# Date 2008-01-16 Time 04:50:18 PST -0800 (1200487818.52 s)
#phil __OFF__

Command line arguments: "../485.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14318
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 485

-------------------------------------------------------------------------------
  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, 45.7567, 84.6622, 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, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.95157
Completeness in resolution range: 0.964215
Completeness with d_max=infinity: 0.961282

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8570
                             d_min =   1.9516

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, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.95157
Completeness in resolution range: 0.964215
Completeness with d_max=infinity: 0.961282

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8574 -  4.1763 [2126/2151]  1916   210   9.9%
  bin  2:  4.1763 -  3.3271 [2050/2070]  1844   206  10.0%
  bin  3:  3.3271 -  2.9101 [2033/2052]  1827   206  10.1%
  bin  4:  2.9101 -  2.6457 [2004/2034]  1809   195   9.7%
  bin  5:  2.6457 -  2.4570 [1999/2018]  1800   199  10.0%
  bin  6:  2.4570 -  2.3127 [1991/2016]  1785   206  10.3%
  bin  7:  2.3127 -  2.1972 [1949/1977]  1755   194  10.0%
  bin  8:  2.1972 -  2.1019 [1982/2018]  1782   200  10.1%
  bin  9:  2.1019 -  2.0212 [1956/1998]  1762   194   9.9%
  bin 10:  2.0212 -  1.9516 [1499/1982]  1350   149   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_485/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:
        1.53 -     2.20: 33
        2.20 -     2.88: 1329
        2.88 -     3.55: 4600
        3.55 -     4.23: 9442
        4.23 -     4.90: 13657
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.528 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.555 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.615 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.716 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 29056 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_485/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_485/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 45.75675 84.6622 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4779   r_free= 0.4784   ksol= 0.00   Bsol= 0.00   scale= 0.899    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.289405                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6582 0.99   1390  155 0.3970 0.4032      6.5983      6.6285|
|  2:  4.6582 -  3.7164 0.99   1334  147 0.4252 0.4206      6.8372      6.7812|
|  3:  3.7164 -  3.2523 0.99   1303  142 0.4574 0.4424      6.7192      6.7928|
|  4:  3.2523 -  2.9575 0.99   1305  153 0.4640 0.4525      6.5546      6.4996|
|  5:  2.9575 -  2.7469 0.99   1293  142 0.5071 0.4863      6.3825      6.3884|
|  6:  2.7469 -  2.5859 0.99   1283  138 0.5068 0.5535      6.2908      6.2533|
|  7:  2.5859 -  2.4570 0.99   1288  139 0.5024 0.5017      6.2502      6.2397|
|  8:  2.4570 -  2.3504 0.98   1262  148 0.5162 0.4918      6.1875      6.1637|
|  9:  2.3504 -  2.2603 0.98   1269  142 0.5237 0.5340      6.1315      6.1401|
| 10:  2.2603 -  2.1825 1.00   1285  138 0.5066 0.5450      6.1002      6.1529|
| 11:  2.1825 -  2.1145 0.97   1251  140 0.5155 0.5268      6.0385      6.0703|
| 12:  2.1145 -  2.0542 0.98   1251  141 0.5064 0.4788      5.9767      6.0094|
| 13:  2.0542 -  2.0003 0.99   1288  141 0.5049 0.4986      5.8775      5.8124|
| 14:  2.0003 -  1.9516 0.66    828   93 0.5353 0.4475      5.8906       5.766|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6582  1390   155  0.65  38.33   0.82     0.72      86480.84|
|  2:  4.6582 -  3.7164  1334   147  0.66  38.46   0.90     0.79     124483.71|
|  3:  3.7164 -  3.2523  1303   142  0.56  46.87   0.92     0.76     129383.60|
|  4:  3.2523 -  2.9575  1305   153  0.47  54.60   0.93     0.66     115313.20|
|  5:  2.9575 -  2.7469  1293   142  0.37  61.80   0.88     0.54      89274.90|
|  6:  2.7469 -  2.5859  1283   138  0.30  67.16   0.89     0.43      81618.33|
|  7:  2.5859 -  2.4570  1288   139  0.26  70.19   0.92     0.37      73784.74|
|  8:  2.4570 -  2.3504  1262   148  0.24  72.21   0.93     0.36      69152.27|
|  9:  2.3504 -  2.2603  1269   142  0.28  68.77   0.91     0.41      58764.13|
| 10:  2.2603 -  2.1825  1285   138  0.32  65.79   0.96     0.48      51534.97|
| 11:  2.1825 -  2.1145  1251   140  0.32  65.71   0.97     0.50      47558.32|
| 12:  2.1145 -  2.0542  1251   141  0.35  63.59   1.00     0.57      42910.49|
| 13:  2.0542 -  2.0003  1288   141  0.39  60.49   0.97     0.63      34097.40|
| 14:  2.0003 -  1.9516   828    93  0.52  50.97   0.98     0.74      22093.71|
|alpha:            min =        0.36 max =            0.79 mean =         0.57|
|beta:             min =    22093.71 max =       129383.60 mean =     75097.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.89|
|phase err.(test): min =        0.00 max =           89.97 mean =        59.00|
|-----------------------------------------------------------------------------|

============================== 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 = 14.078817             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.531   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.086327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.977   (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 |  1.528 -  1.865:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.865 -  2.202:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.202 -  2.539:       68 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.539 -  2.877:     1261 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.877 -  3.214:     1999 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.214 -  3.551:     2601 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.551 -  3.888:     4762 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.888 -  4.225:     4680 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.225 -  4.563:     6213 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.563 -  4.900:     7444 |
|-----------------------------------------------------------------------------|
|-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 |        0.197 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.528 |       0.745 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.307)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4779   r_free= 0.4784   ksol= 0.00   Bsol= 0.00   scale= 0.899    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.289405                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4675   r_free= 0.4658   ksol= 0.35   Bsol= 24.74   scale= 0.916   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.59,1.88,0.83,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.284478                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.375641             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.421   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.662249              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.919   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4675      final r-factor (work) = 0.3930          |
| start r-factor (free) = 0.4658      final r-factor (free) = 0.4237          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.9257 = 11.38 * 0.50 * 6.2816 + 1.00 * 0.1970                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.4052 = 11.38 * 0.50 * 6.2017 + 1.00 * 0.1311                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3930      final r-factor (work) = 0.3593          |
| start r-factor (free) = 0.4237      final r-factor (free) = 0.4323          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3148 = 1.66 * 1.00 * 6.2017 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2096 = 1.66 * 1.00 * 6.1279 + 1.00 * 0.0235                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.307)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.64  19.16    None  None   None       |
|    all(noH): 2823   0      0.00    104.64  19.16    None  None   None       |
|    Sol.    : 438    0      0.00    104.64  34.41    None  None   None       |
|    Mac.    : 2385   0      0.00    99.69   16.36    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 -  10.464:  929   |   5:    52.321 -  62.786:   63        |
|      1:    10.464 -  20.929:  872   |   6:    62.786 -  73.250:   32        |
|      2:    20.929 -  31.393:  528   |   7:    73.250 -  83.714:    8        |
|      3:    31.393 -  41.857:  263   |   8:    83.714 -  94.179:    2        |
