# Date 2008-01-16 Time 04:26:04 PST -0800 (1200486364.15 s)
#phil __OFF__

Command line arguments: "../313.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22570
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 313

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.1647, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.829 1.97067
Completeness in resolution range: 0.954211
Completeness with d_max=infinity: 0.951246

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8290
                             d_min =   1.9707

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.829 1.97067
Completeness in resolution range: 0.954211
Completeness with d_max=infinity: 0.951246

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8294 -  4.2162 [2165/2193]  1947   218  10.1%
  bin  2:  4.2162 -  3.3593 [2058/2077]  1855   203   9.9%
  bin  3:  3.3593 -  2.9384 [2050/2070]  1845   205  10.0%
  bin  4:  2.9384 -  2.6715 [2024/2049]  1823   201   9.9%
  bin  5:  2.6715 -  2.4809 [2016/2036]  1805   211  10.5%
  bin  6:  2.4809 -  2.3353 [1997/2043]  1804   193   9.7%
  bin  7:  2.3353 -  2.2187 [1992/2025]  1796   196   9.8%
  bin  8:  2.2187 -  2.1224 [2001/2036]  1796   205  10.2%
  bin  9:  2.1224 -  2.0409 [1954/1984]  1756   198  10.1%
  bin 10:  2.0409 -  1.9707 [1332/2016]  1203   129   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_313/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.69 -     2.33: 16
        2.33 -     2.97: 1785
        2.97 -     3.61: 4564
        3.61 -     4.26: 9224
        4.26 -     4.90: 12855
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.686 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.777 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.927 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.931 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28439 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_313/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_313/model_refine_001.geo

