# Date 2008-01-16 Time 03:48:13 PST -0800 (1200484093.15 s)
#phil __OFF__

Command line arguments: "../51.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18357
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 51

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.6953, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.756 1.95084
Completeness in resolution range: 0.934768
Completeness with d_max=infinity: 0.931922

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7560
                             d_min =   1.9508

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.756 1.95084
Completeness in resolution range: 0.934768
Completeness with d_max=infinity: 0.931922

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7564 -  4.1742 [2203/2231]  1982   221  10.0%
  bin  2:  4.1742 -  3.3257 [2111/2130]  1897   214  10.1%
  bin  3:  3.3257 -  2.9090 [2083/2104]  1881   202   9.7%
  bin  4:  2.9090 -  2.6447 [2064/2088]  1857   207  10.0%
  bin  5:  2.6447 -  2.4560 [2054/2075]  1844   210  10.2%
  bin  6:  2.4560 -  2.3118 [2033/2079]  1826   207  10.2%
  bin  7:  2.3118 -  2.1964 [2033/2066]  1843   190   9.3%
  bin  8:  2.1964 -  2.1011 [2032/2066]  1816   216  10.6%
  bin  9:  2.1011 -  2.0204 [2024/2055]  1827   197   9.7%
  bin 10:  2.0204 -  1.9508 [ 952/2062]   857    95  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_51/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.39 -     2.09: 20
        2.09 -     2.79: 719
        2.79 -     3.50: 4556
        3.50 -     4.20: 9464
        4.20 -     4.90: 13973
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.389 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.403 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.409 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.447 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.490 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28727 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_51/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_51/model_refine_001.geo