|      4:    41.857 -  52.321:  123   |   9:    94.179 - 104.643:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3593 r_free = 0.4323             target_work(ml) = 6.135         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3590 r_free = 0.4334             target_work(ml) = 6.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3590   r_free= 0.4334   ksol= 0.35   Bsol= 24.74   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.59,1.88,0.83,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.134666                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3583   r_free= 0.4323   ksol= 0.36   Bsol= 45.79   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,1.13,0.38,0.00,0.00,0.00); trace/3= 0.10                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.136884                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.248605             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.125  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631800              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.906  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3583      final r-factor (work) = 0.3082          |
| start r-factor (free) = 0.4323      final r-factor (free) = 0.3836          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.5468 = 10.25 * 0.50 * 6.1307 + 1.00 * 0.1311                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.2697 = 10.25 * 0.50 * 6.0847 + 1.00 * 0.0898                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3082      final r-factor (work) = 0.2980          |
| start r-factor (free) = 0.3836      final r-factor (free) = 0.3731          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8676 = 0.63 * 1.00 * 6.0847 + 1.00 * 0.0233                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8127 = 0.63 * 1.00 * 6.0140 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.307)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.64  17.99    None  None   None       |
|    all(noH): 2823   0      0.00    106.64  17.99    None  None   None       |
|    Sol.    : 438    0      0.00    106.64  32.91    None  None   None       |
|    Mac.    : 2385   0      0.00    97.93   15.25    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 -  10.664:  985   |   5:    53.318 -  63.982:   37        |
|      1:    10.664 -  21.327:  977   |   6:    63.982 -  74.646:   13        |
|      2:    21.327 -  31.991:  469   |   7:    74.646 -  85.309:    5        |
|      3:    31.991 -  42.655:  225   |   8:    85.309 -  95.973:    1        |
|      4:    42.655 -  53.318:  108   |   9:    95.973 - 106.637:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2980 r_free = 0.3731             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2978 r_free = 0.3737             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2978   r_free= 0.3737   ksol= 0.36   Bsol= 45.79   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,1.13,0.38,0.00,0.00,0.00); trace/3= 0.10                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.002776                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2979   r_free= 0.3736   ksol= 0.34   Bsol= 47.97   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,0.19,0.21,0.00,0.00,0.00); trace/3= -0.11                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.001989                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.847289              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.154  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.729842              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.865  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2979      final r-factor (work) = 0.2487          |
| start r-factor (free) = 0.3736      final r-factor (free) = 0.3232          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6733 = 5.85 * 0.50 * 6.0142 + 1.00 * 0.0898                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4250 = 5.85 * 0.50 * 5.9327 + 1.00 * 0.0798                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2487      final r-factor (work) = 0.2366          |
| start r-factor (free) = 0.3232      final r-factor (free) = 0.3194          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2793 = 1.73 * 1.00 * 5.9327 + 1.00 * 0.0166                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1248 = 1.73 * 1.00 * 5.8276 + 1.00 * 0.0441                              |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.307)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.09  17.78    None  None   None       |
|    all(noH): 2823   0      0.00    107.09  17.78    None  None   None       |
|    Sol.    : 438    0      1.39    107.09  34.57    None  None   None       |
|    Mac.    : 2385   0      0.00    98.78   14.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.709: 1030   |   5:    53.545 -  64.254:   39        |
|      1:    10.709 -  21.418:  953   |   6:    64.254 -  74.963:   13        |
|      2:    21.418 -  32.127:  436   |   7:    74.963 -  85.672:    5        |
|      3:    32.127 -  42.836:  226   |   8:    85.672 -  96.381:    2        |
|      4:    42.836 -  53.545:  116   |   9:    96.381 - 107.090:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2366 r_free = 0.3194             target_work(ml) = 5.820         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2361 r_free = 0.3189             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2361   r_free= 0.3189   ksol= 0.34   Bsol= 47.97   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,0.19,0.21,0.00,0.00,0.00); trace/3= -0.11                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.819121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2364   r_free= 0.3180   ksol= 0.34   Bsol= 47.97   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.37,0.06,-0.00,0.00,0.00); trace/3= -0.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.817542                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.663484              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.047   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.989547              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.708   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2364      final r-factor (work) = 0.1965          |
| start r-factor (free) = 0.3180      final r-factor (free) = 0.2673          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5817 = 5.66 * 0.50 * 5.8275 + 1.00 * 0.0798                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3381 = 5.66 * 0.50 * 5.7441 + 1.00 * 0.0723                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1965      final r-factor (work) = 0.1692          |
| start r-factor (free) = 0.2673      final r-factor (free) = 0.2333          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7016 = 0.99 * 1.00 * 5.7441 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5397 = 0.99 * 1.00 * 5.5855 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.307)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.76  17.64    None  None   None       |
|    all(noH): 2823   0      0.00    105.76  17.64    None  None   None       |
|    Sol.    : 438    0      3.64    104.81  42.72    None  None   None       |
|    Mac.    : 2385   0      0.00    105.76  13.03    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 -  10.576: 1259   |   5:    52.879 -  63.455:  104        |
|      1:    10.576 -  21.152:  891   |   6:    63.455 -  74.031:   43        |
|      2:    21.152 -  31.727:  226   |   7:    74.031 -  84.606:    7        |
|      3:    31.727 -  42.303:  154   |   8:    84.606 -  95.182:    6        |
|      4:    42.303 -  52.879:  130   |   9:    95.182 - 105.758:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1692 r_free = 0.2333             target_work(ml) = 5.514         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1690 r_free = 0.2323             target_work(ml) = 5.513         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1690   r_free= 0.2323   ksol= 0.34   Bsol= 47.97   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.37,0.06,-0.00,0.00,0.00); trace/3= -0.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.512744                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1689   r_free= 0.2310   ksol= 0.33   Bsol= 47.97   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-1.21,-0.32,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.510380                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.749278              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.383  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.176282              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.970  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1689      final r-factor (work) = 0.1398          |
