# Date 2008-01-16 Time 03:52:58 PST -0800 (1200484378.20 s)
#phil __OFF__

Command line arguments: "../89.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19565
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 89

-------------------------------------------------------------------------------
  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: (68.4938, 47.6339, 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: 2.77, per 1000 atoms: 0.98


================================== 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: (68.4938, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.95064
Completeness in resolution range: 0.944048
Completeness with d_max=infinity: 0.941191

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8666
                             d_min =   1.9506

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: (68.4938, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.95064
Completeness in resolution range: 0.944048
Completeness with d_max=infinity: 0.941191

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8670 -  4.1744 [2180/2209]  1960   220  10.1%
  bin  2:  4.1744 -  3.3256 [2091/2114]  1883   208   9.9%
  bin  3:  3.3256 -  2.9088 [2067/2092]  1859   208  10.1%
  bin  4:  2.9088 -  2.6444 [2024/2042]  1828   196   9.7%
  bin  5:  2.6444 -  2.4558 [2037/2079]  1824   213  10.5%
  bin  6:  2.4558 -  2.3116 [2026/2054]  1834   192   9.5%
  bin  7:  2.3116 -  2.1962 [2003/2039]  1798   205  10.2%
  bin  8:  2.1962 -  2.1009 [1998/2040]  1806   192   9.6%
  bin  9:  2.1009 -  2.0202 [1984/2042]  1780   204  10.3%
  bin 10:  2.0202 -  1.9506 [1179/2039]  1058   121  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_89/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: 0.12 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:
        1.06 -     1.83: 15
        1.83 -     2.59: 107
        2.59 -     3.36: 4206
        3.36 -     4.13: 9539
        4.13 -     4.90: 14983
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.056 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.322 3.040 -x+1,y+1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.367 3.270 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.393 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.431 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28845 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_89/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_89/model_refine_001.geo

CPU time processing inputs: 8.03


============================ 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 = 68.49375 47.63395 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4760   r_free= 0.4783   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.278829                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6562 0.99   1414  159 0.3814 0.3894      6.5671      6.6217|
|  2:  4.6562 -  3.7147 0.99   1360  151 0.4110 0.3987      6.7937      6.7833|
|  3:  3.7147 -  3.2508 0.99   1336  147 0.4328 0.4352      6.6568      6.7575|
|  4:  3.2508 -  2.9561 0.99   1323  139 0.4593 0.4581      6.5077       6.488|
|  5:  2.9561 -  2.7456 0.99   1316  152 0.4866 0.4600      6.3592      6.3532|
|  6:  2.7456 -  2.5846 0.99   1308  147 0.5006 0.5168      6.2677      6.1708|
|  7:  2.5846 -  2.4558 0.98   1297  150 0.5186 0.4884      6.2594      6.1929|
|  8:  2.4558 -  2.3493 0.98   1320  135 0.5282 0.5397        6.18      6.2207|
|  9:  2.3493 -  2.2592 0.99   1290  145 0.5472 0.5529      6.1303      6.1553|
| 10:  2.2592 -  2.1815 0.98   1297  144 0.5290 0.5736      6.1149      6.1381|
| 11:  2.1815 -  2.1135 0.97   1270  145 0.5434 0.5796      6.0298      6.0409|
| 12:  2.1135 -  2.0532 0.98   1283  148 0.5323 0.5330      5.9653      6.0059|
| 13:  2.0532 -  1.9993 0.92   1221  128 0.5303 0.5512       5.896      5.8783|
| 14:  1.9993 -  1.9506 0.46    595   69 0.5484 0.5045      5.8399      5.6973|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8670 -  4.6562  1414   159  0.66  37.27   0.83     0.69      78575.15|
|  2:  4.6562 -  3.7147  1360   151  0.67  37.44   0.91     0.78     113715.05|
|  3:  3.7147 -  3.2508  1336   147  0.58  45.22   0.93     0.78     119517.66|
|  4:  3.2508 -  2.9561  1323   139  0.51  51.48   0.93     0.72     102685.63|
|  5:  2.9561 -  2.7456  1316   152  0.44  56.41   0.89     0.65      81650.34|
|  6:  2.7456 -  2.5846  1308   147  0.40  60.01   0.90     0.57      70026.95|
|  7:  2.5846 -  2.4558  1297   150  0.36  63.05   0.89     0.50      67129.19|
|  8:  2.4558 -  2.3493  1320   135  0.30  67.75   0.91     0.44      63345.98|
|  9:  2.3493 -  2.2592  1290   145  0.24  71.81   0.90     0.38      61840.83|
| 10:  2.2592 -  2.1815  1297   144  0.22  73.93   0.95     0.32      56811.34|
| 11:  2.1815 -  2.1135  1270   145  0.17  77.38   0.92     0.27      55230.29|
| 12:  2.1135 -  2.0532  1283   148  0.16  78.47   0.95     0.26      51029.87|
| 13:  2.0532 -  1.9993  1221   128  0.15  78.79   0.95     0.25      44038.99|
| 14:  1.9993 -  1.9506   595    69  0.17  77.21   0.90     0.24      33970.85|
|alpha:            min =        0.24 max =            0.78 mean =         0.50|
|beta:             min =    33970.85 max =       119517.66 mean =     73401.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.58|
|phase err.(test): min =        0.00 max =           90.00 mean =        61.78|
|-----------------------------------------------------------------------------|