CPU time processing inputs: 9.05


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.16465 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2804   r_free= 0.2739   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.927411                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8294 -  4.7023 0.99   1401  157 0.2647 0.2729      6.2998      6.3361|
|  2:  4.7023 -  3.7522 0.99   1347  151 0.2143 0.1914      6.2807      6.2243|
|  3:  3.7522 -  3.2838 0.99   1323  148 0.2337 0.2159      6.1778      6.1877|
|  4:  3.2838 -  2.9862 0.99   1310  135 0.2525 0.2689      6.0767       6.104|
|  5:  2.9862 -  2.7737 0.99   1309  150 0.2815 0.2484      5.9694      5.8997|
|  6:  2.7737 -  2.6111 0.98   1296  144 0.2938 0.3248       5.913      5.8587|
|  7:  2.6111 -  2.4809 0.99   1289  153 0.2926 0.2465      5.8791      5.7491|
|  8:  2.4809 -  2.3734 0.98   1309  134 0.2994 0.2908      5.8352      5.8337|
|  9:  2.3734 -  2.2824 0.98   1284  146 0.3128 0.3062      5.7981       5.809|
| 10:  2.2824 -  2.2039 0.97   1255  140 0.3092 0.2937      5.7901      5.7105|
| 11:  2.2039 -  2.1352 0.99   1293  145 0.3241 0.3402      5.7524      5.8091|
| 12:  2.1352 -  2.0743 0.98   1272  141 0.3274 0.3138      5.7054      5.7308|
| 13:  2.0743 -  2.0198 0.97   1254  134 0.3351 0.3283      5.6488      5.5575|
| 14:  2.0198 -  1.9707 0.54    688   81 0.3524 0.3169      5.6638      5.4671|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8294 -  4.7023  1401   157  0.79  25.74   0.87     0.80      40597.93|
|  2:  4.7023 -  3.7522  1347   151  0.87  19.29   1.00     0.93      35531.06|
|  3:  3.7522 -  3.2838  1323   148  0.86  20.92   1.01     0.99      30543.11|
|  4:  3.2838 -  2.9862  1310   135  0.84  22.78   1.01     0.98      26394.38|
|  5:  2.9862 -  2.7737  1309   150  0.79  27.35   1.02     0.96      22643.58|
|  6:  2.7737 -  2.6111  1296   144  0.78  28.07   1.02     0.96      19691.01|
|  7:  2.6111 -  2.4809  1289   153  0.80  26.64   1.03     0.99      17099.74|
|  8:  2.4809 -  2.3734  1309   134  0.80  26.79   1.04     1.01      15772.74|
|  9:  2.3734 -  2.2824  1284   146  0.79  28.25   1.05     1.02      15092.61|
| 10:  2.2824 -  2.2039  1255   140  0.77  29.63   1.08     1.00      14828.62|
| 11:  2.2039 -  2.1352  1293   145  0.76  30.65   1.05     1.02      14973.20|
| 12:  2.1352 -  2.0743  1272   141  0.75  31.43   1.09     1.03      14215.62|
| 13:  2.0743 -  2.0198  1254   134  0.74  32.46   1.07     1.01      12572.54|
| 14:  2.0198 -  1.9707   688    81  0.76  30.58   1.05     0.96       9892.03|
|alpha:            min =        0.80 max =            1.03 mean =         0.97|
|beta:             min =     9892.03 max =        40597.93 mean =     21303.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.79|
|phase err.(work): min =        0.00 max =           89.97 mean =        27.00|
|phase err.(test): min =        0.00 max =           89.97 mean =        27.00|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.055870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.516   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.457487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.335   (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 |  1.686 -  2.007:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.007 -  2.329:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.329 -  2.650:       62 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.650 -  2.972:     1723 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.972 -  3.293:     1890 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.293 -  3.614:     2674 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.614 -  3.936:     4771 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.936 -  4.257:     4453 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.257 -  4.579:     5832 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.579 -  4.900:     7023 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.686 |       0.274 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.749)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2804   r_free= 0.2739   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.927411                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2664   r_free= 0.2581   ksol= 0.33   Bsol= 50.00   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-1.75,-1.56,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.898947                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.806541              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.357   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.062   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2664      final r-factor (work) = 0.1568          |
| start r-factor (free) = 0.2581      final r-factor (free) = 0.1742          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4885 = 2.81 * 0.50 * 5.9292 + 1.00 * 0.1683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8896 = 2.81 * 0.50 * 5.5796 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1568      final r-factor (work) = 0.1439          |
| start r-factor (free) = 0.1742      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3641 = 0.24 * 1.00 * 5.5796 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3224 = 0.24 * 1.00 * 5.3177 + 1.00 * 0.0282                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.749)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.45   16.65    None  None   None       |
|    all(noH): 2823   0      0.00    63.45   16.65    None  None   None       |
|    Sol.    : 438    0      6.74    62.80   37.43    None  None   None       |
|    Mac.    : 2385   0      0.00    63.45   12.84    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 -   6.345:  201   |   5:    31.723 -  38.068:   98        |
|      1:     6.345 -  12.689: 1278   |   6:    38.068 -  44.413:  102        |
|      2:    12.689 -  19.034:  652   |   7:    44.413 -  50.757:   85        |
|      3:    19.034 -  25.379:  216   |   8:    50.757 -  57.102:   55        |
|      4:    25.379 -  31.723:  118   |   9:    57.102 -  63.446:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1439 r_free = 0.1774             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1435 r_free = 0.1775             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1775   ksol= 0.33   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-1.75,-1.56,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.329225                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1416   r_free= 0.1759   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.47,-1.83,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.323313                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.880869              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.770  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.183473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.097   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1416      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1759      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7370 = 2.88 * 0.50 * 5.3297 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5951 = 2.88 * 0.50 * 5.2289 + 1.00 * 0.0633                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1508          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5346 = 0.18 * 1.00 * 5.2289 + 1.00 * 0.5752                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9498 = 0.18 * 1.00 * 5.1397 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.749)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.93    63.08   16.54    None  None   None       |
|    all(noH): 2823   0      1.93    63.08   16.54    None  None   None       |
|    Sol.    : 438    0      3.36    63.08   37.23    None  None   None       |
|    Mac.    : 2385   0      1.93    58.96   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.930 -   8.045:  471   |   5:    32.506 -  38.621:   99        |
|      1:     8.045 -  14.160: 1308   |   6:    38.621 -  44.736:   88        |
|      2:    14.160 -  20.275:  436   |   7:    44.736 -  50.851:   89        |
|      3:    20.275 -  26.391:  153   |   8:    50.851 -  56.967:   60        |
|      4:    26.391 -  32.506:  103   |   9:    56.967 -  63.082:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1508             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1507             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1507   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.47,-1.83,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1502   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-2.28,-1.46,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.304778              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.298  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.396565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.510  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1502      final r-factor (free) = 0.1509          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4167 = 1.30 * 0.50 * 5.1402 + 1.00 * 0.0633                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3977 = 1.30 * 0.50 * 5.1329 + 1.00 * 0.0491                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1509      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.5739 = 4.40 * 1.00 * 5.1329 + 1.00 * 0.0068                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.5350 = 4.40 * 1.00 * 5.1234 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.749)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.45   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    86.45   17.24    None  None   None       |
|    Sol.    : 438    0      3.91    78.20   40.25    None  None   None       |
|    Mac.    : 2385   0      0.00    86.45   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.645:  692   |   5:    43.226 -  51.871:  110        |
|      1:     8.645 -  17.290: 1351   |   6:    51.871 -  60.516:   75        |
|      2:    17.290 -  25.935:  294   |   7:    60.516 -  69.161:   41        |
|      3:    25.935 -  34.580:  128   |   8:    69.161 -  77.806:   16        |
