# Date 2008-01-16 Time 04:21:08 PST -0800 (1200486068.65 s)
#phil __OFF__

Command line arguments: "../279.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15621
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 279

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.4607, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8093 1.97057
Completeness in resolution range: 0.972352
Completeness with d_max=infinity: 0.969273

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8093
                             d_min =   1.9706

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8093 1.97057
Completeness in resolution range: 0.972352
Completeness with d_max=infinity: 0.969273

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8097 -  4.2159 [2118/2142]  1904   214  10.1%
  bin  2:  4.2159 -  3.3591 [2036/2055]  1835   201   9.9%
  bin  3:  3.3591 -  2.9383 [2008/2027]  1809   199   9.9%
  bin  4:  2.9383 -  2.6713 [1982/2012]  1777   205  10.3%
  bin  5:  2.6713 -  2.4808 [1982/2001]  1786   196   9.9%
  bin  6:  2.4808 -  2.3351 [1967/1992]  1773   194   9.9%
  bin  7:  2.3351 -  2.2186 [1950/1978]  1755   195  10.0%
  bin  8:  2.2186 -  2.1223 [1947/1983]  1752   195  10.0%
  bin  9:  2.1223 -  2.0408 [1934/1976]  1739   195  10.1%
  bin 10:  2.0408 -  1.9706 [1665/1980]  1500   165   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_279/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: 0.15 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:
        1.62 -     2.27: 18
        2.27 -     2.93: 1604
        2.93 -     3.59: 4548
        3.59 -     4.24: 9397
        4.24 -     4.90: 13182
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.618 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.726 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.847 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.992 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28744 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_279/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_279/model_refine_001.geo

CPU time processing inputs: 9.43


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.4607 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3469   r_free= 0.3442   ksol= 0.00   Bsol= 0.00   scale= 0.976    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.089549                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.7018 0.99   1380  153 0.2960 0.2895      6.3706      6.3435|
|  2:  4.7018 -  3.7520 0.99   1312  149 0.2707 0.2613      6.4648      6.4514|
|  3:  3.7520 -  3.2836 0.99   1305  145 0.3001 0.3039      6.3989      6.4815|
|  4:  3.2836 -  2.9861 0.99   1290  136 0.3169 0.3498      6.2761       6.367|
|  5:  2.9861 -  2.7735 0.99   1270  144 0.3493 0.3246      6.1409      6.0613|
|  6:  2.7735 -  2.6109 0.99   1276  145 0.3642 0.3652      6.1011      6.0189|
|  7:  2.6109 -  2.4808 0.99   1278  143 0.3674 0.3384      6.0392      5.9468|
|  8:  2.4808 -  2.3733 0.98   1264  135 0.3884 0.3994      6.0271       6.082|
|  9:  2.3733 -  2.2823 0.98   1251  143 0.3884 0.4020      5.9745      5.9491|
| 10:  2.2823 -  2.2038 0.99   1267  136 0.4003 0.3984      5.9759      5.9242|
| 11:  2.2038 -  2.1351 0.98   1259  142 0.3955 0.3982      5.9017      5.9314|
| 12:  2.1351 -  2.0742 0.97   1227  139 0.4158 0.3682      5.8977      5.8521|
| 13:  2.0742 -  2.0197 1.00   1264  137 0.4033 0.3876      5.7782        5.72|
| 14:  2.0197 -  1.9706 0.78    987  112 0.4160 0.3915      5.7774      5.6213|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8097 -  4.7018  1380   153  0.77  27.46   0.87     0.80      46710.98|
|  2:  4.7018 -  3.7520  1312   149  0.83  23.57   0.98     0.92      53365.55|
|  3:  3.7520 -  3.2836  1305   145  0.78  28.02   1.01     0.95      53503.93|
|  4:  3.2836 -  2.9861  1290   136  0.75  31.22   1.00     0.93      47334.49|
|  5:  2.9861 -  2.7735  1270   144  0.70  35.23   0.99     0.91      37844.74|
|  6:  2.7735 -  2.6109  1276   145  0.71  34.73   0.98     0.92      31573.80|
|  7:  2.6109 -  2.4808  1278   143  0.70  35.51   1.00     0.93      28679.68|
|  8:  2.4808 -  2.3733  1264   135  0.69  36.97   1.02     0.91      27653.03|
|  9:  2.3733 -  2.2823  1251   143  0.67  38.51   1.01     0.90      26775.04|
| 10:  2.2823 -  2.2038  1267   136  0.66  39.33   1.04     0.90      25153.73|
| 11:  2.2038 -  2.1351  1259   142  0.65  40.13   1.04     0.92      23632.47|
| 12:  2.1351 -  2.0742  1227   139  0.66  39.41   1.04     0.93      20896.34|
| 13:  2.0742 -  2.0197  1264   137  0.66  39.34   1.05     0.92      17466.87|
| 14:  2.0197 -  1.9706   987   112  0.70  35.81   1.04     0.90      12913.78|
|alpha:            min =        0.80 max =            0.95 mean =         0.91|
|beta:             min =    12913.78 max =        53503.93 mean =     32949.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.71|
|phase err.(work): min =        0.00 max =           89.96 mean =        34.53|
|phase err.(test): min =        0.00 max =           89.95 mean =        34.37|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.702395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.548   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.728479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.757   (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 |  1.618 -  1.946:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.946 -  2.274:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.274 -  2.602:       62 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.602 -  2.931:     1542 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.931 -  3.259:     1911 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.259 -  3.587:     2637 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.587 -  3.915:     4819 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.915 -  4.244:     4578 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.244 -  4.572:     6012 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.572 -  4.900:     7170 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| 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  1.618 |       0.334 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.527)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3469   r_free= 0.3442   ksol= 0.00   Bsol= 0.00   scale= 0.976    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.089549                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3335   r_free= 0.3294   ksol= 0.32   Bsol= 20.00   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,0.18,-1.39,0.00,-0.00,-0.00); trace/3= -0.70                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.068771                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.146360              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.451   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402500              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.608   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3335      final r-factor (work) = 0.1824          |