CPU time processing inputs: 7.92


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.69535 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3833   r_free= 0.3782   ksol= 0.00   Bsol= 0.00   scale= 0.952    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.168582                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7564 -  4.6557 0.99   1430  158 0.3050 0.3025      6.4192       6.427|
|  2:  4.6557 -  3.7147 0.99   1377  154 0.3013 0.2995      6.5592      6.5938|
|  3:  3.7147 -  3.2509 0.99   1344  151 0.3477 0.3505       6.498      6.5618|
|  4:  3.2509 -  2.9563 0.99   1349  141 0.3622 0.3977      6.3638      6.4544|
|  5:  2.9563 -  2.7458 0.99   1313  156 0.3890 0.3917      6.2236      6.2507|
|  6:  2.7458 -  2.5849 0.98   1334  144 0.4069 0.4238      6.1469      6.0699|
|  7:  2.5849 -  2.4560 0.99   1314  150 0.4172 0.3428      6.1351      5.9957|
|  8:  2.4560 -  2.3495 0.98   1324  141 0.4332 0.4179      6.0898      6.1388|
|  9:  2.3495 -  2.2594 0.98   1307  146 0.4526 0.4462      6.0624      6.0835|
| 10:  2.2594 -  2.1817 0.98   1308  144 0.4412 0.3772      6.0271      5.9728|
| 11:  2.1817 -  2.1137 0.99   1305  154 0.4442 0.4418       5.948      5.9347|
| 12:  2.1137 -  2.0534 0.98   1299  144 0.4449 0.4459      5.9003      5.9171|
| 13:  2.0534 -  1.9995 0.93   1233  125 0.4504 0.4633      5.8241      5.7691|
| 14:  1.9995 -  1.9508 0.30    393   51 0.4906 0.4655      5.8825      5.7352|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7564 -  4.6557  1430   158  0.77  28.24   0.86     0.78      49814.82|
|  2:  4.6557 -  3.7147  1377   154  0.79  27.39   0.97     0.88      68917.86|
|  3:  3.7147 -  3.2509  1344   151  0.71  34.51   0.98     0.89      73194.74|
|  4:  3.2509 -  2.9563  1349   141  0.65  39.32   0.97     0.84      65766.48|
|  5:  2.9563 -  2.7458  1313   156  0.60  43.79   0.97     0.80      52388.22|
|  6:  2.7458 -  2.5849  1334   144  0.60  44.27   0.94     0.80      43622.54|
|  7:  2.5849 -  2.4560  1314   150  0.62  42.61   0.98     0.82      38387.22|
|  8:  2.4560 -  2.3495  1324   141  0.60  44.35   0.98     0.81      35168.27|
|  9:  2.3495 -  2.2594  1307   146  0.59  44.89   0.97     0.82      33675.90|
| 10:  2.2594 -  2.1817  1308   144  0.59  45.43   1.00     0.80      30791.83|
| 11:  2.1817 -  2.1137  1305   154  0.57  46.78   0.98     0.85      30558.38|
| 12:  2.1137 -  2.0534  1299   144  0.54  49.05   1.02     0.83      29042.18|
| 13:  2.0534 -  1.9995  1233   125  0.49  52.75   1.00     0.77      27648.27|
| 14:  1.9995 -  1.9508   393    51  0.47  54.10   1.00     0.62      24387.33|
|alpha:            min =        0.62 max =            0.89 mean =         0.82|
|beta:             min =    24387.33 max =        73194.74 mean =     44400.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.86|
|phase err.(test): min =        0.00 max =           89.62 mean =        41.65|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.388143              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.923302              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.890   (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 |  1.389 -  1.740:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.740 -  2.091:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.091 -  2.442:       34 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.442 -  2.793:      685 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.793 -  3.144:     2142 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.144 -  3.496:     2414 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.496 -  3.847:     4604 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.847 -  4.198:     4860 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.198 -  4.549:     6324 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.549 -  4.900:     7649 |
|-----------------------------------------------------------------------------|
|-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 |        0.211 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.389 |       0.924 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3833   r_free= 0.3782   ksol= 0.00   Bsol= 0.00   scale= 0.952    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.168582                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3729   r_free= 0.3686   ksol= 0.35   Bsol= 50.00   scale= 0.976   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,-2.10,0.30,-0.00,0.00,0.00); trace/3= -0.13                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.152773                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.470437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.630   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.511567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.524   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3729      final r-factor (work) = 0.2233          |
| start r-factor (free) = 0.3686      final r-factor (free) = 0.2574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.1311 = 6.47 * 0.50 * 6.1573 + 1.00 * 0.2108                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2234 = 6.47 * 0.50 * 5.9143 + 1.00 * 0.0893                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2233      final r-factor (work) = 0.2022          |
| start r-factor (free) = 0.2574      final r-factor (free) = 0.2639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0315 = 0.51 * 1.00 * 5.9143 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9009 = 0.51 * 1.00 * 5.6499 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.54   17.70    None  None   None       |
|    all(noH): 2823   0      0.00    77.54   17.70    None  None   None       |
|    Sol.    : 438    0      5.14    76.91   40.25    None  None   None       |
|    Mac.    : 2385   0      0.00    77.54   13.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.754:  560   |   5:    38.769 -  46.523:  106        |
|      1:     7.754 -  15.508: 1184   |   6:    46.523 -  54.277:   91        |
|      2:    15.508 -  23.262:  464   |   7:    54.277 -  62.031:   61        |
|      3:    23.262 -  31.015:  192   |   8:    62.031 -  69.785:   32        |
|      4:    31.015 -  38.769:  125   |   9:    69.785 -  77.538:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2022 r_free = 0.2639             target_work(ml) = 5.663         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2018 r_free = 0.2639             target_work(ml) = 5.662         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2018   r_free= 0.2639   ksol= 0.35   Bsol= 50.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,-2.10,0.30,-0.00,0.00,0.00); trace/3= -0.13                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.662399                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1972   r_free= 0.2602   ksol= 0.33   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.60,-0.88,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.649948                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.998258              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.635   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.148389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.438  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1972      final r-factor (work) = 0.1469          |
| start r-factor (free) = 0.2602      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5760 = 3.00 * 0.50 * 5.6611 + 1.00 * 0.0893                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3631 = 3.00 * 0.50 * 5.5412 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1469      final r-factor (work) = 0.1397          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8328 = 0.15 * 1.00 * 5.5412 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8006 = 0.15 * 1.00 * 5.3488 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    79.82   17.12    None  None   None       |
|    all(noH): 2823   0      1.04    79.82   17.12    None  None   None       |
|    Sol.    : 438    0      5.40    71.65   38.29    None  None   None       |
|    Mac.    : 2385   0      1.04    79.82   13.23    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:     1.035 -   8.913:  675   |   5:    40.425 -  48.303:  117        |
|      1:     8.913 -  16.791: 1293   |   6:    48.303 -  56.182:   71        |
|      2:    16.791 -  24.669:  338   |   7:    56.182 -  64.060:   45        |
|      3:    24.669 -  32.547:  141   |   8:    64.060 -  71.938:   10        |
|      4:    32.547 -  40.425:  131   |   9:    71.938 -  79.816:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1397 r_free = 0.1810             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1394 r_free = 0.1809             target_work(ml) = 5.318         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1809   ksol= 0.33   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.60,-0.88,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.318261                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1805   ksol= 0.33   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-2.61,-1.06,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.316073                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.527537              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.561  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.153179              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.881  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1393      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1805      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1413 = 1.53 * 0.50 * 5.3486 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0676 = 1.53 * 0.50 * 5.2591 + 1.00 * 0.0509                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8125 = 0.15 * 1.00 * 5.2591 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8026 = 0.15 * 1.00 * 5.1946 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.86    82.59   17.03    None  None   None       |
|    all(noH): 2823   0      1.86    82.59   17.03    None  None   None       |
|    Sol.    : 438    0      4.91    70.71   38.24    None  None   None       |
|    Mac.    : 2385   0      1.86    82.59   13.13    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:     1.861 -   9.935:  911   |   5:    42.227 -  50.300:  113        |
|      1:     9.935 -  18.008: 1181   |   6:    50.300 -  58.373:   76        |
|      2:    18.008 -  26.081:  262   |   7:    58.373 -  66.446:   26        |
|      3:    26.081 -  34.154:  118   |   8:    66.446 -  74.520:    7        |
