# Date 2008-01-16 Time 04:58:38 PST -0800 (1200488318.01 s)
#phil __OFF__

Command line arguments: "../540.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3405
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 540

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96122
Completeness in resolution range: 0.954909
Completeness with d_max=infinity: 0.951939

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8570
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96122
Completeness in resolution range: 0.954909
Completeness with d_max=infinity: 0.951939

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8574 -  4.1966 [2152/2180]  1940   212   9.9%
  bin  2:  4.1966 -  3.3434 [2068/2087]  1858   210  10.2%
  bin  3:  3.3434 -  2.9245 [2045/2065]  1841   204  10.0%
  bin  4:  2.9245 -  2.6587 [2033/2058]  1835   198   9.7%
  bin  5:  2.6587 -  2.4691 [2011/2030]  1806   205  10.2%
  bin  6:  2.4691 -  2.3241 [2001/2048]  1801   200  10.0%
  bin  7:  2.3241 -  2.2081 [1976/2008]  1776   200  10.1%
  bin  8:  2.2081 -  2.1123 [1988/2024]  1789   199  10.0%
  bin  9:  2.1123 -  2.0311 [1991/2020]  1795   196   9.8%
  bin 10:  2.0311 -  1.9612 [1324/1994]  1189   135  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_540/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:
        1.77 -     2.40: 33
        2.40 -     3.02: 2104
        3.02 -     3.65: 4716
        3.65 -     4.27: 9164
        4.27 -     4.90: 12642
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.773 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.792 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.833 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.890 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28654 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_540/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_540/model_refine_001.geo

CPU time processing inputs: 9.76


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 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: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3290   r_free= 0.3289   ksol= 0.00   Bsol= 0.00   scale= 0.976    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.071413                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6806 0.99   1394  154 0.2909 0.2953      6.3828      6.3543|
|  2:  4.6806 -  3.7346 0.99   1359  148 0.2637 0.2444      6.4778       6.445|
|  3:  3.7346 -  3.2682 0.99   1310  153 0.2851 0.2894      6.3654       6.524|
|  4:  3.2682 -  2.9720 0.99   1326  143 0.2953 0.3044      6.2382      6.2478|
|  5:  2.9720 -  2.7605 0.99   1303  145 0.3297 0.2908      6.1345      6.0871|
|  6:  2.7605 -  2.5986 0.98   1286  144 0.3471 0.3563      6.0545      6.0414|
|  7:  2.5986 -  2.4691 0.99   1302  142 0.3482 0.3152      6.0481       5.982|
|  8:  2.4691 -  2.3621 0.98   1273  146 0.3544 0.3505      5.9922      6.0177|
|  9:  2.3621 -  2.2715 0.98   1299  143 0.3633 0.3652       5.957      5.9544|
| 10:  2.2715 -  2.1933 0.98   1272  136 0.3680 0.4135      5.9295        6.02|
| 11:  2.1933 -  2.1249 0.99   1271  146 0.3798 0.4209      5.8931       5.995|
| 12:  2.1249 -  2.0644 0.98   1273  139 0.3621 0.3579      5.8185      5.8418|
| 13:  2.0644 -  2.0102 0.97   1267  140 0.3824 0.4002      5.7361      5.7273|
| 14:  2.0102 -  1.9612 0.55    695   80 0.4340 0.4188      5.7561      5.6407|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6806  1394   154  0.78  27.36   0.87     0.79      46293.55|
|  2:  4.6806 -  3.7346  1359   148  0.82  23.72   0.98     0.91      51872.69|
|  3:  3.7346 -  3.2682  1310   153  0.79  27.48   1.00     0.96      50809.88|
|  4:  3.2682 -  2.9720  1326   143  0.75  30.90   1.01     0.95      44235.82|
|  5:  2.9720 -  2.7605  1303   145  0.70  35.33   0.98     0.92      37328.43|
|  6:  2.7605 -  2.5986  1286   144  0.69  36.59   0.99     0.90      33111.82|
|  7:  2.5986 -  2.4691  1302   142  0.70  36.08   1.00     0.91      30754.71|
|  8:  2.4691 -  2.3621  1273   146  0.67  38.50   1.01     0.89      29100.62|
|  9:  2.3621 -  2.2715  1299   143  0.65  40.29   1.04     0.86      27550.46|
| 10:  2.2715 -  2.1933  1272   136  0.62  42.69   1.05     0.84      27700.21|
| 11:  2.1933 -  2.1249  1271   146  0.61  43.34   1.05     0.85      26120.69|
| 12:  2.1249 -  2.0644  1273   139  0.62  42.75   1.07     0.89      24887.19|
| 13:  2.0644 -  2.0102  1267   140  0.59  44.82   1.04     0.85      21489.18|
| 14:  2.0102 -  1.9612   695    80  0.57  46.34   1.02     0.76      19006.79|
|alpha:            min =        0.76 max =            0.96 mean =         0.88|
|beta:             min =    19006.79 max =        51872.69 mean =     34310.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           90.00 mean =        36.39|
|phase err.(test): min =        0.00 max =           89.92 mean =        36.43|
|-----------------------------------------------------------------------------|