| start r-factor (free) = 0.3294      final r-factor (free) = 0.2054          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7751 = 4.15 * 0.50 * 6.0796 + 1.00 * 0.1710                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0071 = 4.15 * 0.50 * 5.7586 + 1.00 * 0.0686                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1824      final r-factor (work) = 0.1664          |
| start r-factor (free) = 0.2054      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3237 = 0.40 * 1.00 * 5.7586 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2043 = 0.40 * 1.00 * 5.4538 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.527)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.44   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    74.44   17.30    None  None   None       |
|    Sol.    : 438    0      7.46    74.44   39.49    None  None   None       |
|    Mac.    : 2385   0      0.00    72.31   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:     0.000 -   7.444:  445   |   5:    37.222 -  44.666:  118        |
|      1:     7.444 -  14.889: 1323   |   6:    44.666 -  52.110:   90        |
|      2:    14.889 -  22.333:  463   |   7:    52.110 -  59.554:   78        |
|      3:    22.333 -  29.777:  161   |   8:    59.554 -  66.999:   28        |
|      4:    29.777 -  37.222:  108   |   9:    66.999 -  74.443:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1664 r_free = 0.2149             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1661 r_free = 0.2146             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1661   r_free= 0.2146   ksol= 0.32   Bsol= 20.00   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,0.18,-1.39,0.00,-0.00,-0.00); trace/3= -0.70                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.470494                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1632   r_free= 0.2115   ksol= 0.32   Bsol= 36.37   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.99,-1.70,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.461109                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.743154              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.101   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.102105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.628  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1632      final r-factor (work) = 0.1284          |
| start r-factor (free) = 0.2115      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8362 = 1.74 * 0.50 * 5.4701 + 1.00 * 0.0686                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7191 = 1.74 * 0.50 * 5.3587 + 1.00 * 0.0485                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1256          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5563 = 0.10 * 1.00 * 5.3587 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5402 = 0.10 * 1.00 * 5.2303 + 1.00 * 0.0061                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.527)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.68    74.81   16.68    None  None   None       |
|    all(noH): 2823   0      1.68    74.81   16.68    None  None   None       |
|    Sol.    : 438    0      6.66    73.19   36.75    None  None   None       |
|    Mac.    : 2385   0      1.68    74.81   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:     1.683 -   8.996:  675   |   5:    38.247 -  45.560:  108        |
|      1:     8.996 -  16.309: 1294   |   6:    45.560 -  52.873:   85        |
|      2:    16.309 -  23.621:  345   |   7:    52.873 -  60.186:   41        |
|      3:    23.621 -  30.934:  120   |   8:    60.186 -  67.499:   15        |
|      4:    30.934 -  38.247:  137   |   9:    67.499 -  74.812:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1256 r_free = 0.1615             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1254 r_free = 0.1614             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1614   ksol= 0.32   Bsol= 36.37   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.99,-1.70,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.205276                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1612   ksol= 0.32   Bsol= 37.68   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.41,-1.46,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.204399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.107322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.761  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.445499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.659  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1512          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5587 = 2.11 * 0.50 * 5.2295 + 1.00 * 0.0485                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4827 = 2.11 * 0.50 * 5.1499 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1509          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3004 = 0.45 * 1.00 * 5.1499 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2822 = 0.45 * 1.00 * 5.1051 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.527)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    82.48   17.01    None  None   None       |
|    all(noH): 2823   0      1.04    82.48   17.01    None  None   None       |
|    Sol.    : 438    0      6.35    75.57   38.97    None  None   None       |
|    Mac.    : 2385   0      1.04    82.48   12.97    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:     1.038 -   9.183:  779   |   5:    41.760 -  49.905:  100        |
|      1:     9.183 -  17.327: 1272   |   6:    49.905 -  58.049:   82        |
|      2:    17.327 -  25.471:  286   |   7:    58.049 -  66.194:   42        |
|      3:    25.471 -  33.616:  117   |   8:    66.194 -  74.338:    9        |
|      4:    33.616 -  41.760:  130   |   9:    74.338 -  82.483:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1509             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1509             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1509   ksol= 0.32   Bsol= 37.68   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.41,-1.46,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1508   ksol= 0.32   Bsol= 40.76   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.41,-1.46,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104854                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.312791              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.567  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.232398              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.808  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1508      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4073 = 1.31 * 0.50 * 5.1048 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4009 = 1.31 * 0.50 * 5.1082 + 1.00 * 0.0479                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1515          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1950 = 0.23 * 1.00 * 5.1082 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1954 = 0.23 * 1.00 * 5.1109 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.527)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    83.66   16.80    None  None   None       |