| start r-factor (free) = 0.2310      final r-factor (free) = 0.1964          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5449 = 3.75 * 0.50 * 5.5865 + 1.00 * 0.0723                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2510 = 3.75 * 0.50 * 5.4357 + 1.00 * 0.0611                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1398      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.1964      final r-factor (free) = 0.1820          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9707 = 0.18 * 1.00 * 5.4357 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9470 = 0.18 * 1.00 * 5.3262 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.307)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    99.76   16.52    None  None   None       |
|    all(noH): 2823   0      1.14    99.76   16.52    None  None   None       |
|    Sol.    : 438    0      5.91    98.54   40.16    None  None   None       |
|    Mac.    : 2385   0      1.14    99.76   12.18    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:     1.142 -  11.004: 1433   |   5:    50.452 -  60.314:   87        |
|      1:    11.004 -  20.866:  807   |   6:    60.314 -  70.176:   44        |
|      2:    20.866 -  30.728:  187   |   7:    70.176 -  80.038:   12        |
|      3:    30.728 -  40.590:  136   |   8:    80.038 -  89.900:    3        |
|      4:    40.590 -  50.452:  111   |   9:    89.900 -  99.761:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1329 r_free = 0.1820             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1812             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1812   ksol= 0.33   Bsol= 47.97   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-1.21,-0.32,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.281619                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6582 0.99   1390  155 0.1042 0.1387      5.4331      5.6364|
|  2:  4.6582 -  3.7164 0.99   1334  147 0.0963 0.1309      5.5612       5.783|
|  3:  3.7164 -  3.2523 0.99   1303  142 0.1242 0.1667      5.6208      5.9743|
|  4:  3.2523 -  2.9575 0.99   1305  153 0.1465 0.1959      5.6235      5.7859|
|  5:  2.9575 -  2.7469 0.99   1293  142 0.1538 0.2051      5.4478      5.6931|
|  6:  2.7469 -  2.5859 0.99   1283  138 0.1443 0.1838      5.3294      5.4558|
|  7:  2.5859 -  2.4570 0.99   1288  139 0.1490 0.1905      5.2932      5.5143|
|  8:  2.4570 -  2.3504 0.98   1262  148 0.1490 0.2138      5.2404      5.5192|
|  9:  2.3504 -  2.2603 0.98   1269  142 0.1468 0.2001      5.1913      5.3653|
| 10:  2.2603 -  2.1825 1.00   1285  138 0.1382 0.2129       5.125      5.3831|
| 11:  2.1825 -  2.1145 0.97   1251  140 0.1373 0.2123      5.0964      5.4016|
| 12:  2.1145 -  2.0542 0.98   1251  141 0.1352 0.1802      5.0114      5.2573|
| 13:  2.0542 -  2.0003 0.99   1288  141 0.1350 0.2091      4.9126      5.2106|
| 14:  2.0003 -  1.9516 0.66    828   93 0.1421 0.1686      4.8593      4.9989|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6582  1390   155  0.93  10.64   0.99     0.97       8668.35|
|  2:  4.6582 -  3.7164  1334   147  0.94   9.74   1.04     1.03      11776.30|
|  3:  3.7164 -  3.2523  1303   142  0.91  13.98   1.06     1.04      14135.47|
|  4:  3.2523 -  2.9575  1305   153  0.89  16.86   1.04     1.01      14694.12|
|  5:  2.9575 -  2.7469  1293   142  0.88  17.96   1.02     0.98      10118.10|
|  6:  2.7469 -  2.5859  1283   138  0.88  18.01   1.01     0.98       8625.09|
|  7:  2.5859 -  2.4570  1288   139  0.88  18.17   1.03     0.99       7809.44|
|  8:  2.4570 -  2.3504  1262   148  0.88  18.62   1.02     1.00       7260.98|
|  9:  2.3504 -  2.2603  1269   142  0.88  18.56   1.03     1.00       6808.76|
| 10:  2.2603 -  2.1825  1285   138  0.87  19.07   1.03     0.99       6182.63|
| 11:  2.1825 -  2.1145  1251   140  0.87  19.23   1.04     0.99       5804.90|
| 12:  2.1145 -  2.0542  1251   141  0.89  18.01   1.05     1.03       5049.69|
| 13:  2.0542 -  2.0003  1288   141  0.88  18.76   1.05     1.04       4142.34|
| 14:  2.0003 -  1.9516   828    93  0.90  16.96   1.02     1.00       3331.24|
|alpha:            min =        0.97 max =            1.04 mean =         1.00|
|beta:             min =     3331.24 max =        14694.12 mean =      8337.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        16.68|
|phase err.(test): min =        0.00 max =           89.67 mean =        16.01|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1329   r_free= 0.1811   ksol= 0.33   Bsol= 47.93   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,-1.66,-0.64,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.282384                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1329   r_free= 0.1811   ksol= 0.33   Bsol= 47.93   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,-1.66,-0.64,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.282384                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6582 0.99   1390  155 0.1053 0.1417      5.4407      5.6315|
|  2:  4.6582 -  3.7164 0.99   1334  147 0.0970 0.1327      5.5673      5.7928|
|  3:  3.7164 -  3.2523 0.99   1303  142 0.1251 0.1671      5.6226      5.9753|
|  4:  3.2523 -  2.9575 0.99   1305  153 0.1469 0.1966      5.6257      5.7886|
|  5:  2.9575 -  2.7469 0.99   1293  142 0.1540 0.2051      5.4474      5.6927|
|  6:  2.7469 -  2.5859 0.99   1283  138 0.1441 0.1827      5.3285      5.4514|
|  7:  2.5859 -  2.4570 0.99   1288  139 0.1489 0.1902      5.2919      5.5141|
|  8:  2.4570 -  2.3504 0.98   1262  148 0.1487 0.2142      5.2391      5.5184|
|  9:  2.3504 -  2.2603 0.98   1269  142 0.1467 0.2000      5.1906       5.364|
| 10:  2.2603 -  2.1825 1.00   1285  138 0.1381 0.2132      5.1244      5.3839|
| 11:  2.1825 -  2.1145 0.97   1251  140 0.1371 0.2119      5.0953      5.3999|
| 12:  2.1145 -  2.0542 0.98   1251  141 0.1351 0.1798      5.0107      5.2571|
| 13:  2.0542 -  2.0003 0.99   1288  141 0.1349 0.2091      4.9121      5.2103|
| 14:  2.0003 -  1.9516 0.66    828   93 0.1421 0.1680       4.858      4.9965|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6582  1390   155  0.93  10.62   0.98     0.96       8799.06|
|  2:  4.6582 -  3.7164  1334   147  0.94   9.76   1.04     1.02      11865.02|
|  3:  3.7164 -  3.2523  1303   142  0.91  13.99   1.05     1.03      14163.97|
|  4:  3.2523 -  2.9575  1305   153  0.89  16.88   1.03     1.00      14753.26|
|  5:  2.9575 -  2.7469  1293   142  0.88  17.96   1.01     0.97      10103.06|
|  6:  2.7469 -  2.5859  1283   138  0.88  17.95   0.99     0.97       8597.37|
|  7:  2.5859 -  2.4570  1288   139  0.88  18.11   1.01     0.98       7767.28|
|  8:  2.4570 -  2.3504  1262   148  0.88  18.60   1.00     0.98       7247.01|
|  9:  2.3504 -  2.2603  1269   142  0.88  18.55   1.01     0.98       6805.20|
| 10:  2.2603 -  2.1825  1285   138  0.87  19.06   1.01     0.97       6179.01|
| 11:  2.1825 -  2.1145  1251   140  0.87  19.21   1.02     0.97       5798.74|
| 12:  2.1145 -  2.0542  1251   141  0.89  17.99   1.02     1.01       5042.18|
| 13:  2.0542 -  2.0003  1288   141  0.88  18.73   1.02     1.02       4132.13|
| 14:  2.0003 -  1.9516   828    93  0.90  16.92   1.00     0.98       3313.93|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     3313.93 max =        14753.26 mean =      8350.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.67|
|phase err.(test): min =        0.00 max =           89.94 mean =        16.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.307)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.10    99.72   16.48    None  None   None       |
|    all(noH): 2823   0      1.10    99.72   16.48    None  None   None       |
|    Sol.    : 438    0      5.87    98.50   40.12    None  None   None       |
|    Mac.    : 2385   0      1.10    99.72   12.14    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:     1.102 -  10.964: 1433   |   5:    50.412 -  60.274:   87        |
|      1:    10.964 -  20.826:  807   |   6:    60.274 -  70.136:   44        |
|      2:    20.826 -  30.688:  187   |   7:    70.136 -  79.998:   12        |
|      3:    30.688 -  40.550:  136   |   8:    79.998 -  89.860:    3        |
|      4:    40.550 -  50.412:  111   |   9:    89.860 -  99.722:    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)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.719
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 320
   mapped sites are within: 0.735 - 5.719

peak=    8.356 closest distance to " O   HOH Z 390 " =    1.321