============================== 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 = 4.519546              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.395   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.803021              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.767   (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 |  1.773 -  2.086:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.086 -  2.399:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.399 -  2.711:      139 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.711 -  3.024:     1965 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.024 -  3.337:     1910 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.337 -  3.649:     2806 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.649 -  3.962:     4714 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.962 -  4.275:     4450 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.275 -  4.587:     5744 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.587 -  4.900:     6898 |
|-----------------------------------------------------------------------------|
|-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 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.773 |       0.316 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    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: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3290   r_free= 0.3289   ksol= 0.00   Bsol= 0.00   scale= 0.976    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.071413                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3110   r_free= 0.3094   ksol= 0.33   Bsol= 30.58   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.85,2.78,-0.00,0.00,0.00); trace/3= -1.03                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.049319                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.787934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.333   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402078              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.739   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3110      final r-factor (work) = 0.1997          |
| start r-factor (free) = 0.3094      final r-factor (free) = 0.2243          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6356 = 3.79 * 0.50 * 6.0537 + 1.00 * 0.1701                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0530 = 3.79 * 0.50 * 5.7973 + 1.00 * 0.0732                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1997      final r-factor (work) = 0.1856          |
| start r-factor (free) = 0.2243      final r-factor (free) = 0.2311          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3372 = 0.40 * 1.00 * 5.7973 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2794 = 0.40 * 1.00 * 5.5617 + 1.00 * 0.0432                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.68   16.76    None  None   None       |
|    all(noH): 2823   0      0.00    74.68   16.76    None  None   None       |
|    Sol.    : 438    0      6.81    62.74   37.72    None  None   None       |
|    Mac.    : 2385   0      0.00    74.68   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.468:  452   |   5:    37.338 -  44.806:  135        |
|      1:     7.468 -  14.935: 1280   |   6:    44.806 -  52.273:   87        |
|      2:    14.935 -  22.403:  532   |   7:    52.273 -  59.741:   56        |
|      3:    22.403 -  29.871:  148   |   8:    59.741 -  67.209:    4        |
|      4:    29.871 -  37.338:  128   |   9:    67.209 -  74.676:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1856 r_free = 0.2311             target_work(ml) = 5.576         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1851 r_free = 0.2315             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1851   r_free= 0.2315   ksol= 0.33   Bsol= 30.58   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.85,2.78,-0.00,0.00,0.00); trace/3= -1.03                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.574170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1812   r_free= 0.2269   ksol= 0.32   Bsol= 36.42   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.75,-0.67,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.557497                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.488941              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.868   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.327681              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.953   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1812      final r-factor (work) = 0.1314          |
| start r-factor (free) = 0.2269      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7715 = 3.49 * 0.50 * 5.5594 + 1.00 * 0.0732                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5170 = 3.49 * 0.50 * 5.4217 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1314      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8029 = 0.33 * 1.00 * 5.4217 + 1.00 * 0.0263                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7199 = 0.33 * 1.00 * 5.2245 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.91   17.05    None  None   None       |
|    all(noH): 2823   0      0.00    73.91   17.05    None  None   None       |
|    Sol.    : 438    0      4.50    69.67   39.03    None  None   None       |
|    Mac.    : 2385   0      0.00    73.91   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.391:  359   |   5:    36.953 -  44.343:  112        |
|      1:     7.391 -  14.781: 1456   |   6:    44.343 -  51.734:  110        |
|      2:    14.781 -  22.172:  450   |   7:    51.734 -  59.125:   63        |
|      3:    22.172 -  29.562:  132   |   8:    59.125 -  66.515:   26        |
|      4:    29.562 -  36.953:  104   |   9:    66.515 -  73.906:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1635             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1634             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1634   ksol= 0.32   Bsol= 36.42   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.75,-0.67,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.195477                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1623   ksol= 0.32   Bsol= 39.49   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.47,-1.48,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.192038                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.426798              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.153  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.510055              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.106  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7855 = 1.43 * 0.50 * 5.2237 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7379 = 1.43 * 0.50 * 5.1719 + 1.00 * 0.0483                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6459 = 0.51 * 1.00 * 5.1719 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6319 = 0.51 * 1.00 * 5.1434 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.74    85.70   17.14    None  None   None       |
|    all(noH): 2823   0      0.74    85.70   17.14    None  None   None       |
|    Sol.    : 438    0      3.46    74.08   39.63    None  None   None       |
|    Mac.    : 2385   0      0.74    85.70   13.00    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:     0.741 -   9.237:  812   |   5:    43.220 -  51.715:  124        |
|      1:     9.237 -  17.732: 1251   |   6:    51.715 -  60.211:   69        |
|      2:    17.732 -  26.228:  275   |   7:    60.211 -  68.707:   31        |
|      3:    26.228 -  34.724:  141   |   8:    68.707 -  77.203:   12        |
|      4:    34.724 -  43.220:  103   |   9:    77.203 -  85.699:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1554             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1554             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1554   ksol= 0.32   Bsol= 39.49   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.47,-1.48,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1553   ksol= 0.32   Bsol= 39.49   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.28,-1.68,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141337                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.312286              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.613  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.204458              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.817  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4226 = 1.31 * 0.50 * 5.1430 + 1.00 * 0.0480                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4149 = 1.31 * 0.50 * 5.1297 + 1.00 * 0.0491                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0573 = 0.20 * 1.00 * 5.1297 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0554 = 0.20 * 1.00 * 5.1253 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    85.31   16.71    None  None   None       |
|    all(noH): 2823   0      1.63    85.31   16.71    None  None   None       |
|    Sol.    : 438    0      4.78    74.17   37.93    None  None   None       |
