  15.76   0.99     0.96       6862.14|
|  7:  2.5857 -  2.4568  1315   147  0.91  14.96   0.99     0.96       5785.80|
|  8:  2.4568 -  2.3503  1307   147  0.91  15.43   1.01     0.98       5394.42|
|  9:  2.3503 -  2.2601  1315   144  0.90  16.28   1.00     0.97       4898.87|
| 10:  2.2601 -  2.1824  1306   145  0.91  14.82   1.00     0.97       4395.50|
| 11:  2.1824 -  2.1143  1278   139  0.90  16.21   1.01     0.97       4210.84|
| 12:  2.1143 -  2.0541  1302   153  0.92  14.72   1.01     1.00       3692.92|
| 13:  2.0541 -  2.0001  1242   136  0.90  16.08   1.01     1.00       3226.44|
| 14:  2.0001 -  1.9514   430    45  0.90  15.79   0.99     0.96       2568.41|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2568.41 max =        10233.98 mean =      6239.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.92|
|phase err.(test): min =        0.00 max =           89.23 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    94.26   16.94    None  None   None       |
|    all(noH): 2823   0      1.42    94.26   16.94    None  None   None       |
|    Sol.    : 438    0      5.45    82.26   39.44    None  None   None       |
|    Mac.    : 2385   0      1.42    94.26   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.421 -  10.706: 1198   |   5:    47.842 -  57.126:  104        |
|      1:    10.706 -  19.990:  995   |   6:    57.126 -  66.410:   42        |
|      2:    19.990 -  29.274:  212   |   7:    66.410 -  75.695:   16        |
|      3:    29.274 -  38.558:  125   |   8:    75.695 -  84.979:    6        |
|      4:    38.558 -  47.842:  122   |   9:    84.979 -  94.263:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 293         
Filter by distance & map next to the model:
   mapped sites are within: 0.425 - 5.921
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 289 from: 293
   mapped sites are within: 0.720 - 5.921

peak=    5.757 closest distance to " O   HOH Z 113 " =    2.164
peak=    5.338 closest distance to " O   HOH Z 126 " =    1.842
peak=    5.320 closest distance to " CB  GLN A 223 " =    1.449
peak=    5.296 closest distance to " CB  SER A  63 " =    1.157
peak=    5.227 closest distance to " CG  PRO A  54 " =    1.159
peak=    5.101 closest distance to " CB  ARG A 275 " =    0.908
peak=    4.857 closest distance to " O   HOH Z 142 " =    1.623
peak=    4.855 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.795 closest distance to " CB  GLN A 183 " =    1.332
peak=    4.715 closest distance to " O   HOH Z 234 " =    3.670
peak=    4.661 closest distance to " CB  GLU A 152 " =    1.186
peak=    4.660 closest distance to " O   HOH Z 193 " =    1.759
peak=    4.610 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.598 closest distance to " NE2 GLN A  11 " =    1.035
peak=    4.556 closest distance to " CB  SER A   3 " =    1.308
peak=    4.545 closest distance to " CG  PRO A 213 " =    1.162
peak=    4.523 closest distance to " O   HOH Z  15 " =    2.092
peak=    4.503 closest distance to " O   HOH Z 124 " =    1.393
peak=    4.472 closest distance to " CA  TYR A  30 " =    0.954
peak=    4.472 closest distance to " O   HOH Z 389 " =    1.861
peak=    4.461 closest distance to " O   HOH Z 236 " =    1.909
peak=    4.446 closest distance to " CB  ASN A 148 " =    1.659
peak=    4.441 closest distance to " C   PRO A 198 " =    1.510
peak=    4.419 closest distance to " O   HOH Z 368 " =    2.056
peak=    4.416 closest distance to " OD1 ASN A  69 " =    2.551
peak=    4.411 closest distance to " OD2 ASP A 286 " =    2.757
peak=    4.407 closest distance to " O   HOH Z  97 " =    2.639
peak=    4.401 closest distance to " O   HOH Z 298 " =    1.886
peak=    4.390 closest distance to " O   HOH Z 403 " =    1.731
peak=    4.364 closest distance to " O   HOH Z 203 " =    1.766
peak=    4.333 closest distance to " CB  GLU A 277 " =    3.499
peak=    4.322 closest distance to " CB  TYR A 169 " =    0.742
peak=    4.309 closest distance to " CB  GLU A 128 " =    1.170
peak=    4.284 closest distance to " O   SER A  87 " =    2.239
peak=    4.234 closest distance to " CA  ALA A  21 " =    1.164
peak=    4.231 closest distance to " O   HOH Z 278 " =    1.029
peak=    4.231 closest distance to " O   HOH Z 426 " =    1.508
peak=    4.231 closest distance to " NH2BARG A 145 " =    2.005
peak=    4.215 closest distance to " CB  ARG A  79 " =    1.433
peak=    4.212 closest distance to " O   HOH Z 180 " =    2.264
peak=    4.176 closest distance to " O   HOH Z 344 " =    2.898
peak=    4.169 closest distance to " O   HOH Z 134 " =    1.481
peak=    4.167 closest distance to " O   HOH Z  97 " =    1.829
peak=    4.156 closest distance to " O   HOH Z 427 " =    2.781
peak=    4.144 closest distance to " CA  THR A 221 " =    0.957
peak=    4.138 closest distance to " O   HOH Z 128 " =    1.996
peak=    4.125 closest distance to " O   HOH Z  78 " =    1.710
peak=    4.125 closest distance to " O   HOH Z 132 " =    1.099
peak=    4.122 closest distance to " O   HOH Z 326 " =    1.556
peak=    4.108 closest distance to " O   HOH Z 108 " =    1.338
peak=    4.107 closest distance to " O   HOH Z 279 " =    2.099
peak=    4.090 closest distance to " CB  PRO A  54 " =    0.841
peak=    4.086 closest distance to " O   HOH Z 316 " =    2.842
peak=    4.082 closest distance to " O   HOH Z 197 " =    2.572
peak=    4.050 closest distance to " O   HOH Z 371 " =    3.404
peak=    4.043 closest distance to " O   HOH Z  59 " =    2.362
peak=    4.041 closest distance to " CG1 ILE A  33 " =    1.277