|    all(noH): 2823   0      1.29    83.66   16.80    None  None   None       |
|    Sol.    : 438    0      6.32    76.22   38.39    None  None   None       |
|    Mac.    : 2385   0      1.29    83.66   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.287 -   9.524:  905   |   5:    42.472 -  50.709:  101        |
|      1:     9.524 -  17.761: 1182   |   6:    50.709 -  58.946:   72        |
|      2:    17.761 -  25.998:  263   |   7:    58.946 -  67.183:   29        |
|      3:    25.998 -  34.235:  124   |   8:    67.183 -  75.419:    8        |
|      4:    34.235 -  42.472:  135   |   9:    75.419 -  83.656:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1095 r_free = 0.1515             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1516             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1516   ksol= 0.32   Bsol= 40.76   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.41,-1.46,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1515   ksol= 0.32   Bsol= 41.26   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.33,-1.25,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111254                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.274194              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.741  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.279307              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.173  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1056          |
| start r-factor (free) = 0.1515      final r-factor (free) = 0.1504          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8601 = 2.27 * 0.50 * 5.1114 + 1.00 * 0.0479                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8527 = 2.27 * 0.50 * 5.0950 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1056      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1504      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5257 = 1.28 * 1.00 * 5.0950 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5168 = 1.28 * 1.00 * 5.0872 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.527)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    86.69   16.85    None  None   None       |
|    all(noH): 2823   0      0.54    86.69   16.85    None  None   None       |
|    Sol.    : 438    0      6.11    78.36   39.21    None  None   None       |
|    Mac.    : 2385   0      0.54    86.69   12.74    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:     0.540 -   9.156:  858   |   5:    43.617 -  52.232:  109        |
|      1:     9.156 -  17.771: 1230   |   6:    52.232 -  60.848:   72        |
|      2:    17.771 -  26.386:  264   |   7:    60.848 -  69.463:   24        |
|      3:    26.386 -  35.002:  121   |   8:    69.463 -  78.078:   12        |
|      4:    35.002 -  43.617:  129   |   9:    78.078 -  86.694:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1051 r_free = 0.1517             target_work(ml) = 5.092         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1051 r_free = 0.1516             target_work(ml) = 5.092         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1051   r_free= 0.1516   ksol= 0.32   Bsol= 41.26   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.33,-1.25,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.091879                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.7018 0.99   1380  153 0.0979 0.1217       5.363      5.4921|
|  2:  4.7018 -  3.7520 0.99   1312  149 0.0821 0.1097      5.4054      5.6008|
|  3:  3.7520 -  3.2836 0.99   1305  145 0.1014 0.1488      5.4388      5.8244|
|  4:  3.2836 -  2.9861 0.99   1290  136 0.1128 0.1502      5.3933      5.5406|
|  5:  2.9861 -  2.7735 0.99   1270  144 0.1209 0.1659      5.2645      5.4937|
|  6:  2.7735 -  2.6109 0.99   1276  145 0.1112 0.1752      5.1531      5.3962|
|  7:  2.6109 -  2.4808 0.99   1278  143 0.1164 0.1579      5.1046      5.3293|
|  8:  2.4808 -  2.3733 0.98   1264  135 0.1092 0.1643       5.026      5.3153|
|  9:  2.3733 -  2.2823 0.98   1251  143 0.1098 0.1708       4.976      5.2526|
| 10:  2.2823 -  2.2038 0.99   1267  136 0.1035 0.1661      4.9106      5.1636|
| 11:  2.2038 -  2.1351 0.98   1259  142 0.1046 0.1649      4.8912      5.1924|
| 12:  2.1351 -  2.0742 0.97   1227  139 0.1053 0.1565      4.8321      5.1832|
| 13:  2.0742 -  2.0197 1.00   1264  137 0.1016 0.1652      4.7398      5.0171|
| 14:  2.0197 -  1.9706 0.78    987  112 0.0967 0.1723      4.6195      4.9205|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8097 -  4.7018  1380   153  0.94   8.75   0.98     0.96       6632.15|
|  2:  4.7018 -  3.7520  1312   149  0.96   7.50   1.03     1.02       8479.14|
|  3:  3.7520 -  3.2836  1305   145  0.94  10.54   1.04     1.03       9587.16|
|  4:  3.2836 -  2.9861  1290   136  0.93  12.39   1.01     1.00       9126.31|
|  5:  2.9861 -  2.7735  1270   144  0.91  14.77   1.00     0.98       7460.01|
|  6:  2.7735 -  2.6109  1276   145  0.91  14.92   0.99     0.96       6369.49|
|  7:  2.6109 -  2.4808  1278   143  0.91  14.97   0.99     0.96       5637.01|
|  8:  2.4808 -  2.3733  1264   135  0.92  13.88   1.00     0.98       4816.87|
|  9:  2.3733 -  2.2823  1251   143  0.92  14.40   1.01     0.99       4534.93|
| 10:  2.2823 -  2.2038  1267   136  0.91  14.76   1.00     0.96       3999.79|
| 11:  2.2038 -  2.1351  1259   142  0.91  15.17   1.00     0.97       4092.78|
| 12:  2.1351 -  2.0742  1227   139  0.91  14.70   1.01     1.00       3646.52|
| 13:  2.0742 -  2.0197  1264   137  0.91  14.64   1.00     0.99       3066.05|
| 14:  2.0197 -  1.9706   987   112  0.92  13.54   0.98     0.95       2339.70|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2339.70 max =         9587.16 mean =      5786.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.15|
|phase err.(test): min =        0.00 max =           87.51 mean =        12.76|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1516   ksol= 0.32   Bsol= 42.92   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.16,-1.04,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.091811                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1516   ksol= 0.32   Bsol= 42.92   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.16,-1.04,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.091811                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.7018 0.99   1380  153 0.0980 0.1220      5.3641      5.4934|