============================== 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 = 20.827109             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.246   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.357775              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.210   (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 |  1.056 -  1.441:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.441 -  1.825:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.825 -  2.209:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.209 -  2.594:       68 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.594 -  2.978:     1810 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.978 -  3.362:     2396 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.362 -  3.747:     3959 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.747 -  4.131:     5580 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.131 -  4.516:     6640 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.516 -  4.900:     8343 |
|-----------------------------------------------------------------------------|
|-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 |        0.248 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.056 |       1.481 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4760   r_free= 0.4783   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.278829                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4696   r_free= 0.4698   ksol= 0.30   Bsol= 20.00   scale= 0.936   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,1.20,0.95,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.273793                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.418409             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.947   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.541409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.824   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4696      final r-factor (work) = 0.3228          |
| start r-factor (free) = 0.4698      final r-factor (free) = 0.3479          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.8914 = 17.42 * 0.50 * 6.2743 + 1.00 * 0.2476                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.7346 = 17.42 * 0.50 * 6.1509 + 1.00 * 0.1655                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3228      final r-factor (work) = 0.2906          |
| start r-factor (free) = 0.3479      final r-factor (free) = 0.3554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4879 = 1.54 * 1.00 * 6.1509 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2345 = 1.54 * 1.00 * 5.9482 + 1.00 * 0.0659                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.58  19.27    None  None   None       |
|    all(noH): 2823   0      0.00    119.58  19.27    None  None   None       |
|    Sol.    : 438    0      2.04    77.23   41.13    None  None   None       |
|    Mac.    : 2385   0      0.00    119.58  15.26    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 -  11.958: 1154   |   5:    59.789 -  71.747:   48        |
|      1:    11.958 -  23.916:  843   |   6:    71.747 -  83.704:    4        |
|      2:    23.916 -  35.873:  402   |   7:    83.704 -  95.662:    0        |
|      3:    35.873 -  47.831:  228   |   8:    95.662 - 107.620:    0        |
|      4:    47.831 -  59.789:  143   |   9:   107.620 - 119.578:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2906 r_free = 0.3554             target_work(ml) = 5.957         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2905 r_free = 0.3560             target_work(ml) = 5.957         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2905   r_free= 0.3560   ksol= 0.30   Bsol= 20.00   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,1.20,0.95,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.956534                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2871   r_free= 0.3517   ksol= 0.33   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-0.15,-0.60,-0.00,-0.00,-0.00); trace/3= -0.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.950844                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.255081              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.481   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.882906              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.150   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2871      final r-factor (work) = 0.2077          |
| start r-factor (free) = 0.3517      final r-factor (free) = 0.2604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7135 = 8.26 * 0.50 * 5.9474 + 1.00 * 0.1655                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1606 = 8.26 * 0.50 * 5.8331 + 1.00 * 0.0841                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2077      final r-factor (work) = 0.1823          |
| start r-factor (free) = 0.2604      final r-factor (free) = 0.2375          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1870 = 0.88 * 1.00 * 5.8331 + 1.00 * 0.0369                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9690 = 0.88 * 1.00 * 5.6136 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.55   18.63    None  None   None       |
|    all(noH): 2823   0      0.00    96.55   18.63    None  None   None       |
|    Sol.    : 438    0      4.92    96.55   43.33    None  None   None       |
|    Mac.    : 2385   0      0.00    81.99   14.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.655:  949   |   5:    48.273 -  57.928:  103        |
|      1:     9.655 -  19.309: 1042   |   6:    57.928 -  67.582:   83        |
|      2:    19.309 -  28.964:  304   |   7:    67.582 -  77.237:   27        |
|      3:    28.964 -  38.619:  151   |   8:    77.237 -  86.892:    8        |
|      4:    38.619 -  48.273:  155   |   9:    86.892 -  96.546:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1823 r_free = 0.2375             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1820 r_free = 0.2378             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1820   r_free= 0.2378   ksol= 0.33   Bsol= 50.00   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-0.15,-0.60,-0.00,-0.00,-0.00); trace/3= -0.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.563876                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1821   r_free= 0.2359   ksol= 0.32   Bsol= 41.08   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-0.84,-1.23,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.560889                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.365546              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.639  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.997266              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.855  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1821      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.2359      final r-factor (free) = 0.1966          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5333 = 3.37 * 0.50 * 5.6153 + 1.00 * 0.0841                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2727 = 3.37 * 0.50 * 5.4724 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1455      final r-factor (work) = 0.1350          |
| start r-factor (free) = 0.1966      final r-factor (free) = 0.1890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.8876 = 4.00 * 1.00 * 5.4724 + 1.00 * 0.0128                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.3756 = 4.00 * 1.00 * 5.3442 + 1.00 * 0.0133                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.98  18.79    None  None   None       |
|    all(noH): 2823   0      0.00    121.98  18.79    None  None   None       |
|    Sol.    : 438    0      5.69    121.98  46.75    None  None   None       |
|    Mac.    : 2385   0      0.00    106.64  13.65    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 -  12.198: 1452   |   5:    60.989 -  73.187:   77        |
|      1:    12.198 -  24.396:  804   |   6:    73.187 -  85.385:   48        |
|      2:    24.396 -  36.594:  184   |   7:    85.385 -  97.583:   13        |
|      3:    36.594 -  48.791:  124   |   8:    97.583 - 109.781:    4        |
|      4:    48.791 -  60.989:  115   |   9:   109.781 - 121.978:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1350 r_free = 0.1890             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1349 r_free = 0.1891             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1349   r_free= 0.1891   ksol= 0.32   Bsol= 41.08   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-0.84,-1.23,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.318969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1888   ksol= 0.32   Bsol= 41.08   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.29,-1.57,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.319644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.944192              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.972  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181510              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.481  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1356      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1888      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6090 = 3.94 * 0.50 * 5.3472 + 1.00 * 0.0639                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4696 = 3.94 * 0.50 * 5.2719 + 1.00 * 0.0729                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1749      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9701 = 0.18 * 1.00 * 5.2719 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9563 = 0.18 * 1.00 * 5.2211 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.12    100.98  17.38    None  None   None       |