|      4:    34.154 -  42.227:  127   |   9:    74.520 -  82.593:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1587             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1587             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1587   ksol= 0.33   Bsol= 50.00   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-2.61,-1.06,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1587   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.46,-2.69,-1.19,-0.00,-0.00,-0.00); trace/3= -2.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190142                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.284295              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.686  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.136253              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.095  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5807 = 3.28 * 0.50 * 5.1943 + 1.00 * 0.0509                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5282 = 3.28 * 0.50 * 5.1498 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7085 = 0.14 * 1.00 * 5.1498 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7053 = 0.14 * 1.00 * 5.1286 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.35    82.56   16.76    None  None   None       |
|    all(noH): 2823   0      2.35    82.56   16.76    None  None   None       |
|    Sol.    : 438    0      4.09    71.17   37.39    None  None   None       |
|    Mac.    : 2385   0      2.35    82.56   12.98    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:     2.351 -  10.373: 1034   |   5:    42.457 -  50.478:  104        |
|      1:    10.373 -  18.394: 1092   |   6:    50.478 -  58.500:   66        |
|      2:    18.394 -  26.415:  242   |   7:    58.500 -  66.521:   18        |
|      3:    26.415 -  34.436:  128   |   8:    66.521 -  74.542:    8        |
|      4:    34.436 -  42.457:  129   |   9:    74.542 -  82.563:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1524             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1524             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1524   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.46,-2.69,-1.19,-0.00,-0.00,-0.00); trace/3= -2.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125966                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1523   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.44,-2.63,-1.09,-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: 5.124214                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.909563              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.231  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.687282              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.507  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9675 = 1.91 * 0.50 * 5.1278 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9543 = 1.91 * 0.50 * 5.1300 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5322 = 0.69 * 1.00 * 5.1300 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5305 = 0.69 * 1.00 * 5.1249 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    86.73   17.09    None  None   None       |
|    all(noH): 2823   0      1.31    86.73   17.09    None  None   None       |
|    Sol.    : 438    0      5.40    74.15   39.39    None  None   None       |
|    Mac.    : 2385   0      1.31    86.73   12.99    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:     1.314 -   9.855:  957   |   5:    44.022 -  52.564:   99        |
|      1:     9.855 -  18.397: 1155   |   6:    52.564 -  61.106:   79        |
|      2:    18.397 -  26.939:  252   |   7:    61.106 -  69.647:   26        |
|      3:    26.939 -  35.480:  119   |   8:    69.647 -  78.189:    8        |
|      4:    35.480 -  44.022:  126   |   9:    78.189 -  86.731:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1543             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1543             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1543   ksol= 0.33   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.44,-2.63,-1.09,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130318                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7564 -  4.6557 0.99   1430  158 0.0991 0.1285      5.3891      5.5421|
|  2:  4.6557 -  3.7147 0.99   1377  154 0.0855 0.1104      5.4281      5.6073|
|  3:  3.7147 -  3.2509 0.99   1344  151 0.1042 0.1477      5.4446       5.804|
|  4:  3.2509 -  2.9563 0.99   1349  141 0.1178 0.1481      5.4105      5.5545|
|  5:  2.9563 -  2.7458 0.99   1313  156 0.1231 0.1555      5.2714       5.479|
|  6:  2.7458 -  2.5849 0.98   1334  144 0.1211 0.1929       5.181      5.4573|
|  7:  2.5849 -  2.4560 0.99   1314  150 0.1212 0.1639      5.1394      5.3242|
|  8:  2.4560 -  2.3495 0.98   1324  141 0.1127 0.1544      5.0564      5.2499|
|  9:  2.3495 -  2.2594 0.98   1307  146 0.1126 0.1961      4.9987      5.3703|
| 10:  2.2594 -  2.1817 0.98   1308  144 0.1104 0.1644      4.9348      5.1535|
| 11:  2.1817 -  2.1137 0.99   1305  154 0.1105 0.1754      4.8997      5.2436|
| 12:  2.1137 -  2.0534 0.98   1299  144 0.1126 0.1658      4.8711       5.115|
| 13:  2.0534 -  1.9995 0.93   1233  125 0.1025 0.1720      4.7411       4.976|
| 14:  1.9995 -  1.9508 0.30    393   51 0.0913 0.1780      4.6164      4.9775|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7564 -  4.6557  1430   158  0.94   9.07   0.98     0.95       7108.40|
|  2:  4.6557 -  3.7147  1377   154  0.96   7.62   1.02     1.01       8687.98|
|  3:  3.7147 -  3.2509  1344   151  0.94  10.97   1.03     1.03       9624.24|
|  4:  3.2509 -  2.9563  1349   141  0.93  12.90   1.01     1.01       9477.94|
|  5:  2.9563 -  2.7458  1313   156  0.91  15.08   0.99     0.97       7611.36|
|  6:  2.7458 -  2.5849  1334   144  0.90  16.16   0.98     0.95       6657.78|
|  7:  2.5849 -  2.4560  1314   150  0.91  15.25   0.98     0.95       5896.85|
|  8:  2.4560 -  2.3495  1324   141  0.91  14.94   1.00     0.97       5308.84|
|  9:  2.3495 -  2.2594  1307   146  0.91  15.60   1.00     0.96       4785.50|
| 10:  2.2594 -  2.1817  1308   144  0.90  15.69   0.99     0.96       4288.59|
| 11:  2.1817 -  2.1137  1305   154  0.90  15.77   0.99     0.96       4157.18|
| 12:  2.1137 -  2.0534  1299   144  0.90  16.25   1.01     1.00       4000.39|
| 13:  2.0534 -  1.9995  1233   125  0.91  15.67   0.99     0.97       3187.49|
| 14:  1.9995 -  1.9508   393    51  0.93  12.78   0.98     0.94       2313.15|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2313.15 max =         9624.24 mean =      6172.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.49 mean =        13.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1543   ksol= 0.33   Bsol= 49.95   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,-2.38,-0.86,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1543   ksol= 0.33   Bsol= 49.95   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,-2.38,-0.86,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130336                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7564 -  4.6557 0.99   1430  158 0.0991 0.1286      5.3886      5.5425|
|  2:  4.6557 -  3.7147 0.99   1377  154 0.0856 0.1105      5.4286      5.6071|
|  3:  3.7147 -  3.2509 0.99   1344  151 0.1042 0.1477      5.4445      5.8041|
|  4:  3.2509 -  2.9563 0.99   1349  141 0.1178 0.1481      5.4104      5.5544|
|  5:  2.9563 -  2.7458 0.99   1313  156 0.1231 0.1555      5.2714      5.4786|
|  6:  2.7458 -  2.5849 0.98   1334  144 0.1211 0.1929      5.1811      5.4573|
|  7:  2.5849 -  2.4560 0.99   1314  150 0.1212 0.1638      5.1394       5.324|
|  8:  2.4560 -  2.3495 0.98   1324  141 0.1127 0.1544      5.0565      5.2498|
|  9:  2.3495 -  2.2594 0.98   1307  146 0.1126 0.1961      4.9989      5.3704|
| 10:  2.2594 -  2.1817 0.98   1308  144 0.1104 0.1643      4.9349      5.1535|
| 11:  2.1817 -  2.1137 0.99   1305  154 0.1106 0.1755      4.8998      5.2439|
| 12:  2.1137 -  2.0534 0.98   1299  144 0.1126 0.1658      4.8709      5.1146|
| 13:  2.0534 -  1.9995 0.93   1233  125 0.1025 0.1721      4.7411      4.9759|
| 14:  1.9995 -  1.9508 0.30    393   51 0.0913 0.1780      4.6167      4.9776|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7564 -  4.6557  1430   158  0.94   9.05   0.98     0.95       7091.16|
|  2:  4.6557 -  3.7147  1377   154  0.96   7.62   1.02     1.01       8684.47|
|  3:  3.7147 -  3.2509  1344   151  0.94  10.98   1.03     1.03       9624.79|
|  4:  3.2509 -  2.9563  1349   141  0.93  12.90   1.02     1.01       9476.35|
|  5:  2.9563 -  2.7458  1313   156  0.91  15.09   1.00     0.97       7611.25|
|  6:  2.7458 -  2.5849  1334   144  0.90  16.16   0.98     0.96       6657.69|
|  7:  2.5849 -  2.4560  1314   150  0.91  15.25   0.99     0.96       5896.52|
|  8:  2.4560 -  2.3495  1324   141  0.91  14.94   1.00     0.97       5308.84|
|  9:  2.3495 -  2.2594  1307   146  0.91  15.60   1.01     0.97       4784.56|
| 10:  2.2594 -  2.1817  1308   144  0.90  15.70   1.00     0.96       4287.96|
| 11:  2.1817 -  2.1137  1305   154  0.90  15.77   1.00     0.97       4156.08|
| 12:  2.1137 -  2.0534  1299   144  0.90  16.26   1.02     1.01       4000.08|
| 13:  2.0534 -  1.9995  1233   125  0.91  15.68   1.00     0.98       3188.44|
| 14:  1.9995 -  1.9508   393    51  0.93  12.80   0.99     0.95       2314.79|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2314.79 max =         9624.79 mean =      6170.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.83|
|phase err.(test): min =        0.00 max =           89.62 mean =        13.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.27    86.68   17.04    None  None   None       |
|    all(noH): 2823   0      1.27    86.68   17.04    None  None   None       |
|    Sol.    : 438    0      5.35    74.10   39.34    None  None   None       |
|    Mac.    : 2385   0      1.27    86.68   12.95    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:     1.267 -   9.809:  957   |   5:    43.976 -  52.518:   99        |
|      1:     9.809 -  18.351: 1155   |   6:    52.518 -  61.059:   79        |
|      2:    18.351 -  26.892:  252   |   7:    61.059 -  69.601:   26        |
|      3:    26.892 -  35.434:  119   |   8:    69.601 -  78.143:    8        |
|      4:    35.434 -  43.976:  126   |   9:    78.143 -  86.684:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 280         
Filter by distance & map next to the model:
   mapped sites are within: 0.503 - 5.499
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 272 from: 280
   mapped sites are within: 0.704 - 5.499