|  2:  4.7018 -  3.7520 0.99   1312  149 0.0823 0.1098      5.4069      5.6017|
|  3:  3.7520 -  3.2836 0.99   1305  145 0.1015 0.1488      5.4394      5.8251|
|  4:  3.2836 -  2.9861 0.99   1290  136 0.1127 0.1500       5.393      5.5398|
|  5:  2.9861 -  2.7735 0.99   1270  144 0.1209 0.1657      5.2637      5.4928|
|  6:  2.7735 -  2.6109 0.99   1276  145 0.1111 0.1749      5.1523      5.3948|
|  7:  2.6109 -  2.4808 0.99   1278  143 0.1164 0.1578      5.1039      5.3288|
|  8:  2.4808 -  2.3733 0.98   1264  135 0.1091 0.1642      5.0254      5.3143|
|  9:  2.3733 -  2.2823 0.98   1251  143 0.1097 0.1709      4.9758      5.2528|
| 10:  2.2823 -  2.2038 0.99   1267  136 0.1035 0.1662      4.9107      5.1635|
| 11:  2.2038 -  2.1351 0.98   1259  142 0.1045 0.1649      4.8911      5.1922|
| 12:  2.1351 -  2.0742 0.97   1227  139 0.1052 0.1565       4.832      5.1832|
| 13:  2.0742 -  2.0197 1.00   1264  137 0.1017 0.1652      4.7396      5.0168|
| 14:  2.0197 -  1.9706 0.78    987  112 0.0967 0.1721      4.6189      4.9195|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8097 -  4.7018  1380   153  0.94   8.77   0.99     0.96       6653.68|
|  2:  4.7018 -  3.7520  1312   149  0.96   7.51   1.03     1.02       8498.42|
|  3:  3.7520 -  3.2836  1305   145  0.94  10.54   1.04     1.03       9594.40|
|  4:  3.2836 -  2.9861  1290   136  0.93  12.38   1.02     1.01       9116.56|
|  5:  2.9861 -  2.7735  1270   144  0.91  14.76   1.01     0.98       7447.59|
|  6:  2.7735 -  2.6109  1276   145  0.91  14.90   0.99     0.96       6357.95|
|  7:  2.6109 -  2.4808  1278   143  0.91  14.95   0.99     0.96       5624.63|
|  8:  2.4808 -  2.3733  1264   135  0.92  13.87   1.00     0.98       4809.42|
|  9:  2.3733 -  2.2823  1251   143  0.92  14.40   1.02     0.99       4533.02|
| 10:  2.2823 -  2.2038  1267   136  0.91  14.75   1.01     0.97       4001.13|
| 11:  2.2038 -  2.1351  1259   142  0.91  15.18   1.01     0.98       4092.48|
| 12:  2.1351 -  2.0742  1227   139  0.91  14.69   1.02     1.01       3645.39|
| 13:  2.0742 -  2.0197  1264   137  0.91  14.63   1.02     1.00       3063.30|
| 14:  2.0197 -  1.9706   987   112  0.92  13.53   0.99     0.96       2336.28|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2336.28 max =         9594.40 mean =      5785.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.15|
|phase err.(test): min =        0.00 max =           87.75 mean =        12.76|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.527)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    86.68   16.83    None  None   None       |
|    all(noH): 2823   0      0.52    86.68   16.83    None  None   None       |
|    Sol.    : 438    0      6.10    78.34   39.20    None  None   None       |
|    Mac.    : 2385   0      0.52    86.68   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.523 -   9.138:  858   |   5:    43.600 -  52.215:  109        |
|      1:     9.138 -  17.754: 1230   |   6:    52.215 -  60.830:   72        |
|      2:    17.754 -  26.369:  264   |   7:    60.830 -  69.446:   24        |
|      3:    26.369 -  34.984:  121   |   8:    69.446 -  78.061:   12        |
|      4:    34.984 -  43.600:  129   |   9:    78.061 -  86.677:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 275         
Filter by distance & map next to the model:
   mapped sites are within: 0.405 - 4.606
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 271 from: 275
   mapped sites are within: 0.790 - 4.606

peak=    5.965 closest distance to " NE2 GLN A  11 " =    1.160
peak=    5.951 closest distance to " O   HOH Z 144 " =    1.856
peak=    5.623 closest distance to " O   HOH Z 126 " =    1.939
peak=    5.455 closest distance to " CB  ARG A 275 " =    0.955
peak=    5.272 closest distance to " CG  PRO A  54 " =    1.222
peak=    5.172 closest distance to " NH2 ARG A  56 " =    2.101
peak=    4.922 closest distance to " O   HOH Z  78 " =    1.789
peak=    4.829 closest distance to " CB  GLN A 183 " =    1.217
peak=    4.824 closest distance to " O   HOH Z 427 " =    2.701
peak=    4.803 closest distance to " CB  GLU A 152 " =    1.263
peak=    4.789 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.783 closest distance to " CB  SER A  63 " =    1.172
peak=    4.736 closest distance to " O   HOH Z 236 " =    1.396
peak=    4.694 closest distance to " CB  GLN A 223 " =    1.504
peak=    4.663 closest distance to " O   HOH Z 250 " =    2.427
peak=    4.627 closest distance to " C   PRO A 198 " =    1.421
peak=    4.526 closest distance to " O   HOH Z 193 " =    1.749
peak=    4.514 closest distance to " O   HOH Z 209 " =    2.210
peak=    4.493 closest distance to " O   HOH Z 402 " =    1.414
peak=    4.476 closest distance to " O   HOH Z 369 " =    2.206
peak=    4.459 closest distance to " O   HOH Z 272 " =    1.842
peak=    4.441 closest distance to " O   HOH Z  78 " =    2.090
peak=    4.433 closest distance to " CB  ARG A  79 " =    1.381
peak=    4.336 closest distance to " CA  TYR A  30 " =    0.922
peak=    4.315 closest distance to " ND2 ASN A 187 " =    1.433
peak=    4.311 closest distance to " O   HOH Z 289 " =    1.674
peak=    4.273 closest distance to " NZ  LYS A 117 " =    3.080
peak=    4.259 closest distance to " CB  VAL A 265 " =    1.315
peak=    4.249 closest distance to " O   HOH Z  44 " =    1.783
peak=    4.249 closest distance to " O   HOH Z 234 " =    3.567
peak=    4.225 closest distance to " O   HOH Z 287 " =    1.986
peak=    4.219 closest distance to " CD2 TRP A 179 " =    1.352
peak=    4.208 closest distance to " O   HOH Z  15 " =    2.339
peak=    4.197 closest distance to " CB  ASN A 148 " =    1.406
peak=    4.188 closest distance to " CB  PRO A  54 " =    0.949
peak=    4.186 closest distance to " OG ASER A 258 " =    3.010
peak=    4.174 closest distance to " O   HOH Z 303 " =    2.133
peak=    4.170 closest distance to " O   HOH Z 298 " =    1.874
peak=    4.156 closest distance to " CG2 VAL A 257 " =    0.829
peak=    4.138 closest distance to " O   HOH Z 203 " =    1.681
peak=    4.109 closest distance to " O   SER A  87 " =    2.214
peak=    4.106 closest distance to " O   HOH Z 250 " =    1.498
peak=    4.073 closest distance to " O   HOH Z 158 " =    2.952
peak=    4.062 closest distance to " O   HOH Z 371 " =    1.685
peak=    4.046 closest distance to " O   HOH Z  61 " =    1.639
peak=    4.045 closest distance to " CB  SER A   3 " =    1.270
peak=    4.032 closest distance to " CG  ARG A  66 " =    2.584
peak=    4.010 closest distance to " O   HOH Z   1 " =    1.961
peak=    4.003 closest distance to " O   HOH Z 407 " =    2.284
peak=    3.997 closest distance to " O   HOH Z 392 " =    3.099
peak=    3.986 closest distance to " O   HOH Z 425 " =    2.114
peak=    3.974 closest distance to " O   HOH Z 189 " =    2.132
peak=    3.960 closest distance to " O   HOH Z  93 " =    2.346
peak=    3.958 closest distance to " CG1 ILE A  33 " =    1.206