|    all(noH): 2823   0      2.12    100.98  17.38    None  None   None       |
|    Sol.    : 438    0      3.79    98.08   41.19    None  None   None       |
|    Mac.    : 2385   0      2.12    100.98  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:     2.119 -  12.005: 1466   |   5:    51.548 -  61.434:   76        |
|      1:    12.005 -  21.891:  795   |   6:    61.434 -  71.319:   40        |
|      2:    21.891 -  31.776:  172   |   7:    71.319 -  81.205:   20        |
|      3:    31.776 -  41.662:  129   |   8:    81.205 -  91.091:    9        |
|      4:    41.662 -  51.548:  112   |   9:    91.091 - 100.977:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1670             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1670             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1670   ksol= 0.32   Bsol= 41.08   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.29,-1.57,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.194440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1671   ksol= 0.32   Bsol= 41.08   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.41,-1.56,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.194755                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.335483              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.728  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289796              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.553  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1692 = 2.34 * 0.50 * 5.2206 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1186 = 2.34 * 0.50 * 5.1863 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5116 = 0.29 * 1.00 * 5.1863 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5067 = 0.29 * 1.00 * 5.1697 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.12    100.98  17.10    None  None   None       |
|    all(noH): 2823   0      2.12    100.98  17.10    None  None   None       |
|    Sol.    : 438    0      5.35    90.90   40.45    None  None   None       |
|    Mac.    : 2385   0      2.12    100.98  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:     2.125 -  12.010: 1507   |   5:    51.552 -  61.438:   78        |
|      1:    12.010 -  21.896:  763   |   6:    61.438 -  71.323:   28        |
|      2:    21.896 -  31.781:  164   |   7:    71.323 -  81.209:   18        |
|      3:    31.781 -  41.667:  130   |   8:    81.209 -  91.094:    8        |
|      4:    41.667 -  51.552:  124   |   9:    91.094 - 100.980:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1639             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1640             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1640   ksol= 0.32   Bsol= 41.08   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.41,-1.56,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170419                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6562 0.99   1414  159 0.0993 0.1341      5.3913      5.5731|
|  2:  4.6562 -  3.7147 0.99   1360  151 0.0840 0.1093      5.4305       5.636|
|  3:  3.7147 -  3.2508 0.99   1336  147 0.1047 0.1560      5.4607      5.8373|
|  4:  3.2508 -  2.9561 0.99   1323  139 0.1274 0.1597       5.479      5.6538|
|  5:  2.9561 -  2.7456 0.99   1316  152 0.1337 0.1744      5.3436      5.5321|
|  6:  2.7456 -  2.5846 0.99   1308  147 0.1349 0.2107      5.2658      5.4963|
|  7:  2.5846 -  2.4558 0.98   1297  150 0.1204 0.1612      5.1622      5.3641|
|  8:  2.4558 -  2.3493 0.98   1320  135 0.1218 0.1709      5.1153      5.3538|
|  9:  2.3493 -  2.2592 0.99   1290  145 0.1209 0.1998      5.0593      5.3597|
| 10:  2.2592 -  2.1815 0.98   1297  144 0.1167 0.1824      5.0118       5.242|
| 11:  2.1815 -  2.1135 0.97   1270  145 0.1158 0.1826       4.949       5.243|
| 12:  2.1135 -  2.0532 0.98   1283  148 0.1136 0.1756       4.872       5.145|
| 13:  2.0532 -  1.9993 0.92   1221  128 0.1130 0.1795      4.8037      5.0855|
| 14:  1.9993 -  1.9506 0.46    595   69 0.1099 0.1841      4.7156      4.9575|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8670 -  4.6562  1414   159  0.94   9.28   0.98     0.96       7390.49|
|  2:  4.6562 -  3.7147  1360   151  0.95   8.00   1.03     1.02       9133.40|
|  3:  3.7147 -  3.2508  1336   147  0.93  11.35   1.03     1.02      10215.25|
|  4:  3.2508 -  2.9561  1323   139  0.92  14.13   1.02     1.01      10767.98|
|  5:  2.9561 -  2.7456  1316   152  0.89  16.59   1.00     0.97       8710.19|
|  6:  2.7456 -  2.5846  1308   147  0.89  17.01   0.98     0.94       7643.58|
|  7:  2.5846 -  2.4558  1297   150  0.90  15.93   0.99     0.95       6340.58|
|  8:  2.4558 -  2.3493  1320   135  0.90  16.04   1.01     0.99       5985.52|
|  9:  2.3493 -  2.2592  1290   145  0.89  16.85   1.00     0.96       5400.38|
| 10:  2.2592 -  2.1815  1297   144  0.90  16.45   1.01     0.97       4983.62|
| 11:  2.1815 -  2.1135  1270   145  0.90  16.61   1.01     0.98       4601.73|
| 12:  2.1135 -  2.0532  1283   148  0.91  15.67   1.01     0.99       3905.36|
| 13:  2.0532 -  1.9993  1221   128  0.90  16.52   1.01     1.00       3501.98|
| 14:  1.9993 -  1.9506   595    69  0.90  15.91   0.99     0.95       2868.82|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2868.82 max =        10767.98 mean =      6728.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.61|
|phase err.(test): min =        0.00 max =           89.98 mean =        14.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1641   ksol= 0.32   Bsol= 42.21   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.32,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171025                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1641   ksol= 0.32   Bsol= 42.21   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.32,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6562 0.99   1414  159 0.0988 0.1339      5.3895      5.5646|
|  2:  4.6562 -  3.7147 0.99   1360  151 0.0860 0.1110      5.4415      5.6532|
|  3:  3.7147 -  3.2508 0.99   1336  147 0.1047 0.1554      5.4648       5.831|
|  4:  3.2508 -  2.9561 0.99   1323  139 0.1272 0.1591      5.4789      5.6485|
|  5:  2.9561 -  2.7456 0.99   1316  152 0.1340 0.1745      5.3437      5.5308|
|  6:  2.7456 -  2.5846 0.99   1308  147 0.1343 0.2101      5.2643      5.4938|
|  7:  2.5846 -  2.4558 0.98   1297  150 0.1203 0.1618      5.1609      5.3648|
|  8:  2.4558 -  2.3493 0.98   1320  135 0.1214 0.1705      5.1146      5.3541|
|  9:  2.3493 -  2.2592 0.99   1290  145 0.1206 0.1996      5.0576      5.3582|
| 10:  2.2592 -  2.1815 0.98   1297  144 0.1164 0.1827      5.0117      5.2423|
| 11:  2.1815 -  2.1135 0.97   1270  145 0.1156 0.1823      4.9478      5.2426|
| 12:  2.1135 -  2.0532 0.98   1283  148 0.1134 0.1759       4.872      5.1469|
| 13:  2.0532 -  1.9993 0.92   1221  128 0.1128 0.1800      4.8041      5.0871|
| 14:  1.9993 -  1.9506 0.46    595   69 0.1100 0.1845      4.7167      4.9578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8670 -  4.6562  1414   159  0.94   9.23   0.98     0.96       7331.31|
|  2:  4.6562 -  3.7147  1360   151  0.95   8.10   1.03     1.02       9229.98|
|  3:  3.7147 -  3.2508  1336   147  0.93  11.39   1.04     1.03      10326.13|
|  4:  3.2508 -  2.9561  1323   139  0.92  14.08   1.02     1.01      10709.93|
|  5:  2.9561 -  2.7456  1316   152  0.89  16.52   1.01     0.97       8660.47|
|  6:  2.7456 -  2.5846  1308   147  0.89  17.03   0.98     0.94       7646.13|
|  7:  2.5846 -  2.4558  1297   150  0.90  15.90   0.99     0.95       6317.50|
|  8:  2.4558 -  2.3493  1320   135  0.90  16.04   1.01     0.99       5989.75|
|  9:  2.3493 -  2.2592  1290   145  0.89  16.84   1.01     0.96       5394.50|
| 10:  2.2592 -  2.1815  1297   144  0.90  16.47   1.01     0.97       4988.60|
| 11:  2.1815 -  2.1135  1270   145  0.90  16.60   1.01     0.98       4592.36|
| 12:  2.1135 -  2.0532  1283   148  0.91  15.68   1.01     0.99       3909.55|
| 13:  2.0532 -  1.9993  1221   128  0.90  16.53   1.01     1.00       3509.58|
| 14:  1.9993 -  1.9506   595    69  0.90  15.93   0.99     0.95       2874.98|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2874.98 max =        10709.93 mean =      6730.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.62|
|phase err.(test): min =        0.00 max =           89.85 mean =        14.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.05    100.90  17.02    None  None   None       |
|    all(noH): 2823   0      2.05    100.90  17.02    None  None   None       |
|    Sol.    : 438    0      5.27    90.82   40.38    None  None   None       |
|    Mac.    : 2385   0      2.05    100.90  12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.048 -  11.934: 1507   |   5:    51.475 -  61.361:   78        |
|      1:    11.934 -  21.819:  763   |   6:    61.361 -  71.246:   28        |
|      2:    21.819 -  31.704:  164   |   7:    71.246 -  81.132:   18        |
|      3:    31.704 -  41.590:  130   |   8:    81.132 -  91.017:    8        |
|      4:    41.590 -  51.475:  124   |   9:    91.017 - 100.903:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.523 - 4.469
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 302
   mapped sites are within: 0.707 - 4.469