|      4:    34.580 -  43.226:  110   |   9:    77.806 -  86.451:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1533             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1532             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1532   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-2.28,-1.46,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132747                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1532   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.05,-1.21,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132850                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.457520              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.626  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.093512              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.582  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3455 = 2.46 * 0.50 * 5.1242 + 1.00 * 0.0491                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3452 = 2.46 * 0.50 * 5.1137 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1063      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1515          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4880 = 0.09 * 1.00 * 5.1137 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4853 = 0.09 * 1.00 * 5.1240 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.749)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.48    79.50   16.19    None  None   None       |
|    all(noH): 2823   0      2.48    79.50   16.19    None  None   None       |
|    Sol.    : 438    0      5.82    69.40   35.61    None  None   None       |
|    Mac.    : 2385   0      2.48    79.50   12.62    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:     2.481 -  10.183: 1078   |   5:    40.992 -  48.695:   85        |
|      1:    10.183 -  17.885: 1043   |   6:    48.695 -  56.397:   61        |
|      2:    17.885 -  25.588:  242   |   7:    56.397 -  64.099:   19        |
|      3:    25.588 -  33.290:  131   |   8:    64.099 -  71.802:    7        |
|      4:    33.290 -  40.992:  155   |   9:    71.802 -  79.504:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1515             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1515             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1515   ksol= 0.33   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.05,-1.21,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116989                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1517   ksol= 0.32   Bsol= 42.11   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.99,-1.07,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117477                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.533392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.375  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.475686              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.956  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9902 = 1.53 * 0.50 * 5.1240 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9807 = 1.53 * 0.50 * 5.1238 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5674 = 1.48 * 1.00 * 5.1238 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5599 = 1.48 * 1.00 * 5.1170 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.749)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    88.26   16.74    None  None   None       |
|    all(noH): 2823   0      0.66    88.26   16.74    None  None   None       |
|    Sol.    : 438    0      5.61    78.71   38.82    None  None   None       |
|    Mac.    : 2385   0      0.66    88.26   12.68    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:     0.664 -   9.424:  935   |   5:    44.464 -  53.224:  106        |
|      1:     9.424 -  18.184: 1183   |   6:    53.224 -  61.984:   66        |
|      2:    18.184 -  26.944:  250   |   7:    61.984 -  70.744:   25        |
|      3:    26.944 -  35.704:  130   |   8:    70.744 -  79.504:    6        |
|      4:    35.704 -  44.464:  117   |   9:    79.504 -  88.264:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1534             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1084 r_free = 0.1535             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1535   ksol= 0.32   Bsol= 42.11   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.99,-1.07,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123123                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8294 -  4.7023 0.99   1401  157 0.0980 0.1251      5.3695      5.5224|
|  2:  4.7023 -  3.7522 0.99   1347  151 0.0838 0.1081      5.4159      5.6043|
|  3:  3.7522 -  3.2838 0.99   1323  148 0.1035 0.1488      5.4472      5.8344|
|  4:  3.2838 -  2.9862 0.99   1310  135 0.1161 0.1467      5.4171      5.5588|
|  5:  2.9862 -  2.7737 0.99   1309  150 0.1279 0.1618      5.2941      5.4879|
|  6:  2.7737 -  2.6111 0.98   1296  144 0.1215 0.1990      5.1942      5.4785|
|  7:  2.6111 -  2.4809 0.99   1289  153 0.1185 0.1517       5.132      5.2921|
|  8:  2.4809 -  2.3734 0.98   1309  134 0.1114 0.1636       5.055      5.3003|
|  9:  2.3734 -  2.2824 0.98   1284  146 0.1140 0.1888      4.9994      5.3314|
| 10:  2.2824 -  2.2039 0.97   1255  140 0.1102 0.1539      4.9467      5.1299|
| 11:  2.2039 -  2.1352 0.99   1293  145 0.1088 0.1793      4.9021      5.2488|
| 12:  2.1352 -  2.0743 0.98   1272  141 0.1062 0.1617      4.8316      5.1387|
| 13:  2.0743 -  2.0198 0.97   1254  134 0.1062 0.1713      4.7616      5.0245|
| 14:  2.0198 -  1.9707 0.54    688   81 0.1012 0.1710      4.6853      4.9369|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8294 -  4.7023  1401   157  0.94   8.81   0.98     0.95       6707.68|
|  2:  4.7023 -  3.7522  1347   151  0.96   7.63   1.02     1.00       8506.92|
|  3:  3.7522 -  3.2838  1323   148  0.94  10.84   1.02     1.02       9762.51|
|  4:  3.2838 -  2.9862  1310   135  0.93  12.79   1.01     1.00       9645.63|
|  5:  2.9862 -  2.7737  1309   150  0.90  15.32   0.99     0.96       7754.84|
|  6:  2.7737 -  2.6111  1296   144  0.90  16.04   0.98     0.95       6766.83|
|  7:  2.6111 -  2.4809  1289   153  0.91  14.91   0.98     0.96       5825.27|
|  8:  2.4809 -  2.3734  1309   134  0.91  14.56   0.99     0.97       5252.81|
|  9:  2.3734 -  2.2824  1284   146  0.91  15.34   1.00     0.96       4738.96|
| 10:  2.2824 -  2.2039  1255   140  0.90  15.49   0.99     0.95       4318.28|
| 11:  2.2039 -  2.1352  1293   145  0.91  15.56   0.99     0.96       4120.44|
| 12:  2.1352 -  2.0743  1272   141  0.92  14.64   1.00     0.99       3639.08|
| 13:  2.0743 -  2.0198  1254   134  0.91  15.65   1.00     0.98       3248.16|
| 14:  2.0198 -  1.9707   688    81  0.91  15.15   0.97     0.92       2711.16|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2711.16 max =         9762.51 mean =      6075.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.65|
|phase err.(test): min =        0.00 max =           89.50 mean =        13.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1534   ksol= 0.32   Bsol= 45.27   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-1.80,-0.90,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122708                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1534   ksol= 0.32   Bsol= 45.27   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-1.80,-0.90,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122708                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8294 -  4.7023 0.99   1401  157 0.0980 0.1255       5.369      5.5231|
|  2:  4.7023 -  3.7522 0.99   1347  151 0.0842 0.1083      5.4183       5.606|
|  3:  3.7522 -  3.2838 0.99   1323  148 0.1036 0.1488      5.4482      5.8347|
|  4:  3.2838 -  2.9862 0.99   1310  135 0.1159 0.1462      5.4159      5.5567|
|  5:  2.9862 -  2.7737 0.99   1309  150 0.1276 0.1616      5.2923      5.4864|
|  6:  2.7737 -  2.6111 0.98   1296  144 0.1213 0.1986      5.1927      5.4763|
|  7:  2.6111 -  2.4809 0.99   1289  153 0.1185 0.1515      5.1308      5.2909|
|  8:  2.4809 -  2.3734 0.98   1309  134 0.1113 0.1633      5.0541      5.2986|
|  9:  2.3734 -  2.2824 0.98   1284  146 0.1140 0.1893      4.9991      5.3328|
| 10:  2.2824 -  2.2039 0.97   1255  140 0.1102 0.1538      4.9465       5.129|
| 11:  2.2039 -  2.1352 0.99   1293  145 0.1087 0.1790      4.9017      5.2483|
| 12:  2.1352 -  2.0743 0.98   1272  141 0.1062 0.1617      4.8311      5.1383|
| 13:  2.0743 -  2.0198 0.97   1254  134 0.1062 0.1712      4.7612      5.0241|
| 14:  2.0198 -  1.9707 0.54    688   81 0.1013 0.1708      4.6849      4.9361|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8294 -  4.7023  1401   157  0.94   8.80   0.98     0.95       6692.59|
|  2:  4.7023 -  3.7522  1347   151  0.96   7.63   1.02     1.00       8522.68|
|  3:  3.7522 -  3.2838  1323   148  0.94  10.86   1.03     1.02       9784.15|
|  4:  3.2838 -  2.9862  1310   135  0.93  12.77   1.01     1.01       9622.74|
|  5:  2.9862 -  2.7737  1309   150  0.90  15.29   1.00     0.97       7730.19|
|  6:  2.7737 -  2.6111  1296   144  0.90  16.01   0.98     0.95       6744.75|
|  7:  2.6111 -  2.4809  1289   153  0.91  14.89   0.99     0.96       5802.74|
|  8:  2.4809 -  2.3734  1309   134  0.91  14.55   1.00     0.98       5239.50|
|  9:  2.3734 -  2.2824  1284   146  0.91  15.32   1.01     0.97       4732.23|
| 10:  2.2824 -  2.2039  1255   140  0.90  15.48   1.00     0.96       4315.92|
| 11:  2.2039 -  2.1352  1293   145  0.91  15.54   1.00     0.96       4114.34|
| 12:  2.1352 -  2.0743  1272   141  0.92  14.62   1.01     1.00       3634.01|
| 13:  2.0743 -  2.0198  1254   134  0.91  15.63   1.01     0.99       3244.51|
| 14:  2.0198 -  1.9707   688    81  0.91  15.15   0.98     0.93       2707.58|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2707.58 max =         9784.15 mean =      6067.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.64|
|phase err.(test): min =        0.00 max =           89.25 mean =        13.26|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.749)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.64    88.24   16.72    None  None   None       |
|    all(noH): 2823   0      0.64    88.24   16.72    None  None   None       |
|    Sol.    : 438    0      5.58    78.68   38.80    None  None   None       |
|    Mac.    : 2385   0      0.64    88.24   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.642 -   9.402:  935   |   5:    44.442 -  53.202:  106        |
|      1:     9.402 -  18.162: 1183   |   6:    53.202 -  61.962:   66        |
|      2:    18.162 -  26.922:  250   |   7:    61.962 -  70.722:   25        |
|      3:    26.922 -  35.682:  130   |   8:    70.722 -  79.482:    6        |
|      4:    35.682 -  44.442:  117   |   9:    79.482 -  88.242:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 285         
Filter by distance & map next to the model:
   mapped sites are within: 0.499 - 5.410
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 285
   mapped sites are within: 0.731 - 5.410