peak=    4.040 closest distance to " CB  TRP A 179 " =    1.296
peak=    4.039 closest distance to " O   HOH Z  54 " =    1.737
peak=    4.037 closest distance to " NZ  LYS A 117 " =    3.218
peak=    4.027 closest distance to " CB  LEU A 228 " =    1.142
peak=    4.025 closest distance to " O   HOH Z 313 " =    1.765
peak=    3.996 closest distance to " O   HOH Z  49 " =    2.113
peak=    3.957 closest distance to " CG  PRO A  90 " =    1.123
peak=    3.946 closest distance to " OG BSER A 164 " =    2.452
peak=    3.943 closest distance to " O   HOH Z 374 " =    2.540
peak=    3.924 closest distance to " O   MET A 105 " =    1.810
peak=    3.918 closest distance to " O   HOH Z 369 " =    1.975
peak=    3.913 closest distance to " O   HOH Z   6 " =    2.190
peak=    3.902 closest distance to " CB  ARG A 139 " =    0.966
peak=    3.898 closest distance to " O   HOH Z 207 " =    1.900
peak=    3.864 closest distance to " O   HOH Z  68 " =    1.799
peak=    3.861 closest distance to " O   HOH Z 261 " =    2.212
peak=    3.841 closest distance to " O   HOH Z 132 " =    2.155
peak=    3.839 closest distance to " ND2 ASN A 187 " =    1.548
peak=    3.838 closest distance to " O   HOH Z  40 " =    1.578
peak=    3.835 closest distance to " O   HOH Z 193 " =    2.157
peak=    3.831 closest distance to " CG1BVAL A  72 " =    1.620
peak=    3.831 closest distance to " O   HOH Z 411 " =    3.732
peak=    3.830 closest distance to " CD2 LEU A 297 " =    0.893
peak=    3.824 closest distance to " CA  ASN A 176 " =    1.186
peak=    3.818 closest distance to " O   HOH Z 284 " =    2.862
peak=    3.808 closest distance to " CA  ASN A 215 " =    1.206
peak=    3.799 closest distance to " CB  VAL A 202 " =    1.565
peak=    3.797 closest distance to " CB  ARG A 190 " =    1.656
peak=    3.795 closest distance to " O   HOH Z  10 " =    1.870
peak=    3.780 closest distance to " CG  ARG A  66 " =    2.686
peak=    3.779 closest distance to " O   HOH Z  21 " =    1.705
peak=    3.753 closest distance to " O   HOH Z 423 " =    2.030
peak=    3.745 closest distance to " CG2 THR A 221 " =    1.133
peak=    3.736 closest distance to " O   HOH Z 416 " =    2.713
peak=    3.721 closest distance to " O   HOH Z 263 " =    2.243
peak=    3.714 closest distance to " O   HOH Z  80 " =    1.632
peak=    3.710 closest distance to " O   HOH Z  43 " =    2.038
peak=    3.707 closest distance to " NH2 ARG A 156 " =    1.159
peak=    3.707 closest distance to " CA  ARG A  36 " =    1.100
peak=    3.690 closest distance to " O   HOH Z 227 " =    1.629
peak=    3.689 closest distance to " O   HOH Z 214 " =    2.124
peak=    3.688 closest distance to " O   HOH Z 346 " =    1.691
peak=    3.688 closest distance to " OD2 ASP A 298 " =    4.017
peak=    3.687 closest distance to " O   HOH Z  44 " =    2.026
peak=    3.675 closest distance to " NZ  LYS A 119 " =    1.705
peak=    3.672 closest distance to " O   HOH Z 334 " =    1.416
peak=    3.671 closest distance to " O   HOH Z 173 " =    1.980
peak=    3.658 closest distance to " N   ASN A  39 " =    1.262
peak=    3.657 closest distance to " O   HOH Z 303 " =    1.921
peak=    3.656 closest distance to " O   HOH Z 133 " =    1.417
peak=    3.655 closest distance to " O   HOH Z  88 " =    3.230
peak=    3.650 closest distance to " O   HOH Z  63 " =    1.969
peak=    3.644 closest distance to " CB  VAL A 265 " =    1.253
peak=    3.643 closest distance to " CG  PRO A 243 " =    1.213
peak=    3.622 closest distance to " CD2 TRP A 179 " =    1.417
peak=    3.619 closest distance to " NH1AARG A 145 " =    1.166
peak=    3.614 closest distance to " O   HOH Z  19 " =    1.913
peak=    3.610 closest distance to " CG2 ILE A 120 " =    1.181
peak=    3.604 closest distance to " CB  ASN A 148 " =    1.146
peak=    3.602 closest distance to " O   HOH Z 427 " =    3.036
peak=    3.601 closest distance to " O   HOH Z 380 " =    2.035
peak=    3.596 closest distance to " CA  MET A  40 " =    1.031
peak=    3.593 closest distance to " O   HOH Z 250 " =    1.357
peak=    3.592 closest distance to " O   HOH Z 365 " =    2.949
peak=    3.591 closest distance to " O   HOH Z 261 " =    2.005
peak=    3.588 closest distance to " O   HOH Z  61 " =    1.625
peak=    3.586 closest distance to " O   HOH Z 108 " =    2.019
peak=    3.586 closest distance to " O   HOH Z 345 " =    2.995
peak=    3.585 closest distance to " O   HOH Z 189 " =    1.678
peak=    3.585 closest distance to " O   HOH Z  85 " =    1.738
peak=    3.582 closest distance to " O   HOH Z 128 " =    2.243
peak=    3.576 closest distance to " O   HOH Z  61 " =    1.520
peak=    3.576 closest distance to " NH2AARG A 190 " =    1.244
peak=    3.576 closest distance to " O   ALA A 165 " =    1.377
peak=    3.570 closest distance to " CA  ALA A  51 " =    0.869
peak=    3.568 closest distance to " CD  LYS A 166 " =    1.327
peak=    3.563 closest distance to " O   HOH Z 291 " =    1.453
peak=    3.559 closest distance to " O   HOH Z 327 " =    1.764
peak=    3.558 closest distance to " O   HOH Z 183 " =    1.507
peak=    3.549 closest distance to " CG  GLN A  58 " =    2.548
peak=    3.549 closest distance to " O   HOH Z 411 " =    1.675
peak=    3.546 closest distance to " O   HOH Z 402 " =    1.406
peak=    3.533 closest distance to " O   HOH Z 163 " =    1.899
peak=    3.527 closest distance to " O   HOH Z 147 " =    1.710
peak=    3.526 closest distance to " OG  SER A  22 " =    2.721
peak=    3.519 closest distance to " CB  SER A 141 " =    1.042