peak=    8.993 closest distance to " CB  SER A 216 " =    1.220
peak=    8.358 closest distance to " O   HOH Z  92 " =    2.240
peak=    7.481 closest distance to " O   HOH Z 178 " =    1.245
peak=    6.411 closest distance to " O   HOH Z 401 " =    1.616
peak=    6.133 closest distance to " O   HOH Z  52 " =    1.496
peak=    5.795 closest distance to " O   HOH Z 124 " =    1.617
peak=    5.563 closest distance to " CB  ARG A 275 " =    0.939
peak=    5.427 closest distance to " NH2 ARG A  56 " =    2.291
peak=    5.218 closest distance to " O   HOH Z 193 " =    1.844
peak=    5.038 closest distance to " O   HOH Z  97 " =    1.768
peak=    4.964 closest distance to " CG  PRO A 213 " =    1.302
peak=    4.909 closest distance to " O   HOH Z 403 " =    1.975
peak=    4.894 closest distance to " O   HOH Z 406 " =    1.454
peak=    4.881 closest distance to " O   HOH Z 272 " =    1.857
peak=    4.865 closest distance to " CB  ASN A 187 " =    1.828
peak=    4.861 closest distance to " O   HOH Z 142 " =    1.662
peak=    4.849 closest distance to " O   HOH Z  80 " =    1.766
peak=    4.822 closest distance to " O   HOH Z 132 " =    1.666
peak=    4.795 closest distance to " O   HOH Z 234 " =    3.556
peak=    4.738 closest distance to " CB  SER A  63 " =    1.105
peak=    4.705 closest distance to " CB  GLN A 223 " =    1.443
peak=    4.611 closest distance to " O   SER A  87 " =    2.196
peak=    4.567 closest distance to " CB  GLN A 183 " =    1.299
peak=    4.556 closest distance to " O   HOH Z  63 " =    1.855
peak=    4.528 closest distance to " O   HOH Z 232 " =    2.324
peak=    4.512 closest distance to " O   HOH Z 278 " =    1.136
peak=    4.502 closest distance to " CD  ARG A 269 " =    1.128
peak=    4.478 closest distance to " O   HOH Z 389 " =    1.882
peak=    4.452 closest distance to " O   HOH Z 402 " =    1.469
peak=    4.432 closest distance to " O   HOH Z  85 " =    1.674
peak=    4.428 closest distance to " O   HOH Z 298 " =    1.848
peak=    4.420 closest distance to " C   PRO A 198 " =    1.578
peak=    4.418 closest distance to " O   HOH Z 209 " =    2.351
peak=    4.393 closest distance to " O   HOH Z 261 " =    1.649
peak=    4.391 closest distance to " NZ  LYS A 117 " =    2.996
peak=    4.387 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.315 closest distance to " O   HOH Z 163 " =    1.995
peak=    4.306 closest distance to " CG  ARG A  66 " =    2.896
peak=    4.256 closest distance to " O   HOH Z 154 " =    1.605
peak=    4.244 closest distance to " O   HOH Z  15 " =    2.170
peak=    4.219 closest distance to " NE2 GLN A  11 " =    1.050
peak=    4.211 closest distance to " OE1 GLU A   2 " =    2.288
peak=    4.177 closest distance to " O   HOH Z 134 " =    1.737
peak=    4.175 closest distance to " CB  ARG A  79 " =    1.413
peak=    4.155 closest distance to " CB  GLU A 152 " =    1.183
peak=    4.154 closest distance to " NH2BARG A 145 " =    2.170
peak=    4.145 closest distance to " O   HOH Z 416 " =    1.158
peak=    4.136 closest distance to " O   HOH Z 411 " =    3.704
peak=    4.130 closest distance to " N   ASN A  39 " =    1.219
peak=    4.130 closest distance to " O   HOH Z 189 " =    1.650
peak=    4.106 closest distance to " O   HOH Z 132 " =    1.966
peak=    4.099 closest distance to " O   HOH Z  49 " =    2.151
peak=    4.098 closest distance to " O   HOH Z  43 " =    2.242
peak=    4.090 closest distance to " CB  GLU A 277 " =    3.503
peak=    4.089 closest distance to " CG  PRO A 243 " =    1.199
peak=    4.076 closest distance to " CG  ARG A  66 " =    1.120
peak=    4.061 closest distance to " O   HOH Z 426 " =    1.443
peak=    4.050 closest distance to " O   HOH Z 326 " =    1.606
peak=    4.049 closest distance to " O   HOH Z 154 " =    2.164
peak=    4.040 closest distance to " O   HOH Z  54 " =    1.689
peak=    4.035 closest distance to " ND2 ASN A 187 " =    1.530
peak=    4.032 closest distance to " O   HOH Z 303 " =    1.970
peak=    4.021 closest distance to " O   HOH Z  40 " =    1.773
peak=    4.017 closest distance to " O   HOH Z 245 " =    1.413
peak=    4.008 closest distance to " O   HOH Z  47 " =    1.605
peak=    4.001 closest distance to " CG AARG A 275 " =    1.027
peak=    4.000 closest distance to " CG  PRO A 198 " =    1.285
peak=    3.992 closest distance to " CG1 ILE A  33 " =    1.255
peak=    3.986 closest distance to " O   HOH Z 247 " =    1.285
peak=    3.965 closest distance to " O   HOH Z 334 " =    1.426
peak=    3.958 closest distance to " CB  GLU A 128 " =    1.210
peak=    3.957 closest distance to " CG2BVAL A  41 " =    0.855
peak=    3.952 closest distance to " O   HOH Z 163 " =    1.429
peak=    3.947 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.943 closest distance to " O   HOH Z 345 " =    1.924
peak=    3.936 closest distance to " CB  SER A   3 " =    1.207
peak=    3.912 closest distance to " O   HOH Z 404 " =    1.236
peak=    3.906 closest distance to " CG  PRO A  90 " =    1.228
peak=    3.893 closest distance to " CA  ASN A 176 " =    1.081
peak=    3.892 closest distance to " CB  ASN A 148 " =    1.464
peak=    3.881 closest distance to " O   HOH Z 345 " =    2.349
peak=    3.876 closest distance to " CE  LYS A 119 " =    1.152
peak=    3.862 closest distance to " O   HOH Z 369 " =    2.456
peak=    3.860 closest distance to " O   HOH Z 315 " =    1.881
peak=    3.857 closest distance to " O   HOH Z  43 " =    1.356
peak=    3.855 closest distance to " O   HOH Z 423 " =    1.977
peak=    3.845 closest distance to " O  BHOH Z  74 " =    1.360
peak=    3.823 closest distance to " O   HOH Z 427 " =    2.629
peak=    3.815 closest distance to " CB  ASN A 148 " =    1.762
peak=    3.801 closest distance to " O   HOH Z 327 " =    1.869
peak=    3.796 closest distance to " CB  ARG A 139 " =    0.851
peak=    3.786 closest distance to " O   HOH Z  44 " =    1.982
peak=    3.776 closest distance to " O   HOH Z 368 " =    2.027
peak=    3.775 closest distance to " O   ALA A 165 " =    1.374
peak=    3.773 closest distance to " CB  SER A 141 " =    1.017
peak=    3.771 closest distance to " O   HOH Z 394 " =    1.561
peak=    3.765 closest distance to " NZ  LYS A 119 " =    1.696
peak=    3.759 closest distance to " CG2 ILE A 120 " =    1.316
peak=    3.758 closest distance to " O   HOH Z 346 " =    1.535
peak=    3.756 closest distance to " O   HOH Z 316 " =    2.912
peak=    3.755 closest distance to " O   HOH Z 227 " =    1.713
peak=    3.755 closest distance to " O   HOH Z 203 " =    1.904
peak=    3.750 closest distance to " O   HOH Z 287 " =    1.963
peak=    3.743 closest distance to " O   HOH Z 408 " =    1.761
peak=    3.725 closest distance to " O   HOH Z 173 " =    2.141
peak=    3.717 closest distance to " O   HOH Z 427 " =    3.032
peak=    3.715 closest distance to " O   HOH Z 421 " =    1.772
peak=    3.709 closest distance to " O   HOH Z 313 " =    1.791
peak=    3.702 closest distance to " CB  TRP A 179 " =    1.085
peak=    3.695 closest distance to " O   HOH Z  54 " =    2.199
peak=    3.691 closest distance to " CA  ARG A  36 " =    1.048
peak=    3.690 closest distance to " O   HOH Z 118 " =    1.162
peak=    3.690 closest distance to " O   HOH Z 155 " =    2.841
peak=    3.686 closest distance to " O   HOH Z 155 " =    1.633
peak=    3.680 closest distance to " CB  TYR A 169 " =    0.707
peak=    3.679 closest distance to " O   HOH Z 132 " =    2.576
peak=    3.678 closest distance to " O   HOH Z  39 " =    1.211
peak=    3.672 closest distance to " CA  ARG A  66 " =    1.217
peak=    3.664 closest distance to " O   HOH Z  68 " =    1.765
peak=    3.659 closest distance to " CA  ALA A  21 " =    1.155
peak=    3.650 closest distance to " CB  ALA A 248 " =    1.339
peak=    3.644 closest distance to " CD  GLN A 194 " =    1.567
peak=    3.637 closest distance to " O   HOH Z 128 " =    1.963
peak=    3.631 closest distance to " O   HOH Z  78 " =    1.741
peak=    3.628 closest distance to " O   HOH Z   9 " =    2.103
peak=    3.624 closest distance to " O   HOH Z 279 " =    2.111
peak=    3.624 closest distance to " O   HOH Z 197 " =    2.441
peak=    3.618 closest distance to " OG  SER A  62 " =    2.842
peak=    3.618 closest distance to " O   HOH Z 414 " =    1.540
peak=    3.618 closest distance to " CD2 TRP A 179 " =    1.441
peak=    3.606 closest distance to " O   HOH Z 365 " =    2.638
peak=    3.603 closest distance to " O   HOH Z  35 " =    2.265
peak=    3.599 closest distance to " O   HOH Z 336 " =    1.713
peak=    3.598 closest distance to " OD2 ASP A 286 " =    2.727
peak=    3.589 closest distance to " O   HOH Z 273 " =    2.715
peak=    3.584 closest distance to " CB  ARG A 190 " =    1.806
peak=    3.576 closest distance to " O   HOH Z 284 " =    2.758
peak=    3.572 closest distance to " O   HOH Z 274 " =    1.659
peak=    3.572 closest distance to " O   HOH Z 114 " =    1.208
peak=    3.570 closest distance to " O   HOH Z 291 " =    1.675
peak=    3.554 closest distance to " O   HOH Z 425 " =    1.377
peak=    3.546 closest distance to " CB  ALA A   1 " =    1.268
peak=    3.541 closest distance to " O   HOH Z 173 " =    1.716
peak=    3.541 closest distance to " CB  THR A  31 " =    1.893
peak=    3.534 closest distance to " O   HOH Z 156 " =    3.276
peak=    3.530 closest distance to " O   HOH Z 108 " =    2.418
peak=    3.526 closest distance to " CA  THR A 221 " =    0.981
peak=    3.501 closest distance to " CA  ASN A 215 " =    1.042
peak=    3.500 closest distance to " O   HOH Z 214 " =    1.131
peak=    3.499 closest distance to " O   HOH Z  97 " =    2.203