|    Mac.    : 2385   0      1.63    85.31   12.81    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:     1.627 -   9.996: 1012   |   5:    43.469 -  51.837:  107        |
|      1:     9.996 -  18.364: 1121   |   6:    51.837 -  60.206:   52        |
|      2:    18.364 -  26.732:  230   |   7:    60.206 -  68.574:   21        |
|      3:    26.732 -  35.101:  142   |   8:    68.574 -  76.942:    8        |
|      4:    35.101 -  43.469:  125   |   9:    76.942 -  85.311:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1099 r_free = 0.1526             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1526             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1526   ksol= 0.32   Bsol= 39.49   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.28,-1.68,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.123764                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1526   ksol= 0.32   Bsol= 40.06   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.13,-1.61,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.123779                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.913538              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.048  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298791              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.527  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9530 = 1.91 * 0.50 * 5.1255 + 1.00 * 0.0491                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9461 = 1.91 * 0.50 * 5.1111 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5346 = 0.30 * 1.00 * 5.1111 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5343 = 0.30 * 1.00 * 5.1095 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.41    85.58   16.62    None  None   None       |
|    all(noH): 2823   0      1.41    85.58   16.62    None  None   None       |
|    Sol.    : 438    0      5.88    74.10   37.92    None  None   None       |
|    Mac.    : 2385   0      1.41    85.58   12.71    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:     1.413 -   9.830: 1001   |   5:    43.498 -  51.915:  107        |
|      1:     9.830 -  18.247: 1122   |   6:    51.915 -  60.332:   53        |
|      2:    18.247 -  26.664:  240   |   7:    60.332 -  68.749:   20        |
|      3:    26.664 -  35.081:  139   |   8:    68.749 -  77.166:    8        |
|      4:    35.081 -  43.498:  128   |   9:    77.166 -  85.583:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1066 r_free = 0.1531             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1066 r_free = 0.1531             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1531   ksol= 0.32   Bsol= 40.06   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.13,-1.61,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111241                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6806 0.99   1394  154 0.0989 0.1226       5.369      5.5078|
|  2:  4.6806 -  3.7346 0.99   1359  148 0.0829 0.1095      5.4055      5.6095|
|  3:  3.7346 -  3.2682 0.99   1310  153 0.1015 0.1483      5.4382      5.8319|
|  4:  3.2682 -  2.9720 0.99   1326  143 0.1167 0.1539      5.4253      5.5911|
|  5:  2.9720 -  2.7605 0.99   1303  145 0.1199 0.1621      5.2642      5.4664|
|  6:  2.7605 -  2.5986 0.98   1286  144 0.1160 0.1734      5.1621      5.3892|
|  7:  2.5986 -  2.4691 0.99   1302  142 0.1164 0.1592      5.1092      5.3424|
|  8:  2.4691 -  2.3621 0.98   1273  146 0.1096 0.1708       5.031      5.2938|
|  9:  2.3621 -  2.2715 0.98   1299  143 0.1132 0.1760      4.9969      5.2933|
| 10:  2.2715 -  2.1933 0.98   1272  136 0.1077 0.1721      4.9315      5.1869|
| 11:  2.1933 -  2.1249 0.99   1271  146 0.1086 0.1722       4.905      5.2614|
| 12:  2.1249 -  2.0644 0.98   1273  139 0.1040 0.1601      4.8282      5.0836|
| 13:  2.0644 -  2.0102 0.97   1267  140 0.1073 0.1731      4.7607      5.0552|
| 14:  2.0102 -  1.9612 0.55    695   80 0.1027 0.1564      4.6504      4.8676|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6806  1394   154  0.94   8.62   0.99     0.96       6491.52|
|  2:  4.6806 -  3.7346  1359   148  0.96   7.53   1.02     1.01       8399.42|
|  3:  3.7346 -  3.2682  1310   153  0.94  11.00   1.03     1.03       9869.67|
|  4:  3.2682 -  2.9720  1326   143  0.92  13.35   1.01     0.99       9993.81|
|  5:  2.9720 -  2.7605  1303   145  0.91  14.94   1.00     0.97       7448.67|
|  6:  2.7605 -  2.5986  1286   144  0.91  15.23   0.99     0.96       6463.63|
|  7:  2.5986 -  2.4691  1302   142  0.92  14.25   0.99     0.96       5494.21|
|  8:  2.4691 -  2.3621  1273   146  0.91  14.78   1.00     0.98       5106.86|
|  9:  2.3621 -  2.2715  1299   143  0.92  14.58   1.01     0.98       4611.85|
| 10:  2.2715 -  2.1933  1272   136  0.91  15.16   1.00     0.97       4214.96|
| 11:  2.1933 -  2.1249  1271   146  0.90  15.87   1.00     0.97       4139.62|
| 12:  2.1249 -  2.0644  1273   139  0.92  14.28   1.01     0.98       3621.68|
| 13:  2.0644 -  2.0102  1267   140  0.91  15.54   1.01     1.01       3200.17|
| 14:  2.0102 -  1.9612   695    80  0.91  14.84   0.99     0.96       2478.00|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2478.00 max =         9993.81 mean =      5973.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.46|
|phase err.(test): min =        0.00 max =           88.86 mean =        13.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1531   ksol= 0.32   Bsol= 40.01   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.98,-1.48,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111294                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1531   ksol= 0.32   Bsol= 40.01   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.98,-1.48,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111294                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6806 0.99   1394  154 0.0990 0.1227      5.3697      5.5087|
|  2:  4.6806 -  3.7346 0.99   1359  148 0.0829 0.1095      5.4057      5.6093|
|  3:  3.7346 -  3.2682 0.99   1310  153 0.1015 0.1483      5.4382       5.832|
|  4:  3.2682 -  2.9720 0.99   1326  143 0.1167 0.1540      5.4253      5.5912|
|  5:  2.9720 -  2.7605 0.99   1303  145 0.1199 0.1621      5.2642      5.4663|
|  6:  2.7605 -  2.5986 0.98   1286  144 0.1160 0.1735      5.1622      5.3895|
|  7:  2.5986 -  2.4691 0.99   1302  142 0.1165 0.1592      5.1094      5.3425|
|  8:  2.4691 -  2.3621 0.98   1273  146 0.1097 0.1708      5.0311      5.2938|
|  9:  2.3621 -  2.2715 0.98   1299  143 0.1132 0.1760      4.9969      5.2934|
| 10:  2.2715 -  2.1933 0.98   1272  136 0.1077 0.1720      4.9315      5.1865|
| 11:  2.1933 -  2.1249 0.99   1271  146 0.1085 0.1721      4.9049      5.2612|
| 12:  2.1249 -  2.0644 0.98   1273  139 0.1040 0.1601      4.8281      5.0836|
| 13:  2.0644 -  2.0102 0.97   1267  140 0.1072 0.1730      4.7604      5.0546|
| 14:  2.0102 -  1.9612 0.55    695   80 0.1027 0.1564      4.6504      4.8681|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6806  1394   154  0.94   8.63   0.99     0.96       6502.60|
|  2:  4.6806 -  3.7346  1359   148  0.96   7.54   1.02     1.01       8405.63|
|  3:  3.7346 -  3.2682  1310   153  0.94  11.00   1.03     1.03       9869.35|
|  4:  3.2682 -  2.9720  1326   143  0.92  13.35   1.01     0.99       9992.62|
|  5:  2.9720 -  2.7605  1303   145  0.91  14.94   1.00     0.97       7449.53|
|  6:  2.7605 -  2.5986  1286   144  0.91  15.23   0.99     0.96       6464.35|
|  7:  2.5986 -  2.4691  1302   142  0.92  14.25   1.00     0.96       5495.80|
|  8:  2.4691 -  2.3621  1273   146  0.91  14.78   1.00     0.99       5106.89|
|  9:  2.3621 -  2.2715  1299   143  0.92  14.58   1.01     0.98       4612.26|
| 10:  2.2715 -  2.1933  1272   136  0.91  15.16   1.00     0.97       4214.57|
| 11:  2.1933 -  2.1249  1271   146  0.90  15.87   1.01     0.98       4138.80|
| 12:  2.1249 -  2.0644  1273   139  0.92  14.27   1.01     0.99       3619.74|
| 13:  2.0644 -  2.0102  1267   140  0.91  15.54   1.02     1.02       3199.01|
| 14:  2.0102 -  1.9612   695    80  0.91  14.84   1.00     0.96       2478.15|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2478.15 max =         9992.62 mean =      5975.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.46|
|phase err.(test): min =        0.00 max =           88.86 mean =        13.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    85.53   16.57    None  None   None       |
|    all(noH): 2823   0      1.36    85.53   16.57    None  None   None       |
|    Sol.    : 438    0      5.83    74.05   37.87    None  None   None       |
|    Mac.    : 2385   0      1.36    85.53   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.363 -   9.780: 1001   |   5:    43.448 -  51.865:  107        |
|      1:     9.780 -  18.197: 1122   |   6:    51.865 -  60.282:   53        |
|      2:    18.197 -  26.614:  240   |   7:    60.282 -  68.699:   20        |
|      3:    26.614 -  35.031:  139   |   8:    68.699 -  77.116:    8        |
|      4:    35.031 -  43.448:  128   |   9:    77.116 -  85.533:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.698 - 5.476
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 299
   mapped sites are within: 0.707 - 5.476