peak=    6.191 closest distance to " CB  ARG A 275 " =    0.957
peak=    5.574 closest distance to " NH2 ARG A  56 " =    2.156
peak=    5.325 closest distance to " O   HOH Z 142 " =    1.616
peak=    5.206 closest distance to " CG  PRO A  54 " =    1.278
peak=    5.160 closest distance to " NE2 GLN A  11 " =    1.145
peak=    5.149 closest distance to " O   HOH Z 417 " =    1.642
peak=    5.114 closest distance to " O   HOH Z 232 " =    2.399
peak=    4.993 closest distance to " O   HOH Z 126 " =    1.880
peak=    4.765 closest distance to " CB  PRO A  54 " =    0.998
peak=    4.701 closest distance to " O   HOH Z 402 " =    1.433
peak=    4.686 closest distance to " O   HOH Z  78 " =    1.870
peak=    4.600 closest distance to " CG  PRO A 213 " =    1.272
peak=    4.568 closest distance to " CB  GLN A 223 " =    1.499
peak=    4.544 closest distance to " O   HOH Z 369 " =    2.248
peak=    4.535 closest distance to " O   HOH Z 287 " =    1.883
peak=    4.513 closest distance to " CB  ARG A  79 " =    1.334
peak=    4.507 closest distance to " CG  PRO A  90 " =    1.188
peak=    4.496 closest distance to " CG2 VAL A 257 " =    0.866
peak=    4.419 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.407 closest distance to " O   HOH Z 250 " =    1.519
peak=    4.395 closest distance to " CA  TYR A  30 " =    0.896
peak=    4.368 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.367 closest distance to " O   HOH Z  40 " =    1.840
peak=    4.329 closest distance to " ND2 ASN A 187 " =    1.475
peak=    4.303 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.297 closest distance to " O   SER A  87 " =    2.223
peak=    4.275 closest distance to " CB  ASN A 148 " =    1.465
peak=    4.273 closest distance to " CD2 TRP A 179 " =    1.338
peak=    4.271 closest distance to " CB  SER A  63 " =    1.195
peak=    4.253 closest distance to " NZ  LYS A 117 " =    2.964
peak=    4.243 closest distance to " CB  VAL A 265 " =    1.232
peak=    4.237 closest distance to " CB  GLU A 152 " =    1.209
peak=    4.185 closest distance to " O   HOH Z 189 " =    2.716
peak=    4.183 closest distance to " O   HOH Z  15 " =    2.325
peak=    4.179 closest distance to " O   HOH Z 303 " =    2.142
peak=    4.177 closest distance to " O   HOH Z 427 " =    2.936
peak=    4.171 closest distance to " O   HOH Z 126 " =    2.020
peak=    4.170 closest distance to " C   PRO A 198 " =    1.501
peak=    4.155 closest distance to " CG  PRO A 243 " =    1.009
peak=    4.134 closest distance to " O   HOH Z  66 " =    2.158
peak=    4.121 closest distance to " O   HOH Z 403 " =    1.727
peak=    4.107 closest distance to " O   HOH Z 209 " =    2.231
peak=    4.090 closest distance to " O   HOH Z  97 " =    2.054
peak=    4.083 closest distance to " O   HOH Z 234 " =    3.576
peak=    4.082 closest distance to " O   HOH Z 346 " =    1.704
peak=    4.064 closest distance to " CB  ARG A 190 " =    1.685
peak=    4.063 closest distance to " O   HOH Z 298 " =    1.770
peak=    4.060 closest distance to " O   HOH Z  44 " =    1.838
peak=    4.026 closest distance to " O   HOH Z 132 " =    2.658
peak=    4.017 closest distance to " OG ASER A 258 " =    2.950
peak=    4.005 closest distance to " O   HOH Z 327 " =    1.563
peak=    3.984 closest distance to " O   HOH Z 112 " =    1.184
peak=    3.984 closest distance to " O   HOH Z  97 " =    2.205
peak=    3.978 closest distance to " CZ  PHE A 218 " =    1.081
peak=    3.977 closest distance to " NH2AARG A 190 " =    1.951
peak=    3.958 closest distance to " O   HOH Z 193 " =    1.644
peak=    3.956 closest distance to " CB  ASN A 110 " =    1.068
peak=    3.956 closest distance to " O  BHOH Z  74 " =    1.331
peak=    3.940 closest distance to " CA  ASN A 215 " =    0.995
peak=    3.940 closest distance to " O   HOH Z 158 " =    3.075
peak=    3.914 closest distance to " O   HOH Z 357 " =    1.957
peak=    3.901 closest distance to " CB  VAL A 202 " =    1.533
peak=    3.892 closest distance to " O   HOH Z 128 " =    2.125
peak=    3.884 closest distance to " O   HOH Z 248 " =    1.572
peak=    3.883 closest distance to " O   HOH Z  61 " =    1.631
peak=    3.881 closest distance to " CG2 ILE A 120 " =    1.229
peak=    3.879 closest distance to " O   HOH Z 173 " =    2.056
peak=    3.874 closest distance to " O   HOH Z  59 " =    1.781
peak=    3.855 closest distance to " O   HOH Z 423 " =    1.935
peak=    3.854 closest distance to " CB  THR A  31 " =    1.524
peak=    3.853 closest distance to " O   HOH Z 371 " =    1.707
peak=    3.845 closest distance to " O   HOH Z 128 " =    1.963
peak=    3.844 closest distance to " O   HOH Z 188 " =    1.434
peak=    3.842 closest distance to " CG  ARG A  66 " =    2.475
peak=    3.837 closest distance to " CB  TRP A 266 " =    1.134
peak=    3.825 closest distance to " O   HOH Z 406 " =    1.517
peak=    3.816 closest distance to " CA  ARG A  36 " =    1.011
peak=    3.795 closest distance to " O   HOH Z  43 " =    1.884
peak=    3.783 closest distance to " NH2BARG A 145 " =    2.038
peak=    3.783 closest distance to " OG BSER A 164 " =    2.143
peak=    3.780 closest distance to " O   HOH Z 368 " =    3.612
peak=    3.767 closest distance to " O   HOH Z 265 " =    2.175
peak=    3.764 closest distance to " O   HOH Z 132 " =    2.253
peak=    3.763 closest distance to " O   HOH Z  54 " =    1.722
peak=    3.761 closest distance to " O   HOH Z 337 " =    3.419
peak=    3.739 closest distance to " N   TYR A 116 " =    1.548
peak=    3.737 closest distance to " N   ASN A  39 " =    1.202
peak=    3.735 closest distance to " O   HOH Z 389 " =    1.749
peak=    3.730 closest distance to " O   HOH Z 419 " =    2.119
peak=    3.725 closest distance to " O   HOH Z 365 " =    2.744
peak=    3.705 closest distance to " CB  ILE A 120 " =    1.321
peak=    3.698 closest distance to " O   HOH Z 415 " =    3.622
peak=    3.698 closest distance to " O   HOH Z 368 " =    2.114
peak=    3.698 closest distance to " O   HOH Z 392 " =    2.831
peak=    3.682 closest distance to " O   HOH Z  10 " =    1.801
peak=    3.680 closest distance to " CB  SER A   3 " =    1.208
peak=    3.676 closest distance to " O   HOH Z 261 " =    1.864
peak=    3.672 closest distance to " O  BHOH Z 338 " =    2.300
peak=    3.669 closest distance to " CB  ASP A 140 " =    1.078
peak=    3.665 closest distance to " CG AARG A 275 " =    1.078
peak=    3.656 closest distance to " O   HOH Z 203 " =    1.729
peak=    3.649 closest distance to " CG  MET A 185 " =    1.198
peak=    3.643 closest distance to " CB  GLU A  46 " =    1.052
peak=    3.641 closest distance to " O   HOH Z 291 " =    1.402
peak=    3.639 closest distance to " CA  ALA A  84 " =    1.205
peak=    3.639 closest distance to " O   HOH Z 353 " =    2.606
peak=    3.638 closest distance to " CB  SER A  26 " =    1.718
peak=    3.637 closest distance to " O   HOH Z 342 " =    0.958
peak=    3.637 closest distance to " O   HOH Z 236 " =    1.393
peak=    3.617 closest distance to " CB  ALA A 114 " =    1.035
peak=    3.609 closest distance to " CE  LYS A 119 " =    1.184
peak=    3.606 closest distance to " CB  GLN A  88 " =    1.213
peak=    3.604 closest distance to " CB  GLU A 277 " =    3.513
peak=    3.594 closest distance to " CD  LYS A  76 " =    1.757
peak=    3.592 closest distance to " O   HOH Z  61 " =    1.489
peak=    3.590 closest distance to " N   PHE A 130 " =    1.272
peak=    3.586 closest distance to " CG1 ILE A  33 " =    1.199
peak=    3.584 closest distance to " O   HOH Z 180 " =    2.262
peak=    3.579 closest distance to " CB  GLU A 128 " =    1.016
peak=    3.574 closest distance to " O   HOH Z  88 " =    2.544
peak=    3.563 closest distance to " O   HOH Z 245 " =    1.361
peak=    3.562 closest distance to " O   HOH Z 280 " =    3.005
peak=    3.560 closest distance to " OE1 GLU A   2 " =    2.195
peak=    3.557 closest distance to " O   HOH Z 344 " =    3.192
peak=    3.551 closest distance to " O   HOH Z 305 " =    3.506
peak=    3.549 closest distance to " O   HOH Z 193 " =    1.962
peak=    3.530 closest distance to " O   HOH Z 407 " =    2.506
peak=    3.527 closest distance to " O   HOH Z 214 " =    2.261
peak=    3.527 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.518 closest distance to " CA  ARG A 195 " =    1.236
peak=    3.517 closest distance to " O   HOH Z   3 " =    2.003
peak=    3.511 closest distance to " CB  HIS A 108 " =    0.857
peak=    3.509 closest distance to " CB  TYR A 169 " =    0.770
peak=    3.509 closest distance to " CB  ASN A  39 " =    0.834
peak=    3.507 closest distance to " CG  LEU A 167 " =    1.269
peak=    3.504 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.502 closest distance to " NH1AARG A 145 " =    1.197