peak=    5.961 closest distance to " CB  ARG A 275 " =    0.965
peak=    5.372 closest distance to " CG  PRO A  54 " =    1.270
peak=    5.298 closest distance to " CB  GLN A 223 " =    1.416
peak=    5.042 closest distance to " O   HOH Z 126 " =    1.891
peak=    5.022 closest distance to " NH2 ARG A  56 " =    2.230
peak=    4.988 closest distance to " O   HOH Z 142 " =    1.640
peak=    4.947 closest distance to " CA  TYR A  30 " =    0.903
peak=    4.921 closest distance to " O   HOH Z 232 " =    2.410
peak=    4.757 closest distance to " CB  SER A  63 " =    1.165
peak=    4.658 closest distance to " CG  PRO A  90 " =    1.171
peak=    4.643 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.636 closest distance to " CG  PRO A 213 " =    1.265
peak=    4.612 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.541 closest distance to " CG  PRO A 198 " =    1.240
peak=    4.535 closest distance to " O   HOH Z 209 " =    2.233
peak=    4.528 closest distance to " C   PRO A 198 " =    1.487
peak=    4.517 closest distance to " O   HOH Z 402 " =    1.453
peak=    4.507 closest distance to " O   HOH Z 250 " =    1.489
peak=    4.488 closest distance to " O   HOH Z 236 " =    2.115
peak=    4.451 closest distance to " NE2 GLN A  11 " =    0.997
peak=    4.434 closest distance to " CB  ASN A 148 " =    1.454
peak=    4.415 closest distance to " CB  GLU A 152 " =    1.174
peak=    4.378 closest distance to " CB  ARG A  79 " =    1.302
peak=    4.378 closest distance to " O   HOH Z 427 " =    2.914
peak=    4.356 closest distance to " O   HOH Z 234 " =    3.689
peak=    4.354 closest distance to " CG  PRO A 243 " =    1.057
peak=    4.353 closest distance to " O   HOH Z 272 " =    1.842
peak=    4.346 closest distance to " O   HOH Z 298 " =    1.861
peak=    4.330 closest distance to " CB  ARG A 190 " =    1.715
peak=    4.278 closest distance to " O   HOH Z  15 " =    2.202
peak=    4.269 closest distance to " CZ  PHE A 218 " =    1.066
peak=    4.259 closest distance to " O   HOH Z 303 " =    2.040
peak=    4.243 closest distance to " O   HOH Z  78 " =    1.671
peak=    4.243 closest distance to " O   HOH Z 193 " =    1.744
peak=    4.208 closest distance to " O   HOH Z 369 " =    2.273
peak=    4.195 closest distance to " O   HOH Z 403 " =    1.765
peak=    4.162 closest distance to " O   HOH Z  97 " =    2.442
peak=    4.150 closest distance to " CG2 VAL A 257 " =    0.876
peak=    4.126 closest distance to " O   HOH Z 346 " =    1.692
peak=    4.112 closest distance to " CB  VAL A 265 " =    1.222
peak=    4.112 closest distance to " O   HOH Z 203 " =    1.711
peak=    4.102 closest distance to " CA  ARG A  36 " =    1.014
peak=    4.099 closest distance to " O   SER A  87 " =    2.187
peak=    4.091 closest distance to " ND2 ASN A 187 " =    1.441
peak=    4.081 closest distance to " O   HOH Z  43 " =    1.968
peak=    4.063 closest distance to " O   HOH Z  97 " =    1.969
peak=    4.057 closest distance to " CD2 TRP A 179 " =    1.362
peak=    4.040 closest distance to " O   HOH Z 128 " =    1.923
peak=    4.007 closest distance to " O   HOH Z 392 " =    2.871
peak=    4.003 closest distance to " O   HOH Z 158 " =    3.011
peak=    4.001 closest distance to " CB  TYR A 169 " =    0.738
peak=    3.993 closest distance to " CG1 ILE A  33 " =    1.249
peak=    3.977 closest distance to " O   HOH Z  54 " =    1.741
peak=    3.970 closest distance to " CB  GLU A 128 " =    1.082
peak=    3.956 closest distance to " CA  ASN A 215 " =    1.112
peak=    3.954 closest distance to " OG ASER A 258 " =    3.066
peak=    3.949 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.940 closest distance to " CB  LEU A 228 " =    1.065
peak=    3.917 closest distance to " NZ  LYS A 117 " =    3.164
peak=    3.915 closest distance to " O   HOH Z 389 " =    1.836
peak=    3.913 closest distance to " O   HOH Z 189 " =    2.296
peak=    3.906 closest distance to " CB  TRP A 266 " =    0.990
peak=    3.898 closest distance to " CG2 ILE A 120 " =    1.135
peak=    3.884 closest distance to " O   HOH Z 423 " =    1.968
peak=    3.875 closest distance to " O   HOH Z  40 " =    1.860
peak=    3.872 closest distance to " O   HOH Z 126 " =    2.119
peak=    3.869 closest distance to " CD  ARG A 269 " =    1.004
peak=    3.857 closest distance to " CA  ALA A  21 " =    1.127
peak=    3.856 closest distance to " CB  ARG A  79 " =    0.896
peak=    3.852 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.848 closest distance to " CB  GLU A 277 " =    3.564
peak=    3.844 closest distance to " OD1 ASN A  69 " =    2.554
peak=    3.803 closest distance to " CG  ARG A  66 " =    2.505
peak=    3.798 closest distance to " CB  VAL A 202 " =    1.498
peak=    3.778 closest distance to " CB  SER A   3 " =    1.236
peak=    3.777 closest distance to " NH2BARG A 145 " =    2.031
peak=    3.772 closest distance to " O   HOH Z 280 " =    2.923
peak=    3.750 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.739 closest distance to " O   HOH Z 344 " =    3.084
peak=    3.736 closest distance to " OE1 GLU A   2 " =    2.260
peak=    3.729 closest distance to " CG1BVAL A  72 " =    1.636
peak=    3.728 closest distance to " O   HOH Z 421 " =    1.686
peak=    3.721 closest distance to " O   HOH Z  44 " =    1.877
peak=    3.719 closest distance to " O   HOH Z 407 " =    2.687
peak=    3.716 closest distance to " O   HOH Z 261 " =    2.119
peak=    3.714 closest distance to " O   HOH Z 245 " =    1.306
peak=    3.703 closest distance to " CA  ARG A 195 " =    1.290
peak=    3.700 closest distance to " N   TYR A 116 " =    1.566
peak=    3.697 closest distance to " O   HOH Z  19 " =    2.157
peak=    3.696 closest distance to " CB  ALA A 291 " =    1.243
peak=    3.693 closest distance to " CB  GLU A  46 " =    1.019
peak=    3.690 closest distance to " O   HOH Z  59 " =    2.092
peak=    3.688 closest distance to " O   HOH Z 368 " =    2.092
peak=    3.685 closest distance to " O   HOH Z 227 " =    1.601
peak=    3.657 closest distance to " O   HOH Z 327 " =    1.549
peak=    3.655 closest distance to " O   HOH Z 371 " =    3.248
peak=    3.655 closest distance to " O   HOH Z 132 " =    2.743
peak=    3.655 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.647 closest distance to " OD2 ASP A 286 " =    2.794
peak=    3.631 closest distance to " O   HOH Z 265 " =    2.306
peak=    3.624 closest distance to " CB  THR A  31 " =    1.623
peak=    3.621 closest distance to " O   HOH Z 172 " =    3.773
peak=    3.616 closest distance to " CB  SER A  26 " =    1.667
peak=    3.615 closest distance to " CB  ASN A 110 " =    1.115
peak=    3.614 closest distance to " O   HOH Z  66 " =    2.142
peak=    3.604 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.597 closest distance to " CB  TRP A 179 " =    1.284
peak=    3.593 closest distance to " O   HOH Z 147 " =    1.753
peak=    3.592 closest distance to " CG2 ILE A  20 " =    1.444
peak=    3.589 closest distance to " CB  ASP A 140 " =    1.001
peak=    3.588 closest distance to " O   HOH Z 261 " =    1.720
peak=    3.578 closest distance to " CE1 TYR A 186 " =    1.294
peak=    3.576 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.576 closest distance to " CA  ASN A 176 " =    1.143
peak=    3.573 closest distance to " C   ILE A 106 " =    1.910
peak=    3.572 closest distance to " CD2 LEU A 297 " =    0.884
peak=    3.571 closest distance to " CA  LYS A 117 " =    1.255
peak=    3.570 closest distance to " CA  ALA A  84 " =    1.181
peak=    3.566 closest distance to " CB  SER A  62 " =    0.928
peak=    3.550 closest distance to " O   HOH Z 214 " =    2.099
peak=    3.545 closest distance to " CB  TYR A 169 " =    0.867
peak=    3.544 closest distance to " N   ASN A  39 " =    1.235
peak=    3.540 closest distance to " O   HOH Z 368 " =    3.668
peak=    3.538 closest distance to " O   HOH Z 248 " =    1.651
peak=    3.532 closest distance to " O   HOH Z 406 " =    1.519
peak=    3.532 closest distance to " CA  MET A  40 " =    1.111
peak=    3.531 closest distance to " CB  ILE A 120 " =    1.284
peak=    3.528 closest distance to " CG AARG A 275 " =    1.146
peak=    3.523 closest distance to " CA  MET A 105 " =    1.045
peak=    3.517 closest distance to " O   HOH Z  21 " =    1.818
peak=    3.516 closest distance to " O   HOH Z 417 " =    3.069
peak=    3.513 closest distance to " O   HOH Z 313 " =    1.907
peak=    3.512 closest distance to " O   HOH Z 411 " =    3.846
peak=    3.512 closest distance to " O   HOH Z 357 " =    1.937
peak=    3.510 closest distance to " CB  ALA A 248 " =    1.342
peak=    3.508 closest distance to " O   HOH Z 305 " =    3.550
peak=    3.501 closest distance to " CA  ARG A 275 " =    1.944
peak=    3.491 closest distance to " N   ARG A 156 " =    1.363
peak=    3.489 closest distance to " CD1 LEU A  96 " =    0.744
peak=    3.487 closest distance to " O   THR A 220 " =    1.255
peak=    3.487 closest distance to " CB  GLN A  88 " =    1.136