peak=    7.065 closest distance to " OD1 ASP A 298 " =    2.225
peak=    6.769 closest distance to " O   HOH Z 289 " =    1.657
peak=    6.677 closest distance to " O   HOH Z 130 " =    1.302
peak=    6.509 closest distance to " O   HOH Z 385 " =    1.854
peak=    6.117 closest distance to " O   HOH Z  65 " =    1.944
peak=    6.058 closest distance to " NE2 GLN A  11 " =    1.438
peak=    5.882 closest distance to " O   HOH Z   7 " =    2.085
peak=    5.835 closest distance to " O   HOH Z 222 " =    1.676
peak=    5.720 closest distance to " O   HOH Z 142 " =    1.957
peak=    5.551 closest distance to " O   HOH Z 124 " =    1.719
peak=    5.480 closest distance to " O   HOH Z 278 " =    1.474
peak=    5.433 closest distance to " O   HOH Z 245 " =    1.312
peak=    5.347 closest distance to " O   HOH Z  49 " =    1.659
peak=    5.346 closest distance to " O   HOH Z  28 " =    1.738
peak=    5.226 closest distance to " O   HOH Z  63 " =    1.956
peak=    5.180 closest distance to " O   HOH Z  29 " =    1.329
peak=    5.122 closest distance to " NH2 ARG A  56 " =    2.072
peak=    5.028 closest distance to " O   HOH Z 358 " =    1.385
peak=    5.018 closest distance to " O   HOH Z  54 " =    1.327
peak=    5.002 closest distance to " O   ASN A 285 " =    0.946
peak=    4.989 closest distance to " O   PRO A 198 " =    1.323
peak=    4.980 closest distance to " O   HOH Z 120 " =    0.977
peak=    4.959 closest distance to " O   HOH Z  97 " =    1.491
peak=    4.952 closest distance to " O   HOH Z  78 " =    1.760
peak=    4.944 closest distance to " O   HOH Z 403 " =    1.730
peak=    4.908 closest distance to " O   HOH Z 287 " =    1.815
peak=    4.861 closest distance to " O   HOH Z 415 " =    1.204
peak=    4.791 closest distance to " O   HOH Z 232 " =    1.994
peak=    4.791 closest distance to " O   HOH Z 402 " =    1.558
peak=    4.774 closest distance to " CG  PRO A  90 " =    1.192
peak=    4.754 closest distance to " O   HOH Z 112 " =    1.675
peak=    4.702 closest distance to " O   HOH Z 363 " =    1.219
peak=    4.698 closest distance to " O   HOH Z 214 " =    1.420
peak=    4.685 closest distance to " CG  PRO A  54 " =    1.301
peak=    4.648 closest distance to " O   HOH Z 211 " =    1.447
peak=    4.646 closest distance to " O   HOH Z 417 " =    1.954
peak=    4.643 closest distance to " O   HOH Z 424 " =    1.237
peak=    4.576 closest distance to " O   HOH Z 427 " =    1.272
peak=    4.570 closest distance to " O   HOH Z 400 " =    0.867
peak=    4.569 closest distance to " O   HOH Z 414 " =    1.595
peak=    4.559 closest distance to " O   HOH Z 416 " =    1.434
peak=    4.547 closest distance to " O   HOH Z 427 " =    1.894
peak=    4.536 closest distance to " O   HOH Z 302 " =    1.537
peak=    4.484 closest distance to " O   HOH Z 352 " =    1.654
peak=    4.483 closest distance to " CB  PRO A  54 " =    1.135
peak=    4.405 closest distance to " CB  SER A   3 " =    1.276
peak=    4.397 closest distance to " O   HOH Z 139 " =    1.524
peak=    4.370 closest distance to " OG ASER A 258 " =    2.964
peak=    4.340 closest distance to " O   HOH Z 158 " =    1.531
peak=    4.258 closest distance to " CB  ASN A 148 " =    1.507
peak=    4.252 closest distance to " OD1 ASN A  45 " =    1.193
peak=    4.247 closest distance to " O   HOH Z 244 " =    1.651
peak=    4.234 closest distance to " CG  PRO A 213 " =    1.222
peak=    4.215 closest distance to " CB  ARG A 275 " =    1.068
peak=    4.193 closest distance to " O   HOH Z 276 " =    1.420
peak=    4.191 closest distance to " O   HOH Z  88 " =    2.619
peak=    4.188 closest distance to " O   ASP A 286 " =    2.355
peak=    4.175 closest distance to " O   HOH Z 369 " =    1.717
peak=    4.154 closest distance to " CB  SER A 216 " =    0.972
peak=    4.150 closest distance to " CB  GLU A 128 " =    0.926
peak=    4.147 closest distance to " OD1 ASP A 286 " =    1.111
peak=    4.143 closest distance to " NZ  LYS A 117 " =    1.287
peak=    4.127 closest distance to " O   HOH Z 399 " =    0.897
peak=    4.107 closest distance to " O   HOH Z 236 " =    1.542
peak=    4.106 closest distance to " OE1 GLU A   2 " =    2.056
peak=    4.097 closest distance to " O   HOH Z 371 " =    1.868
peak=    4.089 closest distance to " O   SER A  87 " =    2.237
peak=    4.089 closest distance to " NZ BLYS A 290 " =    1.050
peak=    4.073 closest distance to " O   HOH Z  61 " =    1.385
peak=    4.067 closest distance to " CD  LYS A 166 " =    1.679
peak=    4.055 closest distance to " O   HOH Z 215 " =    1.494
peak=    4.043 closest distance to " CB  GLN A 183 " =    1.066
peak=    4.025 closest distance to " O   HOH Z  63 " =    1.895
peak=    4.017 closest distance to " O   HOH Z   6 " =    1.896
peak=    4.011 closest distance to " O   HOH Z  61 " =    1.600
peak=    4.011 closest distance to " O   HOH Z  47 " =    1.561
peak=    4.002 closest distance to " O   HOH Z  59 " =    1.506
peak=    3.983 closest distance to " O   HOH Z 380 " =    1.969
peak=    3.978 closest distance to " O   HOH Z 234 " =    3.686
peak=    3.978 closest distance to " O   HOH Z 145 " =    2.011
peak=    3.974 closest distance to " O   HOH Z 193 " =    1.838
peak=    3.970 closest distance to " CG1BVAL A 121 " =    1.853
peak=    3.967 closest distance to " O   HOH Z 298 " =    1.941
peak=    3.966 closest distance to " CB  GLU A 277 " =    1.040
peak=    3.959 closest distance to " O   ALA A 165 " =    1.172
peak=    3.950 closest distance to " O   HOH Z 217 " =    2.823
peak=    3.948 closest distance to " CB  GLU A 152 " =    1.171
peak=    3.941 closest distance to " O   HOH Z 132 " =    1.094
peak=    3.932 closest distance to " N   TYR A  15 " =    1.142
peak=    3.927 closest distance to " O   HOH Z 116 " =    1.238
peak=    3.902 closest distance to " O   HOH Z 405 " =    1.638
peak=    3.901 closest distance to " O   HOH Z 293 " =    1.470
peak=    3.899 closest distance to " O   HOH Z  24 " =    1.641
peak=    3.897 closest distance to " CE  MET A  93 " =    1.499
peak=    3.894 closest distance to " NH2 ARG A 219 " =    1.693
peak=    3.889 closest distance to " O   HOH Z 412 " =    2.005
peak=    3.872 closest distance to " O   HOH Z 291 " =    1.614
peak=    3.867 closest distance to " O   HOH Z 392 " =    1.459
peak=    3.860 closest distance to " OG BSER A  12 " =    1.082
peak=    3.857 closest distance to " O   HOH Z 261 " =    1.879
peak=    3.850 closest distance to " O   HOH Z 133 " =    1.284
peak=    3.846 closest distance to " O   HOH Z 426 " =    1.227
peak=    3.842 closest distance to " CB  ALA A 104 " =    1.304
peak=    3.841 closest distance to " O   HOH Z 166 " =    1.633
peak=    3.833 closest distance to " CA  LEU A 282 " =    1.033
peak=    3.825 closest distance to " O   HOH Z 389 " =    1.608
peak=    3.823 closest distance to " CG  TRP A 179 " =    2.179
peak=    3.823 closest distance to " O   HOH Z 223 " =    1.013
peak=    3.816 closest distance to " O   HOH Z 117 " =    1.317
peak=    3.813 closest distance to " O   HOH Z 366 " =    2.512
peak=    3.813 closest distance to " O   HOH Z   9 " =    1.147
peak=    3.801 closest distance to " N   GLU A   2 " =    1.237
peak=    3.795 closest distance to " NH1AARG A 145 " =    1.003
peak=    3.791 closest distance to " CB  ALA A   1 " =    0.989
peak=    3.784 closest distance to " NE AARG A 275 " =    1.382
peak=    3.771 closest distance to " CZ3 TRP A 274 " =    2.062
peak=    3.768 closest distance to " CB  GLN A 223 " =    1.471
peak=    3.754 closest distance to " O   HOH Z 423 " =    1.633
peak=    3.741 closest distance to " O   HOH Z 393 " =    1.485
peak=    3.740 closest distance to " OD2 ASP A 286 " =    2.342
peak=    3.736 closest distance to " N   ALA A   1 " =    1.445
peak=    3.734 closest distance to " CA  TYR A  30 " =    1.062
peak=    3.733 closest distance to " O   HOH Z 394 " =    1.752
peak=    3.731 closest distance to " CD2 TRP A 179 " =    1.546
peak=    3.728 closest distance to " CD  ARG A 138 " =    0.859
peak=    3.698 closest distance to " CD  GLN A  58 " =    5.719
peak=    3.693 closest distance to " N   GLN A 278 " =    1.109
peak=    3.684 closest distance to " O   HOH Z 311 " =    1.554
peak=    3.676 closest distance to " O   HOH Z 105 " =    1.319
peak=    3.674 closest distance to " CG  LYS A 166 " =    1.374
peak=    3.672 closest distance to " CG  ARG A  66 " =    2.682
peak=    3.669 closest distance to " CG  PRO A 243 " =    1.153
peak=    3.668 closest distance to " O   HOH Z 361 " =    2.530
peak=    3.666 closest distance to " CB  SER A 276 " =    1.206
peak=    3.660 closest distance to " N   SER A 210 " =    1.164
peak=    3.655 closest distance to " O   HOH Z 213 " =    1.690
peak=    3.651 closest distance to " NH2BARG A 145 " =    1.977