peak=    5.874 closest distance to " O   HOH Z 126 " =    1.918
peak=    5.390 closest distance to " CB  GLN A 223 " =    1.455
peak=    5.363 closest distance to " CB  SER A  63 " =    1.162
peak=    5.336 closest distance to " CG  PRO A  54 " =    1.197
peak=    5.311 closest distance to " NH2 ARG A  56 " =    2.145
peak=    5.300 closest distance to " CB  ARG A 275 " =    0.912
peak=    5.253 closest distance to " O   HOH Z 144 " =    1.750
peak=    5.175 closest distance to " NE2 GLN A  11 " =    1.098
peak=    4.866 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.834 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.830 closest distance to " CG  PRO A 213 " =    1.223
peak=    4.756 closest distance to " O   HOH Z 236 " =    1.941
peak=    4.731 closest distance to " O   HOH Z 193 " =    1.796
peak=    4.673 closest distance to " C   PRO A 198 " =    1.529
peak=    4.629 closest distance to " O   HOH Z  78 " =    1.712
peak=    4.585 closest distance to " O   HOH Z 427 " =    2.763
peak=    4.571 closest distance to " CB  GLU A 152 " =    1.201
peak=    4.501 closest distance to " CB  GLU A 128 " =    1.061
peak=    4.477 closest distance to " O   HOH Z 234 " =    3.650
peak=    4.475 closest distance to " CB  TYR A 169 " =    0.797
peak=    4.468 closest distance to " CB  PRO A  54 " =    0.938
peak=    4.466 closest distance to " OD1 ASN A  69 " =    2.623
peak=    4.445 closest distance to " CG  PRO A  90 " =    1.121
peak=    4.385 closest distance to " O   HOH Z 298 " =    1.862
peak=    4.326 closest distance to " CB  ASN A 148 " =    1.735
peak=    4.275 closest distance to " O   HOH Z  15 " =    2.232
peak=    4.262 closest distance to " CA  ALA A  21 " =    1.149
peak=    4.243 closest distance to " CA  TYR A  30 " =    0.953
peak=    4.219 closest distance to " CB  SER A   3 " =    1.311
peak=    4.216 closest distance to " OD2 ASP A 286 " =    2.803
peak=    4.203 closest distance to " ND2 ASN A 187 " =    1.480
peak=    4.189 closest distance to " O   HOH Z  54 " =    1.683
peak=    4.160 closest distance to " O   HOH Z 368 " =    1.962
peak=    4.149 closest distance to " O   HOH Z 344 " =    3.036
peak=    4.118 closest distance to " O   HOH Z 346 " =    1.656
peak=    4.116 closest distance to " O   HOH Z 316 " =    3.003
peak=    4.110 closest distance to " O   HOH Z  93 " =    2.452
peak=    4.105 closest distance to " O   HOH Z 389 " =    1.851
peak=    4.087 closest distance to " O   HOH Z  10 " =    1.853
peak=    4.085 closest distance to " CB  LEU A 228 " =    1.080
peak=    4.068 closest distance to " O   HOH Z 303 " =    1.954
peak=    4.068 closest distance to " O   HOH Z 203 " =    1.843
peak=    4.064 closest distance to " CB  ARG A  79 " =    1.393
peak=    4.057 closest distance to " O   HOH Z  97 " =    1.934
peak=    4.019 closest distance to " CA  ASN A 215 " =    1.186
peak=    4.004 closest distance to " O   HOH Z 144 " =    2.205
peak=    3.996 closest distance to " O   SER A  87 " =    2.309
peak=    3.989 closest distance to " CG  PRO A 243 " =    1.130
peak=    3.974 closest distance to " O   HOH Z 207 " =    1.795
peak=    3.947 closest distance to " CB  VAL A 265 " =    1.279
peak=    3.926 closest distance to " O   HOH Z 403 " =    1.697
peak=    3.924 closest distance to " NZ  LYS A 117 " =    3.186
peak=    3.921 closest distance to " CB  TRP A 179 " =    1.266
peak=    3.920 closest distance to " O   HOH Z  40 " =    1.632
peak=    3.920 closest distance to " O   HOH Z 128 " =    1.995
peak=    3.893 closest distance to " CD2 TRP A 179 " =    1.365
peak=    3.888 closest distance to " CA  THR A 221 " =    0.945
peak=    3.878 closest distance to " O   HOH Z 369 " =    1.961
peak=    3.877 closest distance to " O   HOH Z 128 " =    2.132
peak=    3.867 closest distance to " O   HOH Z  61 " =    1.654
peak=    3.861 closest distance to " CG2 VAL A 257 " =    0.926
peak=    3.847 closest distance to " O   HOH Z 132 " =    2.467
peak=    3.836 closest distance to " O   HOH Z 124 " =    1.315
peak=    3.834 closest distance to " CB  ARG A 139 " =    0.943
peak=    3.832 closest distance to " O   HOH Z 402 " =    1.453
peak=    3.828 closest distance to " O   HOH Z 272 " =    1.821
peak=    3.817 closest distance to " CB  TRP A 266 " =    0.982
peak=    3.817 closest distance to " O   HOH Z   6 " =    2.186
peak=    3.817 closest distance to " OG BSER A 164 " =    2.371
peak=    3.805 closest distance to " O   HOH Z 407 " =    2.509
peak=    3.793 closest distance to " O   HOH Z 189 " =    1.637
peak=    3.778 closest distance to " NH2BARG A 145 " =    2.030
peak=    3.777 closest distance to " CG1 ILE A  33 " =    1.223
peak=    3.774 closest distance to " O   HOH Z  21 " =    1.716
peak=    3.768 closest distance to " CB  TYR A 169 " =    0.808
peak=    3.766 closest distance to " O   HOH Z 263 " =    2.257
peak=    3.755 closest distance to " O   HOH Z  61 " =    1.541
peak=    3.752 closest distance to " O   HOH Z 173 " =    1.935
peak=    3.749 closest distance to " CG  PRO A 198 " =    1.261
peak=    3.737 closest distance to " O   HOH Z  43 " =    1.962
peak=    3.736 closest distance to " O   HOH Z  66 " =    2.224
peak=    3.732 closest distance to " CA  THR A 264 " =    0.867
peak=    3.731 closest distance to " N   ASN A  39 " =    1.233
peak=    3.730 closest distance to " CB  ARG A 190 " =    1.725
peak=    3.724 closest distance to " O   HOH Z 158 " =    2.950
peak=    3.721 closest distance to " O   HOH Z 425 " =    1.932
peak=    3.717 closest distance to " O   HOH Z 426 " =    1.537
peak=    3.714 closest distance to " O   HOH Z 250 " =    1.347
peak=    3.711 closest distance to " CG1BVAL A  72 " =    1.535
peak=    3.708 closest distance to " O   HOH Z 371 " =    3.240
peak=    3.704 closest distance to " O   HOH Z 193 " =    2.053
peak=    3.689 closest distance to " O   HOH Z 327 " =    1.688
peak=    3.673 closest distance to " O   HOH Z 392 " =    3.041
peak=    3.673 closest distance to " O   MET A 105 " =    1.822
peak=    3.665 closest distance to " CB  GLU A 277 " =    3.482
peak=    3.657 closest distance to " CG2 ILE A 120 " =    1.211
peak=    3.651 closest distance to " CG2 ILE A  20 " =    1.441
peak=    3.648 closest distance to " NH1BARG A 145 " =    1.285
peak=    3.635 closest distance to " O   HOH Z 279 " =    2.083
peak=    3.630 closest distance to " O   HOH Z 108 " =    2.153
peak=    3.630 closest distance to " CZ2 TRP A 179 " =    1.694
peak=    3.628 closest distance to " O   HOH Z 366 " =    2.944
peak=    3.628 closest distance to " O   HOH Z   9 " =    2.066
peak=    3.622 closest distance to " O   HOH Z 227 " =    1.540
peak=    3.620 closest distance to " O   HOH Z 214 " =    2.044
peak=    3.612 closest distance to " O   HOH Z 273 " =    2.654
peak=    3.609 closest distance to " O   HOH Z  59 " =    2.039
peak=    3.604 closest distance to " O   HOH Z 108 " =    1.168
peak=    3.589 closest distance to " O   HOH Z  44 " =    1.889
peak=    3.589 closest distance to " CD2 LEU A 297 " =    0.919
peak=    3.580 closest distance to " O   HOH Z 291 " =    1.506
peak=    3.576 closest distance to " O   HOH Z 423 " =    1.938
peak=    3.574 closest distance to " NH1AARG A 145 " =    1.126
peak=    3.565 closest distance to " O   HOH Z 172 " =    3.608
peak=    3.563 closest distance to " CB  ASN A  39 " =    0.879
peak=    3.560 closest distance to " CB  SER A 141 " =    1.013
peak=    3.553 closest distance to " CB  VAL A 202 " =    1.613
peak=    3.552 closest distance to " CG  ARG A  66 " =    2.563
peak=    3.550 closest distance to " O   HOH Z 284 " =    2.971
peak=    3.541 closest distance to " CA  ASP A 140 " =    1.095
peak=    3.533 closest distance to " N   ARG A 156 " =    1.280
peak=    3.531 closest distance to " O   HOH Z 374 " =    2.477
peak=    3.530 closest distance to " CD BLYS A 290 " =    1.198
peak=    3.528 closest distance to " CB  SER A  26 " =    1.557
peak=    3.526 closest distance to " CG  LYS A  76 " =    1.025
peak=    3.523 closest distance to " O   HOH Z 209 " =    2.365
peak=    3.520 closest distance to " O   HOH Z 368 " =    3.662
peak=    3.519 closest distance to " O   HOH Z 126 " =    2.183
peak=    3.517 closest distance to " O   HOH Z 163 " =    1.851
peak=    3.515 closest distance to " CD1 ILE A 106 " =    0.936
peak=    3.509 closest distance to " O   HOH Z 219 " =    1.964
peak=    3.508 closest distance to " O   HOH Z 134 " =    1.319
peak=    3.506 closest distance to " O   HOH Z   3 " =    1.703
peak=    3.500 closest distance to " CG  GLN A  77 " =    1.962
peak=    3.492 closest distance to " OG  SER A  22 " =    2.678
peak=    3.491 closest distance to " O   HOH Z 209 " =    2.380
peak=    3.486 closest distance to " CB  ALA A 291 " =    1.316
peak=    3.484 closest distance to " O   HOH Z 245 " =    1.298
peak=    3.480 closest distance to " CB  SER A 216 " =    0.740
peak=    3.478 closest distance to " CB  GLN A  88 " =    1.179
peak=    3.476 closest distance to " CD1 LEU A 300 " =    1.273
peak=    3.471 closest distance to " O   HOH Z 227 " =    2.199
peak=    3.470 closest distance to " O   HOH Z  71 " =    1.949
peak=    3.470 closest distance to " O   HOH Z 183 " =    1.517
peak=    3.469 closest distance to " O   HOH Z  88 " =    3.133
peak=    3.461 closest distance to " NZ  LYS A 119 " =    1.509
peak=    3.451 closest distance to " O   HOH Z   1 " =    1.888
peak=    3.445 closest distance to " O   HOH Z 411 " =    3.772
peak=    3.443 closest distance to " CA  ASN A 176 " =    1.122