peak=    3.518 closest distance to " CZ2 TRP A 179 " =    1.643
peak=    3.516 closest distance to " O   HOH Z 209 " =    2.403
peak=    3.499 closest distance to " O   HOH Z 273 " =    2.756
peak=    3.494 closest distance to " O   HOH Z 299 " =    4.410
peak=    3.493 closest distance to " CG2BVAL A  41 " =    0.865
peak=    3.488 closest distance to " CB  SER A  26 " =    1.575
peak=    3.487 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.481 closest distance to " O   HOH Z 158 " =    2.972
peak=    3.481 closest distance to " CA  ALA A 248 " =    1.178
peak=    3.471 closest distance to " O   HOH Z 368 " =    3.631
peak=    3.467 closest distance to " O   HOH Z 132 " =    3.073
peak=    3.466 closest distance to " O   HOH Z 185 " =    1.717
peak=    3.463 closest distance to " O   HOH Z 214 " =    2.245
peak=    3.462 closest distance to " CB  ASN A  39 " =    0.842
peak=    3.457 closest distance to " O   TRP A 274 " =    1.909
peak=    3.444 closest distance to " CD1 LEU A 300 " =    1.215
peak=    3.444 closest distance to " CA  ASP A 140 " =    1.112
peak=    3.441 closest distance to " O   HOH Z 261 " =    1.554
peak=    3.441 closest distance to " O   HOH Z 357 " =    1.958
peak=    3.435 closest distance to " O   HOH Z 102 " =    1.221
peak=    3.435 closest distance to " OG  SER A  62 " =    3.002
peak=    3.435 closest distance to " O   HOH Z 358 " =    2.179
peak=    3.432 closest distance to " CD  ARG A 269 " =    0.979
peak=    3.428 closest distance to " CD BLYS A 290 " =    1.173
peak=    3.421 closest distance to " OE1 GLN A  11 " =    1.927
peak=    3.421 closest distance to " O   HOH Z 106 " =    2.331
peak=    3.420 closest distance to " O   HOH Z 292 " =    1.628
peak=    3.418 closest distance to " CA  ALA A  84 " =    1.339
peak=    3.413 closest distance to " O   HOH Z  66 " =    2.212
peak=    3.394 closest distance to " O   HOH Z 353 " =    2.662
peak=    3.393 closest distance to " O   HOH Z 260 " =    1.289
peak=    3.393 closest distance to " CA  LYS A 117 " =    1.233
peak=    3.388 closest distance to " O   HOH Z 281 " =    4.288
peak=    3.386 closest distance to " NH2 ARG A 219 " =    1.928
peak=    3.383 closest distance to " O   HOH Z 227 " =    1.613
peak=    3.381 closest distance to " O   HOH Z 126 " =    2.120
peak=    3.379 closest distance to " O   HOH Z 368 " =    2.534
peak=    3.376 closest distance to " CG  GLN A  77 " =    2.079
peak=    3.373 closest distance to " O   HOH Z 245 " =    1.344
peak=    3.372 closest distance to " O   HOH Z 211 " =    2.509
peak=    3.371 closest distance to " CG2 ILE A  20 " =    1.398
peak=    3.371 closest distance to " CE1 TYR A 186 " =    1.206
peak=    3.369 closest distance to " O   HOH Z 341 " =    1.742
peak=    3.368 closest distance to " O   HOH Z   1 " =    2.173
peak=    3.367 closest distance to " CD2 LEU A 255 " =    1.133
peak=    3.363 closest distance to " CB  ALA A 291 " =    1.311
peak=    3.356 closest distance to " O   HOH Z 409 " =    3.340
peak=    3.350 closest distance to " O   HOH Z 286 " =    2.146
peak=    3.333 closest distance to " CG  MET A 185 " =    1.136
peak=    3.333 closest distance to " O   HOH Z 345 " =    1.619
peak=    3.329 closest distance to " O   ALA A   1 " =    1.455
peak=    3.328 closest distance to " O   HOH Z 368 " =    2.509
peak=    3.326 closest distance to " CD  LYS A 119 " =    1.372
peak=    3.326 closest distance to " O   SER A  26 " =    1.726
peak=    3.320 closest distance to " O   HOH Z 337 " =    3.576
peak=    3.318 closest distance to " O   HOH Z  71 " =    1.173
peak=    3.317 closest distance to " O   HOH Z  20 " =    1.506
peak=    3.316 closest distance to " CA  ASN A  74 " =    1.186
peak=    3.316 closest distance to " CG  GLN A  89 " =    1.455
peak=    3.313 closest distance to " CG  GLU A 277 " =    2.207
peak=    3.312 closest distance to " ND1 HIS A  81 " =    1.518
peak=    3.309 closest distance to " CB  ASN A 285 " =    0.910
peak=    3.306 closest distance to " O   HOH Z 250 " =    1.649
peak=    3.299 closest distance to " C   ALA A   1 " =    1.634
peak=    3.298 closest distance to " CB  ARG A 259 " =    1.898
peak=    3.296 closest distance to " CG  PRO A 198 " =    1.294
peak=    3.294 closest distance to " CA  ALA A 291 " =    0.886
peak=    3.293 closest distance to " O   HOH Z 189 " =    1.363
peak=    3.292 closest distance to " CD  ARG A 159 " =    0.765
peak=    3.287 closest distance to " O   HOH Z 425 " =    2.051
peak=    3.284 closest distance to " CA  THR A 264 " =    0.843
peak=    3.281 closest distance to " CB  TYR A 116 " =    0.932
peak=    3.279 closest distance to " CB  ALA A   9 " =    1.554
peak=    3.268 closest distance to " OE1 GLN A  58 " =    5.921
peak=    3.261 closest distance to " CA  ILE A  33 " =    1.528
peak=    3.260 closest distance to " O   HOH Z 267 " =    2.101
peak=    3.259 closest distance to " O   HOH Z 266 " =    2.843
peak=    3.257 closest distance to " O   HOH Z 329 " =    3.432
peak=    3.253 closest distance to " O   HOH Z 417 " =    2.970
peak=    3.250 closest distance to " CG  GLN A  11 " =    1.377
peak=    3.249 closest distance to " OG BSER A 258 " =    3.435
peak=    3.247 closest distance to " CG  LYS A  76 " =    1.159
peak=    3.241 closest distance to " O   HOH Z 438 " =    1.909
peak=    3.239 closest distance to " CB  TRP A 266 " =    0.970
peak=    3.236 closest distance to " O   HOH Z  71 " =    1.942
peak=    3.232 closest distance to " CB  SER A  62 " =    0.801