peak=    3.486 closest distance to " O   HOH Z 185 " =    1.723
peak=    3.471 closest distance to " O   HOH Z 337 " =    3.618
peak=    3.460 closest distance to " O   HOH Z 426 " =    1.557
peak=    3.457 closest distance to " NE2 GLN A  77 " =    3.185
peak=    3.455 closest distance to " O   ALA A 165 " =    1.476
peak=    3.452 closest distance to " CZ2 TRP A 179 " =    1.723
peak=    3.451 closest distance to " O   HOH Z 173 " =    1.975
peak=    3.449 closest distance to " CD1 ILE A 106 " =    0.854
peak=    3.442 closest distance to " O   HOH Z  10 " =    1.782
peak=    3.440 closest distance to " CB  ALA A 114 " =    1.086
peak=    3.426 closest distance to " CG2BVAL A  41 " =    0.857
peak=    3.419 closest distance to " CA  THR A 221 " =    0.994
peak=    3.416 closest distance to " CD  LYS A  76 " =    1.980
peak=    3.410 closest distance to " CA  ALA A 291 " =    0.798
peak=    3.408 closest distance to " CB  SER A 141 " =    1.033
peak=    3.403 closest distance to " CA  ASP A 162 " =    1.061
peak=    3.402 closest distance to " CD  LYS A 166 " =    1.255
peak=    3.396 closest distance to " NH1AARG A 145 " =    1.213
peak=    3.395 closest distance to " O   HOH Z 180 " =    2.226
peak=    3.395 closest distance to " O   HOH Z 365 " =    2.855
peak=    3.391 closest distance to " CA  ASN A 217 " =    1.209
peak=    3.387 closest distance to " CG  LEU A 167 " =    1.252
peak=    3.384 closest distance to " CA  ALA A  51 " =    0.877
peak=    3.382 closest distance to " O   HOH Z 299 " =    4.385
peak=    3.376 closest distance to " CD1AILE A 234 " =    0.960
peak=    3.373 closest distance to " CA  ASP A 140 " =    1.130
peak=    3.372 closest distance to " O   HOH Z 132 " =    2.508
peak=    3.369 closest distance to " O   HOH Z 425 " =    1.948
peak=    3.366 closest distance to " O   HOH Z  80 " =    1.683
peak=    3.366 closest distance to " CB  SER A 212 " =    1.083
peak=    3.365 closest distance to " O   HOH Z 148 " =    3.333
peak=    3.364 closest distance to " O   HOH Z 187 " =    2.257
peak=    3.363 closest distance to " CG  GLN A  58 " =    2.709
peak=    3.363 closest distance to " OH  TYR A 116 " =    1.028
peak=    3.356 closest distance to " CB  GLN A 278 " =    0.882
peak=    3.356 closest distance to " O   HOH Z 325 " =    2.487
peak=    3.345 closest distance to " OG BSER A 164 " =    2.245
peak=    3.336 closest distance to " CG2 VAL A  78 " =    0.887
peak=    3.335 closest distance to " O   HOH Z   1 " =    1.979
peak=    3.332 closest distance to " O   HOH Z 403 " =    1.355
peak=    3.331 closest distance to " C   TYR A 214 " =    1.423
peak=    3.330 closest distance to " CB  ARG A 139 " =    0.870
peak=    3.329 closest distance to " O   HOH Z 108 " =    2.612
peak=    3.327 closest distance to " O   HOH Z 273 " =    2.781
peak=    3.323 closest distance to " O  BHOH Z  74 " =    1.336
peak=    3.321 closest distance to " CB  HIS A 108 " =    0.849
peak=    3.319 closest distance to " CB  GLN A  89 " =    1.361
peak=    3.318 closest distance to " CA  THR A 264 " =    0.885
peak=    3.315 closest distance to " O   HOH Z  49 " =    2.124
peak=    3.315 closest distance to " O   HOH Z  88 " =    2.992
peak=    3.313 closest distance to " CG  MET A 185 " =    1.128
peak=    3.312 closest distance to " O   HOH Z 193 " =    2.045
peak=    3.310 closest distance to " CA  ALA A 248 " =    1.234
peak=    3.308 closest distance to " CD  LYS A 119 " =    1.341
peak=    3.307 closest distance to " O   HOH Z  66 " =    2.138
peak=    3.305 closest distance to " CB  GLN A 205 " =    1.104
peak=    3.303 closest distance to " CB  ALA A  34 " =    1.120
peak=    3.299 closest distance to " CA  ILE A 234 " =    0.929
peak=    3.299 closest distance to " O   HOH Z  88 " =    2.550
peak=    3.295 closest distance to " CA  ALA A  43 " =    1.267
peak=    3.295 closest distance to " O   HOH Z 393 " =    3.229
peak=    3.294 closest distance to " ND2 ASN A 110 " =    1.641
peak=    3.291 closest distance to " CG  GLN A  77 " =    2.067
peak=    3.290 closest distance to " N   PHE A 130 " =    1.233
peak=    3.289 closest distance to " CB  PRO A 198 " =    1.129
peak=    3.287 closest distance to " CG  LYS A  76 " =    0.986
peak=    3.287 closest distance to " O   HOH Z 163 " =    1.893
peak=    3.283 closest distance to " O  BHOH Z 338 " =    2.301
peak=    3.278 closest distance to " CB  ASN A 215 " =    1.184
peak=    3.278 closest distance to " O   HOH Z 435 " =    1.849
peak=    3.277 closest distance to " O   HOH Z 336 " =    1.617
peak=    3.275 closest distance to " CA  GLY A  80 " =    0.859
peak=    3.274 closest distance to " CG2AVAL A 121 " =    2.222
peak=    3.265 closest distance to " O   HOH Z  35 " =    2.429
peak=    3.259 closest distance to " CD BLYS A 290 " =    1.161
peak=    3.252 closest distance to " O   HOH Z 267 " =    2.006
peak=    3.248 closest distance to " CG  GLN A  11 " =    1.449
peak=    3.248 closest distance to " O   HOH Z 279 " =    2.159
peak=    3.246 closest distance to " CG2 VAL A 197 " =    1.114
peak=    3.246 closest distance to " O   HOH Z  61 " =    1.462
peak=    3.239 closest distance to " CG  GLU A  37 " =    0.935
peak=    3.235 closest distance to " O   HOH Z 298 " =    2.300
peak=    3.235 closest distance to " O   HOH Z 345 " =    3.114
peak=    3.227 closest distance to " CE  LYS A 119 " =    1.150
peak=    3.226 closest distance to " CZ  PHE A  38 " =    1.301
peak=    3.221 closest distance to " CE  LYS A  48 " =    1.092
peak=    3.218 closest distance to " CB  MET A  47 " =    0.990
peak=    3.218 closest distance to " O   HOH Z 342 " =    0.878
peak=    3.216 closest distance to " O   HOH Z 359 " =    1.380
peak=    3.213 closest distance to " CB  TYR A 116 " =    0.731
peak=    3.211 closest distance to " CB  SER A 273 " =    0.842
peak=    3.209 closest distance to " OG1 THR A 294 " =    2.397
peak=    3.205 closest distance to " CB  THR A 279 " =    1.617
peak=    3.200 closest distance to " N   VAL A 265 " =    1.099
peak=    3.195 closest distance to " CB  GLN A 103 " =    0.832
peak=    3.194 closest distance to " O   ASN A  74 " =    1.633
peak=    3.189 closest distance to " O   HOH Z 430 " =    5.410
peak=    3.179 closest distance to " O   HOH Z 353 " =    2.591
peak=    3.173 closest distance to " O   HOH Z 380 " =    1.920
peak=    3.168 closest distance to " CA  ARG A 159 " =    1.305
peak=    3.168 closest distance to " CB  VAL A 126 " =    1.101
peak=    3.165 closest distance to " O   ALA A   1 " =    1.701
peak=    3.161 closest distance to " O   HOH Z 329 " =    3.922
peak=    3.160 closest distance to " CD2 HIS A  81 " =    1.062
peak=    3.160 closest distance to " CG  MET A 113 " =    1.081
peak=    3.154 closest distance to " CA  VAL A 125 " =    1.018
peak=    3.153 closest distance to " O   HOH Z 391 " =    2.942
peak=    3.152 closest distance to " ND2 ASN A 249 " =    0.930
peak=    3.152 closest distance to " ND1 HIS A  81 " =    1.622
peak=    3.149 closest distance to " O   HOH Z 171 " =    1.835
peak=    3.146 closest distance to " CD  ARG A  36 " =    0.982
peak=    3.146 closest distance to " O   HOH Z 261 " =    2.278
peak=    3.145 closest distance to " O   HOH Z 257 " =    2.207
peak=    3.144 closest distance to " CB  PRO A 243 " =    1.629
peak=    3.135 closest distance to " CA  ALA A 233 " =    1.385
peak=    3.135 closest distance to " CG1 ILE A 151 " =    1.005
peak=    3.134 closest distance to " O   HOH Z  44 " =    3.328
peak=    3.133 closest distance to " O   HOH Z 392 " =    1.908
peak=    3.132 closest distance to " O   HOH Z 183 " =    1.391
peak=    3.125 closest distance to " O   HOH Z 417 " =    2.206
peak=    3.119 closest distance to " CB  ARG A 269 " =    0.750
peak=    3.116 closest distance to " O   HOH Z 389 " =    1.727
peak=    3.112 closest distance to " CA  ASP A 191 " =    1.211
peak=    3.107 closest distance to " CA  TYR A 116 " =    1.421
peak=    3.106 closest distance to " CD2 TYR A  30 " =    1.011
peak=    3.101 closest distance to " O   HOH Z 433 " =    1.720
peak=    3.093 closest distance to " CD2 TYR A 186 " =    1.069
peak=    3.093 closest distance to " N   ASP A 162 " =    1.221
peak=    3.090 closest distance to " CA  ILE A  33 " =    1.321
peak=    3.088 closest distance to " O   HOH Z 156 " =    2.909
peak=    3.087 closest distance to " O   HOH Z 298 " =    2.693
peak=    3.084 closest distance to " CA  ARG A 102 " =    1.047
peak=    3.080 closest distance to " O   HOH Z 425 " =    1.282
peak=    3.077 closest distance to " NE2 GLN A  58 " =    2.725
peak=    3.074 closest distance to " O   HOH Z 129 " =    3.635
peak=    3.061 closest distance to " O   HOH Z 419 " =    1.957
peak=    3.056 closest distance to " O   HOH Z 271 " =    2.230
peak=    3.054 closest distance to " CA  LYS A 290 " =    1.227
peak=    3.054 closest distance to " O   HOH Z 371 " =    1.505
peak=    3.037 closest distance to " O   HOH Z 285 " =    2.874