peak=    3.438 closest distance to " O   HOH Z 299 " =    4.298
peak=    3.437 closest distance to " CZ  PHE A 218 " =    1.020
peak=    3.437 closest distance to " O   HOH Z 147 " =    1.697
peak=    3.434 closest distance to " CD  ARG A 269 " =    1.012
peak=    3.426 closest distance to " CA  ALA A 291 " =    0.913
peak=    3.413 closest distance to " NH2 ARG A 156 " =    1.168
peak=    3.412 closest distance to " CG  GLU A 277 " =    2.162
peak=    3.411 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.411 closest distance to " O   HOH Z  19 " =    2.364
peak=    3.409 closest distance to " O   HOH Z 295 " =    1.476
peak=    3.402 closest distance to " CA  ASP A 162 " =    1.124
peak=    3.391 closest distance to " O   HOH Z 406 " =    1.620
peak=    3.390 closest distance to " CA  MET A  40 " =    1.079
peak=    3.389 closest distance to " O   HOH Z 334 " =    1.409
peak=    3.387 closest distance to " O   TRP A 274 " =    1.849
peak=    3.384 closest distance to " O   HOH Z 326 " =    1.477
peak=    3.382 closest distance to " CA  ASN A 217 " =    1.285
peak=    3.381 closest distance to " O   HOH Z 180 " =    2.182
peak=    3.378 closest distance to " CD  LYS A 166 " =    1.276
peak=    3.377 closest distance to " O   HOH Z 427 " =    3.042
peak=    3.362 closest distance to " CA  GLY A  80 " =    0.826
peak=    3.355 closest distance to " O   HOH Z 193 " =    1.630
peak=    3.351 closest distance to " CG  MET A 185 " =    1.089
peak=    3.349 closest distance to " O   HOH Z 337 " =    3.673
peak=    3.349 closest distance to " O   HOH Z 248 " =    1.747
peak=    3.346 closest distance to " CG  MET A 185 " =    1.174
peak=    3.346 closest distance to " O   HOH Z 175 " =    2.189
peak=    3.340 closest distance to " C   TYR A 214 " =    1.405
peak=    3.339 closest distance to " CG2BVAL A  41 " =    0.857
peak=    3.339 closest distance to " CD  ARG A 159 " =    0.707
peak=    3.338 closest distance to " O   ALA A   1 " =    1.664
peak=    3.336 closest distance to " O   HOH Z 261 " =    1.507
peak=    3.335 closest distance to " O   HOH Z 329 " =    3.624
peak=    3.331 closest distance to " O   HOH Z 281 " =    4.548
peak=    3.329 closest distance to " O   HOH Z  49 " =    2.068
peak=    3.327 closest distance to " O   HOH Z 433 " =    1.753
peak=    3.324 closest distance to " O   HOH Z 132 " =    2.573
peak=    3.323 closest distance to " O   HOH Z 286 " =    2.199
peak=    3.323 closest distance to " O   ALA A 165 " =    1.394
peak=    3.322 closest distance to " CA  PHE A 283 " =    1.305
peak=    3.322 closest distance to " CG AARG A 275 " =    1.037
peak=    3.321 closest distance to " CG  LEU A 167 " =    1.194
peak=    3.320 closest distance to " OD1 ASP A 231 " =    1.893
peak=    3.319 closest distance to " O   HOH Z 185 " =    1.676
peak=    3.319 closest distance to " O   HOH Z 261 " =    2.013
peak=    3.316 closest distance to " O   HOH Z 357 " =    1.753
peak=    3.313 closest distance to " O   HOH Z 342 " =    0.787
peak=    3.310 closest distance to " CA  ALA A 248 " =    1.387
peak=    3.309 closest distance to " CB  ASP A 140 " =    0.836
peak=    3.309 closest distance to " NH2AARG A 190 " =    1.180
peak=    3.308 closest distance to " O   HOH Z 148 " =    3.127
peak=    3.307 closest distance to " CA  ARG A 195 " =    1.249
peak=    3.306 closest distance to " CG2 VAL A  67 " =    1.100
peak=    3.304 closest distance to " CB  SER A  62 " =    1.297
peak=    3.299 closest distance to " O   HOH Z  59 " =    2.298
peak=    3.296 closest distance to " CA  ARG A  36 " =    1.068
peak=    3.290 closest distance to " O   HOH Z 211 " =    2.570
peak=    3.289 closest distance to " O   HOH Z 286 " =    2.373
peak=    3.286 closest distance to " CE1 TYR A 186 " =    1.277
peak=    3.286 closest distance to " O   HOH Z 163 " =    1.698
peak=    3.283 closest distance to " CB  ALA A  71 " =    1.336
peak=    3.279 closest distance to " CA  ILE A  33 " =    1.431
peak=    3.276 closest distance to " OG  SER A  62 " =    2.893
peak=    3.273 closest distance to " O   HOH Z 368 " =    2.587
peak=    3.270 closest distance to " CG2 THR A 221 " =    1.141
peak=    3.269 closest distance to " O   HOH Z 106 " =    2.289
peak=    3.264 closest distance to " CG1 VAL A 202 " =    1.981
peak=    3.263 closest distance to " O   HOH Z 112 " =    2.672
peak=    3.263 closest distance to " CB  ASN A 215 " =    1.088
peak=    3.257 closest distance to " ND1 HIS A  81 " =    1.524
peak=    3.255 closest distance to " O   HOH Z 265 " =    2.369
peak=    3.255 closest distance to " O   HOH Z 287 " =    2.177
peak=    3.254 closest distance to " CD2 LEU A 255 " =    1.345
peak=    3.252 closest distance to " O   HOH Z  83 " =    1.833
peak=    3.251 closest distance to " CG1 ILE A 151 " =    0.942
peak=    3.251 closest distance to " CA  ALA A  51 " =    0.914
peak=    3.250 closest distance to " CD  PRO A 243 " =    1.541
peak=    3.250 closest distance to " OE1 GLU A 277 " =    1.944
peak=    3.242 closest distance to " O   HOH Z  48 " =    1.368
peak=    3.239 closest distance to " CB  ILE A 120 " =    1.293
peak=    3.238 closest distance to " O   HOH Z 437 " =    1.556
peak=    3.229 closest distance to " O   HOH Z 313 " =    1.608
peak=    3.227 closest distance to " O   HOH Z 234 " =    1.779
peak=    3.226 closest distance to " O   HOH Z 345 " =    3.235
peak=    3.225 closest distance to " O   HOH Z 411 " =    1.716
peak=    3.224 closest distance to " O   HOH Z 250 " =    1.864
peak=    3.224 closest distance to " NE2 GLN A  73 " =    3.770
peak=    3.218 closest distance to " O   ALA A   1 " =    1.446
peak=    3.216 closest distance to " O   HOH Z  35 " =    2.562
peak=    3.216 closest distance to " O   HOH Z  63 " =    2.269
peak=    3.215 closest distance to " O   HOH Z 227 " =    1.665
peak=    3.206 closest distance to " CB  MET A  47 " =    1.069
peak=    3.206 closest distance to " CA  ALA A  43 " =    1.179
peak=    3.204 closest distance to " CG  GLN A  89 " =    1.483
peak=    3.202 closest distance to " CA  ALA A 233 " =    1.242
peak=    3.199 closest distance to " O   HOH Z 192 " =    1.991
peak=    3.197 closest distance to " O   HOH Z 353 " =    2.603
peak=    3.197 closest distance to " O   HOH Z 422 " =    2.753
peak=    3.196 closest distance to " O   HOH Z 266 " =    2.070
peak=    3.194 closest distance to " O   HOH Z 305 " =    3.627
peak=    3.193 closest distance to " NZ  LYS A  76 " =    1.206
peak=    3.192 closest distance to " O   HOH Z 216 " =    2.583
peak=    3.190 closest distance to " N   ASN A 127 " =    1.222
peak=    3.184 closest distance to " O   SER A  26 " =    1.667
peak=    3.184 closest distance to " N   PHE A 130 " =    1.378
peak=    3.182 closest distance to " CD  ARG A  66 " =    2.675
peak=    3.177 closest distance to " O   HOH Z 417 " =    3.216
peak=    3.174 closest distance to " O   HOH Z 133 " =    1.401
peak=    3.174 closest distance to " O   HOH Z 423 " =    3.052
peak=    3.169 closest distance to " O   HOH Z 280 " =    1.757
peak=    3.167 closest distance to " CA  VAL A  41 " =    0.908
peak=    3.159 closest distance to " O   HOH Z 250 " =    1.547
peak=    3.151 closest distance to " O   HOH Z 125 " =    2.244
peak=    3.151 closest distance to " CG  MET A 113 " =    1.173
peak=    3.141 closest distance to " CB  THR A  31 " =    1.750
peak=    3.140 closest distance to " CD  LYS A 119 " =    1.273
peak=    3.135 closest distance to " CB  ASN A 285 " =    0.941
peak=    3.131 closest distance to " N   VAL A 126 " =    1.335
peak=    3.129 closest distance to " CA  ALA A  84 " =    1.364
peak=    3.124 closest distance to " CG2 THR A 294 " =    1.613
peak=    3.122 closest distance to " O   HOH Z 430 " =    5.476
peak=    3.120 closest distance to " O   HOH Z  68 " =    1.493
peak=    3.117 closest distance to " O   HOH Z 403 " =    1.297
peak=    3.116 closest distance to " CB  GLN A 103 " =    0.813
peak=    3.115 closest distance to " CB  GLU A  46 " =    1.072
peak=    3.108 closest distance to " CB  THR A 157 " =    1.080
peak=    3.105 closest distance to " OE2 GLU A  53 " =    2.121
peak=    3.101 closest distance to " N   SER A 135 " =    1.230
peak=    3.098 closest distance to " CB  VAL A 126 " =    1.135
peak=    3.091 closest distance to " CB  ALA A 114 " =    1.221
peak=    3.091 closest distance to " CG2 VAL A 202 " =    1.219
peak=    3.084 closest distance to " CA  LEU A 282 " =    1.108
peak=    3.079 closest distance to " O   HOH Z 409 " =    3.028
peak=    3.078 closest distance to " CD2 HIS A  81 " =    1.160
peak=    3.077 closest distance to " O   HOH Z  40 " =    1.879
peak=    3.074 closest distance to " O   HOH Z 425 " =    1.218
peak=    3.069 closest distance to " CG2 VAL A 126 " =    2.069
peak=    3.069 closest distance to " CD1AILE A 234 " =    1.018
peak=    3.064 closest distance to " CA  SER A  87 " =    0.940
peak=    3.059 closest distance to " O   HOH Z  49 " =    2.353
peak=    3.051 closest distance to " CA  ALA A 158 " =    1.162
peak=    3.049 closest distance to " O   GLY A 147 " =    1.298
peak=    3.048 closest distance to " CB  LEU A 255 " =    0.742
peak=    3.046 closest distance to " OD1BASN A 224 " =    2.337
peak=    3.045 closest distance to " O   HOH Z 367 " =    3.561
peak=    3.044 closest distance to " O   HOH Z 135 " =    1.513
peak=    3.029 closest distance to " N   TYR A 116 " =    1.707
peak=    3.026 closest distance to " O   HOH Z  66 " =    1.948
peak=    2.907 closest distance to " CG2 THR A 294 " =    3.803