peak=    3.649 closest distance to " CB  TRP A 179 " =    1.337
peak=    3.649 closest distance to " CB  ASP A 124 " =    1.024
peak=    3.643 closest distance to " O   HOH Z 158 " =    2.387
peak=    3.639 closest distance to " O   HOH Z 371 " =    3.313
peak=    3.629 closest distance to " O   HOH Z 381 " =    1.207
peak=    3.617 closest distance to " O   HOH Z 119 " =    1.489
peak=    3.605 closest distance to " OG BSER A 258 " =    1.005
peak=    3.604 closest distance to " O   HOH Z  32 " =    2.097
peak=    3.598 closest distance to " O   HOH Z  17 " =    1.785
peak=    3.598 closest distance to " O   HOH Z 326 " =    1.382
peak=    3.584 closest distance to " O   HOH Z 347 " =    1.149
peak=    3.581 closest distance to " O   HOH Z  69 " =    2.296
peak=    3.580 closest distance to " OG BSER A 212 " =    2.714
peak=    3.580 closest distance to " CA  GLU A 152 " =    1.165
peak=    3.578 closest distance to " NE1 TRP A 274 " =    1.151
peak=    3.575 closest distance to " O   HOH Z 250 " =    1.249
peak=    3.568 closest distance to " O   HOH Z 272 " =    1.778
peak=    3.566 closest distance to " O   HOH Z 413 " =    1.643
peak=    3.564 closest distance to " O   HOH Z  22 " =    1.869
peak=    3.553 closest distance to " O   HOH Z 227 " =    2.082
peak=    3.546 closest distance to " OD1 ASP A 238 " =    0.881
peak=    3.544 closest distance to " O   HOH Z 222 " =    2.310
peak=    3.536 closest distance to " O   HOH Z 425 " =    1.478
peak=    3.535 closest distance to " O   HOH Z  53 " =    2.303
peak=    3.535 closest distance to " CG  LEU A 167 " =    1.268
peak=    3.532 closest distance to " CB  ARG A 102 " =    0.865
peak=    3.527 closest distance to " O   HOH Z 368 " =    3.625
peak=    3.527 closest distance to " O   HOH Z 126 " =    1.422
peak=    3.520 closest distance to " NH2AARG A 190 " =    1.495
peak=    3.517 closest distance to " CB  ASP A 200 " =    0.954
peak=    3.516 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.515 closest distance to " CE AMET A  47 " =    1.161
peak=    3.509 closest distance to " CG  PRO A 198 " =    1.373
peak=    3.504 closest distance to " O   HOH Z 282 " =    1.598
peak=    3.504 closest distance to " O   HOH Z  30 " =    1.798
peak=    3.503 closest distance to " CB  TRP A 266 " =    1.011
peak=    3.496 closest distance to " O   HOH Z 236 " =    2.067
peak=    3.491 closest distance to " O   HOH Z 276 " =    2.170
peak=    3.490 closest distance to " O   HOH Z 353 " =    2.147
peak=    3.489 closest distance to " O   HOH Z  44 " =    1.906
peak=    3.487 closest distance to " O   HOH Z 158 " =    2.984
peak=    3.483 closest distance to " NE2 GLN A  58 " =    3.502
peak=    3.477 closest distance to " O   HOH Z 162 " =    2.106
peak=    3.470 closest distance to " CA  PHE A 283 " =    1.217
peak=    3.458 closest distance to " O   HOH Z 153 " =    3.564
peak=    3.457 closest distance to " CG  ARG A 159 " =    0.749
peak=    3.455 closest distance to " O   HOH Z 368 " =    1.823
peak=    3.455 closest distance to " O   HOH Z 181 " =    2.196
peak=    3.453 closest distance to " CB  ASN A  39 " =    0.877
peak=    3.451 closest distance to " O   HOH Z 227 " =    1.763
peak=    3.448 closest distance to " CB  LEU A 300 " =    0.974
peak=    3.445 closest distance to " O   HOH Z 409 " =    1.859
peak=    3.443 closest distance to " O   HOH Z 151 " =    1.831
peak=    3.440 closest distance to " OG ASER A  99 " =    1.198
peak=    3.440 closest distance to " CD1 PHE A 283 " =    1.113
peak=    3.435 closest distance to " ND2 ASN A 285 " =    0.848
peak=    3.433 closest distance to " CG2 THR A 221 " =    1.339
peak=    3.433 closest distance to " CB  VAL A 265 " =    1.307
peak=    3.432 closest distance to " CG2 ILE A 151 " =    1.051
peak=    3.432 closest distance to " O   HOH Z 436 " =    2.204
peak=    3.431 closest distance to " O   SER A 271 " =    1.296
peak=    3.430 closest distance to " CA  PRO A 280 " =    1.507
peak=    3.418 closest distance to " O   HOH Z 116 " =    2.199
peak=    3.415 closest distance to " O   HOH Z 248 " =    2.049
peak=    3.414 closest distance to " CG  ARG A 156 " =    1.080
peak=    3.414 closest distance to " O   HOH Z 193 " =    1.920
peak=    3.411 closest distance to " O   HOH Z 152 " =    2.279
peak=    3.408 closest distance to " CA  ALA A 299 " =    0.921
peak=    3.406 closest distance to " O   HOH Z 258 " =    1.463
peak=    3.401 closest distance to " CB  PRO A 243 " =    1.005
peak=    3.396 closest distance to " O   HOH Z 384 " =    1.327
peak=    3.392 closest distance to " CG2 THR A 279 " =    1.116
peak=    3.375 closest distance to " O   HOH Z   5 " =    1.382
peak=    3.372 closest distance to " O   HOH Z 411 " =    3.445
peak=    3.368 closest distance to " O   HOH Z  10 " =    1.805
peak=    3.367 closest distance to " O   HOH Z 418 " =    0.973
peak=    3.364 closest distance to " O   HOH Z 422 " =    2.693
peak=    3.361 closest distance to " OG  SER A  22 " =    2.663
peak=    3.356 closest distance to " O   HOH Z 419 " =    1.883
peak=    3.350 closest distance to " NH2 ARG A 269 " =    0.735
peak=    3.349 closest distance to " O   HOH Z 109 " =    1.240
peak=    3.347 closest distance to " O   HOH Z  50 " =    1.913
peak=    3.345 closest distance to " O   HOH Z 106 " =    2.471
peak=    3.342 closest distance to " ND1 HIS A  81 " =    1.285
peak=    3.341 closest distance to " O   HOH Z 434 " =    1.485
peak=    3.338 closest distance to " CD  PRO A 243 " =    1.633
peak=    3.331 closest distance to " O   HOH Z  38 " =    1.711
peak=    3.330 closest distance to " O   HOH Z 423 " =    1.717
peak=    3.330 closest distance to " O   HOH Z  46 " =    1.133
peak=    3.322 closest distance to " CB  MET A 105 " =    1.206
peak=    3.321 closest distance to " O   HOH Z 155 " =    2.085
peak=    3.319 closest distance to " O   HOH Z 134 " =    1.453
peak=    3.317 closest distance to " O   HOH Z 385 " =    3.266
peak=    3.316 closest distance to " CA  ASN A 284 " =    1.073
peak=    3.314 closest distance to " O   HOH Z  65 " =    1.290
peak=    3.313 closest distance to " CG  GLN A  88 " =    1.033
peak=    3.310 closest distance to " O   HOH Z 128 " =    2.132
peak=    3.308 closest distance to " CA  ARG A 195 " =    1.494
peak=    3.306 closest distance to " O   HOH Z 119 " =    4.150
peak=    3.304 closest distance to " CD2 LEU A  25 " =    1.179
peak=    3.301 closest distance to " CZ3 TRP A 274 " =    1.367
peak=    3.291 closest distance to " CA  ALA A  21 " =    1.117
peak=    3.291 closest distance to " O   HOH Z 128 " =    1.945
peak=    3.290 closest distance to " CG  GLN A 240 " =    3.406
peak=    3.290 closest distance to " NZ  LYS A 119 " =    1.423
peak=    3.290 closest distance to " O   GLY A 302 " =    1.358
peak=    3.288 closest distance to " O   HOH Z  55 " =    1.809
peak=    3.285 closest distance to " O   HOH Z   7 " =    2.845
peak=    3.285 closest distance to " O   HOH Z  92 " =    1.205
peak=    3.281 closest distance to " O   HOH Z  32 " =    1.703
peak=    3.280 closest distance to " CG  GLN A  89 " =    1.322
peak=    3.280 closest distance to " O   HOH Z 133 " =    2.269
peak=    3.279 closest distance to " CD2 LEU A 167 " =    1.184
peak=    3.277 closest distance to " O   HOH Z 384 " =    1.593
peak=    3.277 closest distance to " O   HOH Z 334 " =    1.341
peak=    3.268 closest distance to " O   HOH Z 369 " =    1.636
peak=    3.255 closest distance to " CB  GLN A  11 " =    1.311
peak=    3.254 closest distance to " CE  LYS A 117 " =    1.753
peak=    3.253 closest distance to " OD2 ASP A  65 " =    2.236
peak=    3.249 closest distance to " CE  LYS A 289 " =    1.155
peak=    3.249 closest distance to " O   HOH Z 410 " =    1.843
peak=    3.244 closest distance to " O   HOH Z 419 " =    1.808
peak=    3.239 closest distance to " O   HOH Z 157 " =    1.733
peak=    3.238 closest distance to " O   HOH Z 247 " =    1.202
peak=    3.236 closest distance to " O   HOH Z 288 " =    1.958
peak=    3.234 closest distance to " N   THR A 246 " =    1.368
peak=    3.234 closest distance to " CG2 THR A 220 " =    0.896
peak=    3.233 closest distance to " CA  ARG A 275 " =    0.759
peak=    3.227 closest distance to " O   HOH Z 167 " =    1.762
peak=    3.225 closest distance to " O   HOH Z  80 " =    1.991
peak=    3.222 closest distance to " OG  SER A  62 " =    3.220
peak=    3.220 closest distance to " CB  MET A  47 " =    1.355
peak=    3.219 closest distance to " OG ASER A 134 " =    1.365
peak=    3.216 closest distance to " O   HOH Z 172 " =    2.054
peak=    3.215 closest distance to " CG1 VAL A 202 " =    2.105
peak=    3.215 closest distance to " O   HOH Z 375 " =    1.011