peak=    3.954 closest distance to " OG BSER A 164 " =    2.250
peak=    3.950 closest distance to " O   HOH Z 344 " =    3.165
peak=    3.945 closest distance to " CG  PRO A  90 " =    1.096
peak=    3.942 closest distance to " O   HOH Z 403 " =    1.688
peak=    3.938 closest distance to " O   HOH Z 327 " =    1.646
peak=    3.938 closest distance to " O   HOH Z 419 " =    2.116
peak=    3.927 closest distance to " CB  ARG A 190 " =    1.647
peak=    3.922 closest distance to " O   HOH Z 132 " =    2.243
peak=    3.882 closest distance to " O   HOH Z 173 " =    1.978
peak=    3.873 closest distance to " O   HOH Z  66 " =    2.123
peak=    3.849 closest distance to " CB  TYR A 169 " =    0.869
peak=    3.848 closest distance to " O   HOH Z  61 " =    1.476
peak=    3.847 closest distance to " CB  TRP A 266 " =    1.081
peak=    3.846 closest distance to " O   HOH Z 417 " =    3.424
peak=    3.839 closest distance to " O   HOH Z  59 " =    1.681
peak=    3.826 closest distance to " OD1 ASN A  69 " =    2.610
peak=    3.826 closest distance to " O   HOH Z 245 " =    1.332
peak=    3.824 closest distance to " OE1 GLU A   2 " =    2.227
peak=    3.819 closest distance to " O   HOH Z 368 " =    3.564
peak=    3.784 closest distance to " O   HOH Z  97 " =    1.993
peak=    3.781 closest distance to " O   HOH Z 128 " =    2.105
peak=    3.772 closest distance to " O   HOH Z 128 " =    2.020
peak=    3.763 closest distance to " O   HOH Z  40 " =    1.626
peak=    3.757 closest distance to " CG  PRO A 243 " =    1.088
peak=    3.755 closest distance to " CB  SER A  26 " =    1.606
peak=    3.752 closest distance to " O  BHOH Z 338 " =    2.360
peak=    3.752 closest distance to " O   HOH Z 298 " =    2.454
peak=    3.734 closest distance to " CB  GLU A 128 " =    1.074
peak=    3.730 closest distance to " CA  ASN A 215 " =    1.118
peak=    3.722 closest distance to " O   HOH Z 368 " =    2.018
peak=    3.709 closest distance to " O   HOH Z 248 " =    1.594
peak=    3.696 closest distance to " CG  PRO A 198 " =    1.233
peak=    3.689 closest distance to " CB  LEU A 228 " =    1.129
peak=    3.685 closest distance to " O   HOH Z 144 " =    2.145
peak=    3.685 closest distance to " CB  VAL A 202 " =    1.559
peak=    3.680 closest distance to " OD2 ASP A 286 " =    2.687
peak=    3.672 closest distance to " CB  ARG A 139 " =    1.014
peak=    3.670 closest distance to " O   HOH Z 132 " =    2.771
peak=    3.669 closest distance to " O   HOH Z   1 " =    1.602
peak=    3.660 closest distance to " CB  TRP A 179 " =    1.248
peak=    3.644 closest distance to " O   HOH Z 371 " =    3.121
peak=    3.638 closest distance to " O   HOH Z  54 " =    1.666
peak=    3.636 closest distance to " O   HOH Z  43 " =    2.019
peak=    3.635 closest distance to " O   HOH Z 193 " =    1.934
peak=    3.633 closest distance to " O   HOH Z  10 " =    1.833
peak=    3.613 closest distance to " CB  GLN A  89 " =    1.450
peak=    3.607 closest distance to " O   HOH Z 286 " =    2.262
peak=    3.598 closest distance to " O   HOH Z  88 " =    2.446
peak=    3.592 closest distance to " O   HOH Z 389 " =    1.702
peak=    3.591 closest distance to " CE  LYS A  76 " =    0.839
peak=    3.584 closest distance to " O   HOH Z 265 " =    2.338
peak=    3.584 closest distance to " CA  ALA A  84 " =    1.283
peak=    3.582 closest distance to " O   HOH Z 365 " =    2.840
peak=    3.580 closest distance to " O   HOH Z 305 " =    3.572
peak=    3.573 closest distance to " O   HOH Z   9 " =    2.055
peak=    3.573 closest distance to " N   PHE A 130 " =    1.303
peak=    3.570 closest distance to " CG2 ILE A 120 " =    1.050
peak=    3.569 closest distance to " NE2 GLN A  73 " =    3.657
peak=    3.563 closest distance to " CG AARG A 275 " =    1.051
peak=    3.552 closest distance to " NH2BARG A 145 " =    1.995
peak=    3.549 closest distance to " CA  ALA A  21 " =    1.084
peak=    3.539 closest distance to " O   HOH Z 284 " =    2.904
peak=    3.526 closest distance to " CB  THR A  31 " =    1.749
peak=    3.520 closest distance to " O   HOH Z 423 " =    2.705
peak=    3.515 closest distance to " CD BLYS A 290 " =    1.308
peak=    3.513 closest distance to " O   HOH Z 180 " =    2.258
peak=    3.511 closest distance to " CG1BVAL A  72 " =    1.454
peak=    3.500 closest distance to " O   HOH Z 433 " =    1.795
peak=    3.500 closest distance to " O   HOH Z 193 " =    1.811
peak=    3.499 closest distance to " NH1AARG A 145 " =    1.186
peak=    3.493 closest distance to " O   HOH Z 207 " =    1.715
peak=    3.476 closest distance to " CA  PHE A 283 " =    1.304
peak=    3.473 closest distance to " N   ASN A  39 " =    1.176
peak=    3.472 closest distance to " CA  ALA A 233 " =    0.979
peak=    3.467 closest distance to " O   HOH Z 172 " =    3.302
peak=    3.464 closest distance to " NH1BARG A 145 " =    1.320
peak=    3.455 closest distance to " CD2 LEU A 297 " =    0.936
peak=    3.454 closest distance to " O   HOH Z 357 " =    1.794
peak=    3.453 closest distance to " CB  ASN A  39 " =    0.837
peak=    3.447 closest distance to " O   HOH Z 261 " =    1.603
peak=    3.445 closest distance to " CG2 ILE A  20 " =    1.482
peak=    3.442 closest distance to " CB  ALA A  34 " =    1.158
peak=    3.441 closest distance to " O   HOH Z  64 " =    2.383
peak=    3.433 closest distance to " O   HOH Z 421 " =    1.756
peak=    3.430 closest distance to " O   HOH Z 353 " =    2.619
peak=    3.428 closest distance to " O   HOH Z  88 " =    2.392
peak=    3.428 closest distance to " CB  ASP A 140 " =    0.931
peak=    3.426 closest distance to " CB  ASN A 110 " =    1.078
peak=    3.421 closest distance to " CB  GLU A 277 " =    3.480
peak=    3.412 closest distance to " CB  ALA A 291 " =    1.331
peak=    3.410 closest distance to " O   HOH Z 302 " =    1.765
peak=    3.409 closest distance to " CB  ALA A  21 " =    1.968
peak=    3.409 closest distance to " CD1 ILE A 106 " =    0.877
peak=    3.402 closest distance to " O   HOH Z 214 " =    2.186
peak=    3.400 closest distance to " N   ARG A 156 " =    1.269
peak=    3.391 closest distance to " CB  THR A 157 " =    1.077
peak=    3.391 closest distance to " O   HOH Z 345 " =    3.320
peak=    3.390 closest distance to " O   HOH Z 337 " =    3.563
peak=    3.389 closest distance to " O   HOH Z  21 " =    1.762
peak=    3.387 closest distance to " O   HOH Z 219 " =    2.223
peak=    3.384 closest distance to " O   HOH Z 147 " =    1.715
peak=    3.381 closest distance to " O   HOH Z 426 " =    1.828
peak=    3.378 closest distance to " NH2AARG A 190 " =    1.925
peak=    3.378 closest distance to " O   HOH Z   3 " =    1.919
peak=    3.371 closest distance to " CB  SER A  62 " =    1.390
peak=    3.367 closest distance to " CA  ARG A 195 " =    1.219
peak=    3.367 closest distance to " O   HOH Z 423 " =    1.900
peak=    3.360 closest distance to " O   HOH Z  89 " =    2.116
peak=    3.357 closest distance to " O   HOH Z  44 " =    2.976