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.777 - 5.172
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.777 - 5.172

peak=   -4.909 closest distance to " O   HOH Z 266 " =    4.373
peak=   -4.352 closest distance to " O   HOH Z 290 " =    1.026
peak=   -4.284 closest distance to " O   HOH Z 372 " =    2.395
peak=   -4.278 closest distance to " CD  ARG A 156 " =    1.985
peak=   -4.222 closest distance to " O   ILE A 109 " =    2.576
peak=   -4.221 closest distance to " SG  CYS A 254 " =    3.222
peak=   -4.138 closest distance to " C   HIS A 108 " =    1.073
peak=   -4.137 closest distance to " CB  PRO A 243 " =    2.590
peak=   -4.125 closest distance to " O   VAL A  67 " =    2.685
peak=   -4.107 closest distance to " N   GLN A  58 " =    1.625
peak=   -4.037 closest distance to " O   HOH Z 198 " =    2.082
peak=   -4.028 closest distance to " CG  GLN A 223 " =    1.821
peak=   -4.026 closest distance to " CG1 VAL A 112 " =    2.756
peak=   -4.013 closest distance to " O   HOH Z 377 " =    2.125
peak=   -3.993 closest distance to " O   HOH Z 353 " =    2.204
peak=   -3.987 closest distance to " OXT GLY A 302 " =    2.722
peak=   -3.982 closest distance to " O   HOH Z 126 " =    1.823
peak=   -3.963 closest distance to " OG  SER A  97 " =    2.104
peak=   -3.949 closest distance to " CA  VAL A  67 " =    2.678
peak=   -3.944 closest distance to " CZ  TYR A 169 " =    1.701
peak=   -3.919 closest distance to " O   VAL A 153 " =    2.410
peak=   -3.886 closest distance to " CE2 TYR A  30 " =    2.815
peak=   -3.882 closest distance to " CG  ASP A 231 " =    0.799
peak=   -3.860 closest distance to " CZ3 TRP A 179 " =    1.238
peak=   -3.857 closest distance to " OG BSER A 134 " =    1.196
peak=   -3.837 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.831 closest distance to " C   ALA A 158 " =    1.254
peak=   -3.830 closest distance to " O   HOH Z 118 " =    3.111
peak=   -3.829 closest distance to " CZ  PHE A  59 " =    1.565
peak=   -3.823 closest distance to " O   HOH Z 185 " =    2.234
peak=   -3.818 closest distance to " CB  ASN A  39 " =    2.157
peak=   -3.816 closest distance to " ND2 ASN A  45 " =    0.989
peak=   -3.815 closest distance to " N   ALA A  43 " =    2.404
peak=   -3.788 closest distance to " CD  ARG A 139 " =    1.492
peak=   -3.782 closest distance to " CD1 PHE A  59 " =    1.872
peak=   -3.781 closest distance to " O   HOH Z  13 " =    1.499
peak=   -3.763 closest distance to " O   HOH Z 407 " =    2.980
peak=   -3.756 closest distance to " O   PRO A 163 " =    2.006
peak=   -3.756 closest distance to " O   HOH Z  43 " =    1.613
peak=   -3.750 closest distance to " N   ALA A 248 " =    1.581
peak=   -3.748 closest distance to " NH1 ARG A 195 " =    2.538
peak=   -3.746 closest distance to " CG  PHE A 283 " =    2.670
peak=   -3.739 closest distance to " CB  TYR A  15 " =    2.196
peak=   -3.736 closest distance to " CD2 LEU A 300 " =    2.898
peak=   -3.709 closest distance to " O   HOH Z 231 " =    2.111
peak=   -3.705 closest distance to " O   HOH Z 166 " =    1.468
peak=   -3.673 closest distance to " O   SER A 210 " =    1.953
peak=   -3.670 closest distance to " CE  MET A 105 " =    2.182
peak=   -3.654 closest distance to " CD1 LEU A 228 " =    2.151
peak=   -3.634 closest distance to " OG  SER A   3 " =    1.687
peak=   -3.632 closest distance to " O   HOH Z  52 " =    1.396
peak=   -3.620 closest distance to " O   HOH Z  47 " =    1.558
peak=   -3.596 closest distance to " O   HOH Z 435 " =    2.711
peak=   -3.587 closest distance to " NH2AARG A 275 " =    5.120
peak=   -3.580 closest distance to " O   HOH Z  10 " =    1.413
peak=   -3.565 closest distance to " O   HOH Z 102 " =    1.703
peak=   -3.563 closest distance to " O   ALA A 161 " =    1.555
peak=   -3.560 closest distance to " CD1 LEU A 101 " =    2.408
peak=   -3.551 closest distance to " OG BSER A 134 " =    1.713
peak=   -3.548 closest distance to " CB  ALA A 291 " =    2.407
peak=   -3.542 closest distance to " O   HOH Z  11 " =    1.998
peak=   -3.534 closest distance to " O   HOH Z 198 " =    1.403
peak=   -3.534 closest distance to " CA  GLY A 203 " =    2.239
peak=   -3.526 closest distance to " CB  PHE A 192 " =    1.855
peak=   -3.519 closest distance to " O   HOH Z 385 " =    1.894
peak=   -3.518 closest distance to " N   ASP A 286 " =    2.366
peak=   -3.516 closest distance to " CB  ALA A 248 " =    1.947
peak=   -3.515 closest distance to " OG  SER A  62 " =    1.532
peak=   -3.505 closest distance to " O   GLY A 196 " =    0.962
peak=   -3.501 closest distance to " O   HOH Z 389 " =    1.740
peak=   -3.497 closest distance to " O   VAL A 174 " =    1.990
peak=   -3.494 closest distance to " O   MET A  40 " =    2.766
peak=   -3.490 closest distance to " N   GLN A 122 " =    1.436
peak=   -3.487 closest distance to " C   LEU A 143 " =    1.055
peak=   -3.482 closest distance to " CD1 ILE A 239 " =    2.492
peak=   -3.465 closest distance to " O   HOH Z   3 " =    1.994
peak=   -3.464 closest distance to " CB  ASP A 132 " =    2.268
peak=   -3.459 closest distance to " O   SER A 135 " =    1.541
peak=   -3.448 closest distance to " CA  GLY A  98 " =    1.936
peak=   -3.446 closest distance to " O   HOH Z 388 " =    2.041
peak=   -3.444 closest distance to " O   PHE A 218 " =    1.598
peak=   -3.437 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.434 closest distance to " OXT GLY A 302 " =    3.309
peak=   -3.426 closest distance to " O   HOH Z 313 " =    2.077
peak=   -3.423 closest distance to " O   HOH Z 311 " =    3.534
peak=   -3.420 closest distance to " CB  CYS A 201 " =    2.582
peak=   -3.420 closest distance to " O   HOH Z 351 " =    1.492
peak=   -3.419 closest distance to " OD1 ASP A 191 " =    1.445
peak=   -3.415 closest distance to " CG  ARG A 269 " =    2.326
peak=   -3.414 closest distance to " ND2 ASN A 187 " =    1.447
peak=   -3.413 closest distance to " N   HIS A 115 " =    1.848
peak=   -3.407 closest distance to " NH2 ARG A  79 " =    1.932
peak=   -3.405 closest distance to " N   THR A 235 " =    1.344
peak=   -3.403 closest distance to " CD2 LEU A 237 " =    2.621
peak=   -3.402 closest distance to " CB  PRO A 163 " =    2.543
peak=   -3.400 closest distance to " O   HOH Z 211 " =    1.671
peak=   -3.398 closest distance to " CA  GLY A 133 " =    1.911
peak=   -3.398 closest distance to " O   HOH Z  11 " =    1.775
peak=   -3.386 closest distance to " SG ACYS A 201 " =    1.912