peak=    3.231 closest distance to " CB  SER A  62 " =    1.238
peak=    3.231 closest distance to " CA  ARG A 195 " =    1.292
peak=    3.229 closest distance to " O   HOH Z 118 " =    1.271
peak=    3.224 closest distance to " CB  MET A  47 " =    1.074
peak=    3.223 closest distance to " CB  ALA A   1 " =    1.194
peak=    3.217 closest distance to " O   HOH Z 126 " =    1.609
peak=    3.213 closest distance to " O   HOH Z 266 " =    1.648
peak=    3.213 closest distance to " CA  ASP A 191 " =    0.864
peak=    3.213 closest distance to " O   HOH Z 403 " =    1.398
peak=    3.210 closest distance to " O   ALA A 158 " =    1.230
peak=    3.206 closest distance to " O   HOH Z 336 " =    1.748
peak=    3.205 closest distance to " O   HOH Z 189 " =    2.806
peak=    3.202 closest distance to " NH1BARG A 145 " =    1.201
peak=    3.201 closest distance to " CG2 VAL A 197 " =    1.077
peak=    3.199 closest distance to " O   SER A 164 " =    1.001
peak=    3.195 closest distance to " O   HOH Z 194 " =    1.897
peak=    3.193 closest distance to " CA  VAL A 126 " =    1.051
peak=    3.193 closest distance to " CA  ALA A 233 " =    1.206
peak=    3.185 closest distance to " O   HOH Z 135 " =    1.694
peak=    3.182 closest distance to " O   HOH Z 175 " =    2.194
peak=    3.182 closest distance to " CG AARG A 275 " =    0.986
peak=    3.177 closest distance to " CB  GLN A 278 " =    0.863
peak=    3.176 closest distance to " O   HOH Z  85 " =    1.969
peak=    3.175 closest distance to " CD1 ILE A 106 " =    0.933
peak=    3.173 closest distance to " N   ASN A 127 " =    1.253
peak=    3.171 closest distance to " OD1 ASP A 286 " =    1.596
peak=    3.170 closest distance to " CB  SER A 212 " =    1.035
peak=    3.164 closest distance to " CA  ASP A 162 " =    1.166
peak=    3.157 closest distance to " O   HOH Z 380 " =    1.839
peak=    3.156 closest distance to " CA  LEU A 282 " =    1.211
peak=    3.149 closest distance to " O   HOH Z 227 " =    2.167
peak=    3.148 closest distance to " CB  ASP A 140 " =    0.883
peak=    3.142 closest distance to " N   PHE A 130 " =    1.388
peak=    3.140 closest distance to " O   HOH Z 299 " =    2.261
peak=    3.137 closest distance to " O   HOH Z 163 " =    1.644
peak=    3.135 closest distance to " NZ  LYS A  76 " =    1.240
peak=    3.133 closest distance to " O   HOH Z 125 " =    2.285
peak=    3.133 closest distance to " O   HOH Z 422 " =    2.658
peak=    3.132 closest distance to " O   HOH Z 112 " =    1.645
peak=    3.131 closest distance to " O   HOH Z  35 " =    2.506
peak=    3.122 closest distance to " CB  ALA A 100 " =    1.150
peak=    3.110 closest distance to " CA  GLY A  80 " =    0.934
peak=    3.099 closest distance to " O   HOH Z 367 " =    3.424
peak=    3.098 closest distance to " O   HOH Z 359 " =    1.741
peak=    3.097 closest distance to " CG  MET A 185 " =    1.077
peak=    3.092 closest distance to " CB  TYR A  30 " =    1.434
peak=    3.091 closest distance to " O   HOH Z 435 " =    1.840
peak=    3.089 closest distance to " CA  VAL A  41 " =    0.884
peak=    3.079 closest distance to " C   ALA A 299 " =    0.931
peak=    3.076 closest distance to " CB  GLN A 205 " =    1.273
peak=    3.076 closest distance to " O   HOH Z 423 " =    3.196
peak=    3.075 closest distance to " CD1AILE A 234 " =    0.992
peak=    3.066 closest distance to " CB  ILE A 120 " =    1.354
peak=    3.065 closest distance to " OG BSER A  99 " =    2.250
peak=    3.062 closest distance to " CA  GLU A  46 " =    0.720
peak=    3.058 closest distance to " N   ARG A 156 " =    1.330
peak=    3.055 closest distance to " OD1 ASP A 238 " =    0.960
peak=    3.047 closest distance to " N   SER A 135 " =    1.309
peak=    3.046 closest distance to " O   HOH Z 271 " =    2.157
peak=    3.043 closest distance to " CA  ALA A 158 " =    1.161

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.869 - 5.149
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.869 - 5.149

peak=   -4.687 closest distance to " O   HOH Z 266 " =    4.109
peak=   -4.320 closest distance to " CD  ARG A 156 " =    2.022
peak=   -4.200 closest distance to " N   GLN A  58 " =    1.637
peak=   -4.193 closest distance to " O   HOH Z  13 " =    1.549
peak=   -4.179 closest distance to " O   VAL A  67 " =    2.813
peak=   -4.161 closest distance to " OXT GLY A 302 " =    2.782
peak=   -4.156 closest distance to " O   ILE A 109 " =    2.589
peak=   -4.133 closest distance to " C   HIS A 108 " =    1.095
peak=   -4.127 closest distance to " CD1 LEU A 101 " =    2.474
peak=   -4.117 closest distance to " O   HOH Z 372 " =    2.317
peak=   -4.104 closest distance to " SG  CYS A 254 " =    3.258
peak=   -4.087 closest distance to " O   PRO A 163 " =    2.067
peak=   -4.045 closest distance to " CA  VAL A  67 " =    2.746
peak=   -4.032 closest distance to " CB  PRO A 243 " =    2.564
peak=   -4.010 closest distance to " O   HOH Z  10 " =    1.544
peak=   -3.998 closest distance to " OG  SER A  97 " =    2.124
peak=   -3.987 closest distance to " CH2 TRP A 179 " =    1.334
peak=   -3.961 closest distance to " CD  ARG A 139 " =    1.627
peak=   -3.957 closest distance to " CB  ALA A 291 " =    2.355
peak=   -3.920 closest distance to " N   ALA A 248 " =    1.693
peak=   -3.919 closest distance to " O   HOH Z 377 " =    2.061
peak=   -3.911 closest distance to " O   HOH Z 198 " =    2.261
peak=   -3.899 closest distance to " NE2 GLN A  58 " =    1.100
peak=   -3.899 closest distance to " O   HOH Z 388 " =    2.019
peak=   -3.897 closest distance to " CD1 PHE A 130 " =    2.279