peak=    3.213 closest distance to " CB  GLN A  77 " =    0.744
peak=    3.212 closest distance to " O   HOH Z 116 " =    5.577
peak=    3.212 closest distance to " NZ  LYS A 289 " =    2.255
peak=    3.211 closest distance to " O   HOH Z 189 " =    2.731
peak=    3.208 closest distance to " CA  ALA A  51 " =    1.125
peak=    3.207 closest distance to " CG2 THR A 251 " =    1.757
peak=    3.206 closest distance to " CB  ALA A   7 " =    1.169
peak=    3.204 closest distance to " O   HOH Z 112 " =    2.192
peak=    3.204 closest distance to " O   HOH Z 327 " =    1.897
peak=    3.203 closest distance to " OG BSER A  99 " =    2.264
peak=    3.203 closest distance to " O   HOH Z 378 " =    1.160
peak=    3.199 closest distance to " O   HOH Z 355 " =    1.689
peak=    3.189 closest distance to " CB  MET A  40 " =    1.013
peak=    3.187 closest distance to " O   HOH Z 434 " =    5.583
peak=    3.184 closest distance to " CG2 THR A 294 " =    1.027
peak=    3.180 closest distance to " CG2BVAL A  72 " =    1.154
peak=    3.178 closest distance to " CG AARG A 275 " =    1.114
peak=    3.175 closest distance to " O   HOH Z 212 " =    1.254
peak=    3.175 closest distance to " CB  LYS A 290 " =    1.437
peak=    3.169 closest distance to " O   HOH Z 108 " =    1.552
peak=    3.168 closest distance to " CA  ARG A  36 " =    1.271
peak=    3.163 closest distance to " NZ  LYS A  76 " =    1.289
peak=    3.163 closest distance to " CG  GLN A  11 " =    2.064
peak=    3.160 closest distance to " O   ALA A  84 " =    0.994
peak=    3.159 closest distance to " CB  ASN A 285 " =    1.096
peak=    3.157 closest distance to " O   HOH Z 357 " =    1.617
peak=    3.143 closest distance to " O   HOH Z 271 " =    1.917
peak=    3.135 closest distance to " O   HOH Z 137 " =    1.898
peak=    3.133 closest distance to " O   HOH Z 365 " =    5.261
peak=    3.132 closest distance to " CE BLYS A 290 " =    0.811
peak=    3.117 closest distance to " O   HOH Z 147 " =    1.391
peak=    3.115 closest distance to " O   HOH Z 272 " =    1.976
peak=    3.107 closest distance to " O   GLY A 302 " =    2.377
peak=    3.107 closest distance to " CG  MET A 188 " =    0.909
peak=    3.104 closest distance to " CA  ILE A 263 " =    1.140
peak=    3.093 closest distance to " O   HOH Z 166 " =    1.534
peak=    3.089 closest distance to " O   HOH Z 356 " =    1.437
peak=    3.085 closest distance to " CG2 VAL A 232 " =    1.319
peak=    3.085 closest distance to " O   HOH Z 162 " =    3.692
peak=    3.073 closest distance to " O   GLN A 278 " =    1.390
peak=    3.072 closest distance to " O   HOH Z   9 " =    1.500
peak=    3.058 closest distance to " O   HOH Z 230 " =    1.507
peak=    3.057 closest distance to " CA  ILE A 234 " =    1.152
peak=    3.052 closest distance to " O   HOH Z 303 " =    1.754
peak=    3.040 closest distance to " CD1 TRP A 179 " =    1.096

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.450 - 4.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 202
   mapped sites are within: 0.702 - 4.875

peak=   -4.855 closest distance to " O   PRO A 198 " =    1.156
peak=   -4.585 closest distance to " O   HOH Z 347 " =    0.721
peak=   -4.489 closest distance to " O   HOH Z  60 " =    1.844
peak=   -4.439 closest distance to " O   HOH Z 290 " =    1.070
peak=   -4.214 closest distance to " O   HOH Z  24 " =    1.244
peak=   -4.192 closest distance to " OG  SER A  97 " =    2.117
peak=   -4.175 closest distance to " O   HOH Z 409 " =    3.109
peak=   -4.140 closest distance to " O   HOH Z 264 " =    0.962
peak=   -4.133 closest distance to " O   HOH Z 385 " =    0.858
peak=   -4.087 closest distance to " O   HOH Z 197 " =    3.397
peak=   -4.081 closest distance to " CD1 TRP A 179 " =    1.112
peak=   -4.052 closest distance to " O   HOH Z  88 " =    1.915
peak=   -4.047 closest distance to " CG  MET A 105 " =    0.950
peak=   -4.030 closest distance to " O   SER A  22 " =    2.554
peak=   -4.010 closest distance to " O   SER A 135 " =    1.677
peak=   -4.006 closest distance to " ND2 ASN A 209 " =    1.717
peak=   -3.962 closest distance to " O   HOH Z 372 " =    2.614
peak=   -3.927 closest distance to " O   HOH Z 425 " =    0.783
peak=   -3.914 closest distance to " CB  ALA A 248 " =    1.988
peak=   -3.913 closest distance to " O   HOH Z 381 " =    0.823
peak=   -3.909 closest distance to " CA  GLY A  98 " =    1.836
peak=   -3.892 closest distance to " CZ  PHE A  59 " =    1.579
peak=   -3.879 closest distance to " CB  PRO A 243 " =    2.447
peak=   -3.869 closest distance to " N   VAL A  72 " =    1.748
peak=   -3.851 closest distance to " O   HOH Z 221 " =    0.842
peak=   -3.839 closest distance to " O   PRO A 198 " =    0.961
peak=   -3.814 closest distance to " O   ILE A  49 " =    1.555
peak=   -3.811 closest distance to " O   HOH Z  13 " =    1.376
peak=   -3.806 closest distance to " CD2 LEU A 237 " =    2.336
peak=   -3.802 closest distance to " CA  GLY A 133 " =    1.856
peak=   -3.774 closest distance to " N   GLN A  58 " =    1.172
peak=   -3.771 closest distance to " CD  ARG A  14 " =    2.904
peak=   -3.754 closest distance to " O   HOH Z 393 " =    3.128
peak=   -3.717 closest distance to " O   TRP A  70 " =    1.406
peak=   -3.711 closest distance to " O   HOH Z 250 " =    1.277
peak=   -3.703 closest distance to " CB  CYS A 201 " =    2.091
peak=   -3.702 closest distance to " O   HOH Z 163 " =    1.836
peak=   -3.700 closest distance to " O   HOH Z 208 " =    0.839
peak=   -3.663 closest distance to " O   HOH Z 185 " =    1.774
peak=   -3.660 closest distance to " O   HOH Z  76 " =    1.120
peak=   -3.647 closest distance to " CG  ARG A 219 " =    2.174
peak=   -3.635 closest distance to " O   ASN A 215 " =    1.736
peak=   -3.632 closest distance to " O   VAL A 189 " =    2.394
peak=   -3.632 closest distance to " OE1 GLU A 277 " =    2.118
peak=   -3.621 closest distance to " O   HOH Z  14 " =    1.502
peak=   -3.607 closest distance to " O   HOH Z 416 " =    0.798
peak=   -3.606 closest distance to " NH2 ARG A  79 " =    1.881
peak=   -3.604 closest distance to " O   HOH Z 390 " =    1.022
peak=   -3.579 closest distance to " ND2 ASN A  60 " =    1.253
peak=   -3.567 closest distance to " CG  GLN A  88 " =    0.843
peak=   -3.555 closest distance to " OXT GLY A 302 " =    3.139
peak=   -3.553 closest distance to " O   SER A 146 " =    1.315
peak=   -3.552 closest distance to " N   THR A 157 " =    1.590
peak=   -3.539 closest distance to " O   HOH Z 205 " =    0.855
peak=   -3.531 closest distance to " O   HOH Z 266 " =    4.195
peak=   -3.530 closest distance to " O   HOH Z   1 " =    3.629
peak=   -3.517 closest distance to " CB  TYR A  15 " =    2.023
peak=   -3.514 closest distance to " O   MET A  40 " =    2.812
peak=   -3.509 closest distance to " CE3 TRP A 123 " =    1.419
peak=   -3.494 closest distance to " O   HOH Z 415 " =    1.087
peak=   -3.491 closest distance to " O   HOH Z 397 " =    1.282
peak=   -3.490 closest distance to " O   HOH Z  46 " =    0.710
peak=   -3.487 closest distance to " CG  ASP A 231 " =    0.803
peak=   -3.480 closest distance to " O   HOH Z 244 " =    1.467
peak=   -3.480 closest distance to " CD2 TYR A 293 " =    1.924
peak=   -3.479 closest distance to " CB  ASN A 285 " =    1.813
peak=   -3.474 closest distance to " O   THR A 235 " =    1.382
peak=   -3.469 closest distance to " NE2 GLN A  55 " =    0.727
peak=   -3.467 closest distance to " OG  SER A 245 " =    1.129
peak=   -3.460 closest distance to " OG ASER A 134 " =    1.282
peak=   -3.458 closest distance to " OG  SER A   3 " =    0.997
peak=   -3.456 closest distance to " CD2 LEU A 297 " =    1.180
peak=   -3.438 closest distance to " O   GLN A 194 " =    1.310
peak=   -3.425 closest distance to " O   HOH Z 426 " =    1.436
peak=   -3.421 closest distance to " O   HOH Z 143 " =    2.185
peak=   -3.418 closest distance to " OD1 ASN A 301 " =    1.940
peak=   -3.416 closest distance to " C   GLN A 205 " =    2.008
peak=   -3.416 closest distance to " O   HOH Z 211 " =    0.702
peak=   -3.414 closest distance to " OG1 THR A 279 " =    1.287
peak=   -3.411 closest distance to " O   HOH Z  61 " =    0.840
peak=   -3.410 closest distance to " C   ILE A 239 " =    2.091
peak=   -3.404 closest distance to " OD1 ASP A 191 " =    1.953
peak=   -3.398 closest distance to " C   ALA A 114 " =    2.006
peak=   -3.384 closest distance to " O   HOH Z 322 " =    0.745
peak=   -3.382 closest distance to " O   HOH Z 234 " =    4.732
peak=   -3.368 closest distance to " CB  ALA A 227 " =    2.193
peak=   -3.368 closest distance to " OE2 GLU A   2 " =    0.823
peak=   -3.367 closest distance to " CD1 LEU A 101 " =    2.286
peak=   -3.366 closest distance to " CA  GLY A 211 " =    1.490