peak=    3.352 closest distance to " CA  ASP A 162 " =    1.063
peak=    3.350 closest distance to " NZ  LYS A  76 " =    1.549
peak=    3.347 closest distance to " N   TYR A 116 " =    1.558
peak=    3.345 closest distance to " CZ  PHE A 218 " =    1.044
peak=    3.332 closest distance to " O   HOH Z 336 " =    1.810
peak=    3.326 closest distance to " CB  ALA A 248 " =    1.439
peak=    3.323 closest distance to " CD2 LEU A 255 " =    1.355
peak=    3.323 closest distance to " O   HOH Z 148 " =    3.377
peak=    3.322 closest distance to " O   HOH Z 261 " =    2.301
peak=    3.321 closest distance to " CG  MET A 185 " =    1.194
peak=    3.315 closest distance to " CG2 THR A 294 " =    1.585
peak=    3.314 closest distance to " O   HOH Z  71 " =    2.075
peak=    3.312 closest distance to " ND1 HIS A  86 " =    1.828
peak=    3.309 closest distance to " CB  LYS A 117 " =    1.207
peak=    3.308 closest distance to " CB  ILE A 120 " =    1.323
peak=    3.308 closest distance to " CB  THR A 279 " =    1.667
peak=    3.307 closest distance to " OH  TYR A 116 " =    1.052
peak=    3.299 closest distance to " CB  HIS A 108 " =    0.820
peak=    3.298 closest distance to " O   HOH Z 411 " =    3.704
peak=    3.298 closest distance to " O   HOH Z 257 " =    2.131
peak=    3.294 closest distance to " O   HOH Z 437 " =    1.483
peak=    3.294 closest distance to " CB  SER A 212 " =    1.017
peak=    3.292 closest distance to " CG  LYS A  76 " =    0.987
peak=    3.289 closest distance to " O   HOH Z  49 " =    2.128
peak=    3.288 closest distance to " O   HOH Z 291 " =    1.525
peak=    3.287 closest distance to " O   ALA A   1 " =    1.660
peak=    3.285 closest distance to " CA  ARG A  36 " =    0.983
peak=    3.283 closest distance to " O   HOH Z 325 " =    3.700
peak=    3.282 closest distance to " CB  LYS A 290 " =    0.969
peak=    3.280 closest distance to " CB  GLN A  88 " =    1.226
peak=    3.278 closest distance to " CA  THR A 264 " =    0.852
peak=    3.275 closest distance to " OG  SER A  62 " =    2.815
peak=    3.274 closest distance to " CA  LYS A 117 " =    1.205
peak=    3.274 closest distance to " CD1 ILE A 263 " =    1.361
peak=    3.269 closest distance to " CA  MET A  40 " =    1.095
peak=    3.263 closest distance to " CE AMET A  47 " =    1.389
peak=    3.262 closest distance to " OD1BASN A 224 " =    2.263
peak=    3.258 closest distance to " O   HOH Z 291 " =    1.761
peak=    3.257 closest distance to " CA  ALA A 299 " =    0.929
peak=    3.256 closest distance to " O   HOH Z 146 " =    1.564
peak=    3.255 closest distance to " OG  SER A  22 " =    2.616
peak=    3.255 closest distance to " O   HOH Z  40 " =    1.972
peak=    3.254 closest distance to " CH2 TRP A  92 " =    2.058
peak=    3.251 closest distance to " OG BSER A  99 " =    2.333
peak=    3.248 closest distance to " CD  ARG A  66 " =    2.530
peak=    3.244 closest distance to " CG2 THR A 221 " =    1.092
peak=    3.237 closest distance to " O   HOH Z 286 " =    2.415
peak=    3.237 closest distance to " O   HOH Z 234 " =    1.905
peak=    3.226 closest distance to " O   HOH Z 175 " =    2.035
peak=    3.225 closest distance to " O   HOH Z 271 " =    2.248
peak=    3.224 closest distance to " CB  VAL A 126 " =    1.117
peak=    3.224 closest distance to " C   ILE A 106 " =    1.874
peak=    3.223 closest distance to " O   HOH Z  53 " =    2.531
peak=    3.222 closest distance to " O   HOH Z 329 " =    3.846
peak=    3.215 closest distance to " CG  MET A 113 " =    1.066
peak=    3.212 closest distance to " CA  THR A 221 " =    1.008
peak=    3.206 closest distance to " N   SER A 134 " =    1.463
peak=    3.201 closest distance to " CA  SER A 146 " =    1.755
peak=    3.199 closest distance to " O   HOH Z  47 " =    1.776
peak=    3.192 closest distance to " CB  TYR A 116 " =    0.790
peak=    3.192 closest distance to " O   HOH Z 130 " =    2.253
peak=    3.188 closest distance to " CG2BVAL A  41 " =    0.847
peak=    3.187 closest distance to " CG  LEU A 167 " =    1.236
peak=    3.184 closest distance to " CA  MET A 105 " =    0.967
peak=    3.181 closest distance to " OG1 THR A 294 " =    2.420
peak=    3.180 closest distance to " O   ASP A 124 " =    1.285
peak=    3.179 closest distance to " O   HOH Z 124 " =    1.266
peak=    3.162 closest distance to " N   GLU A   2 " =    1.477
peak=    3.160 closest distance to " N   ASP A 162 " =    1.185
peak=    3.153 closest distance to " CB  MET A  47 " =    1.240
peak=    3.151 closest distance to " OG BSER A 134 " =    2.865
peak=    3.151 closest distance to " CB  ASN A 215 " =    1.086
peak=    3.150 closest distance to " O   HOH Z 391 " =    2.926
peak=    3.149 closest distance to " O   HOH Z 128 " =    2.010
peak=    3.148 closest distance to " O   HOH Z 273 " =    2.748
peak=    3.146 closest distance to " O   HOH Z 153 " =    1.555
peak=    3.144 closest distance to " CB  SER A 216 " =    0.794
peak=    3.142 closest distance to " CB  GLN A 278 " =    0.813
peak=    3.139 closest distance to " CB  ALA A 114 " =    1.418
peak=    3.135 closest distance to " CG  GLN A  89 " =    1.482
peak=    3.129 closest distance to " CB  MET A 188 " =    1.545
peak=    3.128 closest distance to " O   HOH Z 409 " =    2.755
peak=    3.127 closest distance to " O   HOH Z 435 " =    1.866
peak=    3.127 closest distance to " CG  GLN A  77 " =    2.181
peak=    3.125 closest distance to " CA  ALA A 291 " =    0.820
peak=    3.117 closest distance to " NH1 ARG A 138 " =    1.213
peak=    3.114 closest distance to " O   HOH Z 175 " =    2.103
peak=    3.112 closest distance to " O   HOH Z 290 " =    0.994
peak=    3.112 closest distance to " CG2 VAL A 197 " =    1.060
peak=    3.109 closest distance to " O   HOH Z 272 " =    2.194
peak=    3.109 closest distance to " O   HOH Z 406 " =    1.514
peak=    3.100 closest distance to " N   GLN A 278 " =    1.168
peak=    3.098 closest distance to " CB  LEU A 300 " =    0.912
peak=    3.091 closest distance to " CA  ALA A  51 " =    0.928
peak=    3.087 closest distance to " CB  ALA A   1 " =    4.606
peak=    3.084 closest distance to " CA  ALA A 233 " =    1.643
peak=    3.078 closest distance to " O   HOH Z 153 " =    3.747
peak=    3.078 closest distance to " CA  LYS A 290 " =    1.328
peak=    3.071 closest distance to " ND2 ASN A 249 " =    0.875
peak=    3.070 closest distance to " CG BARG A 102 " =    1.688
peak=    3.060 closest distance to " O   HOH Z 156 " =    2.791
peak=    3.053 closest distance to " O   HOH Z 132 " =    3.470
peak=    3.052 closest distance to " CG  LYS A  76 " =    1.362
peak=    3.045 closest distance to " O   HOH Z  66 " =    1.907
peak=    3.042 closest distance to " O   HOH Z 191 " =    2.315
peak=    3.038 closest distance to " CB  TRP A 179 " =    1.384
peak=    3.032 closest distance to " O   HOH Z 365 " =    3.231
peak=    3.021 closest distance to " O  BHOH Z  74 " =    1.376

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.796 - 5.848