peak=   -3.885 closest distance to " CG  ASP A 231 " =    0.869
peak=   -3.874 closest distance to " O   HOH Z 292 " =    4.463
peak=   -3.858 closest distance to " CD1 LEU A 228 " =    2.248
peak=   -3.848 closest distance to " O   HOH Z 234 " =    4.084
peak=   -3.836 closest distance to " O   HOH Z  52 " =    1.486
peak=   -3.834 closest distance to " O   PRO A 198 " =    1.342
peak=   -3.833 closest distance to " O   HOH Z 353 " =    2.243
peak=   -3.824 closest distance to " OG BSER A 134 " =    1.283
peak=   -3.796 closest distance to " CD2 LEU A 300 " =    2.837
peak=   -3.787 closest distance to " CB  TYR A  15 " =    2.215
peak=   -3.786 closest distance to " O   SER A 210 " =    1.896
peak=   -3.784 closest distance to " CZ  TYR A 169 " =    1.844
peak=   -3.782 closest distance to " OG BSER A 134 " =    1.720
peak=   -3.777 closest distance to " N   SER A 276 " =    1.335
peak=   -3.771 closest distance to " CD1 PHE A  59 " =    1.912
peak=   -3.760 closest distance to " ND2 ASN A 187 " =    1.520
peak=   -3.753 closest distance to " O   HOH Z  11 " =    1.799
peak=   -3.743 closest distance to " CG  ASP A  50 " =    2.386
peak=   -3.740 closest distance to " OE1 GLN A 223 " =    2.116
peak=   -3.739 closest distance to " O   HOH Z  43 " =    1.615
peak=   -3.732 closest distance to " N   ALA A  43 " =    2.558
peak=   -3.731 closest distance to " OE2 GLU A   2 " =    1.927
peak=   -3.725 closest distance to " O   HOH Z 126 " =    1.920
peak=   -3.720 closest distance to " O   HOH Z 407 " =    3.111
peak=   -3.704 closest distance to " C   ALA A 158 " =    1.201
peak=   -3.701 closest distance to " NH1 ARG A 195 " =    2.542
peak=   -3.693 closest distance to " O   HOH Z 290 " =    1.039
peak=   -3.688 closest distance to " NH2 ARG A  79 " =    1.882
peak=   -3.686 closest distance to " N   GLN A 122 " =    1.513
peak=   -3.677 closest distance to " O   HOH Z 166 " =    1.421
peak=   -3.653 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.644 closest distance to " NH2 ARG A  66 " =    4.909
peak=   -3.626 closest distance to " O   VAL A 153 " =    2.331
peak=   -3.626 closest distance to " CB  ASN A  39 " =    2.285
peak=   -3.625 closest distance to " O   HOH Z 118 " =    2.881
peak=   -3.623 closest distance to " O   HOH Z 395 " =    5.149
peak=   -3.621 closest distance to " O   HOH Z 385 " =    1.994
peak=   -3.608 closest distance to " O   HOH Z 102 " =    1.752
peak=   -3.592 closest distance to " O   ASN A  45 " =    1.838
peak=   -3.584 closest distance to " O   HOH Z 185 " =    2.241
peak=   -3.574 closest distance to " O   MET A  40 " =    2.719
peak=   -3.572 closest distance to " CD2 LEU A 237 " =    2.652
peak=   -3.568 closest distance to " O   HOH Z  19 " =    2.057
peak=   -3.561 closest distance to " O   VAL A 174 " =    2.087
peak=   -3.558 closest distance to " CE2 TYR A  30 " =    2.786
peak=   -3.558 closest distance to " O   HOH Z 165 " =    2.004
peak=   -3.555 closest distance to " ND2 ASN A  45 " =    0.955
peak=   -3.553 closest distance to " O   HOH Z 311 " =    3.525
peak=   -3.553 closest distance to " OG ASER A 134 " =    1.264
peak=   -3.547 closest distance to " O   HOH Z  11 " =    1.834
peak=   -3.537 closest distance to " CB  PHE A 192 " =    1.883
peak=   -3.535 closest distance to " CG  PHE A 283 " =    2.552
peak=   -3.522 closest distance to " O   HOH Z 283 " =    1.755
peak=   -3.514 closest distance to " NH2 ARG A  66 " =    1.826
peak=   -3.510 closest distance to " O   HOH Z  15 " =    1.578
peak=   -3.503 closest distance to " OG  SER A  62 " =    1.485
peak=   -3.502 closest distance to " O   HOH Z  38 " =    1.537
peak=   -3.491 closest distance to " O   HOH Z 166 " =    1.956
peak=   -3.490 closest distance to " O   HOH Z  90 " =    2.916
peak=   -3.488 closest distance to " O   ALA A 161 " =    1.804
peak=   -3.474 closest distance to " O   HOH Z 196 " =    1.909
peak=   -3.466 closest distance to " O   HOH Z  76 " =    1.978
peak=   -3.465 closest distance to " O   TRP A  92 " =    1.822
peak=   -3.464 closest distance to " O   HOH Z  17 " =    1.578
peak=   -3.460 closest distance to " N   HIS A 115 " =    2.009
peak=   -3.458 closest distance to " CD  LYS A 289 " =    2.449
peak=   -3.440 closest distance to " O   HOH Z 148 " =    3.649
peak=   -3.430 closest distance to " O   SER A 135 " =    1.574
peak=   -3.430 closest distance to " CA  ASP A 298 " =    1.079
peak=   -3.422 closest distance to " CE  MET A 105 " =    1.999
peak=   -3.420 closest distance to " O   HOH Z 435 " =    2.690
peak=   -3.415 closest distance to " CE  MET A  93 " =    1.194
peak=   -3.415 closest distance to " O   HOH Z  88 " =    1.841
peak=   -3.403 closest distance to " O   ALA A 160 " =    1.458
peak=   -3.396 closest distance to " O   HOH Z  97 " =    1.600
peak=   -3.396 closest distance to " CB  SER A 245 " =    2.466
peak=   -3.395 closest distance to " O   HOH Z 427 " =    1.424
peak=   -3.390 closest distance to " OE1 GLN A  77 " =    1.733
peak=   -3.387 closest distance to " O   HOH Z  93 " =    1.506
peak=   -3.384 closest distance to " O   PHE A 218 " =    1.577
peak=   -3.384 closest distance to " SG ACYS A 201 " =    2.102
peak=   -3.382 closest distance to " C   LEU A 143 " =    1.128
peak=   -3.372 closest distance to " O   HOH Z 281 " =    2.712
peak=   -3.368 closest distance to " CG  ARG A  66 " =    2.453
peak=   -3.352 closest distance to " CZ  PHE A  59 " =    1.647
peak=   -3.345 closest distance to " CB  SER A 258 " =    2.030