peak=    3.494 closest distance to " ND2 ASN A 249 " =    0.928
peak=    3.491 closest distance to " O   HOH Z 234 " =    2.035
peak=    3.488 closest distance to " CB  ALA A 291 " =    1.189
peak=    3.486 closest distance to " O   HOH Z   1 " =    1.839
peak=    3.481 closest distance to " OD1 ASN A  69 " =    2.530
peak=    3.472 closest distance to " CA  ASP A 124 " =    0.704
peak=    3.470 closest distance to " O   HOH Z  88 " =    2.709
peak=    3.459 closest distance to " O   HOH Z 371 " =    3.005
peak=    3.458 closest distance to " CD  LYS A 166 " =    1.253
peak=    3.454 closest distance to " O   THR A 220 " =    1.284
peak=    3.448 closest distance to " O   HOH Z 433 " =    1.882
peak=    3.446 closest distance to " CB  ASN A 142 " =    1.096
peak=    3.445 closest distance to " CB  LYS A 290 " =    1.015
peak=    3.444 closest distance to " O   HOH Z 234 " =    2.211
peak=    3.443 closest distance to " O   ASN A  74 " =    1.455
peak=    3.425 closest distance to " CB  GLN A  89 " =    1.385
peak=    3.420 closest distance to " O   HOH Z 425 " =    1.979
peak=    3.412 closest distance to " CB  ARG A 139 " =    1.083
peak=    3.409 closest distance to " N   ARG A 156 " =    1.298
peak=    3.409 closest distance to " O   HOH Z 148 " =    3.428
peak=    3.401 closest distance to " O   HOH Z 411 " =    3.878
peak=    3.387 closest distance to " O   HOH Z  44 " =    2.956
peak=    3.370 closest distance to " CB  SER A 212 " =    1.115
peak=    3.370 closest distance to " CA  ALA A 233 " =    1.097
peak=    3.370 closest distance to " CD2 LEU A 297 " =    0.937
peak=    3.369 closest distance to " O   HOH Z   1 " =    1.566
peak=    3.366 closest distance to " O   ALA A   1 " =    1.713
peak=    3.359 closest distance to " C   PHE A  59 " =    0.912
peak=    3.358 closest distance to " O   HOH Z  92 " =    2.419
peak=    3.358 closest distance to " O   HOH Z 109 " =    1.149
peak=    3.356 closest distance to " O   HOH Z 286 " =    2.300
peak=    3.356 closest distance to " O   HOH Z  89 " =    2.116
peak=    3.353 closest distance to " CA  LEU A 300 " =    1.011
peak=    3.347 closest distance to " O   HOH Z 359 " =    1.490
peak=    3.345 closest distance to " CA  ALA A  51 " =    0.877
peak=    3.342 closest distance to " CB  TRP A 179 " =    1.316
peak=    3.341 closest distance to " O   HOH Z  80 " =    1.651
peak=    3.339 closest distance to " O   HOH Z 394 " =    3.836
peak=    3.338 closest distance to " CA  MET A  40 " =    1.144
peak=    3.337 closest distance to " CA  ILE A 234 " =    1.011
peak=    3.332 closest distance to " O   HOH Z  47 " =    1.537
peak=    3.329 closest distance to " CA  TYR A 116 " =    1.366
peak=    3.329 closest distance to " CG1BVAL A  72 " =    1.549
peak=    3.325 closest distance to " CA  ASN A 217 " =    1.232
peak=    3.321 closest distance to " OG1 THR A 264 " =    0.797
peak=    3.321 closest distance to " OG  SER A  62 " =    2.742
peak=    3.320 closest distance to " N   CYS A 260 " =    0.945
peak=    3.318 closest distance to " O   HOH Z 421 " =    1.803
peak=    3.301 closest distance to " O   HOH Z 380 " =    1.890
peak=    3.299 closest distance to " O   HOH Z 257 " =    2.085
peak=    3.292 closest distance to " O   HOH Z 329 " =    3.981
peak=    3.290 closest distance to " CG  LYS A 119 " =    1.133
peak=    3.288 closest distance to " O   ALA A 165 " =    1.513
peak=    3.284 closest distance to " CD1 ILE A 106 " =    0.882
peak=    3.284 closest distance to " O   HOH Z 126 " =    1.541
peak=    3.280 closest distance to " O   HOH Z  85 " =    1.352
peak=    3.277 closest distance to " CB  LEU A 300 " =    0.956
peak=    3.272 closest distance to " CB  LEU A  83 " =    0.776
peak=    3.271 closest distance to " N   GLN A 278 " =    1.361
peak=    3.270 closest distance to " CB  LYS A 117 " =    1.181
peak=    3.269 closest distance to " OG BSER A 210 " =    1.357
peak=    3.267 closest distance to " CB  TYR A 169 " =    0.811
peak=    3.263 closest distance to " CB  ASN A 215 " =    1.106
peak=    3.261 closest distance to " OD2 ASP A 286 " =    2.772
peak=    3.259 closest distance to " O   HOH Z 261 " =    1.988
peak=    3.258 closest distance to " O   HOH Z  21 " =    1.809
peak=    3.257 closest distance to " OG ASER A  99 " =    1.459
peak=    3.254 closest distance to " NE2 HIS A 207 " =    1.243
peak=    3.252 closest distance to " CG  GLU A  37 " =    0.962
peak=    3.250 closest distance to " N   ASP A 162 " =    1.138
peak=    3.250 closest distance to " CB  SER A  62 " =    1.436
peak=    3.248 closest distance to " CA  ALA A  21 " =    1.113
peak=    3.246 closest distance to " CA  VAL A 125 " =    0.962
peak=    3.246 closest distance to " CA  MET A 105 " =    1.002
peak=    3.244 closest distance to " CA  THR A 264 " =    0.852
peak=    3.244 closest distance to " CD1 ILE A 199 " =    1.131
peak=    3.243 closest distance to " O   HOH Z  97 " =    1.211
peak=    3.242 closest distance to " O   HOH Z 213 " =    1.727
peak=    3.241 closest distance to " O   HOH Z 172 " =    3.347
peak=    3.240 closest distance to " O   HOH Z 325 " =    2.485
peak=    3.231 closest distance to " CA  SER A  32 " =    1.686
peak=    3.230 closest distance to " CB  GLN A 205 " =    1.063
peak=    3.230 closest distance to " O   HOH Z  85 " =    2.366
peak=    3.220 closest distance to " CB  LEU A 228 " =    1.072
peak=    3.216 closest distance to " O   HOH Z 183 " =    1.644
peak=    3.213 closest distance to " CB  SER A 141 " =    1.000
peak=    3.211 closest distance to " O   HOH Z  78 " =    2.068
peak=    3.211 closest distance to " O   HOH Z 153 " =    3.823
peak=    3.204 closest distance to " CA  ASP A 162 " =    1.077
peak=    3.202 closest distance to " NH1BARG A 145 " =    1.306
peak=    3.202 closest distance to " CG  GLN A  77 " =    2.116
peak=    3.199 closest distance to " CG  LYS A  76 " =    0.915
peak=    3.197 closest distance to " O   HOH Z 273 " =    2.842
peak=    3.195 closest distance to " O   HOH Z  94 " =    1.970
peak=    3.194 closest distance to " CA  ARG A 159 " =    1.252
peak=    3.194 closest distance to " CD2 TYR A 186 " =    1.100
peak=    3.190 closest distance to " CG  ARG A 269 " =    1.260
peak=    3.190 closest distance to " CA  ASN A 127 " =    1.155
peak=    3.186 closest distance to " CB  VAL A 268 " =    0.864
peak=    3.185 closest distance to " CG2 ILE A  20 " =    1.487
peak=    3.185 closest distance to " CG  MET A 113 " =    1.001
peak=    3.180 closest distance to " CB  SER A 273 " =    0.843
peak=    3.179 closest distance to " OG1 THR A 294 " =    2.333
peak=    3.178 closest distance to " O   GLY A  91 " =    1.564
peak=    3.171 closest distance to " O   HOH Z 361 " =    3.097
peak=    3.167 closest distance to " O   HOH Z 345 " =    3.235
peak=    3.161 closest distance to " O   HOH Z 332 " =    1.505
peak=    3.156 closest distance to " O   HOH Z  47 " =    1.737
peak=    3.156 closest distance to " O   HOH Z  66 " =    2.091
peak=    3.151 closest distance to " CA  LYS A 117 " =    1.201
peak=    3.145 closest distance to " CA  ASP A 140 " =    1.082
peak=    3.144 closest distance to " O   HOH Z  48 " =    1.532
peak=    3.140 closest distance to " O   HOH Z 394 " =    1.634
peak=    3.139 closest distance to " NH2BARG A 190 " =    1.644
peak=    3.130 closest distance to " O   HOH Z 227 " =    1.499
peak=    3.128 closest distance to " CG2 THR A 294 " =    1.655
peak=    3.124 closest distance to " O   HOH Z 426 " =    1.770
peak=    3.123 closest distance to " CB  ALA A 248 " =    1.396
peak=    3.123 closest distance to " CG  GLN A  58 " =    0.949
peak=    3.114 closest distance to " N   SER A 135 " =    1.264
peak=    3.105 closest distance to " CB  GLN A 278 " =    0.793
peak=    3.097 closest distance to " CB  SER A 210 " =    0.760
peak=    3.088 closest distance to " CD1AILE A 234 " =    0.907
peak=    3.086 closest distance to " CB  TYR A 116 " =    0.805
peak=    3.084 closest distance to " O   HOH Z  62 " =    2.236
peak=    3.084 closest distance to " CB  ARG A 219 " =    0.873
peak=    3.082 closest distance to " OG  SER A  62 " =    3.578
peak=    3.072 closest distance to " O   HOH Z  59 " =    2.350
peak=    3.070 closest distance to " O   HOH Z 188 " =    2.033
peak=    3.062 closest distance to " O   HOH Z 285 " =    2.397
peak=    3.061 closest distance to " CB  ALA A 114 " =    0.960
peak=    3.060 closest distance to " O   HOH Z 172 " =    5.499
peak=    3.058 closest distance to " CB  ARG A 138 " =    0.831
peak=    3.052 closest distance to " O   HOH Z 194 " =    1.939
peak=    3.015 closest distance to " CG  LYS A  76 " =    0.883