peak=    3.498 closest distance to " OG BSER A 164 " =    2.432
peak=    3.496 closest distance to " CB  PRO A 163 " =    3.843
peak=    3.495 closest distance to " CA  ALA A  84 " =    1.136
peak=    3.489 closest distance to " O   HOH Z 214 " =    2.372
peak=    3.487 closest distance to " O   HOH Z  88 " =    3.371
peak=    3.487 closest distance to " CD  ARG A 195 " =    0.880
peak=    3.486 closest distance to " CB  VAL A 265 " =    1.273
peak=    3.485 closest distance to " O   HOH Z 361 " =    3.194
peak=    3.484 closest distance to " O   HOH Z  19 " =    1.381
peak=    3.479 closest distance to " CB  SER A  62 " =    0.896
peak=    3.479 closest distance to " O   HOH Z 194 " =    1.857
peak=    3.478 closest distance to " CA  ALA A  51 " =    0.889
peak=    3.477 closest distance to " NH2AARG A 145 " =    2.154
peak=    3.470 closest distance to " CB  ASP A 191 " =    1.236
peak=    3.470 closest distance to " C   ALA A   1 " =    1.547
peak=    3.463 closest distance to " CD1 LEU A  96 " =    0.797
peak=    3.459 closest distance to " CD2 PHE A 225 " =    1.164
peak=    3.459 closest distance to " N   HIS A 108 " =    1.843
peak=    3.454 closest distance to " CA  ARG A 195 " =    1.239
peak=    3.453 closest distance to " N   ASP A 162 " =    1.416
peak=    3.442 closest distance to " O   HOH Z 147 " =    1.817
peak=    3.439 closest distance to " O   HOH Z  63 " =    2.120
peak=    3.434 closest distance to " O   HOH Z  30 " =    2.167
peak=    3.434 closest distance to " CA  LYS A 117 " =    1.298
peak=    3.425 closest distance to " CD  ARG A 159 " =    0.743
peak=    3.424 closest distance to " CA  ASP A 162 " =    1.103
peak=    3.413 closest distance to " CD ALYS A 290 " =    1.094
peak=    3.406 closest distance to " O   HOH Z  59 " =    1.673
peak=    3.405 closest distance to " CB  PRO A 198 " =    1.317
peak=    3.401 closest distance to " O   HOH Z 260 " =    1.396
peak=    3.400 closest distance to " O   HOH Z 255 " =    1.621
peak=    3.395 closest distance to " O   HOH Z 357 " =    1.644
peak=    3.394 closest distance to " O   HOH Z 337 " =    3.484
peak=    3.393 closest distance to " OD1 ASP A 253 " =    1.883
peak=    3.393 closest distance to " O   HOH Z 374 " =    2.566
peak=    3.392 closest distance to " O   HOH Z 144 " =    2.034
peak=    3.392 closest distance to " O   HOH Z 282 " =    1.948
peak=    3.387 closest distance to " O   HOH Z 298 " =    2.436
peak=    3.386 closest distance to " O   HOH Z 425 " =    1.965
peak=    3.385 closest distance to " O   SER A  26 " =    1.669
peak=    3.384 closest distance to " O   HOH Z 250 " =    1.458
peak=    3.375 closest distance to " O   HOH Z 257 " =    2.098
peak=    3.373 closest distance to " CD  ARG A 139 " =    1.523
peak=    3.362 closest distance to " CG2 VAL A 257 " =    0.825
peak=    3.362 closest distance to " CB  SER A  26 " =    1.695
peak=    3.362 closest distance to " CB  LEU A 228 " =    1.171
peak=    3.354 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.354 closest distance to " CB  ARG A 269 " =    0.736
peak=    3.343 closest distance to " O   HOH Z 428 " =    3.808
peak=    3.330 closest distance to " CG2 VAL A  78 " =    0.983
peak=    3.330 closest distance to " O   GLY A 211 " =    1.313
peak=    3.329 closest distance to " OE1 GLN A  11 " =    1.843
peak=    3.329 closest distance to " O   GLY A  91 " =    1.415
peak=    3.327 closest distance to " OG BSER A 210 " =    1.277
peak=    3.325 closest distance to " O   HOH Z 194 " =    2.002
peak=    3.324 closest distance to " CD  PRO A  54 " =    0.907
peak=    3.320 closest distance to " O   HOH Z 380 " =    1.755
peak=    3.317 closest distance to " O   HOH Z 251 " =    1.585
peak=    3.313 closest distance to " O   HOH Z 105 " =    2.545
peak=    3.310 closest distance to " CG2 ILE A  20 " =    1.345
peak=    3.309 closest distance to " O   HOH Z 119 " =    4.469
peak=    3.305 closest distance to " O   HOH Z 419 " =    1.552
peak=    3.305 closest distance to " CG2 VAL A 197 " =    1.134
peak=    3.303 closest distance to " CD  LYS A  76 " =    1.828
peak=    3.301 closest distance to " OD1 ASP A 286 " =    1.663
peak=    3.299 closest distance to " OG1 THR A 294 " =    2.328
peak=    3.296 closest distance to " O   HOH Z 185 " =    1.658
peak=    3.296 closest distance to " O   HOH Z  10 " =    1.832
peak=    3.294 closest distance to " O   HOH Z  64 " =    1.697
peak=    3.287 closest distance to " O   HOH Z  59 " =    1.763
peak=    3.284 closest distance to " CH2 TRP A 274 " =    2.095
peak=    3.282 closest distance to " CZ  PHE A  38 " =    1.392
peak=    3.282 closest distance to " N   CYS A 260 " =    0.792
peak=    3.280 closest distance to " CA  GLN A 194 " =    0.944
peak=    3.272 closest distance to " CB  ASN A  39 " =    0.770
peak=    3.269 closest distance to " NH2 ARG A 156 " =    1.073
peak=    3.267 closest distance to " CG1BVAL A  72 " =    1.579
peak=    3.264 closest distance to " O   HOH Z 406 " =    2.849
peak=    3.263 closest distance to " O   HOH Z  18 " =    1.479
peak=    3.262 closest distance to " CG  GLN A  77 " =    2.062
peak=    3.260 closest distance to " OG  SER A 245 " =    1.392
peak=    3.257 closest distance to " OG BSER A 258 " =    3.057
peak=    3.256 closest distance to " OD1 ASN A  60 " =    1.345
peak=    3.255 closest distance to " O   HOH Z 422 " =    2.571
peak=    3.252 closest distance to " O   HOH Z 261 " =    1.934
peak=    3.251 closest distance to " O   HOH Z   1 " =    2.320
peak=    3.239 closest distance to " CB  GLN A 278 " =    0.755
peak=    3.237 closest distance to " O   HOH Z 148 " =    3.116
peak=    3.236 closest distance to " O   HOH Z 375 " =    2.197
peak=    3.230 closest distance to " N   TRP A 150 " =    1.506
peak=    3.228 closest distance to " CD  LYS A 119 " =    1.880
peak=    3.227 closest distance to " CD  GLN A 240 " =    1.380
peak=    3.225 closest distance to " CA  ASP A 140 " =    1.115
peak=    3.224 closest distance to " CB  ALA A  34 " =    0.935
peak=    3.221 closest distance to " CB  ALA A 291 " =    1.236
peak=    3.220 closest distance to " O   HOH Z 280 " =    2.555
peak=    3.216 closest distance to " CG1 VAL A 153 " =    1.055
peak=    3.214 closest distance to " CD2 LEU A 297 " =    0.980
peak=    3.209 closest distance to " O   HOH Z  66 " =    2.203
peak=    3.204 closest distance to " N   TYR A  15 " =    0.863
peak=    3.194 closest distance to " CG2 ILE A 106 " =    0.796
peak=    3.185 closest distance to " CB  ALA A   9 " =    1.535
peak=    3.185 closest distance to " NH2AARG A 190 " =    1.338
peak=    3.184 closest distance to " C   PRO A 163 " =    1.675
peak=    3.178 closest distance to " OG BSER A 212 " =    2.781
peak=    3.176 closest distance to " O   HOH Z 343 " =    2.282
peak=    3.168 closest distance to " O   HOH Z 162 " =    1.854
peak=    3.162 closest distance to " O   HOH Z  85 " =    2.155
peak=    3.160 closest distance to " CA  MET A  40 " =    1.063
peak=    3.160 closest distance to " O   HOH Z 305 " =    3.614
peak=    3.160 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.158 closest distance to " C   THR A  82 " =    1.938
peak=    3.157 closest distance to " O   HOH Z 423 " =    3.372
peak=    3.157 closest distance to " O   HOH Z 383 " =    1.936
peak=    3.155 closest distance to " O   HOH Z 118 " =    1.223
peak=    3.155 closest distance to " CB  TRP A 266 " =    1.203
peak=    3.150 closest distance to " CA  ASP A 191 " =    0.826
peak=    3.149 closest distance to " O   HOH Z 299 " =    4.289
peak=    3.148 closest distance to " CG  MET A  93 " =    1.071
peak=    3.147 closest distance to " CB  TYR A  30 " =    1.475
peak=    3.136 closest distance to " O   HOH Z 325 " =    1.865
peak=    3.134 closest distance to " CA  VAL A 126 " =    1.125
peak=    3.133 closest distance to " O   HOH Z  48 " =    1.684
peak=    3.129 closest distance to " OD2 ASP A 298 " =    4.036
peak=    3.126 closest distance to " CG  LYS A 119 " =    1.104
peak=    3.119 closest distance to " O   HOH Z 195 " =    1.988
peak=    3.116 closest distance to " O   HOH Z 424 " =    3.436
peak=    3.103 closest distance to " O   HOH Z 156 " =    2.822
peak=    3.101 closest distance to " CG  PRO A  54 " =    1.483
peak=    3.101 closest distance to " CB  LYS A 289 " =    1.022
peak=    3.100 closest distance to " O   HOH Z  71 " =    1.290
peak=    3.099 closest distance to " CA  GLY A  80 " =    0.815
peak=    3.098 closest distance to " O   HOH Z  95 " =    1.519
peak=    3.096 closest distance to " O   HOH Z 234 " =    2.234
peak=    3.096 closest distance to " OD1 ASN A  45 " =    1.280
peak=    3.085 closest distance to " N   ARG A 156 " =    1.442
peak=    3.083 closest distance to " OG1 THR A 221 " =    1.255
peak=    3.081 closest distance to " O   HOH Z 402 " =    2.955
peak=    3.079 closest distance to " NH1AARG A 275 " =    1.099
peak=    3.078 closest distance to " CA  ALA A 248 " =    1.134
peak=    3.071 closest distance to " N   PHE A 130 " =    1.385
peak=    3.066 closest distance to " NZ  LYS A 117 " =    1.637
peak=    3.062 closest distance to " O   HOH Z 435 " =    1.874
peak=    3.059 closest distance to " O   HOH Z 128 " =    1.655
peak=    3.058 closest distance to " O   HOH Z  85 " =    1.733
peak=    3.047 closest distance to " CE3 TRP A 274 " =    2.404
peak=    3.043 closest distance to " CB  MET A  47 " =    1.121
peak=    3.018 closest distance to " O   HOH Z  40 " =    2.644
peak=    3.016 closest distance to " NH1AARG A 145 " =    1.266
peak=    2.983 closest distance to " CD  LYS A 119 " =    2.096