peak=   -3.344 closest distance to " O   HOH Z 361 " =    3.442
peak=   -3.337 closest distance to " OG BSER A 210 " =    2.018
peak=   -3.336 closest distance to " O   GLY A 196 " =    0.985
peak=   -3.332 closest distance to " C   ASN A 285 " =    2.427
peak=   -3.328 closest distance to " O   LEU A 167 " =    1.477
peak=   -3.327 closest distance to " CA  GLY A 133 " =    1.854
peak=   -3.326 closest distance to " OD2 ASP A 171 " =    2.293
peak=   -3.321 closest distance to " O   SER A 146 " =    0.919
peak=   -3.321 closest distance to " O   HOH Z 265 " =    1.951
peak=   -3.321 closest distance to " CD  GLN A  88 " =    1.920
peak=   -3.319 closest distance to " O   HOH Z 417 " =    2.552
peak=   -3.311 closest distance to " OD1 ASP A 171 " =    1.585
peak=   -3.307 closest distance to " CG  GLU A  53 " =    1.485
peak=   -3.304 closest distance to " CG1 VAL A 112 " =    2.741
peak=   -3.303 closest distance to " ND2 ASN A  39 " =    1.304
peak=   -3.300 closest distance to " O   PRO A 198 " =    1.311
peak=   -3.299 closest distance to " OD1 ASN A 148 " =    1.615
peak=   -3.296 closest distance to " CG2 ILE A 263 " =    2.235
peak=   -3.296 closest distance to " CG2 VAL A 189 " =    2.168
peak=   -3.287 closest distance to " OG1 THR A 178 " =    1.244
peak=   -3.287 closest distance to " CB  CYS A 201 " =    2.546
peak=   -3.281 closest distance to " CG  PRO A 163 " =    2.573
peak=   -3.274 closest distance to " ND2 ASN A 209 " =    1.774
peak=   -3.271 closest distance to " CG  GLU A 152 " =    2.167
peak=   -3.270 closest distance to " O   HOH Z  60 " =    1.934
peak=   -3.270 closest distance to " O   HOH Z 263 " =    2.933
peak=   -3.269 closest distance to " O   HOH Z 396 " =    1.512
peak=   -3.264 closest distance to " CB  PRO A 163 " =    2.689
peak=   -3.258 closest distance to " OG  SER A  87 " =    1.344
peak=   -3.255 closest distance to " O   ASN A 187 " =    1.456
peak=   -3.253 closest distance to " CB  PHE A 208 " =    2.219
peak=   -3.253 closest distance to " OD1 ASP A 191 " =    1.801
peak=   -3.250 closest distance to " O   ALA A 256 " =    1.519
peak=   -3.237 closest distance to " O   HOH Z   6 " =    1.708
peak=   -3.235 closest distance to " OD2 ASP A 171 " =    1.656
peak=   -3.235 closest distance to " CD2 PHE A  59 " =    2.374
peak=   -3.232 closest distance to " CB  CYS A 254 " =    2.537
peak=   -3.232 closest distance to " O   HOH Z 145 " =    3.039
peak=   -3.232 closest distance to " O   HOH Z 313 " =    0.971
peak=   -3.231 closest distance to " O   HOH Z 423 " =    2.274
peak=   -3.229 closest distance to " O   HOH Z 250 " =    1.399
peak=   -3.228 closest distance to " N   GLN A  58 " =    1.465
peak=   -3.226 closest distance to " CG  LEU A  83 " =    1.933
peak=   -3.226 closest distance to " O   HOH Z  71 " =    1.455
peak=   -3.226 closest distance to " OD1 ASN A 187 " =    1.726
peak=   -3.210 closest distance to " OG  SER A  26 " =    1.220
peak=   -3.207 closest distance to " O   HOH Z 378 " =    1.239
peak=   -3.203 closest distance to " O   ALA A  34 " =    2.576
peak=   -3.201 closest distance to " CD2 LEU A 237 " =    2.615
peak=   -3.196 closest distance to " O   VAL A 125 " =    2.197
peak=   -3.194 closest distance to " OG  SER A 206 " =    1.767
peak=   -3.190 closest distance to " OG1 THR A 279 " =    1.342
peak=   -3.188 closest distance to " O   ASP A 231 " =    2.518
peak=   -3.183 closest distance to " NH2 ARG A  66 " =    4.601
peak=   -3.180 closest distance to " NE2 GLN A 103 " =    1.636
peak=   -3.173 closest distance to " O   HOH Z 411 " =    3.518
peak=   -3.172 closest distance to " O   HOH Z 151 " =    1.389
peak=   -3.171 closest distance to " O   HOH Z  41 " =    2.352
peak=   -3.170 closest distance to " CB  ASP A 286 " =    2.105
peak=   -3.169 closest distance to " N   VAL A 189 " =    1.680
peak=   -3.169 closest distance to " CB  ALA A  10 " =    2.136
peak=   -3.166 closest distance to " N   THR A 157 " =    1.569
peak=   -3.159 closest distance to " C   GLN A 205 " =    1.879
peak=   -3.158 closest distance to " O   HOH Z  98 " =    2.049
peak=   -3.156 closest distance to " OH  TYR A 214 " =    1.312
peak=   -3.150 closest distance to " O   ILE A 120 " =    1.395
peak=   -3.147 closest distance to " OE1 GLN A 223 " =    1.902
peak=   -3.139 closest distance to " O   HOH Z 412 " =    4.477
peak=   -3.137 closest distance to " O   HOH Z 297 " =    2.810
peak=   -3.125 closest distance to " O   HOH Z  61 " =    1.601
peak=   -3.124 closest distance to " OD1 ASP A 200 " =    1.298
peak=   -3.121 closest distance to " O   HOH Z 266 " =    4.525
peak=   -3.115 closest distance to " O   ASN A 301 " =    1.309
peak=   -3.109 closest distance to " CE3 TRP A 274 " =    2.431
peak=   -3.108 closest distance to " CE1 HIS A  81 " =    1.395
peak=   -3.102 closest distance to " OXT GLY A 302 " =    3.021
peak=   -3.096 closest distance to " O   HOH Z 264 " =    1.820
peak=   -3.095 closest distance to " SD  MET A 188 " =    2.255
peak=   -3.086 closest distance to " CA  GLY A 241 " =    3.150
peak=   -3.084 closest distance to " CG  GLU A 152 " =    1.405
peak=   -3.084 closest distance to " CG  ARG A 259 " =    2.785
peak=   -3.083 closest distance to " OG1 THR A  82 " =    1.446
peak=   -3.082 closest distance to " O   HOH Z 317 " =    2.580
peak=   -3.080 closest distance to " CD1 TYR A 247 " =    2.410
peak=   -3.076 closest distance to " CG  LYS A 119 " =    2.887
peak=   -3.067 closest distance to " O   HOH Z 211 " =    1.842