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 184         
Filter by distance & map next to the model:
   mapped sites are within: 0.774 - 5.826
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 184
   mapped sites are within: 0.774 - 5.826

peak=   -4.600 closest distance to " CG  GLN A  58 " =    1.034
peak=   -4.512 closest distance to " C   HIS A 108 " =    1.123
peak=   -4.486 closest distance to " CD  ARG A  14 " =    3.387
peak=   -4.400 closest distance to " OG BSER A 134 " =    1.310
peak=   -4.342 closest distance to " O   HOH Z 266 " =    5.213
peak=   -4.267 closest distance to " CG  GLN A 223 " =    2.049
peak=   -4.250 closest distance to " CG1 VAL A 112 " =    2.793
peak=   -4.227 closest distance to " CB  PRO A 243 " =    2.662
peak=   -4.205 closest distance to " CD  ARG A 156 " =    2.058
peak=   -4.193 closest distance to " O   HOH Z 372 " =    2.191
peak=   -4.139 closest distance to " O   HOH Z 198 " =    1.559
peak=   -4.102 closest distance to " O   PRO A 198 " =    1.242
peak=   -4.099 closest distance to " O   HOH Z 377 " =    2.127
peak=   -4.073 closest distance to " CB  PHE A 192 " =    1.955
peak=   -4.055 closest distance to " CE  MET A 105 " =    2.389
peak=   -4.007 closest distance to " CA  VAL A  67 " =    2.917
peak=   -3.968 closest distance to " O   HOH Z 231 " =    2.266
peak=   -3.967 closest distance to " CB  ASN A  39 " =    2.331
peak=   -3.926 closest distance to " N   ALA A 248 " =    1.604
peak=   -3.902 closest distance to " OXT GLY A 302 " =    2.874
peak=   -3.882 closest distance to " O   HOH Z 313 " =    1.791
peak=   -3.853 closest distance to " O   HOH Z 351 " =    1.435
peak=   -3.853 closest distance to " CE2 TYR A  30 " =    2.796
peak=   -3.851 closest distance to " ND2 ASN A  45 " =    1.199
peak=   -3.848 closest distance to " O   VAL A  67 " =    2.639
peak=   -3.847 closest distance to " O   HOH Z 290 " =    1.160
peak=   -3.837 closest distance to " OD2 ASP A 191 " =    1.371
peak=   -3.824 closest distance to " O   HOH Z 102 " =    1.680
peak=   -3.823 closest distance to " CZ  TYR A 169 " =    1.796
peak=   -3.809 closest distance to " CB  ALA A  43 " =    2.445
peak=   -3.805 closest distance to " O   ALA A 161 " =    1.636
peak=   -3.797 closest distance to " CZ3 TRP A 179 " =    1.260
peak=   -3.792 closest distance to " N   GLN A  58 " =    1.659
peak=   -3.783 closest distance to " ND2 ASN A 187 " =    1.489
peak=   -3.765 closest distance to " OG  SER A  97 " =    2.200
peak=   -3.765 closest distance to " O   HOH Z  63 " =    1.576
peak=   -3.736 closest distance to " CD2 TYR A 247 " =    2.388
peak=   -3.735 closest distance to " O   HOH Z 165 " =    2.120
peak=   -3.688 closest distance to " O   HOH Z 407 " =    2.587
peak=   -3.683 closest distance to " O   HOH Z 429 " =    1.978
peak=   -3.677 closest distance to " CD1 LEU A 255 " =    2.705
peak=   -3.649 closest distance to " CG2 ILE A 263 " =    2.215
peak=   -3.624 closest distance to " CG  PHE A 283 " =    2.639
peak=   -3.613 closest distance to " CD  ARG A 139 " =    1.509
peak=   -3.611 closest distance to " NE  ARG A 156 " =    1.899
peak=   -3.608 closest distance to " O   SER A 210 " =    2.004
peak=   -3.606 closest distance to " OE1 GLN A 183 " =    1.537
peak=   -3.605 closest distance to " CD1 LEU A 101 " =    2.321
peak=   -3.584 closest distance to " O   HOH Z 185 " =    2.308
peak=   -3.583 closest distance to " CB  PHE A 208 " =    2.222
peak=   -3.580 closest distance to " O   HOH Z 139 " =    5.087
peak=   -3.580 closest distance to " O   VAL A 174 " =    2.191
peak=   -3.574 closest distance to " O   PHE A 218 " =    1.626
peak=   -3.547 closest distance to " O   SER A  95 " =    1.482
peak=   -3.543 closest distance to " CZ  ARG A  66 " =    1.172
peak=   -3.537 closest distance to " O   HOH Z 362 " =    5.826
peak=   -3.536 closest distance to " CB  ALA A 161 " =    2.386
peak=   -3.534 closest distance to " OD1 ASP A 171 " =    1.586
peak=   -3.532 closest distance to " O   HOH Z  13 " =    1.639
peak=   -3.527 closest distance to " CB  ASP A 132 " =    2.255
peak=   -3.525 closest distance to " O   PRO A 163 " =    1.921
peak=   -3.518 closest distance to " CE BMET A  47 " =    1.221
peak=   -3.514 closest distance to " CB  ALA A 248 " =    2.240
peak=   -3.500 closest distance to " O   HOH Z  38 " =    1.753
peak=   -3.486 closest distance to " CD2 TYR A 293 " =    1.952
peak=   -3.476 closest distance to " CD1 PHE A  59 " =    1.983
peak=   -3.474 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.468 closest distance to " O   HOH Z 183 " =    1.571
peak=   -3.466 closest distance to " O   HOH Z 421 " =    3.211
peak=   -3.466 closest distance to " CG1 VAL A  78 " =    2.833
peak=   -3.464 closest distance to " O   GLN A  89 " =    1.475
peak=   -3.457 closest distance to " CB  ASP A 286 " =    2.214
peak=   -3.456 closest distance to " CD2 PHE A 225 " =    1.257
peak=   -3.449 closest distance to " OD2 ASP A 171 " =    2.235
peak=   -3.442 closest distance to " O   HOH Z   6 " =    2.057
peak=   -3.439 closest distance to " OE2 GLU A 152 " =    1.248
peak=   -3.434 closest distance to " O   ALA A  34 " =    2.163
peak=   -3.434 closest distance to " CA  GLY A 241 " =    2.326
peak=   -3.430 closest distance to " O   HOH Z 353 " =    2.276
peak=   -3.429 closest distance to " O   MET A  40 " =    2.780
peak=   -3.427 closest distance to " O   TRP A  70 " =    1.405
peak=   -3.424 closest distance to " CZ3 TRP A 274 " =    2.275
peak=   -3.418 closest distance to " CB  ALA A 291 " =    2.182
peak=   -3.408 closest distance to " OD1 ASN A 301 " =    1.897
peak=   -3.408 closest distance to " O   HOH Z 389 " =    1.891
peak=   -3.405 closest distance to " O   HOH Z 126 " =    1.946
peak=   -3.398 closest distance to " O   ALA A  10 " =    1.704
peak=   -3.398 closest distance to " CB  PRO A 163 " =    2.463
peak=   -3.396 closest distance to " O   HOH Z  11 " =    1.754
peak=   -3.396 closest distance to " O   HOH Z 394 " =    1.421