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.853
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.713 - 5.853

peak=   -4.692 closest distance to " C   HIS A 108 " =    1.093
peak=   -4.594 closest distance to " O   HOH Z 102 " =    0.767
peak=   -4.531 closest distance to " O   HOH Z 266 " =    4.176
peak=   -4.301 closest distance to " O   TRP A  92 " =    1.800
peak=   -4.292 closest distance to " O   HOH Z  13 " =    1.666
peak=   -4.281 closest distance to " CG  MET A  93 " =    2.391
peak=   -4.281 closest distance to " C   THR A 279 " =    1.251
peak=   -4.266 closest distance to " CD  ARG A 156 " =    2.063
peak=   -4.213 closest distance to " OXT GLY A 302 " =    2.980
peak=   -4.204 closest distance to " CD2 LEU A 237 " =    2.535
peak=   -4.162 closest distance to " N   ALA A 248 " =    1.818
peak=   -4.155 closest distance to " O   PRO A 163 " =    1.999
peak=   -4.120 closest distance to " O   VAL A  67 " =    2.706
peak=   -4.052 closest distance to " CG  LYS A 193 " =    2.281
peak=   -4.026 closest distance to " OG BSER A 134 " =    1.473
peak=   -3.975 closest distance to " ND2 ASN A  45 " =    0.962
peak=   -3.955 closest distance to " CB  ALA A 161 " =    2.530
peak=   -3.946 closest distance to " O   PRO A 198 " =    1.347
peak=   -3.945 closest distance to " O   HOH Z  52 " =    1.521
peak=   -3.943 closest distance to " ND2 ASN A  69 " =    1.552
peak=   -3.938 closest distance to " SG  CYS A 254 " =    3.202
peak=   -3.929 closest distance to " O   HOH Z 165 " =    1.873
peak=   -3.927 closest distance to " CD  ARG A 195 " =    5.121
peak=   -3.897 closest distance to " CD2 LEU A 300 " =    2.816
peak=   -3.854 closest distance to " CZ  TYR A 169 " =    1.859
peak=   -3.844 closest distance to " O   HOH Z 401 " =    0.810
peak=   -3.830 closest distance to " O   HOH Z  52 " =    0.717
peak=   -3.830 closest distance to " O   HOH Z 234 " =    3.950
peak=   -3.824 closest distance to " N   SER A 276 " =    1.377
peak=   -3.808 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.804 closest distance to " O   HOH Z 377 " =    1.996
peak=   -3.790 closest distance to " CD1 PHE A  59 " =    1.957
peak=   -3.785 closest distance to " O   HOH Z  97 " =    1.202
peak=   -3.760 closest distance to " O   HOH Z 407 " =    2.768
peak=   -3.720 closest distance to " NH2 ARG A  66 " =    4.873
peak=   -3.719 closest distance to " O   HOH Z  71 " =    1.303
peak=   -3.715 closest distance to " CA  GLY A 133 " =    1.732
peak=   -3.712 closest distance to " O   PHE A 218 " =    1.575
peak=   -3.690 closest distance to " O   ARG A  56 " =    1.563
peak=   -3.683 closest distance to " CD  GLN A  58 " =    1.236
peak=   -3.680 closest distance to " OD2 ASP A 191 " =    1.434
peak=   -3.676 closest distance to " ND2 ASN A  39 " =    1.145
peak=   -3.662 closest distance to " N   ALA A 226 " =    1.870
peak=   -3.653 closest distance to " O   ASN A 187 " =    1.485
peak=   -3.652 closest distance to " O   SER A 146 " =    0.966
peak=   -3.638 closest distance to " CG  GLU A  53 " =    1.381
peak=   -3.628 closest distance to " O   HOH Z 126 " =    1.742
peak=   -3.625 closest distance to " O   ASN A  45 " =    1.820
peak=   -3.619 closest distance to " OD2 ASP A 171 " =    2.273
peak=   -3.618 closest distance to " O   HOH Z 423 " =    2.338
peak=   -3.613 closest distance to " O   HOH Z 290 " =    0.874
peak=   -3.611 closest distance to " CB  TYR A  15 " =    2.247
peak=   -3.609 closest distance to " CB  PHE A 192 " =    1.994
peak=   -3.609 closest distance to " O   PRO A  54 " =    1.560
peak=   -3.606 closest distance to " O   VAL A 174 " =    2.031
peak=   -3.605 closest distance to " O   HOH Z 250 " =    1.351
peak=   -3.597 closest distance to " OE1 GLN A 223 " =    2.372
peak=   -3.596 closest distance to " O   HOH Z 251 " =    1.341
peak=   -3.594 closest distance to " O   HOH Z  11 " =    1.757
peak=   -3.584 closest distance to " O   HOH Z  18 " =    1.237
peak=   -3.579 closest distance to " CE1 TYR A 247 " =    2.619
peak=   -3.578 closest distance to " CG  ASP A 132 " =    2.245
peak=   -3.571 closest distance to " CD2 TYR A  30 " =    2.778
peak=   -3.567 closest distance to " N   GLN A  58 " =    1.760
peak=   -3.566 closest distance to " OD2 ASP A  50 " =    1.349
peak=   -3.558 closest distance to " CD1 LEU A  25 " =    2.503
peak=   -3.555 closest distance to " O   HOH Z 351 " =    1.449
peak=   -3.534 closest distance to " ND2 ASN A 187 " =    1.410
peak=   -3.528 closest distance to " NH2 ARG A  79 " =    2.052
peak=   -3.521 closest distance to " CB  PRO A 163 " =    2.778
peak=   -3.516 closest distance to " CB  ASN A  39 " =    2.248
peak=   -3.508 closest distance to " O   HOH Z 311 " =    3.372
peak=   -3.497 closest distance to " O   HOH Z  92 " =    1.692
peak=   -3.486 closest distance to " CD  GLN A 223 " =    0.999
peak=   -3.482 closest distance to " N   THR A 220 " =    2.182
peak=   -3.480 closest distance to " C   ALA A 158 " =    1.126
peak=   -3.478 closest distance to " O  BHOH Z 338 " =    1.391
peak=   -3.474 closest distance to " C   GLY A  91 " =    1.314
peak=   -3.470 closest distance to " CE1 HIS A  81 " =    1.458
peak=   -3.470 closest distance to " O   ALA A 161 " =    1.438
peak=   -3.460 closest distance to " O   HOH Z  11 " =    1.741
peak=   -3.455 closest distance to " CD2 TYR A 293 " =    2.030
peak=   -3.455 closest distance to " O   HOH Z 384 " =    3.420
peak=   -3.455 closest distance to " N   GLN A 122 " =    1.588
peak=   -3.447 closest distance to " C   GLY A  80 " =    2.337
peak=   -3.441 closest distance to " CD1 LEU A 228 " =    2.156
peak=   -3.440 closest distance to " CH2 TRP A 179 " =    1.363
peak=   -3.429 closest distance to " O   HOH Z 348 " =    2.275
peak=   -3.428 closest distance to " O   ALA A  34 " =    2.416
peak=   -3.428 closest distance to " O   LEU A 167 " =    1.608
peak=   -3.420 closest distance to " O   HOH Z 427 " =    1.361
peak=   -3.419 closest distance to " O   HOH Z 396 " =    1.678
peak=   -3.417 closest distance to " O   HOH Z 118 " =    3.401
peak=   -3.411 closest distance to " O   HOH Z 174 " =    4.093
peak=   -3.399 closest distance to " C   ASN A 285 " =    2.069
peak=   -3.397 closest distance to " OG BSER A 216 " =    0.868
peak=   -3.397 closest distance to " O   HOH Z  35 " =    2.185
peak=   -3.394 closest distance to " O   PRO A 198 " =    1.236
peak=   -3.394 closest distance to " CD  GLN A  58 " =    1.173
peak=   -3.391 closest distance to " O   HOH Z 362 " =    5.622
peak=   -3.389 closest distance to " O   HOH Z 197 " =    1.947
peak=   -3.381 closest distance to " O   SER A   3 " =    1.013