peak=   -3.360 closest distance to " N   ALA A   1 " =    1.390
peak=   -3.359 closest distance to " N   GLN A  88 " =    1.640
peak=   -3.354 closest distance to " O   HOH Z  43 " =    1.576
peak=   -3.351 closest distance to " O   HOH Z  22 " =    2.535
peak=   -3.348 closest distance to " CG  ARG A  66 " =    2.300
peak=   -3.344 closest distance to " N   ASN A 127 " =    1.341
peak=   -3.343 closest distance to " OXT GLY A 302 " =    0.855
peak=   -3.338 closest distance to " N   ARG A  14 " =    1.072
peak=   -3.337 closest distance to " O   ASN A 301 " =    1.327
peak=   -3.337 closest distance to " O   HOH Z 298 " =    0.963
peak=   -3.336 closest distance to " CD  LYS A 289 " =    2.408
peak=   -3.336 closest distance to " O   HOH Z  73 " =    1.539
peak=   -3.335 closest distance to " O   HOH Z 213 " =    1.159
peak=   -3.333 closest distance to " N   GLN A  58 " =    1.886
peak=   -3.329 closest distance to " O   HOH Z 426 " =    1.929
peak=   -3.329 closest distance to " O   ALA A  51 " =    1.386
peak=   -3.324 closest distance to " O   HOH Z 404 " =    1.522
peak=   -3.323 closest distance to " O   HOH Z  93 " =    1.571
peak=   -3.323 closest distance to " O   HOH Z  51 " =    1.029
peak=   -3.321 closest distance to " O   HOH Z 132 " =    0.881
peak=   -3.319 closest distance to " NH2 ARG A 159 " =    2.446
peak=   -3.315 closest distance to " CE2 TYR A  30 " =    2.603
peak=   -3.313 closest distance to " O   HOH Z  22 " =    1.018
peak=   -3.312 closest distance to " OG BSER A 134 " =    1.415
peak=   -3.308 closest distance to " O   HOH Z 292 " =    1.449
peak=   -3.305 closest distance to " CG BLYS A 290 " =    0.820
peak=   -3.304 closest distance to " O   LEU A 297 " =    0.746
peak=   -3.302 closest distance to " OD2 ASP A 171 " =    2.167
peak=   -3.300 closest distance to " O   HOH Z 137 " =    1.428
peak=   -3.292 closest distance to " C   HIS A 108 " =    1.160
peak=   -3.291 closest distance to " O   VAL A  72 " =    1.193
peak=   -3.290 closest distance to " O   HOH Z 139 " =    2.478
peak=   -3.285 closest distance to " O   GLU A  44 " =    1.857
peak=   -3.279 closest distance to " ND2 ASN A 173 " =    1.655
peak=   -3.273 closest distance to " C   LEU A 143 " =    1.204
peak=   -3.272 closest distance to " O   HOH Z 111 " =    4.399
peak=   -3.271 closest distance to " OG BSER A 210 " =    1.742
peak=   -3.266 closest distance to " O   PRO A  54 " =    1.346
peak=   -3.266 closest distance to " N   GLY A  35 " =    1.808
peak=   -3.264 closest distance to " CD  ARG A 156 " =    1.940
peak=   -3.263 closest distance to " O   ARG A 145 " =    1.485
peak=   -3.262 closest distance to " O   ASN A 170 " =    1.957
peak=   -3.256 closest distance to " CB  ALA A 291 " =    2.153
peak=   -3.254 closest distance to " O   HOH Z  64 " =    0.955
peak=   -3.252 closest distance to " O   HOH Z 296 " =    0.778
peak=   -3.251 closest distance to " O   HOH Z  52 " =    0.881
peak=   -3.247 closest distance to " C   VAL A 265 " =    0.856
peak=   -3.243 closest distance to " O   HOH Z  39 " =    1.582
peak=   -3.242 closest distance to " O   ALA A 161 " =    1.835
peak=   -3.241 closest distance to " CG  GLN A  77 " =    1.300
peak=   -3.240 closest distance to " CB  ALA A   7 " =    1.915
peak=   -3.237 closest distance to " O   HOH Z 236 " =    2.180
peak=   -3.235 closest distance to " O   HOH Z 198 " =    2.307
peak=   -3.234 closest distance to " O   HOH Z 429 " =    2.087
peak=   -3.232 closest distance to " O   HOH Z  77 " =    1.636
peak=   -3.230 closest distance to " O   HOH Z 417 " =    2.828
peak=   -3.230 closest distance to " O   HOH Z 419 " =    3.745
peak=   -3.222 closest distance to " O   HOH Z 150 " =    2.697
peak=   -3.221 closest distance to " O   PHE A 218 " =    1.339
peak=   -3.219 closest distance to " NH1 ARG A  56 " =    2.441
peak=   -3.208 closest distance to " CB  SER A 273 " =    2.400
peak=   -3.203 closest distance to " O   HOH Z 105 " =    1.090
peak=   -3.198 closest distance to " OG  SER A  32 " =    0.870
peak=   -3.196 closest distance to " O   GLN A  77 " =    2.078
peak=   -3.196 closest distance to " O   HOH Z 383 " =    0.712
peak=   -3.196 closest distance to " O   HOH Z  97 " =    1.011
peak=   -3.190 closest distance to " CD1 TYR A 214 " =    1.418
peak=   -3.188 closest distance to " NH1BARG A 145 " =    3.533
peak=   -3.184 closest distance to " O   HOH Z  56 " =    1.721
peak=   -3.184 closest distance to " OG1 THR A 246 " =    1.393
peak=   -3.181 closest distance to " O   HOH Z 336 " =    4.875
peak=   -3.180 closest distance to " CD  PRO A 198 " =    1.242
peak=   -3.170 closest distance to " O   HOH Z   5 " =    1.003
peak=   -3.164 closest distance to " O   VAL A 197 " =    1.491
peak=   -3.162 closest distance to " O   HOH Z 300 " =    1.087
peak=   -3.162 closest distance to " CD  GLN A  11 " =    0.828
peak=   -3.160 closest distance to " NH2 ARG A 156 " =    0.862
peak=   -3.157 closest distance to " CG2 THR A 294 " =    2.514
peak=   -3.153 closest distance to " O   TRP A  85 " =    2.210
peak=   -3.144 closest distance to " O   ALA A   1 " =    1.166
peak=   -3.144 closest distance to " CE3 TRP A 274 " =    2.561
peak=   -3.138 closest distance to " OD1 ASP A 171 " =    1.426
peak=   -3.131 closest distance to " OG1 THR A 178 " =    1.009
peak=   -3.131 closest distance to " CG  PRO A 163 " =    2.495
peak=   -3.131 closest distance to " NH2 ARG A 219 " =    1.854
peak=   -3.130 closest distance to " O   HOH Z 168 " =    0.956
peak=   -3.127 closest distance to " O   THR A  29 " =    1.803
peak=   -3.123 closest distance to " CD  GLN A 223 " =    1.486
peak=   -3.116 closest distance to " CG  PHE A 283 " =    2.436
peak=   -3.116 closest distance to " O   HOH Z 231 " =    1.341
peak=   -3.113 closest distance to " O   HOH Z 437 " =    0.780
peak=   -3.093 closest distance to " CD  LYS A 289 " =    1.477
peak=   -3.093 closest distance to " O   HOH Z 246 " =    1.659
peak=   -3.082 closest distance to " O   ARG A  56 " =    1.474
peak=   -3.080 closest distance to " O   HOH Z 392 " =    1.292
peak=   -3.079 closest distance to " CB  ASP A 162 " =    2.412
peak=   -3.078 closest distance to " O   HOH Z 231 " =    0.810
peak=   -3.077 closest distance to " CE  LYS A 166 " =    1.128
peak=   -3.076 closest distance to " OD1 ASP A 200 " =    1.375
peak=   -3.074 closest distance to " O   HOH Z 174 " =    4.791
peak=   -3.069 closest distance to " CD1 TRP A 274 " =    1.001
peak=   -3.060 closest distance to " O   HOH Z 235 " =    1.029
peak=   -3.054 closest distance to " CG1 ILE A 234 " =    1.768
peak=   -3.048 closest distance to " NE  ARG A 269 " =    1.825
peak=   -3.047 closest distance to " O   SER A  97 " =    1.338
peak=   -3.041 closest distance to " CA  ASN A 148 " =    1.824
peak=   -3.031 closest distance to " C   ASP A 124 " =    1.173

================= 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    :  0.4779 0.4784   6.289405e+00   6.282227e+00
   1_bss:  0.4675 0.4658   6.284478e+00   6.269439e+00
   1_xyz:  0.3930 0.4237   6.173929e+00   6.222142e+00
   1_adp:  0.3593 0.4323   6.135124e+00   6.231063e+00
   1_occ:  0.3590 0.4334   6.134666e+00   6.231078e+00
   2_bss:  0.3583 0.4323   6.136884e+00   6.231538e+00
   2_xyz:  0.3082 0.3836   6.023661e+00   6.159056e+00
   2_adp:  0.2980 0.3731   6.002698e+00   6.142981e+00
   2_occ:  0.2978 0.3737   6.002776e+00   6.143491e+00
   3_bss:  0.2979 0.3736   6.001989e+00   6.143083e+00
   3_xyz:  0.2487 0.3232   5.850208e+00   6.021012e+00
   3_adp:  0.2366 0.3194   5.819911e+00   6.010302e+00
   3_occ:  0.2361 0.3189   5.819121e+00   6.009912e+00
   4_bss:  0.2364 0.3180   5.817542e+00   6.007301e+00
   4_xyz:  0.1965 0.2673   5.646630e+00   5.860596e+00
   4_adp:  0.1692 0.2333   5.514161e+00   5.747722e+00
   4_occ:  0.1690 0.2323   5.512744e+00   5.745997e+00
   5_bss:  0.1689 0.2310   5.510380e+00   5.742845e+00
   5_xyz:  0.1398 0.1964   5.341246e+00   5.591802e+00
   5_adp:  0.1329 0.1820   5.283648e+00   5.517176e+00
   5_occ:  0.1326 0.1812   5.281619e+00   5.514959e+00
   5_bss:  0.1329 0.1811   5.282384e+00   5.514880e+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:  0.354  24.740  -3.585   1.876   0.835   0.000   0.000   0.000
   1_xyz:  0.354  24.740  -3.585   1.876   0.835   0.000   0.000   0.000
   1_adp:  0.354  24.740  -3.585   1.876   0.835   0.000   0.000   0.000
   1_occ:  0.354  24.740  -3.585   1.876   0.835   0.000   0.000   0.000
   2_bss:  0.357  45.788  -1.223   1.132   0.377   0.000   0.000   0.000
   2_xyz:  0.357  45.788  -1.223   1.132   0.377   0.000   0.000   0.000
   2_adp:  0.357  45.788  -1.223   1.132   0.377   0.000   0.000   0.000
   2_occ:  0.357  45.788  -1.223   1.132   0.377   0.000   0.000   0.000