peak=   -3.392 closest distance to " CB  TRP A  85 " =    2.452
peak=   -3.387 closest distance to " O   HOH Z 211 " =    1.616
peak=   -3.387 closest distance to " O   ILE A  49 " =    1.727
peak=   -3.378 closest distance to " O   HOH Z 281 " =    2.772
peak=   -3.367 closest distance to " CZ  ARG A 259 " =    0.957
peak=   -3.366 closest distance to " CA  GLY A 241 " =    3.179
peak=   -3.366 closest distance to " O   HOH Z 393 " =    3.509
peak=   -3.366 closest distance to " CZ  PHE A  59 " =    1.477
peak=   -3.360 closest distance to " ND2 ASN A 249 " =    2.314
peak=   -3.357 closest distance to " O   HOH Z 317 " =    1.516
peak=   -3.353 closest distance to " OG  SER A   3 " =    1.724
peak=   -3.350 closest distance to " CA  ASP A 298 " =    1.091
peak=   -3.348 closest distance to " CB  ASP A 132 " =    2.388
peak=   -3.347 closest distance to " O   TRP A  92 " =    1.885
peak=   -3.346 closest distance to " OD1 ASP A 191 " =    1.626
peak=   -3.342 closest distance to " ND2 ASN A  39 " =    1.144
peak=   -3.340 closest distance to " CB  SER A 210 " =    1.170
peak=   -3.338 closest distance to " CG2 ILE A  49 " =    2.737
peak=   -3.336 closest distance to " NE2 GLN A 278 " =    1.734
peak=   -3.335 closest distance to " C   SER A  22 " =    2.450
peak=   -3.334 closest distance to " O   SER A 135 " =    1.470
peak=   -3.333 closest distance to " O   HOH Z  15 " =    1.506
peak=   -3.329 closest distance to " O   HOH Z 369 " =    2.178
peak=   -3.327 closest distance to " CG  GLU A 277 " =    1.328
peak=   -3.326 closest distance to " CB  ALA A 291 " =    2.173
peak=   -3.325 closest distance to " ND2 ASN A  60 " =    4.119
peak=   -3.320 closest distance to " CA  GLY A  57 " =    2.154
peak=   -3.311 closest distance to " N   ALA A  43 " =    2.556
peak=   -3.305 closest distance to " CB  GLN A  55 " =    1.265
peak=   -3.304 closest distance to " NE2 GLN A 194 " =    1.854
peak=   -3.300 closest distance to " CG  ARG A  66 " =    2.455
peak=   -3.299 closest distance to " CD1 ILE A 106 " =    2.217
peak=   -3.297 closest distance to " O   PRO A 198 " =    1.233
peak=   -3.295 closest distance to " OE1 GLN A  88 " =    1.075
peak=   -3.294 closest distance to " O   HOH Z 114 " =    3.131
peak=   -3.293 closest distance to " O   ALA A 292 " =    2.094
peak=   -3.293 closest distance to " CD  GLN A 223 " =    0.893
peak=   -3.291 closest distance to " O   GLU A 152 " =    1.338
peak=   -3.289 closest distance to " CE2 PHE A  61 " =    2.611
peak=   -3.286 closest distance to " O   HOH Z 385 " =    1.890
peak=   -3.283 closest distance to " C   GLN A 205 " =    1.736
peak=   -3.275 closest distance to " O   SER A   3 " =    1.002
peak=   -3.271 closest distance to " O   HOH Z 256 " =    1.332
peak=   -3.260 closest distance to " CZ2 TRP A 274 " =    0.990
peak=   -3.249 closest distance to " OD2 ASP A  50 " =    1.440
peak=   -3.236 closest distance to " N   ASN A 127 " =    1.434
peak=   -3.234 closest distance to " O   HOH Z 198 " =    1.635
peak=   -3.232 closest distance to " O   HOH Z 131 " =    4.082
peak=   -3.232 closest distance to " O   HOH Z 123 " =    2.287
peak=   -3.229 closest distance to " OH  TYR A 172 " =    1.800
peak=   -3.229 closest distance to " CE3 TRP A 150 " =    2.227
peak=   -3.228 closest distance to " OD1 ASN A 148 " =    1.485
peak=   -3.227 closest distance to " O   HOH Z 137 " =    1.424
peak=   -3.224 closest distance to " O   HOH Z 253 " =    3.627
peak=   -3.221 closest distance to " CB  ASP A 286 " =    1.793
peak=   -3.218 closest distance to " O   HOH Z 243 " =    1.929
peak=   -3.217 closest distance to " CG2 THR A 178 " =    2.253
peak=   -3.209 closest distance to " O   VAL A 189 " =    2.626
peak=   -3.203 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.202 closest distance to " O   ALA A 227 " =    1.562
peak=   -3.196 closest distance to " CG1 VAL A 230 " =    1.934
peak=   -3.194 closest distance to " CB  GLN A  11 " =    1.843
peak=   -3.177 closest distance to " O   HOH Z 134 " =    3.131
peak=   -3.175 closest distance to " NE  ARG A  36 " =    1.966
peak=   -3.172 closest distance to " CD2 LEU A 237 " =    2.761
peak=   -3.166 closest distance to " O   HOH Z   6 " =    1.442
peak=   -3.164 closest distance to " O  BHOH Z 338 " =    1.365
peak=   -3.164 closest distance to " C   GLY A  17 " =    0.972
peak=   -3.164 closest distance to " CG1 VAL A 268 " =    2.424
peak=   -3.163 closest distance to " CD2 PHE A  61 " =    2.371
peak=   -3.160 closest distance to " O   ILE A 106 " =    1.934
peak=   -3.159 closest distance to " O   HOH Z 427 " =    1.516
peak=   -3.146 closest distance to " O   LEU A 167 " =    1.536
peak=   -3.145 closest distance to " O   HOH Z 326 " =    1.681
peak=   -3.140 closest distance to " C   MET A 188 " =    1.430
peak=   -3.136 closest distance to " O   HOH Z 250 " =    1.367
peak=   -3.134 closest distance to " O   HOH Z 298 " =    2.404
peak=   -3.130 closest distance to " CA  GLY A 133 " =    2.027
peak=   -3.121 closest distance to " O   HOH Z 197 " =    5.073
peak=   -3.119 closest distance to " CG  ARG A 269 " =    2.170
peak=   -3.118 closest distance to " O   LYS A  76 " =    1.817
peak=   -3.118 closest distance to " N   PHE A  59 " =    1.774
peak=   -3.118 closest distance to " CG1 VAL A 250 " =    2.583
peak=   -3.115 closest distance to " O   HOH Z 139 " =    3.173
peak=   -3.103 closest distance to " C   ALA A 158 " =    1.449
peak=   -3.101 closest distance to " C   ARG A 195 " =    1.720
peak=   -3.101 closest distance to " C   ALA A 114 " =    2.238
peak=   -3.099 closest distance to " O   HOH Z  33 " =    2.658
peak=   -3.098 closest distance to " O   HOH Z  60 " =    2.046
peak=   -3.089 closest distance to " N   ASP A 286 " =    2.118
peak=   -3.076 closest distance to " OG1 THR A 246 " =    1.402
peak=   -3.026 closest distance to " N   ALA A 226 " =    1.891
peak=   -3.016 closest distance to " O   PRO A 163 " =    1.293
peak=   -3.006 closest distance to " CG1AVAL A  41 " =    2.353