peak=   -3.066 closest distance to " O   HOH Z 378 " =    1.635
peak=   -3.058 closest distance to " CB  ASP A 132 " =    2.335
peak=   -3.039 closest distance to " ND2 ASN A  60 " =    1.497
peak=   -3.034 closest distance to " CD1 ILE A 239 " =    2.363
peak=   -3.027 closest distance to " CG1AVAL A  41 " =    2.846
peak=   -3.019 closest distance to " O   HOH Z 422 " =    1.510

================= 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    :  0.4092 0.4053   6.211215e+00   6.211815e+00
   1_bss:  0.3970 0.3922   6.199572e+00   6.189524e+00
   1_xyz:  0.2755 0.3018   5.895108e+00   5.971426e+00
   1_adp:  0.2506 0.3113   5.841592e+00   5.993164e+00
   1_occ:  0.2501 0.3117   5.840870e+00   5.992630e+00
   2_bss:  0.2471 0.3080   5.834495e+00   5.987385e+00
   2_xyz:  0.1810 0.2363   5.562027e+00   5.760747e+00
   2_adp:  0.1668 0.2189   5.489601e+00   5.691751e+00
   2_occ:  0.1665 0.2188   5.489113e+00   5.691420e+00
   3_bss:  0.1664 0.2171   5.484918e+00   5.686578e+00
   3_xyz:  0.1293 0.1741   5.257628e+00   5.481404e+00
   3_adp:  0.1215 0.1651   5.202755e+00   5.424148e+00
   3_occ:  0.1213 0.1649   5.202071e+00   5.423664e+00
   4_bss:  0.1219 0.1653   5.205733e+00   5.426542e+00
   4_xyz:  0.1144 0.1579   5.157632e+00   5.383915e+00
   4_adp:  0.1119 0.1582   5.148664e+00   5.383208e+00
   4_occ:  0.1119 0.1581   5.148337e+00   5.383179e+00
   5_bss:  0.1119 0.1581   5.148139e+00   5.383057e+00
   5_xyz:  0.1071 0.1564   5.122580e+00   5.371147e+00
   5_adp:  0.1064 0.1568   5.121792e+00   5.374276e+00
   5_occ:  0.1064 0.1568   5.121858e+00   5.374614e+00
   5_bss:  0.1063 0.1568   5.121907e+00   5.374623e+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:  0.316  24.695  -3.208   0.014   3.045   0.000   0.000   0.000
   1_xyz:  0.316  24.695  -3.208   0.014   3.045   0.000   0.000   0.000
   1_adp:  0.316  24.695  -3.208   0.014   3.045   0.000   0.000   0.000
   1_occ:  0.316  24.695  -3.208   0.014   3.045   0.000   0.000   0.000
   2_bss:  0.324  45.729  -2.854  -1.096   0.130  -0.000   0.000   0.000
   2_xyz:  0.324  45.729  -2.854  -1.096   0.130  -0.000   0.000   0.000
   2_adp:  0.324  45.729  -2.854  -1.096   0.130  -0.000   0.000   0.000
   2_occ:  0.324  45.729  -2.854  -1.096   0.130  -0.000   0.000   0.000
   3_bss:  0.319  40.786  -2.638  -1.561  -1.202  -0.000  -0.000  -0.000
   3_xyz:  0.319  40.786  -2.638  -1.561  -1.202  -0.000  -0.000  -0.000
   3_adp:  0.319  40.786  -2.638  -1.561  -1.202  -0.000  -0.000  -0.000
   3_occ:  0.319  40.786  -2.638  -1.561  -1.202  -0.000  -0.000  -0.000
   4_bss:  0.319  42.463  -2.808  -1.972  -1.867  -0.000  -0.000  -0.000
   4_xyz:  0.319  42.463  -2.808  -1.972  -1.867  -0.000  -0.000  -0.000
   4_adp:  0.319  42.463  -2.808  -1.972  -1.867  -0.000  -0.000  -0.000
   4_occ:  0.319  42.463  -2.808  -1.972  -1.867  -0.000  -0.000  -0.000
   5_bss:  0.321  43.676  -2.744  -1.965  -1.965  -0.000  -0.000  -0.000
   5_xyz:  0.321  43.676  -2.744  -1.965  -1.965  -0.000  -0.000  -0.000
   5_adp:  0.321  43.676  -2.744  -1.965  -1.965  -0.000  -0.000  -0.000
   5_occ:  0.321  43.676  -2.744  -1.965  -1.965  -0.000  -0.000  -0.000
   5_bss:  0.323  44.459  -2.517  -1.767  -1.759  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.276 0.5423  0.7205    52438.998
   1_bss:  46.610 0.5609  0.7444    48009.517
   1_xyz:  31.012 0.7469  0.9481    24085.421
   1_adp:  32.443 0.7298  0.9336    25733.401
   1_occ:  32.437 0.7298  0.9334    25720.697
   2_bss:  31.969 0.7350  0.9016    25164.506
   2_xyz:  23.338 0.8276  0.9796    14219.258
   2_adp:  20.923 0.8528  0.9909    12119.986
   2_occ:  20.929 0.8528  0.9906    12123.919
   3_bss:  20.732 0.8545  0.9727    11908.220
   3_xyz:  16.288 0.8949  0.9958     7705.420
   3_adp:  15.005 0.9064  0.9981     6950.568
   3_occ:  14.993 0.9065  0.9980     6945.326
   4_bss:  15.047 0.9061  0.9827     7031.521
   4_xyz:  14.085 0.9142  0.9853     6340.176
   4_adp:  14.034 0.9148  0.9819     6324.480
   4_occ:  14.032 0.9148  0.9818     6324.284
   5_bss:  14.026 0.9149  0.9816     6326.296
   5_xyz:  13.839 0.9163  0.9815     6206.699
   5_adp:  13.883 0.9160  0.9766     6234.586
   5_occ:  13.886 0.9160  0.9765     6237.652
   5_bss:  13.887 0.9160  0.9821     6238.908
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8666e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8666e-01
   1_xyz:   1.365  0.011  0.082 15.871  0.005  4.110   1.0371e-01
   1_adp:   1.365  0.011  0.082 15.871  0.005  4.110   1.0371e-01
   1_occ:   1.365  0.011  0.082 15.871  0.005  4.110   1.0371e-01
   2_bss:   1.365  0.011  0.082 15.871  0.005  4.110   1.0371e-01
   2_xyz:   1.067  0.007  0.073 13.991  0.004  4.122   6.1601e-02
   2_adp:   1.067  0.007  0.073 13.991  0.004  4.122   6.1601e-02
   2_occ:   1.067  0.007  0.073 13.991  0.004  4.122   6.1601e-02
   3_bss:   1.067  0.007  0.073 13.991  0.004  4.122   6.1601e-02
   3_xyz:   1.088  0.008  0.074 14.698  0.004  4.115   6.6568e-02
   3_adp:   1.088  0.008  0.074 14.698  0.004  4.115   6.6568e-02
   3_occ:   1.088  0.008  0.074 14.698  0.004  4.115   6.6568e-02
   4_bss:   1.088  0.008  0.074 14.698  0.004  4.115   6.6568e-02
   4_xyz:   1.016  0.007  0.072 14.541  0.004  4.116   5.8898e-02
   4_adp:   1.016  0.007  0.072 14.541  0.004  4.116   5.8898e-02
   4_occ:   1.016  0.007  0.072 14.541  0.004  4.116   5.8898e-02
   5_bss:   1.016  0.007  0.072 14.541  0.004  4.116   5.8898e-02
   5_xyz:   1.112  0.008  0.079 14.800  0.005  4.108   6.9995e-02