peak=   -3.380 closest distance to " O   MET A  40 " =    2.788
peak=   -3.380 closest distance to " OG  SER A   3 " =    1.430
peak=   -3.374 closest distance to " C   LEU A 143 " =    1.145
peak=   -3.373 closest distance to " O   SER A 273 " =    1.188
peak=   -3.370 closest distance to " OG  SER A  97 " =    1.954
peak=   -3.361 closest distance to " O   LEU A 222 " =    1.342
peak=   -3.361 closest distance to " CD1 PHE A 130 " =    2.179
peak=   -3.359 closest distance to " O   ALA A 160 " =    1.425
peak=   -3.354 closest distance to " O   HOH Z 435 " =    2.435
peak=   -3.352 closest distance to " OE2 GLU A   2 " =    1.789
peak=   -3.349 closest distance to " O   HOH Z 364 " =    5.069
peak=   -3.349 closest distance to " CG2 THR A 182 " =    2.253
peak=   -3.347 closest distance to " O   HOH Z 123 " =    2.191
peak=   -3.346 closest distance to " O   HOH Z 193 " =    1.900
peak=   -3.329 closest distance to " NE2 GLN A  94 " =    1.851
peak=   -3.319 closest distance to " O   GLN A  11 " =    1.320
peak=   -3.317 closest distance to " O   HOH Z 198 " =    1.467
peak=   -3.307 closest distance to " O   HOH Z 166 " =    2.035
peak=   -3.305 closest distance to " CA  TYR A  68 " =    2.787
peak=   -3.300 closest distance to " CA  GLY A 133 " =    2.020
peak=   -3.300 closest distance to " NE2 GLN A 278 " =    2.005
peak=   -3.298 closest distance to " CB  PRO A 243 " =    2.616
peak=   -3.297 closest distance to " O   HOH Z  88 " =    4.490
peak=   -3.293 closest distance to " O   VAL A 197 " =    1.184
peak=   -3.285 closest distance to " N   VAL A 189 " =    1.638
peak=   -3.285 closest distance to " O   HOH Z 265 " =    1.997
peak=   -3.278 closest distance to " O   HOH Z 418 " =    1.549
peak=   -3.278 closest distance to " O   HOH Z 424 " =    3.082
peak=   -3.275 closest distance to " CG  GLU A 152 " =    1.025
peak=   -3.273 closest distance to " CE  LYS A 166 " =    2.931
peak=   -3.273 closest distance to " CG  ARG A 259 " =    2.715
peak=   -3.269 closest distance to " OD1 ASP A 200 " =    1.166
peak=   -3.267 closest distance to " O   HOH Z  15 " =    1.518
peak=   -3.266 closest distance to " CG1AVAL A  41 " =    2.562
peak=   -3.258 closest distance to " O   GLY A  75 " =    1.666
peak=   -3.257 closest distance to " OG  SER A  87 " =    1.236
peak=   -3.246 closest distance to " O   HOH Z   6 " =    1.769
peak=   -3.240 closest distance to " O   HOH Z 287 " =    2.091
peak=   -3.236 closest distance to " NH1 ARG A  66 " =    5.059
peak=   -3.236 closest distance to " CG2 VAL A 189 " =    2.218
peak=   -3.235 closest distance to " O   HOH Z 397 " =    1.239
peak=   -3.234 closest distance to " CB  LEU A 167 " =    2.091
peak=   -3.234 closest distance to " O   ALA A   1 " =    1.846
peak=   -3.232 closest distance to " OG  SER A  63 " =    1.166
peak=   -3.228 closest distance to " CZ2 TRP A  92 " =    2.600
peak=   -3.226 closest distance to " CG  PHE A 283 " =    2.594
peak=   -3.222 closest distance to " CD  ARG A 139 " =    1.452
peak=   -3.221 closest distance to " OG ASER A 134 " =    1.339
peak=   -3.220 closest distance to " O   GLY A  80 " =    2.560
peak=   -3.217 closest distance to " O   HOH Z 411 " =    3.601
peak=   -3.216 closest distance to " OE1 GLN A 194 " =    1.439
peak=   -3.214 closest distance to " CG1 VAL A 112 " =    2.700
peak=   -3.212 closest distance to " CD2 HIS A 115 " =    1.024
peak=   -3.211 closest distance to " CD  GLN A  88 " =    1.059
peak=   -3.207 closest distance to " OE1 GLN A 103 " =    1.316
peak=   -3.206 closest distance to " OG BSER A 134 " =    1.744
peak=   -3.203 closest distance to " O   HOH Z 137 " =    1.775
peak=   -3.201 closest distance to " CD  LYS A 289 " =    2.460
peak=   -3.198 closest distance to " NE2 GLN A  58 " =    2.579
peak=   -3.198 closest distance to " O   HOH Z 166 " =    1.511
peak=   -3.195 closest distance to " NH1 ARG A  66 " =    0.773
peak=   -3.193 closest distance to " CE1 TYR A 169 " =    2.188
peak=   -3.191 closest distance to " OD1 ASN A 148 " =    1.618
peak=   -3.189 closest distance to " N   GLY A  17 " =    1.538
peak=   -3.189 closest distance to " O   HOH Z 191 " =    5.853
peak=   -3.175 closest distance to " O   ALA A  51 " =    1.496
peak=   -3.170 closest distance to " CA  ASP A 298 " =    1.133
peak=   -3.169 closest distance to " N   ALA A  43 " =    2.438
peak=   -3.168 closest distance to " CG2 THR A 251 " =    2.040
peak=   -3.167 closest distance to " OG BSER A  99 " =    1.085
peak=   -3.166 closest distance to " NE2 GLN A  55 " =    1.605
peak=   -3.161 closest distance to " CD1 ILE A 109 " =    2.134
peak=   -3.160 closest distance to " O   HOH Z 384 " =    2.050
peak=   -3.157 closest distance to " N   ALA A 248 " =    2.247
peak=   -3.153 closest distance to " O   HOH Z 360 " =    2.512
peak=   -3.152 closest distance to " O   HOH Z 326 " =    1.919
peak=   -3.147 closest distance to " NE2 GLN A  88 " =    1.690
peak=   -3.141 closest distance to " O   HOH Z  20 " =    1.836
peak=   -3.140 closest distance to " CG  ASN A 110 " =    1.086
peak=   -3.136 closest distance to " O   GLY A 196 " =    0.958
peak=   -3.132 closest distance to " O   HOH Z 231 " =    1.148
peak=   -3.131 closest distance to " OXT GLY A 302 " =    3.069
peak=   -3.115 closest distance to " O   HOH Z 113 " =    1.929
peak=   -3.113 closest distance to " O   HOH Z  56 " =    1.445
peak=   -3.111 closest distance to " O   HOH Z 242 " =    1.628
peak=   -3.107 closest distance to " CA  TYR A  68 " =    2.851
peak=   -3.101 closest distance to " CB  ASP A  27 " =    2.426
peak=   -3.100 closest distance to " O   HOH Z 140 " =    0.922
peak=   -3.097 closest distance to " NH1 ARG A 195 " =    2.461
peak=   -3.087 closest distance to " CB  ASP A 162 " =    2.644
peak=   -3.080 closest distance to " O   HOH Z 185 " =    2.248
peak=   -3.078 closest distance to " O   HOH Z 202 " =    1.663
peak=   -3.076 closest distance to " NE2 GLN A 223 " =    1.294
peak=   -3.071 closest distance to " O   GLN A  94 " =    2.279
peak=   -3.071 closest distance to " O   HOH Z 416 " =    0.713
peak=   -3.067 closest distance to " O   HOH Z 128 " =    1.537
peak=   -3.066 closest distance to " CZ  PHE A  16 " =    2.153
peak=   -3.054 closest distance to " O   HOH Z 426 " =    1.699
peak=   -3.054 closest distance to " O   THR A  52 " =    1.827
peak=   -3.054 closest distance to " CG  ASP A  50 " =    2.469
peak=   -3.051 closest distance to " O   ILE A 234 " =    1.259
peak=   -3.042 closest distance to " CG  ASN A 187 " =    1.695
peak=   -3.035 closest distance to " O   ALA A  10 " =    1.658