   3_bss:  0.345  47.968  -0.727   0.190   0.208   0.000   0.000   0.000
   3_xyz:  0.345  47.968  -0.727   0.190   0.208   0.000   0.000   0.000
   3_adp:  0.345  47.968  -0.727   0.190   0.208   0.000   0.000   0.000
   3_occ:  0.345  47.968  -0.727   0.190   0.208   0.000   0.000   0.000
   4_bss:  0.345  47.968  -0.675  -0.373   0.056  -0.000   0.000   0.000
   4_xyz:  0.345  47.968  -0.675  -0.373   0.056  -0.000   0.000   0.000
   4_adp:  0.345  47.968  -0.675  -0.373   0.056  -0.000   0.000   0.000
   4_occ:  0.345  47.968  -0.675  -0.373   0.056  -0.000   0.000   0.000
   5_bss:  0.329  47.968  -1.116  -1.209  -0.323  -0.000  -0.000  -0.000
   5_xyz:  0.329  47.968  -1.116  -1.209  -0.323  -0.000  -0.000  -0.000
   5_adp:  0.329  47.968  -1.116  -1.209  -0.323  -0.000  -0.000  -0.000
   5_occ:  0.329  47.968  -1.116  -1.209  -0.323  -0.000  -0.000  -0.000
   5_bss:  0.329  47.929  -1.472  -1.656  -0.637  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.900 0.4084  0.5672    75100.967
   1_bss:  57.554 0.4243  0.5858    70866.723
   1_xyz:  49.350 0.5282  0.7140    55405.832
   1_adp:  50.560 0.5126  0.6933    57726.213
   1_occ:  50.569 0.5126  0.6928    57811.748
   2_bss:  50.523 0.5132  0.7070    58007.140
   2_xyz:  42.869 0.6076  0.8353    43667.472
   2_adp:  41.074 0.6297  0.8531    41324.919
   2_occ:  41.139 0.6289  0.8517    41359.642
   3_bss:  41.014 0.6301  0.8462    41065.272
   3_xyz:  33.788 0.7148  0.9353    28399.445
   3_adp:  32.824 0.7261  0.9301    27439.652
   3_occ:  32.820 0.7261  0.9293    27368.909
   4_bss:  32.698 0.7272  0.9237    27093.257
   4_xyz:  26.518 0.7948  0.9848    18217.520
   4_adp:  22.652 0.8354  0.9985    13816.520
   4_occ:  22.594 0.8359  0.9987    13736.437
   5_bss:  22.508 0.8366  0.9786    13598.962
   5_xyz:  18.620 0.8741  0.9997     9667.204
   5_adp:  16.675 0.8926  1.0037     8408.838
   5_occ:  16.615 0.8931  1.0038     8338.209
   5_bss:  16.602 0.8932  0.9888     8351.491
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   1.9701e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   1.9701e-01
   1_xyz:   1.596  0.012  0.107 15.764  0.006  4.101   1.3109e-01
   1_adp:   1.596  0.012  0.107 15.764  0.006  4.101   1.3109e-01
   1_occ:   1.596  0.012  0.107 15.764  0.006  4.101   1.3109e-01
   2_bss:   1.596  0.012  0.107 15.764  0.006  4.101   1.3109e-01
   2_xyz:   1.284  0.009  0.085 14.788  0.005  4.103   8.9774e-02
   2_adp:   1.284  0.009  0.085 14.788  0.005  4.103   8.9774e-02
   2_occ:   1.284  0.009  0.085 14.788  0.005  4.103   8.9774e-02
   3_bss:   1.284  0.009  0.085 14.788  0.005  4.103   8.9774e-02
   3_xyz:   1.111  0.009  0.077 14.607  0.004  4.109   7.9803e-02
   3_adp:   1.111  0.009  0.077 14.607  0.004  4.109   7.9803e-02
   3_occ:   1.111  0.009  0.077 14.607  0.004  4.109   7.9803e-02
   4_bss:   1.111  0.009  0.077 14.607  0.004  4.109   7.9803e-02
   4_xyz:   1.138  0.008  0.080 14.502  0.004  4.104   7.2340e-02
   4_adp:   1.138  0.008  0.080 14.502  0.004  4.104   7.2340e-02
   4_occ:   1.138  0.008  0.080 14.502  0.004  4.104   7.2340e-02
   5_bss:   1.138  0.008  0.080 14.502  0.004  4.104   7.2340e-02
   5_xyz:   1.020  0.007  0.068 14.500  0.004  4.105   6.1058e-02
   5_adp:   1.020  0.007  0.068 14.500  0.004  4.105   6.1058e-02
   5_occ:   1.020  0.007  0.068 14.500  0.004  4.105   6.1058e-02
   5_bss:   1.020  0.007  0.068 14.500  0.004  4.105   6.1058e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.528   2.3733e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.528   2.3733e-01
   1_xyz:  10.014  0.103  0.462 84.072  0.047  1.989   1.0088e-01
   1_adp:  10.014  0.103  0.462 84.072  0.047  1.989   1.0088e-01
   1_occ:  10.014  0.103  0.462 84.072  0.047  1.989   1.0088e-01
   2_bss:  10.014  0.103  0.462 84.072  0.047  1.989   1.0088e-01
   2_xyz:   8.373  0.062  0.290 79.430  0.042  2.074   6.8191e-02
   2_adp:   8.373  0.062  0.290 79.430  0.042  2.074   6.8191e-02
   2_occ:   8.373  0.062  0.290 79.430  0.042  2.074   6.8191e-02
   3_bss:   8.373  0.062  0.290 79.430  0.042  2.074   6.8191e-02
   3_xyz:   7.990  0.060  0.284 78.656  0.019  2.301   1.6377e-01
   3_adp:   7.990  0.060  0.284 78.656  0.019  2.301   1.6377e-01
   3_occ:   7.990  0.060  0.284 78.656  0.019  2.301   1.6377e-01
   4_bss:   7.990  0.060  0.284 78.656  0.019  2.301   1.6377e-01
   4_xyz:   8.163  0.042  0.277 77.889  0.025  2.115   6.5620e-02
   4_adp:   8.163  0.042  0.277 77.889  0.025  2.115   6.5620e-02
   4_occ:   8.163  0.042  0.277 77.889  0.025  2.115   6.5620e-02
   5_bss:   8.163  0.042  0.277 77.889  0.025  2.115   6.5620e-02
   5_xyz:   7.674  0.046  0.222 80.590  0.035  2.282   5.7403e-02
   5_adp:   7.674  0.046  0.222 80.590  0.035  2.282   5.7403e-02
   5_occ:   7.674  0.046  0.222 80.590  0.035  2.282   5.7403e-02
   5_bss:   7.674  0.046  0.222 80.590  0.035  2.282   5.7403e-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: 104.64   0.00  19.16  99.69   0.00  16.36 104.64   0.00  34.41
   1_occ: 104.64   0.00  19.16  99.69   0.00  16.36 104.64   0.00  34.41
   2_bss: 104.64   0.00  19.16  99.69   0.00  16.36 104.64   0.00  34.41
   2_xyz: 104.64   0.00  19.16  99.69   0.00  16.36 104.64   0.00  34.41
   2_adp: 106.64   0.00  17.99  97.93   0.00  15.25 106.64   0.00  32.91
   2_occ: 106.64   0.00  17.99  97.93   0.00  15.25 106.64   0.00  32.91
   3_bss: 106.64   0.00  17.99  97.93   0.00  15.25 106.64   0.00  32.91
   3_xyz: 106.64   0.00  17.99  97.93   0.00  15.25 106.64   0.00  32.91
   3_adp: 107.09   0.00  17.78  98.78   0.00  14.69 107.09   1.39  34.57
   3_occ: 107.09   0.00  17.78  98.78   0.00  14.69 107.09   1.39  34.57
   4_bss: 107.09   0.00  17.78  98.78   0.00  14.69 107.09   1.39  34.57
   4_xyz: 107.09   0.00  17.78  98.78   0.00  14.69 107.09   1.39  34.57
   4_adp: 105.76   0.00  17.64 105.76   0.00  13.03 104.81   3.64  42.72
   4_occ: 105.76   0.00  17.64 105.76   0.00  13.03 104.81   3.64  42.72
   5_bss: 105.76   0.00  17.64 105.76   0.00  13.03 104.81   3.64  42.72
   5_xyz: 105.76   0.00  17.64 105.76   0.00  13.03 104.81   3.64  42.72
   5_adp:  99.76   1.14  16.52  99.76   1.14  12.18  98.54   5.91  40.16
   5_occ:  99.76   1.14  16.52  99.76   1.14  12.18  98.54   5.91  40.16
   5_bss:  99.72   1.10  16.48  99.72   1.10  12.14  98.50   5.87  40.12
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.711    0.012    0.320
   1_adp:    1.711    0.012    0.320
   1_occ:    1.711    0.012    0.320
   2_bss:    1.711    0.012    0.320
   2_xyz:    1.632    0.028    0.497
   2_adp:    1.632    0.028    0.497
   2_occ:    1.632    0.028    0.497
   3_bss:    1.632    0.028    0.497
   3_xyz:    1.555    0.017    0.661
   3_adp:    1.555    0.017    0.661
   3_occ:    1.555    0.017    0.661
   4_bss:    1.555    0.017    0.661
   4_xyz:    1.809    0.049    0.782
   4_adp:    1.809    0.049    0.782
   4_occ:    1.809    0.049    0.782
   5_bss:    1.809    0.049    0.782
   5_xyz:    1.812    0.050    0.847
   5_adp:    1.812    0.050    0.847
   5_occ:    1.812    0.050    0.847
   5_bss:    1.812    0.050    0.847
------------------------------------------------------------------------

CPU time actual refinement: 353.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_485/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_485/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_485/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_485/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_485/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.51 
  Macro-tasks:
    bulk solvent and scale       = 43.89  
    individual site refinement   = 151.94 
    weights calculation          = 29.27  
    collect and process          = 6.45   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 231.67 
  Micro-tasks:
    mask                            = 2.95   
    f_calc                          = 112.38 
    alpha_beta                      = 8.35   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 123.31 
    fmodel                         = 7.96   
    r_factors                      = 0.25   
    phase_errors                   = 10.13  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 266.79 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.940 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    658 calls, 112.01 s
gradients_fft:          603 calls, 109.41 s

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

# Date 2008-01-16 Time 04:56:24 PST -0800 (1200488184.85 s)
Start R-work = 0.4779, R-free = 0.4784 (no bulk solvent and anisotropic scale)
Final R-work = 0.1515, R-free = 0.1972 (no bulk solvent and anisotropic scale)

Start R-work = 0.4675, R-free = 0.4658
Final R-work = 0.1329, R-free = 0.1811