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.833 - 5.891
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 192
   mapped sites are within: 0.833 - 5.891

peak=   -4.853 closest distance to " O   HOH Z 266 " =    5.033
peak=   -4.694 closest distance to " C   HIS A 108 " =    1.101
peak=   -4.485 closest distance to " CD  GLN A  58 " =    1.090
peak=   -4.441 closest distance to " SG  CYS A 254 " =    3.401
peak=   -4.438 closest distance to " CD  ARG A 156 " =    2.064
peak=   -4.325 closest distance to " CG  GLN A 223 " =    2.013
peak=   -4.321 closest distance to " OG BSER A 134 " =    1.199
peak=   -4.312 closest distance to " CG1 VAL A 112 " =    2.812
peak=   -4.269 closest distance to " O   HOH Z 198 " =    1.800
peak=   -4.261 closest distance to " CB  PRO A 243 " =    2.635
peak=   -4.243 closest distance to " O   HOH Z 372 " =    2.264
peak=   -4.193 closest distance to " O   VAL A  67 " =    2.681
peak=   -4.132 closest distance to " CB  PRO A 280 " =    2.168
peak=   -4.051 closest distance to " CA  VAL A  67 " =    2.929
peak=   -4.012 closest distance to " O   HOH Z 231 " =    2.264
peak=   -3.995 closest distance to " ND2 ASN A  45 " =    1.363
peak=   -3.944 closest distance to " CZ  TYR A 169 " =    1.776
peak=   -3.916 closest distance to " O   HOH Z 290 " =    1.197
peak=   -3.915 closest distance to " ND2 ASN A  45 " =    1.029
peak=   -3.913 closest distance to " OXT GLY A 302 " =    2.784
peak=   -3.899 closest distance to " CZ3 TRP A 179 " =    1.243
peak=   -3.899 closest distance to " OG  SER A  97 " =    2.159
peak=   -3.889 closest distance to " CB  ASP A 132 " =    2.274
peak=   -3.878 closest distance to " N   ALA A  43 " =    2.625
peak=   -3.878 closest distance to " CB  ALA A 161 " =    2.527
peak=   -3.875 closest distance to " O   PRO A 198 " =    1.238
peak=   -3.875 closest distance to " CB  ASN A  39 " =    2.287
peak=   -3.869 closest distance to " CB  PHE A 192 " =    1.922
peak=   -3.869 closest distance to " O   HOH Z 353 " =    2.147
peak=   -3.854 closest distance to " O   HOH Z  13 " =    1.608
peak=   -3.847 closest distance to " ND2 ASN A 187 " =    1.513
peak=   -3.821 closest distance to " CA  GLY A 203 " =    2.430
peak=   -3.814 closest distance to " CE2 TYR A  30 " =    2.781
peak=   -3.814 closest distance to " CG2 ILE A 263 " =    2.258
peak=   -3.810 closest distance to " O   HOH Z 126 " =    1.879
peak=   -3.788 closest distance to " CD  ARG A 139 " =    1.553
peak=   -3.782 closest distance to " O   HOH Z 407 " =    2.820
peak=   -3.736 closest distance to " O   HOH Z 114 " =    3.193
peak=   -3.726 closest distance to " OD2 ASP A 191 " =    1.409
peak=   -3.720 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.719 closest distance to " N   GLN A  58 " =    1.622
peak=   -3.704 closest distance to " O   HOH Z 165 " =    2.003
peak=   -3.681 closest distance to " CD1 LEU A 255 " =    2.762
peak=   -3.673 closest distance to " CG1 VAL A  78 " =    3.031
peak=   -3.667 closest distance to " OD2 ASP A 171 " =    2.398
peak=   -3.658 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.645 closest distance to " CD1 LEU A 101 " =    2.356
peak=   -3.643 closest distance to " O   PRO A 163 " =    2.054
peak=   -3.633 closest distance to " CB  PHE A 208 " =    2.279
peak=   -3.626 closest distance to " OG  SER A   3 " =    1.697
peak=   -3.625 closest distance to " CG  ASP A 231 " =    0.833
peak=   -3.620 closest distance to " O   HOH Z 389 " =    1.748
peak=   -3.615 closest distance to " O   PHE A 218 " =    1.614
peak=   -3.597 closest distance to " O   HOH Z  63 " =    1.526
peak=   -3.587 closest distance to " N   ALA A 248 " =    1.577
peak=   -3.582 closest distance to " O   HOH Z 196 " =    2.002
peak=   -3.582 closest distance to " O   GLN A  89 " =    1.512
peak=   -3.579 closest distance to " O   SER A 210 " =    1.970
peak=   -3.568 closest distance to " CG  PHE A 283 " =    2.676
peak=   -3.568 closest distance to " CD1 ILE A 239 " =    2.303
peak=   -3.565 closest distance to " O   HOH Z 102 " =    1.593
peak=   -3.556 closest distance to " O   HOH Z 292 " =    4.464
peak=   -3.556 closest distance to " CB  ALA A 291 " =    2.330
peak=   -3.537 closest distance to " O   HOH Z 185 " =    2.348
peak=   -3.536 closest distance to " CB  ALA A 248 " =    2.256
peak=   -3.536 closest distance to " CB  ASP A 286 " =    1.838
peak=   -3.527 closest distance to " CZ  PHE A  59 " =    1.544
peak=   -3.527 closest distance to " CB  ALA A 248 " =    2.038
peak=   -3.524 closest distance to " O   HOH Z  10 " =    1.520
peak=   -3.507 closest distance to " O   HOH Z 362 " =    5.891
peak=   -3.500 closest distance to " O   HOH Z 211 " =    1.690
peak=   -3.500 closest distance to " CD1 LEU A  25 " =    2.503
peak=   -3.489 closest distance to " O   HOH Z 243 " =    2.040
peak=   -3.481 closest distance to " CG  ARG A 269 " =    2.276
peak=   -3.481 closest distance to " NE2 GLN A  88 " =    1.765
peak=   -3.472 closest distance to " O   ALA A 161 " =    1.668
peak=   -3.471 closest distance to " CG  GLU A 277 " =    1.210
peak=   -3.465 closest distance to " O   VAL A 174 " =    2.120
peak=   -3.463 closest distance to " O   ALA A  34 " =    2.302
peak=   -3.462 closest distance to " CD1 PHE A  59 " =    1.889
peak=   -3.462 closest distance to " O   HOH Z 394 " =    1.504
peak=   -3.457 closest distance to " N   THR A  52 " =    1.701
peak=   -3.455 closest distance to " CD  ARG A 195 " =    5.168
peak=   -3.450 closest distance to " CB  ALA A  43 " =    2.450
peak=   -3.448 closest distance to " C   LEU A 143 " =    1.046
peak=   -3.432 closest distance to " O   HOH Z 166 " =    1.922
peak=   -3.421 closest distance to " O   MET A  40 " =    2.740
peak=   -3.418 closest distance to " CD  GLU A 236 " =    1.046
peak=   -3.410 closest distance to " C   THR A 279 " =    1.207
peak=   -3.403 closest distance to " CB  ALA A 291 " =    2.265
peak=   -3.399 closest distance to " OD1 ASN A 148 " =    1.500
peak=   -3.399 closest distance to " CG  GLU A  53 " =    1.437
peak=   -3.393 closest distance to " O   SER A  95 " =    1.576
peak=   -3.393 closest distance to " O   HOH Z 171 " =    2.008
peak=   -3.382 closest distance to " NH2AARG A 275 " =    5.032