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 201
   mapped sites are within: 0.796 - 5.848

peak=   -4.759 closest distance to " O   HOH Z 266 " =    4.881
peak=   -4.597 closest distance to " CB  PRO A 243 " =    2.611
peak=   -4.535 closest distance to " C   HIS A 108 " =    1.106
peak=   -4.495 closest distance to " CD  ARG A 156 " =    2.063
peak=   -4.446 closest distance to " OG BSER A 134 " =    1.253
peak=   -4.443 closest distance to " CG  GLN A 223 " =    1.864
peak=   -4.346 closest distance to " O   VAL A  67 " =    2.595
peak=   -4.290 closest distance to " CA  VAL A  67 " =    2.818
peak=   -4.277 closest distance to " O   HOH Z 290 " =    1.167
peak=   -4.267 closest distance to " CG1 VAL A 112 " =    2.785
peak=   -4.216 closest distance to " O   HOH Z 377 " =    2.144
peak=   -4.121 closest distance to " ND2 ASN A  45 " =    1.623
peak=   -4.106 closest distance to " SG  CYS A 254 " =    3.293
peak=   -4.085 closest distance to " CG  GLN A  58 " =    1.084
peak=   -4.051 closest distance to " CE  MET A 105 " =    2.332
peak=   -4.018 closest distance to " N   GLN A  58 " =    1.581
peak=   -4.017 closest distance to " OD2 ASP A 191 " =    1.400
peak=   -4.016 closest distance to " O   HOH Z 389 " =    1.940
peak=   -3.994 closest distance to " O   HOH Z 435 " =    2.808
peak=   -3.985 closest distance to " OXT GLY A 302 " =    2.808
peak=   -3.985 closest distance to " O   HOH Z 372 " =    2.370
peak=   -3.979 closest distance to " O   HOH Z 198 " =    1.874
peak=   -3.979 closest distance to " CB  ASN A  39 " =    2.309
peak=   -3.967 closest distance to " CG  PHE A 283 " =    2.648
peak=   -3.952 closest distance to " O   ALA A 161 " =    1.639
peak=   -3.912 closest distance to " O   HOH Z 313 " =    1.882
peak=   -3.884 closest distance to " O   HOH Z 351 " =    1.562
peak=   -3.880 closest distance to " OD2 ASP A 171 " =    2.210
peak=   -3.860 closest distance to " CD  ARG A 139 " =    1.494
peak=   -3.853 closest distance to " CE2 PHE A 218 " =    2.424
peak=   -3.852 closest distance to " CB  ALA A 291 " =    2.379
peak=   -3.851 closest distance to " CB  PHE A 192 " =    1.969
peak=   -3.845 closest distance to " O   HOH Z 231 " =    2.287
peak=   -3.842 closest distance to " OD1 ASN A 187 " =    1.632
peak=   -3.840 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.839 closest distance to " CZ  TYR A 169 " =    1.758
peak=   -3.812 closest distance to " O   HOH Z 407 " =    2.828
peak=   -3.805 closest distance to " CB  ALA A 291 " =    2.170
peak=   -3.782 closest distance to " CE2 TYR A  30 " =    2.730
peak=   -3.776 closest distance to " O   HOH Z 185 " =    2.183
peak=   -3.761 closest distance to " O   HOH Z 102 " =    1.623
peak=   -3.727 closest distance to " NE  ARG A 156 " =    1.870
peak=   -3.723 closest distance to " CB  TYR A  15 " =    2.140
peak=   -3.717 closest distance to " CB  ALA A 248 " =    2.097
peak=   -3.711 closest distance to " CZ  PHE A  59 " =    1.447
peak=   -3.709 closest distance to " OD1 ASP A 171 " =    1.591
peak=   -3.706 closest distance to " O   HOH Z 211 " =    1.668
peak=   -3.695 closest distance to " O   HOH Z  63 " =    1.728
peak=   -3.671 closest distance to " N   ALA A 248 " =    1.663
peak=   -3.669 closest distance to " N   ASP A 286 " =    2.331
peak=   -3.666 closest distance to " O   HOH Z  60 " =    2.299
peak=   -3.646 closest distance to " OD1 ASP A 191 " =    1.478
peak=   -3.644 closest distance to " CD1 PHE A  59 " =    1.995
peak=   -3.644 closest distance to " N   ALA A  43 " =    2.531
peak=   -3.640 closest distance to " O   PRO A 163 " =    1.926
peak=   -3.626 closest distance to " CD1 LEU A 101 " =    2.228
peak=   -3.625 closest distance to " O   HOH Z 298 " =    1.254
peak=   -3.625 closest distance to " CB  ALA A 248 " =    2.264
peak=   -3.620 closest distance to " O   HOH Z  13 " =    1.571
peak=   -3.615 closest distance to " O   PHE A 218 " =    1.550
peak=   -3.605 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.603 closest distance to " CZ3 TRP A 179 " =    1.206
peak=   -3.601 closest distance to " CB  ALA A 161 " =    2.419
peak=   -3.599 closest distance to " O   HOH Z 353 " =    2.211
peak=   -3.597 closest distance to " O   HOH Z 385 " =    1.983
peak=   -3.584 closest distance to " O   HOH Z 114 " =    3.005
peak=   -3.573 closest distance to " NH1 ARG A 195 " =    2.600
peak=   -3.572 closest distance to " O   HOH Z 126 " =    1.880
peak=   -3.569 closest distance to " CG2 ILE A 263 " =    2.229
peak=   -3.567 closest distance to " NE2 GLN A 278 " =    1.717
peak=   -3.558 closest distance to " O   HOH Z 362 " =    5.848
peak=   -3.558 closest distance to " O   ARG A 145 " =    1.526
peak=   -3.553 closest distance to " OG  SER A  97 " =    2.117
peak=   -3.546 closest distance to " O   HOH Z 395 " =    5.185
peak=   -3.538 closest distance to " O   SER A 135 " =    1.456
peak=   -3.534 closest distance to " CA  GLY A  98 " =    1.852
peak=   -3.529 closest distance to " CA  GLY A 203 " =    2.298
peak=   -3.523 closest distance to " SG ACYS A 201 " =    1.778
peak=   -3.515 closest distance to " OD1 ASN A 148 " =    1.554
peak=   -3.512 closest distance to " CD1 LEU A 228 " =    1.992
peak=   -3.498 closest distance to " O   SER A 210 " =    2.004
peak=   -3.492 closest distance to " O   SER A  95 " =    1.416
peak=   -3.480 closest distance to " O   HOH Z 166 " =    1.386
peak=   -3.478 closest distance to " O   HOH Z  24 " =    1.331
peak=   -3.473 closest distance to " CB  PRO A 163 " =    2.435
peak=   -3.469 closest distance to " O   HOH Z 165 " =    2.070
peak=   -3.469 closest distance to " O   GLN A  89 " =    1.542
peak=   -3.466 closest distance to " NH2AARG A 275 " =    5.058
peak=   -3.462 closest distance to " CA  GLY A 133 " =    1.948
peak=   -3.462 closest distance to " O   HOH Z 198 " =    1.532
peak=   -3.461 closest distance to " O   SER A 146 " =    1.088
peak=   -3.456 closest distance to " OXT GLY A 302 " =    3.461
peak=   -3.452 closest distance to " CB  ALA A  43 " =    2.392
peak=   -3.448 closest distance to " O   HOH Z 263 " =    2.906
peak=   -3.440 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.437 closest distance to " O   HOH Z 196 " =    2.193
peak=   -3.436 closest distance to " CG2 THR A 178 " =    2.238
peak=   -3.432 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.427 closest distance to " O   ALA A  51 " =    1.249
peak=   -3.425 closest distance to " OE2 GLU A 152 " =    1.199
peak=   -3.421 closest distance to " CG1 VAL A 230 " =    1.997
peak=   -3.421 closest distance to " ND2 ASN A 187 " =    1.561
peak=   -3.408 closest distance to " N   HIS A 115 " =    2.182
peak=   -3.402 closest distance to " CG1 VAL A 268 " =    2.430
peak=   -3.393 closest distance to " O   ALA A 292 " =    1.964
peak=   -3.385 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.383 closest distance to " O   HOH Z  11 " =    1.788