   5_adp:   1.112  0.008  0.079 14.800  0.005  4.108   6.9995e-02
   5_occ:   1.112  0.008  0.079 14.800  0.005  4.108   6.9995e-02
   5_bss:   1.112  0.008  0.079 14.800  0.005  4.108   6.9995e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.494   2.4014e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.494   2.4014e-01
   1_xyz:   8.931  0.065  0.346 86.822  0.029  1.994   1.0147e-01
   1_adp:   8.931  0.065  0.346 86.822  0.029  1.994   1.0147e-01
   1_occ:   8.931  0.065  0.346 86.822  0.029  1.994   1.0147e-01
   2_bss:   8.931  0.065  0.346 86.822  0.029  1.994   1.0147e-01
   2_xyz:   7.188  0.068  0.232 81.484  0.036  2.367   5.1341e-02
   2_adp:   7.188  0.068  0.232 81.484  0.036  2.367   5.1341e-02
   2_occ:   7.188  0.068  0.232 81.484  0.036  2.367   5.1341e-02
   3_bss:   7.188  0.068  0.232 81.484  0.036  2.367   5.1341e-02
   3_xyz:   6.970  0.045  0.306 81.433  0.031  2.312   5.6653e-02
   3_adp:   6.970  0.045  0.306 81.433  0.031  2.312   5.6653e-02
   3_occ:   6.970  0.045  0.306 81.433  0.031  2.312   5.6653e-02
   4_bss:   6.970  0.045  0.306 81.433  0.031  2.312   5.6653e-02
   4_xyz:   6.841  0.038  0.234 82.364  0.038  2.359   4.3259e-02
   4_adp:   6.841  0.038  0.234 82.364  0.038  2.359   4.3259e-02
   4_occ:   6.841  0.038  0.234 82.364  0.038  2.359   4.3259e-02
   5_bss:   6.841  0.038  0.234 82.364  0.038  2.359   4.3259e-02
   5_xyz:   7.348  0.046  0.251 82.315  0.035  2.265   5.7753e-02
   5_adp:   7.348  0.046  0.251 82.315  0.035  2.265   5.7753e-02
   5_occ:   7.348  0.046  0.251 82.315  0.035  2.265   5.7753e-02
   5_bss:   7.348  0.046  0.251 82.315  0.035  2.265   5.7753e-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:  92.71   0.00  18.21  88.93   0.00  14.18  92.71   3.94  40.13
   1_occ:  92.71   0.00  18.21  88.93   0.00  14.18  92.71   3.94  40.13
   2_bss:  92.71   0.00  18.21  88.93   0.00  14.18  92.71   3.94  40.13
   2_xyz:  92.71   0.00  18.21  88.93   0.00  14.18  92.71   3.94  40.13
   2_adp:  83.88   0.00  17.66  83.88   0.00  13.50  82.27   6.01  40.28
   2_occ:  83.88   0.00  17.66  83.88   0.00  13.50  82.27   6.01  40.28
   3_bss:  83.88   0.00  17.66  83.88   0.00  13.50  82.27   6.01  40.28
   3_xyz:  83.88   0.00  17.66  83.88   0.00  13.50  82.27   6.01  40.28
   3_adp:  85.75   2.20  17.22  85.75   2.20  13.10  78.47   4.87  39.67
   3_occ:  85.75   2.20  17.22  85.75   2.20  13.10  78.47   4.87  39.67
   4_bss:  85.75   2.20  17.22  85.75   2.20  13.10  78.47   4.87  39.67
   4_xyz:  85.75   2.20  17.22  85.75   2.20  13.10  78.47   4.87  39.67
   4_adp:  90.38   2.11  17.09  90.38   2.11  12.97  81.36   5.28  39.54
   4_occ:  90.38   2.11  17.09  90.38   2.11  12.97  81.36   5.28  39.54
   5_bss:  90.38   2.11  17.09  90.38   2.11  12.97  81.36   5.28  39.54
   5_xyz:  90.38   2.11  17.09  90.38   2.11  12.97  81.36   5.28  39.54
   5_adp:  94.32   1.47  16.99  94.32   1.47  12.86  82.32   5.50  39.50
   5_occ:  94.32   1.47  16.99  94.32   1.47  12.86  82.32   5.50  39.50
   5_bss:  94.26   1.42  16.94  94.26   1.42  12.80  82.26   5.45  39.44
------------------------------------------------------------------------
 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:    2.025    0.014    0.367
   1_adp:    2.025    0.014    0.367
   1_occ:    2.025    0.014    0.367
   2_bss:    2.025    0.014    0.367
   2_xyz:    1.472    0.029    0.481
   2_adp:    1.472    0.029    0.481
   2_occ:    1.472    0.029    0.481
   3_bss:    1.472    0.029    0.481
   3_xyz:    1.684    0.038    0.577
   3_adp:    1.684    0.038    0.577
   3_occ:    1.684    0.038    0.577
   4_bss:    1.684    0.038    0.577
   4_xyz:    1.772    0.067    0.596
   4_adp:    1.772    0.067    0.596
   4_occ:    1.772    0.067    0.596
   5_bss:    1.772    0.067    0.596
   5_xyz:    1.862    0.094    0.612
   5_adp:    1.862    0.094    0.612
   5_occ:    1.862    0.094    0.612
   5_bss:    1.862    0.094    0.612
------------------------------------------------------------------------

CPU time actual refinement: 341.77


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_561/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_561/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_561/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_561/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_561/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.63 
  Macro-tasks:
    bulk solvent and scale       = 44.27  
    individual site refinement   = 137.58 
    weights calculation          = 30.50  
    collect and process          = 6.89   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.36 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 107.81 
    alpha_beta                      = 8.32   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 115.89 
    fmodel                         = 7.61   
    r_factors                      = 0.21   
    phase_errors                   = 10.88  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 254.00 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.846 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    643 calls, 107.44 s
gradients_fft:          588 calls, 102.77 s

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

# Date 2008-01-16 Time 05:07:29 PST -0800 (1200488849.72 s)
Start R-work = 0.4092, R-free = 0.4053 (no bulk solvent and anisotropic scale)
Final R-work = 0.1314, R-free = 0.1774 (no bulk solvent and anisotropic scale)

Start R-work = 0.3970, R-free = 0.3922
Final R-work = 0.1063, R-free = 0.1568