peak=   -3.385 closest distance to " CD1 ILE A 239 " =    2.108
peak=   -3.378 closest distance to " OG ASER A 134 " =    1.125
peak=   -3.377 closest distance to " OD2 ASP A 171 " =    2.292
peak=   -3.374 closest distance to " N   VAL A 189 " =    1.667
peak=   -3.371 closest distance to " O   LYS A 117 " =    1.594
peak=   -3.363 closest distance to " O   HOH Z  24 " =    1.506
peak=   -3.362 closest distance to " CB  ALA A  43 " =    2.285
peak=   -3.361 closest distance to " O   HOH Z  15 " =    1.577
peak=   -3.357 closest distance to " O   HOH Z 298 " =    1.252
peak=   -3.357 closest distance to " O   HOH Z 292 " =    4.506
peak=   -3.356 closest distance to " CD  GLN A  58 " =    1.241
peak=   -3.353 closest distance to " OD1 ASN A 148 " =    1.633
peak=   -3.340 closest distance to " O   HOH Z 385 " =    2.021
peak=   -3.340 closest distance to " O   HOH Z  76 " =    1.790
peak=   -3.337 closest distance to " CG2 ILE A 263 " =    2.229
peak=   -3.337 closest distance to " O   ALA A  51 " =    1.363
peak=   -3.333 closest distance to " O   HOH Z  93 " =    1.641
peak=   -3.328 closest distance to " N   THR A 157 " =    1.563
peak=   -3.321 closest distance to " O   HOH Z  63 " =    1.431
peak=   -3.318 closest distance to " NE2 GLN A  58 " =    1.221
peak=   -3.311 closest distance to " NH1 ARG A  36 " =    2.071
peak=   -3.310 closest distance to " O   HOH Z 395 " =    5.172
peak=   -3.309 closest distance to " CB  ASP A 286 " =    2.240
peak=   -3.298 closest distance to " NH1 ARG A  56 " =    2.553
peak=   -3.295 closest distance to " CG  ARG A  66 " =    2.434
peak=   -3.294 closest distance to " O   SER A 146 " =    1.044
peak=   -3.286 closest distance to " CA  TYR A  68 " =    2.882
peak=   -3.283 closest distance to " O   TRP A  92 " =    1.644
peak=   -3.283 closest distance to " CA  ASP A 298 " =    1.055
peak=   -3.279 closest distance to " OG1 THR A 178 " =    1.245
peak=   -3.275 closest distance to " CE  MET A  93 " =    1.180
peak=   -3.274 closest distance to " CG  GLU A  53 " =    1.375
peak=   -3.272 closest distance to " CB  ALA A 131 " =    2.074
peak=   -3.270 closest distance to " OG BSER A 210 " =    1.976
peak=   -3.267 closest distance to " N   ALA A 226 " =    2.027
peak=   -3.267 closest distance to " O   HOH Z 282 " =    1.344
peak=   -3.266 closest distance to " O   HOH Z  44 " =    2.167
peak=   -3.262 closest distance to " OD1 ASN A 176 " =    1.215
peak=   -3.258 closest distance to " OD2 ASP A  50 " =    1.445
peak=   -3.256 closest distance to " O   HOH Z 407 " =    3.311
peak=   -3.254 closest distance to " O   HOH Z 148 " =    3.268
peak=   -3.251 closest distance to " O   ASN A  45 " =    1.846
peak=   -3.250 closest distance to " CD2 LEU A 237 " =    2.668
peak=   -3.247 closest distance to " O   HOH Z  90 " =    2.731
peak=   -3.244 closest distance to " O   HOH Z 281 " =    2.682
peak=   -3.244 closest distance to " OE1 GLN A  88 " =    1.251
peak=   -3.238 closest distance to " CG1 VAL A 230 " =    1.943
peak=   -3.237 closest distance to " OD1 ASP A 191 " =    1.737
peak=   -3.235 closest distance to " NH2 ARG A  66 " =    4.886
peak=   -3.234 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.233 closest distance to " O   HOH Z 263 " =    2.906
peak=   -3.232 closest distance to " CB  ALA A 291 " =    2.208
peak=   -3.228 closest distance to " O   HOH Z 250 " =    1.429
peak=   -3.226 closest distance to " O   HOH Z 234 " =    4.058
peak=   -3.225 closest distance to " O   LEU A 167 " =    1.467
peak=   -3.224 closest distance to " C   GLN A 205 " =    1.930
peak=   -3.215 closest distance to " O   HOH Z 361 " =    3.465
peak=   -3.212 closest distance to " O   HOH Z 210 " =    1.123
peak=   -3.203 closest distance to " CD  GLU A 152 " =    2.570
peak=   -3.202 closest distance to " O   PRO A 198 " =    1.240
peak=   -3.195 closest distance to " CE  LYS A  76 " =    2.668
peak=   -3.195 closest distance to " CE3 TRP A 123 " =    1.265
peak=   -3.194 closest distance to " NE2 GLN A  88 " =    1.891
peak=   -3.193 closest distance to " O   HOH Z 278 " =    1.974
peak=   -3.190 closest distance to " O   HOH Z 326 " =    1.609
peak=   -3.185 closest distance to " CE3 TRP A 274 " =    2.411
peak=   -3.185 closest distance to " ND2 ASN A 249 " =    2.293
peak=   -3.175 closest distance to " CE  LYS A  76 " =    2.873
peak=   -3.174 closest distance to " O   HOH Z 322 " =    1.665
peak=   -3.169 closest distance to " O   HOH Z 166 " =    1.926
peak=   -3.167 closest distance to " O   HOH Z  37 " =    1.813
peak=   -3.164 closest distance to " CA  TRP A 274 " =    1.539
peak=   -3.162 closest distance to " CD2 TYR A 293 " =    2.025
peak=   -3.159 closest distance to " CG  GLU A 152 " =    0.870
peak=   -3.156 closest distance to " N   SER A 276 " =    1.190
peak=   -3.154 closest distance to " CA  GLY A 241 " =    3.125
peak=   -3.153 closest distance to " CG  MET A 105 " =    0.941
peak=   -3.149 closest distance to " CD  GLN A  88 " =    0.777
peak=   -3.147 closest distance to " CG  GLU A 277 " =    1.209
peak=   -3.143 closest distance to " OH  TYR A 214 " =    1.221
peak=   -3.121 closest distance to " CD1 TYR A 247 " =    2.602
peak=   -3.118 closest distance to " O   HOH Z 436 " =    1.269
peak=   -3.117 closest distance to " CG  TRP A 266 " =    1.835
peak=   -3.109 closest distance to " O   ALA A   1 " =    1.832
peak=   -3.103 closest distance to " O   HOH Z 317 " =    2.479
peak=   -3.100 closest distance to " OE1 GLN A 223 " =    1.704
peak=   -3.087 closest distance to " ND2 ASN A  39 " =    1.375
peak=   -3.085 closest distance to " O   SER A  62 " =    2.089
peak=   -3.082 closest distance to " O   HOH Z 166 " =    1.944
peak=   -3.081 closest distance to " O   ASP A 162 " =    2.226
peak=   -3.079 closest distance to " O   ASN A 249 " =    1.544
peak=   -3.077 closest distance to " CB  PHE A 208 " =    2.224
peak=   -3.073 closest distance to " OG1 THR A 246 " =    1.427
peak=   -3.067 closest distance to " CG  ASN A 301 " =    1.969
peak=   -3.064 closest distance to " CG  ASP A  50 " =    2.348
peak=   -3.063 closest distance to " O   HOH Z 168 " =    1.693
peak=   -3.063 closest distance to " CZ  PHE A 130 " =    0.893
peak=   -3.049 closest distance to " CD2 LEU A 237 " =    2.184
peak=   -3.039 closest distance to " O   HOH Z 137 " =    1.507
peak=   -3.028 closest distance to " CG1 VAL A 197 " =    2.196
peak=   -3.020 closest distance to " O   HOH Z 429 " =    2.066