peak=   -3.370 closest distance to " CA  GLY A 133 " =    1.988
peak=   -3.370 closest distance to " O   HOH Z 313 " =    1.948
peak=   -3.366 closest distance to " O   HOH Z 317 " =    1.592
peak=   -3.365 closest distance to " O   HOH Z 385 " =    2.105
peak=   -3.363 closest distance to " OG BSER A 134 " =    1.773
peak=   -3.361 closest distance to " O   ALA A  10 " =    1.743
peak=   -3.347 closest distance to " N   ALA A 226 " =    1.949
peak=   -3.339 closest distance to " O   HOH Z 123 " =    2.237
peak=   -3.337 closest distance to " O   HOH Z  11 " =    1.738
peak=   -3.332 closest distance to " NH1 ARG A  66 " =    1.291
peak=   -3.328 closest distance to " O   HOH Z   6 " =    2.134
peak=   -3.327 closest distance to " OD2 ASP A  50 " =    2.300
peak=   -3.325 closest distance to " O   HOH Z  44 " =    2.238
peak=   -3.320 closest distance to " O   LEU A 167 " =    1.488
peak=   -3.320 closest distance to " OE1 GLN A 194 " =    1.742
peak=   -3.312 closest distance to " CE  MET A 105 " =    2.239
peak=   -3.312 closest distance to " CB  GLN A  11 " =    1.773
peak=   -3.309 closest distance to " CB  PRO A 163 " =    2.446
peak=   -3.301 closest distance to " N   ASP A 286 " =    2.363
peak=   -3.298 closest distance to " CD2 LEU A 300 " =    2.833
peak=   -3.290 closest distance to " O   GLY A  75 " =    1.745
peak=   -3.286 closest distance to " CB  TYR A  15 " =    2.188
peak=   -3.283 closest distance to " CG1 VAL A 230 " =    2.022
peak=   -3.283 closest distance to " O   HOH Z 369 " =    2.129
peak=   -3.282 closest distance to " O   HOH Z 252 " =    3.713
peak=   -3.280 closest distance to " O   HOH Z 166 " =    1.577
peak=   -3.266 closest distance to " OD1 ASP A 171 " =    1.528
peak=   -3.266 closest distance to " CD2 TYR A 293 " =    1.993
peak=   -3.265 closest distance to " O   ALA A 292 " =    2.005
peak=   -3.263 closest distance to " OG  SER A  62 " =    1.769
peak=   -3.261 closest distance to " O   HOH Z 111 " =    3.706
peak=   -3.261 closest distance to " CD2 LEU A 237 " =    2.285
peak=   -3.261 closest distance to " O   HOH Z 283 " =    2.335
peak=   -3.240 closest distance to " CE3 TRP A 150 " =    2.136
peak=   -3.239 closest distance to " O   SER A 135 " =    1.516
peak=   -3.238 closest distance to " O   HOH Z  43 " =    1.690
peak=   -3.233 closest distance to " O   HOH Z  71 " =    1.959
peak=   -3.230 closest distance to " O   HOH Z 414 " =    1.449
peak=   -3.230 closest distance to " O   HOH Z  37 " =    1.727
peak=   -3.223 closest distance to " O   HOH Z   6 " =    1.512
peak=   -3.223 closest distance to " O   HOH Z 311 " =    3.583
peak=   -3.218 closest distance to " C   MET A 188 " =    1.423
peak=   -3.217 closest distance to " O   HOH Z 134 " =    2.943
peak=   -3.214 closest distance to " NE2 GLN A 194 " =    1.803
peak=   -3.212 closest distance to " O   HOH Z 244 " =    2.079
peak=   -3.209 closest distance to " O   HOH Z 298 " =    1.227
peak=   -3.205 closest distance to " O   HOH Z 250 " =    1.401
peak=   -3.202 closest distance to " O   HOH Z 191 " =    5.794
peak=   -3.202 closest distance to " C   ALA A 158 " =    1.377
peak=   -3.202 closest distance to " ND2 ASN A 249 " =    2.325
peak=   -3.201 closest distance to " CE2 PHE A 218 " =    2.442
peak=   -3.201 closest distance to " CD2 LEU A 237 " =    2.387
peak=   -3.198 closest distance to " NE2 GLN A 278 " =    1.816
peak=   -3.197 closest distance to " CD2 PHE A 225 " =    1.207
peak=   -3.191 closest distance to " O   GLY A 196 " =    0.961
peak=   -3.187 closest distance to " OD2 ASP A  50 " =    1.506
peak=   -3.187 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.186 closest distance to " CD1 LEU A 228 " =    2.047
peak=   -3.185 closest distance to " O   HOH Z  52 " =    1.449
peak=   -3.182 closest distance to " CA  ASN A 127 " =    1.325
peak=   -3.168 closest distance to " CB  TRP A  85 " =    2.587
peak=   -3.167 closest distance to " CZ  PHE A 130 " =    0.945
peak=   -3.164 closest distance to " OE2 GLU A 152 " =    1.266
peak=   -3.160 closest distance to " SG ACYS A 201 " =    2.038
peak=   -3.160 closest distance to " O   HOH Z 177 " =    1.724
peak=   -3.158 closest distance to " O   LEU A 101 " =    2.151
peak=   -3.157 closest distance to " O   ILE A 120 " =    1.417
peak=   -3.155 closest distance to " O   HOH Z  77 " =    2.161
peak=   -3.155 closest distance to " ND2 ASN A  39 " =    1.214
peak=   -3.153 closest distance to " O   HOH Z 421 " =    3.303
peak=   -3.150 closest distance to " CG2 VAL A 189 " =    2.169
peak=   -3.150 closest distance to " CG  GLU A   2 " =    1.907
peak=   -3.150 closest distance to " NH2 ARG A  79 " =    2.043
peak=   -3.147 closest distance to " CA  GLY A 241 " =    3.250
peak=   -3.146 closest distance to " CG1AVAL A  41 " =    2.815
peak=   -3.143 closest distance to " CB  LEU A  83 " =    2.374
peak=   -3.141 closest distance to " O   HOH Z 174 " =    4.167
peak=   -3.140 closest distance to " O   TRP A  92 " =    1.750
peak=   -3.140 closest distance to " O   ILE A 106 " =    1.794
peak=   -3.130 closest distance to " CA  GLY A 241 " =    2.360
peak=   -3.128 closest distance to " OG1 THR A 246 " =    1.377
peak=   -3.128 closest distance to " NH2 ARG A  79 " =    1.587
peak=   -3.120 closest distance to " O   HOH Z 210 " =    1.098
peak=   -3.114 closest distance to " NH1 ARG A 195 " =    2.573
peak=   -3.113 closest distance to " O   HOH Z 234 " =    4.012
peak=   -3.104 closest distance to " O   HOH Z 377 " =    1.704
peak=   -3.103 closest distance to " C   ASP A 231 " =    2.611
peak=   -3.092 closest distance to " CD2 PHE A  61 " =    2.496
peak=   -3.085 closest distance to " CE1 TYR A 247 " =    2.779
peak=   -3.082 closest distance to " O   HOH Z 339 " =    1.740
peak=   -3.076 closest distance to " O   HOH Z 397 " =    1.153
peak=   -3.067 closest distance to " O   HOH Z  76 " =    1.987
peak=   -3.067 closest distance to " O   HOH Z 361 " =    3.403
peak=   -3.063 closest distance to " O   ALA A  51 " =    1.357
peak=   -3.042 closest distance to " OG  SER A  97 " =    2.038
peak=   -3.023 closest distance to " ND2 ASN A  60 " =    1.369
peak=   -3.001 closest distance to " CB  ASN A  39 " =    2.108