================= 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    :  0.3833 0.3782   6.168582e+00   6.163264e+00
   1_bss:  0.3729 0.3686   6.152773e+00   6.146447e+00
   1_xyz:  0.2233 0.2574   5.713886e+00   5.824872e+00
   1_adp:  0.2022 0.2639   5.662526e+00   5.852641e+00
   1_occ:  0.2018 0.2639   5.662399e+00   5.852481e+00
   2_bss:  0.1972 0.2602   5.649948e+00   5.842683e+00
   2_xyz:  0.1469 0.1910   5.371367e+00   5.575764e+00
   2_adp:  0.1397 0.1810   5.319461e+00   5.515532e+00
   2_occ:  0.1394 0.1809   5.318261e+00   5.514627e+00
   3_bss:  0.1393 0.1805   5.316073e+00   5.511415e+00
   3_xyz:  0.1236 0.1607   5.206967e+00   5.408358e+00
   3_adp:  0.1207 0.1587   5.190497e+00   5.398141e+00
   3_occ:  0.1206 0.1587   5.190366e+00   5.398512e+00
   4_bss:  0.1206 0.1587   5.190142e+00   5.398199e+00
   4_xyz:  0.1104 0.1528   5.130107e+00   5.365060e+00
   4_adp:  0.1100 0.1524   5.126066e+00   5.359656e+00
   4_occ:  0.1099 0.1524   5.125966e+00   5.359857e+00
   5_bss:  0.1097 0.1523   5.124214e+00   5.356966e+00
   5_xyz:  0.1106 0.1530   5.133437e+00   5.364930e+00
   5_adp:  0.1091 0.1543   5.130504e+00   5.372467e+00
   5_occ:  0.1090 0.1543   5.130318e+00   5.372288e+00
   5_bss:  0.1090 0.1543   5.130336e+00   5.372252e+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:  0.345  50.000   1.423  -2.101   0.296  -0.000   0.000   0.000
   1_xyz:  0.345  50.000   1.423  -2.101   0.296  -0.000   0.000   0.000
   1_adp:  0.345  50.000   1.423  -2.101   0.296  -0.000   0.000   0.000
   1_occ:  0.345  50.000   1.423  -2.101   0.296  -0.000   0.000   0.000
   2_bss:  0.327  50.000  -2.229  -2.602  -0.879  -0.000  -0.000  -0.000
   2_xyz:  0.327  50.000  -2.229  -2.602  -0.879  -0.000  -0.000  -0.000
   2_adp:  0.327  50.000  -2.229  -2.602  -0.879  -0.000  -0.000  -0.000
   2_occ:  0.327  50.000  -2.229  -2.602  -0.879  -0.000  -0.000  -0.000
   3_bss:  0.330  50.000  -3.178  -2.605  -1.061  -0.000  -0.000  -0.000
   3_xyz:  0.330  50.000  -3.178  -2.605  -1.061  -0.000  -0.000  -0.000
   3_adp:  0.330  50.000  -3.178  -2.605  -1.061  -0.000  -0.000  -0.000
   3_occ:  0.330  50.000  -3.178  -2.605  -1.061  -0.000  -0.000  -0.000
   4_bss:  0.330  50.000  -3.457  -2.694  -1.194  -0.000  -0.000  -0.000
   4_xyz:  0.330  50.000  -3.457  -2.694  -1.194  -0.000  -0.000  -0.000
   4_adp:  0.330  50.000  -3.457  -2.694  -1.194  -0.000  -0.000  -0.000
   4_occ:  0.330  50.000  -3.457  -2.694  -1.194  -0.000  -0.000  -0.000
   5_bss:  0.330  50.000  -3.439  -2.630  -1.094  -0.000  -0.000  -0.000
   5_xyz:  0.330  50.000  -3.439  -2.630  -1.094  -0.000  -0.000  -0.000
   5_adp:  0.330  50.000  -3.439  -2.630  -1.094  -0.000  -0.000  -0.000
   5_occ:  0.330  50.000  -3.439  -2.630  -1.094  -0.000  -0.000  -0.000
   5_bss:  0.327  49.954  -3.221  -2.379  -0.863  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.837 0.6233  0.8187    44397.257
   1_bss:  40.631 0.6362  0.8398    41183.829
   1_xyz:  25.091 0.8115  1.0082    16929.403
   1_adp:  26.147 0.7996  1.0023    17978.410
   1_occ:  26.177 0.7993  1.0020    18012.774
   2_bss:  25.751 0.8034  0.9419    17415.389
   2_xyz:  18.208 0.8784  0.9884     9403.078
   2_adp:  16.702 0.8926  0.9962     8441.897
   2_occ:  16.679 0.8928  0.9962     8410.922
   3_bss:  16.608 0.8933  0.9818     8331.583
   3_xyz:  14.588 0.9100  0.9883     6703.947
   3_adp:  14.353 0.9122  0.9865     6576.910
   3_occ:  14.359 0.9121  0.9863     6574.732
   4_bss:  14.355 0.9121  0.9802     6569.482
   4_xyz:  13.719 0.9171  0.9819     6132.278
   4_adp:  13.611 0.9180  0.9790     6077.098
   4_occ:  13.613 0.9180  0.9789     6076.700
   5_bss:  13.579 0.9183  0.9812     6024.869
   5_xyz:  13.646 0.9180  0.9807     6126.411
   5_adp:  13.791 0.9168  0.9753     6175.843
   5_occ:  13.787 0.9168  0.9752     6172.108
   5_bss:  13.789 0.9168  0.9817     6170.200
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.1084e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.1084e-01
   1_xyz:   1.282  0.009  0.081 15.414  0.006  4.109   8.9348e-02
   1_adp:   1.282  0.009  0.081 15.414  0.006  4.109   8.9348e-02
   1_occ:   1.282  0.009  0.081 15.414  0.006  4.109   8.9348e-02
   2_bss:   1.282  0.009  0.081 15.414  0.006  4.109   8.9348e-02
   2_xyz:   0.995  0.006  0.071 14.582  0.004  4.116   5.6235e-02
   2_adp:   0.995  0.006  0.071 14.582  0.004  4.116   5.6235e-02
   2_occ:   0.995  0.006  0.071 14.582  0.004  4.116   5.6235e-02
   3_bss:   0.995  0.006  0.071 14.582  0.004  4.116   5.6235e-02
   3_xyz:   0.921  0.005  0.067 14.435  0.004  4.109   5.0940e-02
   3_adp:   0.921  0.005  0.067 14.435  0.004  4.109   5.0940e-02
   3_occ:   0.921  0.005  0.067 14.435  0.004  4.109   5.0940e-02
   4_bss:   0.921  0.005  0.067 14.435  0.004  4.109   5.0940e-02
   4_xyz:   1.124  0.009  0.081 14.988  0.005  4.110   7.1559e-02
   4_adp:   1.124  0.009  0.081 14.988  0.005  4.110   7.1559e-02
   4_occ:   1.124  0.009  0.081 14.988  0.005  4.110   7.1559e-02
   5_bss:   1.124  0.009  0.081 14.988  0.005  4.110   7.1559e-02
   5_xyz:   0.973  0.006  0.073 14.566  0.004  4.110   5.6290e-02
   5_adp:   0.973  0.006  0.073 14.566  0.004  4.110   5.6290e-02
   5_occ:   0.973  0.006  0.073 14.566  0.004  4.110   5.6290e-02
   5_bss:   0.973  0.006  0.073 14.566  0.004  4.110   5.6290e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.389   2.4145e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.389   2.4145e-01
   1_xyz:  11.017  0.041  0.295 84.947  0.046  2.177   9.4844e-02
   1_adp:  11.017  0.041  0.295 84.947  0.046  2.177   9.4844e-02
   1_occ:  11.017  0.041  0.295 84.947  0.046  2.177   9.4844e-02
   2_bss:  11.017  0.041  0.295 84.947  0.046  2.177   9.4844e-02
   2_xyz:   6.839  0.037  0.218 81.123  0.045  2.299   4.5580e-02
   2_adp:   6.839  0.037  0.218 81.123  0.045  2.299   4.5580e-02
   2_occ:   6.839  0.037  0.218 81.123  0.045  2.299   4.5580e-02
   3_bss:   6.839  0.037  0.218 81.123  0.045  2.299   4.5580e-02
   3_xyz:   6.577  0.046  0.207 84.049  0.037  2.407   6.3454e-02
   3_adp:   6.577  0.046  0.207 84.049  0.037  2.407   6.3454e-02
   3_occ:   6.577  0.046  0.207 84.049  0.037  2.407   6.3454e-02
   4_bss:   6.577  0.046  0.207 84.049  0.037  2.407   6.3454e-02
   4_xyz:   7.148  0.052  0.265 83.593  0.037  2.277   5.6729e-02
   4_adp:   7.148  0.052  0.265 83.593  0.037  2.277   5.6729e-02
   4_occ:   7.148  0.052  0.265 83.593  0.037  2.277   5.6729e-02
   5_bss:   7.148  0.052  0.265 83.593  0.037  2.277   5.6729e-02
   5_xyz:   6.644  0.048  0.238 84.353  0.043  2.370   3.8974e-02
   5_adp:   6.644  0.048  0.238 84.353  0.043  2.370   3.8974e-02
   5_occ:   6.644  0.048  0.238 84.353  0.043  2.370   3.8974e-02
   5_bss:   6.644  0.048  0.238 84.353  0.043  2.370   3.8974e-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:  77.54   0.00  17.70  77.54   0.00  13.56  76.91   5.14  40.25
   1_occ:  77.54   0.00  17.70  77.54   0.00  13.56  76.91   5.14  40.25
   2_bss:  77.54   0.00  17.70  77.54   0.00  13.56  76.91   5.14  40.25
   2_xyz:  77.54   0.00  17.70  77.54   0.00  13.56  76.91   5.14  40.25
   2_adp:  79.82   1.04  17.12  79.82   1.04  13.23  71.65   5.40  38.29
   2_occ:  79.82   1.04  17.12  79.82   1.04  13.23  71.65   5.40  38.29
   3_bss:  79.82   1.04  17.12  79.82   1.04  13.23  71.65   5.40  38.29
   3_xyz:  79.82   1.04  17.12  79.82   1.04  13.23  71.65   5.40  38.29
   3_adp:  82.59   1.86  17.03  82.59   1.86  13.13  70.71   4.91  38.24
   3_occ:  82.59   1.86  17.03  82.59   1.86  13.13  70.71   4.91  38.24
   4_bss:  82.59   1.86  17.03  82.59   1.86  13.13  70.71   4.91  38.24
   4_xyz:  82.59   1.86  17.03  82.59   1.86  13.13  70.71   4.91  38.24
   4_adp:  82.56   2.35  16.76  82.56   2.35  12.98  71.17   4.09  37.39
   4_occ:  82.56   2.35  16.76  82.56   2.35  12.98  71.17   4.09  37.39
   5_bss:  82.56   2.35  16.76  82.56   2.35  12.98  71.17   4.09  37.39
   5_xyz:  82.56   2.35  16.76  82.56   2.35  12.98  71.17   4.09  37.39
   5_adp:  86.73   1.31  17.09  86.73   1.31  12.99  74.15   5.40  39.39
   5_occ:  86.73   1.31  17.09  86.73   1.31  12.99  74.15   5.40  39.39
   5_bss:  86.68   1.27  17.04  86.68   1.27  12.95  74.10   5.35  39.34
------------------------------------------------------------------------
 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:    1.583    0.015    0.375
   1_adp:    1.583    0.015    0.375
   1_occ:    1.583    0.015    0.375
   2_bss:    1.583    0.015    0.375
   2_xyz:    1.677    0.018    0.443
   2_adp:    1.677    0.018    0.443
   2_occ:    1.677    0.018    0.443
   3_bss:    1.677    0.018    0.443
   3_xyz:    1.763    0.028    0.494
   3_adp:    1.763    0.028    0.494
   3_occ:    1.763    0.028    0.494
   4_bss:    1.763    0.028    0.494
   4_xyz:    1.784    0.033    0.510
   4_adp:    1.784    0.033    0.510
   4_occ:    1.784    0.033    0.510
   5_bss:    1.784    0.033    0.510
   5_xyz:    1.792    0.031    0.520
   5_adp:    1.792    0.031    0.520
   5_occ:    1.792    0.031    0.520
   5_bss:    1.792    0.031    0.520
------------------------------------------------------------------------

CPU time actual refinement: 268.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_51/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_51/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_51/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_51/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_51/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 268.54 
  Macro-tasks:
    bulk solvent and scale       = 30.80  
    individual site refinement   = 109.93 
    weights calculation          = 24.17  
    collect and process          = 5.46   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 170.44 
  Micro-tasks:
    mask                            = 1.50   
    f_calc                          = 85.64  
    alpha_beta                      = 6.86   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 93.03  
    fmodel                         = 5.35   
    r_factors                      = 0.16   
    phase_errors                   = 9.05   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 202.78 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.821 micro seconds
Total CPU time: 4.67 minutes
from_scatterers_fft:    646 calls, 85.41 s
gradients_fft:          591 calls, 81.54 s

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

# Date 2008-01-16 Time 03:52:52 PST -0800 (1200484372.62 s)
Start R-work = 0.3833, R-free = 0.3782 (no bulk solvent and anisotropic scale)
Final R-work = 0.1360, R-free = 0.1756 (no bulk solvent and anisotropic scale)

Start R-work = 0.3729, R-free = 0.3686
Final R-work = 0.1090, R-free = 0.1543