================= 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    :  0.3290 0.3289   6.071413e+00   6.082302e+00
   1_bss:  0.3110 0.3094   6.049319e+00   6.040355e+00
   1_xyz:  0.1997 0.2243   5.615457e+00   5.712124e+00
   1_adp:  0.1856 0.2311   5.575562e+00   5.743376e+00
   1_occ:  0.1851 0.2315   5.574170e+00   5.742582e+00
   2_bss:  0.1812 0.2269   5.557497e+00   5.727401e+00
   2_xyz:  0.1314 0.1719   5.263226e+00   5.469061e+00
   2_adp:  0.1210 0.1635   5.196469e+00   5.415255e+00
   2_occ:  0.1208 0.1634   5.195477e+00   5.414254e+00
   3_bss:  0.1209 0.1623   5.192038e+00   5.409594e+00
   3_xyz:  0.1147 0.1554   5.151820e+00   5.374136e+00
   3_adp:  0.1127 0.1554   5.142108e+00   5.370566e+00
   3_occ:  0.1126 0.1554   5.141831e+00   5.370480e+00
   4_bss:  0.1125 0.1553   5.141337e+00   5.370256e+00
   4_xyz:  0.1097 0.1531   5.123999e+00   5.360415e+00
   4_adp:  0.1099 0.1526   5.124014e+00   5.358204e+00
   4_occ:  0.1099 0.1526   5.123764e+00   5.358222e+00
   5_bss:  0.1098 0.1526   5.123779e+00   5.358231e+00
   5_xyz:  0.1068 0.1530   5.111076e+00   5.359786e+00
   5_adp:  0.1066 0.1531   5.111318e+00   5.362182e+00
   5_occ:  0.1066 0.1531   5.111241e+00   5.362259e+00
   5_bss:  0.1066 0.1531   5.111294e+00   5.362304e+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:  0.325  30.576  -3.011  -2.853   2.779  -0.000   0.000   0.000
   1_xyz:  0.325  30.576  -3.011  -2.853   2.779  -0.000   0.000   0.000
   1_adp:  0.325  30.576  -3.011  -2.853   2.779  -0.000   0.000   0.000
   1_occ:  0.325  30.576  -3.011  -2.853   2.779  -0.000   0.000   0.000
   2_bss:  0.321  36.424  -2.984  -2.751  -0.669  -0.000  -0.000  -0.000
   2_xyz:  0.321  36.424  -2.984  -2.751  -0.669  -0.000  -0.000  -0.000
   2_adp:  0.321  36.424  -2.984  -2.751  -0.669  -0.000  -0.000  -0.000
   2_occ:  0.321  36.424  -2.984  -2.751  -0.669  -0.000  -0.000  -0.000
   3_bss:  0.319  39.486  -2.796  -2.465  -1.482  -0.000  -0.000  -0.000
   3_xyz:  0.319  39.486  -2.796  -2.465  -1.482  -0.000  -0.000  -0.000
   3_adp:  0.319  39.486  -2.796  -2.465  -1.482  -0.000  -0.000  -0.000
   3_occ:  0.319  39.486  -2.796  -2.465  -1.482  -0.000  -0.000  -0.000
   4_bss:  0.319  39.486  -2.672  -2.281  -1.676  -0.000  -0.000  -0.000
   4_xyz:  0.319  39.486  -2.672  -2.281  -1.676  -0.000  -0.000  -0.000
   4_adp:  0.319  39.486  -2.672  -2.281  -1.676  -0.000  -0.000  -0.000
   4_occ:  0.319  39.486  -2.672  -2.281  -1.676  -0.000  -0.000  -0.000
   5_bss:  0.321  40.060  -2.554  -2.131  -1.606  -0.000  -0.000  -0.000
   5_xyz:  0.321  40.060  -2.554  -2.131  -1.606  -0.000  -0.000  -0.000
   5_adp:  0.321  40.060  -2.554  -2.131  -1.606  -0.000  -0.000  -0.000
   5_occ:  0.321  40.060  -2.554  -2.131  -1.606  -0.000  -0.000  -0.000
   5_bss:  0.321  40.010  -2.399  -1.979  -1.479  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.394 0.6878  0.8820    34310.368
   1_bss:  34.528 0.7072  0.8745    29728.848
   1_xyz:  21.539 0.8477  0.9936    12823.768
   1_adp:  22.682 0.8354  0.9861    13722.897
   1_occ:  22.674 0.8355  0.9862    13693.191
   2_bss:  22.034 0.8418  0.9542    13121.088
   2_xyz:  15.950 0.8980  0.9877     7454.965
   2_adp:  14.789 0.9082  0.9883     6774.585
   2_occ:  14.768 0.9083  0.9882     6756.114
   3_bss:  14.652 0.9093  0.9848     6679.594
   3_xyz:  13.792 0.9164  0.9879     6142.783
   3_adp:  13.674 0.9177  0.9844     6096.266
   3_occ:  13.668 0.9177  0.9844     6094.331
   4_bss:  13.660 0.9178  0.9856     6093.802
   4_xyz:  13.495 0.9189  0.9849     5943.160
   4_adp:  13.410 0.9197  0.9817     5919.751
   4_occ:  13.406 0.9198  0.9816     5918.282
   5_bss:  13.407 0.9198  0.9856     5920.293
   5_xyz:  13.385 0.9200  0.9862     5950.643
   5_adp:  13.424 0.9197  0.9820     5973.297
   5_occ:  13.424 0.9197  0.9819     5973.948
   5_bss:  13.426 0.9197  0.9853     5975.150
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7015e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7015e-01
   1_xyz:   1.132  0.009  0.068 15.194  0.005  4.108   7.3219e-02
   1_adp:   1.132  0.009  0.068 15.194  0.005  4.108   7.3219e-02
   1_occ:   1.132  0.009  0.068 15.194  0.005  4.108   7.3219e-02
   2_bss:   1.132  0.009  0.068 15.194  0.005  4.108   7.3219e-02
   2_xyz:   1.009  0.006  0.069 14.623  0.004  4.112   5.8905e-02
   2_adp:   1.009  0.006  0.069 14.623  0.004  4.112   5.8905e-02
   2_occ:   1.009  0.006  0.069 14.623  0.004  4.112   5.8905e-02
   3_bss:   1.009  0.006  0.069 14.623  0.004  4.112   5.8905e-02
   3_xyz:   0.873  0.005  0.065 14.488  0.004  4.112   4.8298e-02
   3_adp:   0.873  0.005  0.065 14.488  0.004  4.112   4.8298e-02
   3_occ:   0.873  0.005  0.065 14.488  0.004  4.112   4.8298e-02
   4_bss:   0.873  0.005  0.065 14.488  0.004  4.112   4.8298e-02
   4_xyz:   0.901  0.005  0.067 14.414  0.003  4.111   4.9064e-02
   4_adp:   0.901  0.005  0.067 14.414  0.003  4.111   4.9064e-02
   4_occ:   0.901  0.005  0.067 14.414  0.003  4.111   4.9064e-02
   5_bss:   0.901  0.005  0.067 14.414  0.003  4.111   4.9064e-02
   5_xyz:   0.967  0.006  0.072 14.624  0.004  4.111   5.5945e-02
   5_adp:   0.967  0.006  0.072 14.624  0.004  4.111   5.5945e-02
   5_occ:   0.967  0.006  0.072 14.624  0.004  4.111   5.5945e-02
   5_bss:   0.967  0.006  0.072 14.624  0.004  4.111   5.5945e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.773   2.3888e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.773   2.3888e-01
   1_xyz:   8.787  0.043  0.291 85.996  0.031  2.301   7.5802e-02
   1_adp:   8.787  0.043  0.291 85.996  0.031  2.301   7.5802e-02
   1_occ:   8.787  0.043  0.291 85.996  0.031  2.301   7.5802e-02
   2_bss:   8.787  0.043  0.291 85.996  0.031  2.301   7.5802e-02
   2_xyz:   6.253  0.038  0.264 83.353  0.038  2.313   6.4584e-02
   2_adp:   6.253  0.038  0.264 83.353  0.038  2.313   6.4584e-02
   2_occ:   6.253  0.038  0.264 83.353  0.038  2.313   6.4584e-02
   3_bss:   6.253  0.038  0.264 83.353  0.038  2.313   6.4584e-02
   3_xyz:   5.821  0.037  0.214 82.907  0.036  2.362   3.1059e-02
   3_adp:   5.821  0.037  0.214 82.907  0.036  2.362   3.1059e-02
   3_occ:   5.821  0.037  0.214 82.907  0.036  2.362   3.1059e-02
   4_bss:   5.821  0.037  0.214 82.907  0.036  2.362   3.1059e-02
   4_xyz:   6.040  0.036  0.206 82.994  0.031  2.362   2.8673e-02
   4_adp:   6.040  0.036  0.206 82.994  0.031  2.362   2.8673e-02
   4_occ:   6.040  0.036  0.206 82.994  0.031  2.362   2.8673e-02
   5_bss:   6.040  0.036  0.206 82.994  0.031  2.362   2.8673e-02
   5_xyz:   6.620  0.039  0.241 83.085  0.037  2.305   4.1449e-02
   5_adp:   6.620  0.039  0.241 83.085  0.037  2.305   4.1449e-02
   5_occ:   6.620  0.039  0.241 83.085  0.037  2.305   4.1449e-02
   5_bss:   6.620  0.039  0.241 83.085  0.037  2.305   4.1449e-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:  74.68   0.00  16.76  74.68   0.00  12.91  62.74   6.81  37.72
   1_occ:  74.68   0.00  16.76  74.68   0.00  12.91  62.74   6.81  37.72
   2_bss:  74.68   0.00  16.76  74.68   0.00  12.91  62.74   6.81  37.72
   2_xyz:  74.68   0.00  16.76  74.68   0.00  12.91  62.74   6.81  37.72
   2_adp:  73.91   0.00  17.05  73.91   0.00  13.02  69.67   4.50  39.03
   2_occ:  73.91   0.00  17.05  73.91   0.00  13.02  69.67   4.50  39.03
   3_bss:  73.91   0.00  17.05  73.91   0.00  13.02  69.67   4.50  39.03
   3_xyz:  73.91   0.00  17.05  73.91   0.00  13.02  69.67   4.50  39.03
   3_adp:  85.70   0.74  17.14  85.70   0.74  13.00  74.08   3.46  39.63
   3_occ:  85.70   0.74  17.14  85.70   0.74  13.00  74.08   3.46  39.63
   4_bss:  85.70   0.74  17.14  85.70   0.74  13.00  74.08   3.46  39.63
   4_xyz:  85.70   0.74  17.14  85.70   0.74  13.00  74.08   3.46  39.63
   4_adp:  85.31   1.63  16.71  85.31   1.63  12.81  74.17   4.78  37.93
   4_occ:  85.31   1.63  16.71  85.31   1.63  12.81  74.17   4.78  37.93
   5_bss:  85.31   1.63  16.71  85.31   1.63  12.81  74.17   4.78  37.93
   5_xyz:  85.31   1.63  16.71  85.31   1.63  12.81  74.17   4.78  37.93
   5_adp:  85.58   1.41  16.62  85.58   1.41  12.71  74.10   5.88  37.92
   5_occ:  85.58   1.41  16.62  85.58   1.41  12.71  74.10   5.88  37.92
   5_bss:  85.53   1.36  16.57  85.53   1.36  12.66  74.05   5.83  37.87
------------------------------------------------------------------------
 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:    1.586    0.006    0.293
   1_adp:    1.586    0.006    0.293
   1_occ:    1.586    0.006    0.293
   2_bss:    1.586    0.006    0.293
   2_xyz:    1.033    0.016    0.372
   2_adp:    1.033    0.016    0.372
   2_occ:    1.033    0.016    0.372
   3_bss:    1.033    0.016    0.372
   3_xyz:    1.231    0.015    0.388
   3_adp:    1.231    0.015    0.388
   3_occ:    1.231    0.015    0.388
   4_bss:    1.231    0.015    0.388
   4_xyz:    1.254    0.027    0.405
   4_adp:    1.254    0.027    0.405
   4_occ:    1.254    0.027    0.405
   5_bss:    1.254    0.027    0.405
   5_xyz:    1.210    0.020    0.411
   5_adp:    1.210    0.020    0.411
   5_occ:    1.210    0.020    0.411
   5_bss:    1.210    0.020    0.411
------------------------------------------------------------------------

CPU time actual refinement: 320.26


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_540/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_540/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_540/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_540/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_540/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.10 
  Macro-tasks:
    bulk solvent and scale       = 37.16  
    individual site refinement   = 131.75 
    weights calculation          = 29.05  
    collect and process          = 6.41   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 204.45 
  Micro-tasks:
    mask                            = 1.22   
    f_calc                          = 102.51 
    alpha_beta                      = 7.81   
    target                          = 1.10   
    gradients_wrt_atomic_parameters = 110.73 
    fmodel                         = 6.63   
    r_factors                      = 0.20   
    phase_errors                   = 10.72  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 241.11 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.569 micro seconds
Total CPU time: 5.57 minutes
from_scatterers_fft:    641 calls, 102.14 s
gradients_fft:          586 calls,  97.54 s

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

# Date 2008-01-16 Time 05:04:11 PST -0800 (1200488651.84 s)
Start R-work = 0.3290, R-free = 0.3289 (no bulk solvent and anisotropic scale)
Final R-work = 0.1319, R-free = 0.1741 (no bulk solvent and anisotropic scale)

Start R-work = 0.3110, R-free = 0.3094
Final R-work = 0.1066, R-free = 0.1531