================= 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    :  0.2804 0.2739   5.927411e+00   5.895803e+00
   1_bss:  0.2664 0.2581   5.898947e+00   5.866239e+00
   1_xyz:  0.1568 0.1742   5.381540e+00   5.477550e+00
   1_adp:  0.1439 0.1774   5.330278e+00   5.506846e+00
   1_occ:  0.1435 0.1775   5.329225e+00   5.506196e+00
   2_bss:  0.1416 0.1759   5.323313e+00   5.497316e+00
   2_xyz:  0.1160 0.1539   5.154351e+00   5.367064e+00
   2_adp:  0.1127 0.1508   5.128614e+00   5.345427e+00
   2_occ:  0.1126 0.1507   5.128284e+00   5.345262e+00
   3_bss:  0.1126 0.1502   5.127891e+00   5.342844e+00
   3_xyz:  0.1133 0.1509   5.135296e+00   5.349350e+00
   3_adp:  0.1110 0.1533   5.132699e+00   5.363445e+00
   3_occ:  0.1110 0.1532   5.132747e+00   5.363697e+00
   4_bss:  0.1109 0.1532   5.132850e+00   5.363743e+00
   4_xyz:  0.1063 0.1532   5.110584e+00   5.359621e+00
   4_adp:  0.1091 0.1515   5.116898e+00   5.350429e+00
   4_occ:  0.1090 0.1515   5.116989e+00   5.350978e+00
   5_bss:  0.1090 0.1517   5.117477e+00   5.351787e+00
   5_xyz:  0.1105 0.1524   5.127950e+00   5.359852e+00
   5_adp:  0.1085 0.1534   5.122959e+00   5.366950e+00
   5_occ:  0.1084 0.1535   5.123123e+00   5.367324e+00
   5_bss:  0.1083 0.1534   5.122708e+00   5.366820e+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:  0.330  50.000  -0.809  -1.752  -1.563  -0.000  -0.000  -0.000
   1_xyz:  0.330  50.000  -0.809  -1.752  -1.563  -0.000  -0.000  -0.000
   1_adp:  0.330  50.000  -0.809  -1.752  -1.563  -0.000  -0.000  -0.000
   1_occ:  0.330  50.000  -0.809  -1.752  -1.563  -0.000  -0.000  -0.000
   2_bss:  0.327  50.000  -2.867  -2.471  -1.826  -0.000  -0.000  -0.000
   2_xyz:  0.327  50.000  -2.867  -2.471  -1.826  -0.000  -0.000  -0.000
   2_adp:  0.327  50.000  -2.867  -2.471  -1.826  -0.000  -0.000  -0.000
   2_occ:  0.327  50.000  -2.867  -2.471  -1.826  -0.000  -0.000  -0.000
   3_bss:  0.327  50.000  -2.996  -2.275  -1.456  -0.000  -0.000  -0.000
   3_xyz:  0.327  50.000  -2.996  -2.275  -1.456  -0.000  -0.000  -0.000
   3_adp:  0.327  50.000  -2.996  -2.275  -1.456  -0.000  -0.000  -0.000
   3_occ:  0.327  50.000  -2.996  -2.275  -1.456  -0.000  -0.000  -0.000
   4_bss:  0.327  50.000  -2.838  -2.052  -1.210  -0.000  -0.000  -0.000
   4_xyz:  0.327  50.000  -2.838  -2.052  -1.210  -0.000  -0.000  -0.000
   4_adp:  0.327  50.000  -2.838  -2.052  -1.210  -0.000  -0.000  -0.000
   4_occ:  0.327  50.000  -2.838  -2.052  -1.210  -0.000  -0.000  -0.000
   5_bss:  0.321  42.113  -2.811  -1.988  -1.072  -0.000  -0.000  -0.000
   5_xyz:  0.321  42.113  -2.811  -1.988  -1.072  -0.000  -0.000  -0.000
   5_adp:  0.321  42.113  -2.811  -1.988  -1.072  -0.000  -0.000  -0.000
   5_occ:  0.321  42.113  -2.811  -1.988  -1.072  -0.000  -0.000  -0.000
   5_bss:  0.320  45.269  -2.627  -1.803  -0.902  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  26.998 0.7945  0.9746    21302.772
   1_bss:  25.696 0.8067  0.9462    18294.308
   1_xyz:  15.858 0.9002  1.0073     7677.456
   1_adp:  16.540 0.8940  1.0039     8067.536
   1_occ:  16.539 0.8940  1.0036     8060.728
   2_bss:  16.331 0.8957  0.9673     7874.194
   2_xyz:  13.814 0.9162  0.9748     6084.582
   2_adp:  13.363 0.9198  0.9716     5882.131
   2_occ:  13.358 0.9198  0.9715     5871.321
   3_bss:  13.325 0.9201  0.9763     5828.321
   3_xyz:  13.318 0.9205  0.9771     5894.969
   3_adp:  13.582 0.9185  0.9711     6010.108
   3_occ:  13.588 0.9185  0.9710     6012.249
   4_bss:  13.591 0.9185  0.9783     6012.845
   4_xyz:  13.523 0.9189  0.9780     5988.027
   4_adp:  13.306 0.9205  0.9758     5919.209
   4_occ:  13.316 0.9204  0.9757     5923.928
   5_bss:  13.341 0.9203  0.9780     5927.345
   5_xyz:  13.438 0.9197  0.9778     6017.866
   5_adp:  13.611 0.9184  0.9718     6069.656
   5_occ:  13.616 0.9183  0.9718     6074.438
   5_bss:  13.605 0.9184  0.9774     6066.409
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6830e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6830e-01
   1_xyz:   1.016  0.007  0.069 15.088  0.004  4.109   5.9969e-02
   1_adp:   1.016  0.007  0.069 15.088  0.004  4.109   5.9969e-02
   1_occ:   1.016  0.007  0.069 15.088  0.004  4.109   5.9969e-02
   2_bss:   1.016  0.007  0.069 15.088  0.004  4.109   5.9969e-02
   2_xyz:   1.049  0.007  0.077 14.854  0.004  4.115   6.3260e-02
   2_adp:   1.049  0.007  0.077 14.854  0.004  4.115   6.3260e-02
   2_occ:   1.049  0.007  0.077 14.854  0.004  4.115   6.3260e-02
   3_bss:   1.049  0.007  0.077 14.854  0.004  4.115   6.3260e-02
   3_xyz:   0.890  0.005  0.069 14.464  0.004  4.115   4.9077e-02
   3_adp:   0.890  0.005  0.069 14.464  0.004  4.115   4.9077e-02
   3_occ:   0.890  0.005  0.069 14.464  0.004  4.115   4.9077e-02
   4_bss:   0.890  0.005  0.069 14.464  0.004  4.115   4.9077e-02
   4_xyz:   1.017  0.007  0.077 14.760  0.004  4.117   6.1635e-02
   4_adp:   1.017  0.007  0.077 14.760  0.004  4.117   6.1635e-02
   4_occ:   1.017  0.007  0.077 14.760  0.004  4.117   6.1635e-02
   5_bss:   1.017  0.007  0.077 14.760  0.004  4.117   6.1635e-02
   5_xyz:   0.924  0.006  0.072 14.492  0.004  4.116   5.2264e-02
   5_adp:   0.924  0.006  0.072 14.492  0.004  4.116   5.2264e-02
   5_occ:   0.924  0.006  0.072 14.492  0.004  4.116   5.2264e-02
   5_bss:   0.924  0.006  0.072 14.492  0.004  4.116   5.2264e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.686   2.4018e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.686   2.4018e-01
   1_xyz:   6.664  0.040  0.263 83.495  0.038  2.263   5.2083e-02
   1_adp:   6.664  0.040  0.263 83.495  0.038  2.263   5.2083e-02
   1_occ:   6.664  0.040  0.263 83.495  0.038  2.263   5.2083e-02
   2_bss:   6.664  0.040  0.263 83.495  0.038  2.263   5.2083e-02
   2_xyz:   7.140  0.047  0.244 82.449  0.037  2.293   5.0260e-02
   2_adp:   7.140  0.047  0.244 82.449  0.037  2.293   5.0260e-02
   2_occ:   7.140  0.047  0.244 82.449  0.037  2.293   5.0260e-02
   3_bss:   7.140  0.047  0.244 82.449  0.037  2.293   5.0260e-02
   3_xyz:   6.395  0.044  0.218 82.735  0.038  2.400   2.9774e-02
   3_adp:   6.395  0.044  0.218 82.735  0.038  2.400   2.9774e-02
   3_occ:   6.395  0.044  0.218 82.735  0.038  2.400   2.9774e-02
   4_bss:   6.395  0.044  0.218 82.735  0.038  2.400   2.9774e-02
   4_xyz:   7.053  0.051  0.253 82.851  0.036  2.313   5.0532e-02
   4_adp:   7.053  0.051  0.253 82.851  0.036  2.313   5.0532e-02
   4_occ:   7.053  0.051  0.253 82.851  0.036  2.313   5.0532e-02
   5_bss:   7.053  0.051  0.253 82.851  0.036  2.313   5.0532e-02
   5_xyz:   6.669  0.044  0.223 83.340  0.038  2.360   3.1541e-02
   5_adp:   6.669  0.044  0.223 83.340  0.038  2.360   3.1541e-02
   5_occ:   6.669  0.044  0.223 83.340  0.038  2.360   3.1541e-02
   5_bss:   6.669  0.044  0.223 83.340  0.038  2.360   3.1541e-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:  63.45   0.00  16.65  63.45   0.00  12.84  62.80   6.74  37.43
   1_occ:  63.45   0.00  16.65  63.45   0.00  12.84  62.80   6.74  37.43
   2_bss:  63.45   0.00  16.65  63.45   0.00  12.84  62.80   6.74  37.43
   2_xyz:  63.45   0.00  16.65  63.45   0.00  12.84  62.80   6.74  37.43
   2_adp:  63.08   1.93  16.54  58.96   1.93  12.75  63.08   3.36  37.23
   2_occ:  63.08   1.93  16.54  58.96   1.93  12.75  63.08   3.36  37.23
   3_bss:  63.08   1.93  16.54  58.96   1.93  12.75  63.08   3.36  37.23
   3_xyz:  63.08   1.93  16.54  58.96   1.93  12.75  63.08   3.36  37.23
   3_adp:  86.45   0.00  17.24  86.45   0.00  13.02  78.20   3.91  40.25
   3_occ:  86.45   0.00  17.24  86.45   0.00  13.02  78.20   3.91  40.25
   4_bss:  86.45   0.00  17.24  86.45   0.00  13.02  78.20   3.91  40.25
   4_xyz:  86.45   0.00  17.24  86.45   0.00  13.02  78.20   3.91  40.25
   4_adp:  79.50   2.48  16.19  79.50   2.48  12.62  69.40   5.82  35.61
   4_occ:  79.50   2.48  16.19  79.50   2.48  12.62  69.40   5.82  35.61
   5_bss:  79.50   2.48  16.19  79.50   2.48  12.62  69.40   5.82  35.61
   5_xyz:  79.50   2.48  16.19  79.50   2.48  12.62  69.40   5.82  35.61
   5_adp:  88.26   0.66  16.74  88.26   0.66  12.68  78.71   5.61  38.82
   5_occ:  88.26   0.66  16.74  88.26   0.66  12.68  78.71   5.61  38.82
   5_bss:  88.24   0.64  16.72  88.24   0.64  12.66  78.68   5.58  38.80
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.041    0.011    0.252
   1_adp:    1.041    0.011    0.252
   1_occ:    1.041    0.011    0.252
   2_bss:    1.041    0.011    0.252
   2_xyz:    0.731    0.023    0.301
   2_adp:    0.731    0.023    0.301
   2_occ:    0.731    0.023    0.301
   3_bss:    0.731    0.023    0.301
   3_xyz:    0.965    0.022    0.310
   3_adp:    0.965    0.022    0.310
   3_occ:    0.965    0.022    0.310
   4_bss:    0.965    0.022    0.310
   4_xyz:    0.913    0.012    0.320
   4_adp:    0.913    0.012    0.320
   4_occ:    0.913    0.012    0.320
   5_bss:    0.913    0.012    0.320
   5_xyz:    0.967    0.019    0.323
   5_adp:    0.967    0.019    0.323
   5_occ:    0.967    0.019    0.323
   5_bss:    0.967    0.019    0.323
------------------------------------------------------------------------

CPU time actual refinement: 303.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_313/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_313/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_313/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_313/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_313/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 303.53 
  Macro-tasks:
    bulk solvent and scale       = 35.34  
    individual site refinement   = 121.87 
    weights calculation          = 28.30  
    collect and process          = 6.58   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 192.20 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 95.56  
    alpha_beta                      = 8.31   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 104.24 
    fmodel                         = 5.79   
    r_factors                      = 0.20   
    phase_errors                   = 11.36  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 228.01 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.392 micro seconds
Total CPU time: 5.28 minutes
from_scatterers_fft:    618 calls, 95.20 s
gradients_fft:          563 calls, 91.39 s

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

# Date 2008-01-16 Time 04:31:19 PST -0800 (1200486679.52 s)
Start R-work = 0.2804, R-free = 0.2739 (no bulk solvent and anisotropic scale)
Final R-work = 0.1328, R-free = 0.1733 (no bulk solvent and anisotropic scale)

Start R-work = 0.2664, R-free = 0.2581
Final R-work = 0.1083, R-free = 0.1534