================= 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    :  0.4760 0.4783   6.278829e+00   6.279012e+00
   1_bss:  0.4696 0.4698   6.273793e+00   6.267489e+00
   1_xyz:  0.3228 0.3479   6.014584e+00   6.070522e+00
   1_adp:  0.2906 0.3554   5.956774e+00   6.090116e+00
   1_occ:  0.2905 0.3560   5.956534e+00   6.090396e+00
   2_bss:  0.2871 0.3517   5.950844e+00   6.087687e+00
   2_xyz:  0.2077 0.2604   5.668146e+00   5.858105e+00
   2_adp:  0.1823 0.2375   5.564130e+00   5.767919e+00
   2_occ:  0.1820 0.2378   5.563876e+00   5.768283e+00
   3_bss:  0.1821 0.2359   5.560889e+00   5.762769e+00
   3_xyz:  0.1455 0.1966   5.375223e+00   5.598669e+00
   3_adp:  0.1350 0.1890   5.318837e+00   5.550690e+00
   3_occ:  0.1349 0.1891   5.318969e+00   5.550982e+00
   4_bss:  0.1356 0.1888   5.319644e+00   5.549155e+00
   4_xyz:  0.1199 0.1749   5.224442e+00   5.471472e+00
   4_adp:  0.1180 0.1670   5.195034e+00   5.430132e+00
   4_occ:  0.1179 0.1670   5.194440e+00   5.430297e+00
   5_bss:  0.1179 0.1671   5.194755e+00   5.430537e+00
   5_xyz:  0.1150 0.1637   5.173801e+00   5.411292e+00
   5_adp:  0.1140 0.1639   5.170582e+00   5.412817e+00
   5_occ:  0.1139 0.1640   5.170419e+00   5.412992e+00
   5_bss:  0.1141 0.1641   5.171025e+00   5.412700e+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:  0.300  20.000  -0.417   1.201   0.946   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -0.417   1.201   0.946   0.000   0.000   0.000
   1_adp:  0.300  20.000  -0.417   1.201   0.946   0.000   0.000   0.000
   1_occ:  0.300  20.000  -0.417   1.201   0.946   0.000   0.000   0.000
   2_bss:  0.328  50.000  -2.018  -0.147  -0.598  -0.000  -0.000  -0.000
   2_xyz:  0.328  50.000  -2.018  -0.147  -0.598  -0.000  -0.000  -0.000
   2_adp:  0.328  50.000  -2.018  -0.147  -0.598  -0.000  -0.000  -0.000
   2_occ:  0.328  50.000  -2.018  -0.147  -0.598  -0.000  -0.000  -0.000
   3_bss:  0.319  41.082  -2.600  -0.844  -1.235  -0.000  -0.000  -0.000
   3_xyz:  0.319  41.082  -2.600  -0.844  -1.235  -0.000  -0.000  -0.000
   3_adp:  0.319  41.082  -2.600  -0.844  -1.235  -0.000  -0.000  -0.000
   3_occ:  0.319  41.082  -2.600  -0.844  -1.235  -0.000  -0.000  -0.000
   4_bss:  0.319  41.082  -2.924  -1.289  -1.566  -0.000  -0.000  -0.000
   4_xyz:  0.319  41.082  -2.924  -1.289  -1.566  -0.000  -0.000  -0.000
   4_adp:  0.319  41.082  -2.924  -1.289  -1.566  -0.000  -0.000  -0.000
   4_occ:  0.319  41.082  -2.924  -1.289  -1.566  -0.000  -0.000  -0.000
   5_bss:  0.324  41.082  -2.980  -1.407  -1.563  -0.000  -0.000  -0.000
   5_xyz:  0.324  41.082  -2.980  -1.407  -1.563  -0.000  -0.000  -0.000
   5_adp:  0.324  41.082  -2.980  -1.407  -1.563  -0.000  -0.000  -0.000
   5_occ:  0.324  41.082  -2.980  -1.407  -1.563  -0.000  -0.000  -0.000
   5_bss:  0.321  42.214  -2.851  -1.319  -1.417  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.602 0.3719  0.5049    73387.925
   1_bss:  60.498 0.3845  0.5353    69912.234
   1_xyz:  36.839 0.6804  0.9143    32696.763
   1_adp:  38.366 0.6612  0.9015    34311.788
   1_occ:  38.455 0.6601  0.8998    34417.068
   2_bss:  38.105 0.6639  0.8594    33719.638
   2_xyz:  26.999 0.7883  0.9806    17850.083
   2_adp:  23.453 0.8270  0.9974    14572.054
   2_occ:  23.466 0.8269  0.9970    14581.626
   3_bss:  23.301 0.8282  0.9742    14312.578
   3_xyz:  18.978 0.8705  0.9984     9823.526
   3_adp:  17.762 0.8826  0.9933     9069.409
   3_occ:  17.772 0.8825  0.9931     9069.080
   4_bss:  17.734 0.8828  0.9801     9032.641
   4_xyz:  16.099 0.8970  0.9875     7607.672
   4_adp:  15.102 0.9059  0.9875     7052.322
   4_occ:  15.097 0.9059  0.9874     7045.406
   5_bss:  15.104 0.9058  0.9854     7052.956
   5_xyz:  14.599 0.9102  0.9861     6698.333
   5_adp:  14.570 0.9106  0.9809     6728.346
   5_occ:  14.569 0.9106  0.9808     6726.714
   5_bss:  14.571 0.9106  0.9825     6728.841
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   2.4763e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   2.4763e-01
   1_xyz:   1.701  0.014  0.101 16.866  0.007  4.106   1.6546e-01
   1_adp:   1.701  0.014  0.101 16.866  0.007  4.106   1.6546e-01
   1_occ:   1.701  0.014  0.101 16.866  0.007  4.106   1.6546e-01
   2_bss:   1.701  0.014  0.101 16.866  0.007  4.106   1.6546e-01
   2_xyz:   1.257  0.009  0.081 15.692  0.006  4.107   8.4130e-02
   2_adp:   1.257  0.009  0.081 15.692  0.006  4.107   8.4130e-02
   2_occ:   1.257  0.009  0.081 15.692  0.006  4.107   8.4130e-02
   3_bss:   1.257  0.009  0.081 15.692  0.006  4.107   8.4130e-02
   3_xyz:   1.054  0.007  0.069 15.100  0.004  4.112   6.3859e-02
   3_adp:   1.054  0.007  0.069 15.100  0.004  4.112   6.3859e-02
   3_occ:   1.054  0.007  0.069 15.100  0.004  4.112   6.3859e-02
   4_bss:   1.054  0.007  0.069 15.100  0.004  4.112   6.3859e-02
   4_xyz:   1.143  0.008  0.076 15.261  0.005  4.105   7.2905e-02
   4_adp:   1.143  0.008  0.076 15.261  0.005  4.105   7.2905e-02
   4_occ:   1.143  0.008  0.076 15.261  0.005  4.105   7.2905e-02
   5_bss:   1.143  0.008  0.076 15.261  0.005  4.105   7.2905e-02
   5_xyz:   1.050  0.007  0.072 14.940  0.004  4.106   6.2261e-02
   5_adp:   1.050  0.007  0.072 14.940  0.004  4.106   6.2261e-02
   5_occ:   1.050  0.007  0.072 14.940  0.004  4.106   6.2261e-02
   5_bss:   1.050  0.007  0.072 14.940  0.004  4.106   6.2261e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.056   2.4446e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.056   2.4446e-01
   1_xyz:  10.215  0.110  0.307 86.304  0.051  1.975   1.3431e-01
   1_adp:  10.215  0.110  0.307 86.304  0.051  1.975   1.3431e-01
   1_occ:  10.215  0.110  0.307 86.304  0.051  1.975   1.3431e-01
   2_bss:  10.215  0.110  0.307 86.304  0.051  1.975   1.3431e-01
   2_xyz:   9.050  0.052  0.274 83.509  0.053  2.166   8.3367e-02
   2_adp:   9.050  0.052  0.274 83.509  0.053  2.166   8.3367e-02
   2_occ:   9.050  0.052  0.274 83.509  0.053  2.166   8.3367e-02
   3_bss:   9.050  0.052  0.274 83.509  0.053  2.166   8.3367e-02
   3_xyz:   7.648  0.042  0.258 78.656  0.037  2.229   5.1457e-02
   3_adp:   7.648  0.042  0.258 78.656  0.037  2.229   5.1457e-02
   3_occ:   7.648  0.042  0.258 78.656  0.037  2.229   5.1457e-02
   4_bss:   7.648  0.042  0.258 78.656  0.037  2.229   5.1457e-02
   4_xyz:   7.704  0.042  0.223 81.180  0.038  2.187   5.6948e-02
   4_adp:   7.704  0.042  0.223 81.180  0.038  2.187   5.6948e-02
   4_occ:   7.704  0.042  0.223 81.180  0.038  2.187   5.6948e-02
   5_bss:   7.704  0.042  0.223 81.180  0.038  2.187   5.6948e-02
   5_xyz:   7.136  0.035  0.233 81.110  0.040  2.302   3.9971e-02
   5_adp:   7.136  0.035  0.233 81.110  0.040  2.302   3.9971e-02
   5_occ:   7.136  0.035  0.233 81.110  0.040  2.302   3.9971e-02
   5_bss:   7.136  0.035  0.233 81.110  0.040  2.302   3.9971e-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: 119.58   0.00  19.27 119.58   0.00  15.26  77.23   2.04  41.13
   1_occ: 119.58   0.00  19.27 119.58   0.00  15.26  77.23   2.04  41.13
   2_bss: 119.58   0.00  19.27 119.58   0.00  15.26  77.23   2.04  41.13
   2_xyz: 119.58   0.00  19.27 119.58   0.00  15.26  77.23   2.04  41.13
   2_adp:  96.55   0.00  18.63  81.99   0.00  14.10  96.55   4.92  43.33
   2_occ:  96.55   0.00  18.63  81.99   0.00  14.10  96.55   4.92  43.33
   3_bss:  96.55   0.00  18.63  81.99   0.00  14.10  96.55   4.92  43.33
   3_xyz:  96.55   0.00  18.63  81.99   0.00  14.10  96.55   4.92  43.33
   3_adp: 121.98   0.00  18.79 106.64   0.00  13.65 121.98   5.69  46.75
   3_occ: 121.98   0.00  18.79 106.64   0.00  13.65 121.98   5.69  46.75
   4_bss: 121.98   0.00  18.79 106.64   0.00  13.65 121.98   5.69  46.75
   4_xyz: 121.98   0.00  18.79 106.64   0.00  13.65 121.98   5.69  46.75
   4_adp: 100.98   2.12  17.38 100.98   2.12  13.00  98.08   3.79  41.19
   4_occ: 100.98   2.12  17.38 100.98   2.12  13.00  98.08   3.79  41.19
   5_bss: 100.98   2.12  17.38 100.98   2.12  13.00  98.08   3.79  41.19
   5_xyz: 100.98   2.12  17.38 100.98   2.12  13.00  98.08   3.79  41.19
   5_adp: 100.98   2.12  17.10 100.98   2.12  12.81  90.90   5.35  40.45
   5_occ: 100.98   2.12  17.10 100.98   2.12  12.81  90.90   5.35  40.45
   5_bss: 100.90   2.05  17.02 100.90   2.05  12.73  90.82   5.27  40.38
------------------------------------------------------------------------
 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:    3.861    0.029    0.491
   1_adp:    3.861    0.029    0.491
   1_occ:    3.861    0.029    0.491
   2_bss:    3.861    0.029    0.491
   2_xyz:    2.745    0.066    0.639
   2_adp:    2.745    0.066    0.639
   2_occ:    2.745    0.066    0.639
   3_bss:    2.745    0.066    0.639
   3_xyz:    2.709    0.093    0.720
   3_adp:    2.709    0.093    0.720
   3_occ:    2.709    0.093    0.720
   4_bss:    2.709    0.093    0.720
   4_xyz:    2.579    0.068    0.762
   4_adp:    2.579    0.068    0.762
   4_occ:    2.579    0.068    0.762
   5_bss:    2.579    0.068    0.762
   5_xyz:    2.468    0.108    0.772
   5_adp:    2.468    0.108    0.772
   5_occ:    2.468    0.108    0.772
   5_bss:    2.468    0.108    0.772
------------------------------------------------------------------------

CPU time actual refinement: 292.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_89/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_89/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_89/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_89/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_89/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 292.39 
  Macro-tasks:
    bulk solvent and scale       = 35.05  
    individual site refinement   = 121.44 
    weights calculation          = 25.26  
    collect and process          = 5.39   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 187.22 
  Micro-tasks:
    mask                            = 2.05   
    f_calc                          = 93.46  
    alpha_beta                      = 6.90   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 101.88 
    fmodel                         = 6.11   
    r_factors                      = 0.22   
    phase_errors                   = 8.70   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 220.58 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.101 micro seconds
Total CPU time: 5.07 minutes
from_scatterers_fft:    665 calls, 93.21 s
gradients_fft:          610 calls, 90.06 s

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

# Date 2008-01-16 Time 03:58:01 PST -0800 (1200484681.20 s)
Start R-work = 0.4760, R-free = 0.4783 (no bulk solvent and anisotropic scale)
Final R-work = 0.1386, R-free = 0.1844 (no bulk solvent and anisotropic scale)

Start R-work = 0.4696, R-free = 0.4698
Final R-work = 0.1141, R-free = 0.1641