peak=   -3.383 closest distance to " O   HOH Z  52 " =    1.379
peak=   -3.375 closest distance to " O   HOH Z  43 " =    1.842
peak=   -3.373 closest distance to " O   HOH Z 253 " =    3.666
peak=   -3.368 closest distance to " O   HOH Z 123 " =    2.312
peak=   -3.359 closest distance to " CD1 ILE A 239 " =    2.550
peak=   -3.345 closest distance to " OD1 ASP A 191 " =    1.843
peak=   -3.344 closest distance to " OG1 THR A 178 " =    1.278
peak=   -3.343 closest distance to " C   ASP A 231 " =    2.575
peak=   -3.342 closest distance to " O   HOH Z  15 " =    1.496
peak=   -3.339 closest distance to " O   TRP A  70 " =    1.428
peak=   -3.337 closest distance to " CB  ASP A 132 " =    2.366
peak=   -3.336 closest distance to " CB  PHE A 208 " =    2.219
peak=   -3.334 closest distance to " O   HOH Z   3 " =    2.029
peak=   -3.332 closest distance to " O   HOH Z 137 " =    1.433
peak=   -3.331 closest distance to " CG1AVAL A  41 " =    2.722
peak=   -3.327 closest distance to " N   THR A 235 " =    1.366
peak=   -3.319 closest distance to " O   GLN A 240 " =    1.880
peak=   -3.312 closest distance to " O   VAL A 174 " =    2.132
peak=   -3.309 closest distance to " O   HOH Z 351 " =    1.677
peak=   -3.304 closest distance to " O   ALA A  34 " =    2.318
peak=   -3.304 closest distance to " O   HOH Z 193 " =    1.994
peak=   -3.303 closest distance to " CB  ASP A 286 " =    2.166
peak=   -3.301 closest distance to " ND2 ASN A  39 " =    1.313
peak=   -3.295 closest distance to " OG BSER A 134 " =    1.555
peak=   -3.294 closest distance to " CG1 VAL A  78 " =    2.919
peak=   -3.284 closest distance to " OD1 ASN A 176 " =    1.332
peak=   -3.284 closest distance to " NH2 ARG A  79 " =    1.988
peak=   -3.282 closest distance to " CD2 PHE A 225 " =    1.202
peak=   -3.282 closest distance to " O   HOH Z 140 " =    1.721
peak=   -3.280 closest distance to " O   HOH Z 266 " =    4.672
peak=   -3.279 closest distance to " CB  ASP A 132 " =    2.221
peak=   -3.274 closest distance to " O   HOH Z 339 " =    1.822
peak=   -3.268 closest distance to " CE1 TYR A 169 " =    2.447
peak=   -3.268 closest distance to " CB  ASP A 286 " =    1.740
peak=   -3.262 closest distance to " NH2BARG A 275 " =    1.894
peak=   -3.262 closest distance to " O   HOH Z 309 " =    2.519
peak=   -3.257 closest distance to " C   ALA A 158 " =    1.342
peak=   -3.257 closest distance to " O   HOH Z 427 " =    1.478
peak=   -3.256 closest distance to " CB  ALA A 244 " =    2.084
peak=   -3.253 closest distance to " O   HOH Z 139 " =    3.039
peak=   -3.250 closest distance to " O   HOH Z  90 " =    2.391
peak=   -3.244 closest distance to " O   HOH Z  37 " =    1.704
peak=   -3.241 closest distance to " CG  ARG A 269 " =    2.303
peak=   -3.238 closest distance to " O   HOH Z 148 " =    1.891
peak=   -3.235 closest distance to " O   ALA A  10 " =    1.670
peak=   -3.234 closest distance to " O   HOH Z  38 " =    1.846
peak=   -3.229 closest distance to " CD2 TYR A 293 " =    1.968
peak=   -3.229 closest distance to " O   SER A  22 " =    2.325
peak=   -3.226 closest distance to " CZ2 TRP A 274 " =    0.967
peak=   -3.223 closest distance to " CA  GLY A  57 " =    2.179
peak=   -3.217 closest distance to " O   HOH Z   6 " =    1.510
peak=   -3.217 closest distance to " O   MET A  40 " =    2.718
peak=   -3.215 closest distance to " O   HOH Z 250 " =    1.342
peak=   -3.213 closest distance to " CG  GLU A 152 " =    1.050
peak=   -3.203 closest distance to " O   HOH Z 281 " =    2.688
peak=   -3.202 closest distance to " O   HOH Z 134 " =    3.139
peak=   -3.196 closest distance to " CD2 LEU A 237 " =    2.651
peak=   -3.196 closest distance to " OE1 GLN A 223 " =    1.848
peak=   -3.195 closest distance to " O   HOH Z 131 " =    4.045
peak=   -3.185 closest distance to " N   PHE A  59 " =    1.802
peak=   -3.184 closest distance to " CB  TRP A  85 " =    2.478
peak=   -3.183 closest distance to " CB  ALA A   7 " =    2.040
peak=   -3.182 closest distance to " O   HOH Z 244 " =    2.036
peak=   -3.176 closest distance to " O   ALA A 180 " =    1.019
peak=   -3.176 closest distance to " OG  SER A  97 " =    1.706
peak=   -3.174 closest distance to " OG  SER A  26 " =    1.235
peak=   -3.163 closest distance to " C   GLN A 205 " =    1.824
peak=   -3.163 closest distance to " CB  ILE A  33 " =    2.889
peak=   -3.162 closest distance to " CG  PRO A 243 " =    1.631
peak=   -3.160 closest distance to " C   MET A 188 " =    1.412
peak=   -3.158 closest distance to " CB  LEU A  83 " =    2.362
peak=   -3.153 closest distance to " O   HOH Z  60 " =    1.853
peak=   -3.140 closest distance to " O   HOH Z 421 " =    3.022
peak=   -3.140 closest distance to " O   HOH Z  10 " =    1.377
peak=   -3.137 closest distance to " N   GLN A  77 " =    1.731
peak=   -3.135 closest distance to " O   HOH Z 137 " =    1.484
peak=   -3.131 closest distance to " CD1 ILE A 263 " =    2.540
peak=   -3.124 closest distance to " O   HOH Z 394 " =    1.438
peak=   -3.124 closest distance to " CB  TRP A 266 " =    2.044
peak=   -3.109 closest distance to " OD2 ASP A  50 " =    1.535
peak=   -3.108 closest distance to " CB  GLN A  11 " =    1.857
peak=   -3.104 closest distance to " OG1 THR A 246 " =    1.390
peak=   -3.092 closest distance to " O   HOH Z 256 " =    1.385
peak=   -3.079 closest distance to " CD1 ILE A 151 " =    2.096
peak=   -3.076 closest distance to " O   ASN A 249 " =    1.404
peak=   -3.067 closest distance to " CB  ALA A  51 " =    1.894
peak=   -3.063 closest distance to " OG  SER A 245 " =    1.306
peak=   -3.059 closest distance to " OD1AASN A 224 " =    1.818
peak=   -3.058 closest distance to " O   HOH Z 414 " =    1.773
peak=   -3.055 closest distance to " O   HOH Z 371 " =    1.623
peak=   -3.053 closest distance to " OE1 GLN A 194 " =    1.598
peak=   -3.034 closest distance to " CE  LYS A  76 " =    2.807
peak=   -3.022 closest distance to " O   HOH Z 357 " =    2.045
peak=   -3.011 closest distance to " CD2 LEU A 300 " =    2.771

================= 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    :  0.3469 0.3442   6.089549e+00   6.064263e+00
   1_bss:  0.3335 0.3294   6.068771e+00   6.033966e+00
   1_xyz:  0.1824 0.2054   5.523015e+00   5.626231e+00
   1_adp:  0.1664 0.2149   5.471717e+00   5.665673e+00
   1_occ:  0.1661 0.2146   5.470494e+00   5.664385e+00
   2_bss:  0.1632 0.2115   5.461109e+00   5.652733e+00
   2_xyz:  0.1284 0.1702   5.239770e+00   5.447246e+00
   2_adp:  0.1256 0.1615   5.206240e+00   5.401990e+00
   2_occ:  0.1254 0.1614   5.205276e+00   5.401874e+00
   3_bss:  0.1254 0.1612   5.204399e+00   5.399142e+00
   3_xyz:  0.1123 0.1512   5.120357e+00   5.341609e+00
   3_adp:  0.1091 0.1509   5.105318e+00   5.339880e+00
   3_occ:  0.1091 0.1509   5.105378e+00   5.340147e+00
   4_bss:  0.1091 0.1508   5.104854e+00   5.339512e+00
   4_xyz:  0.1096 0.1517   5.111485e+00   5.346842e+00
   4_adp:  0.1095 0.1515   5.111256e+00   5.347179e+00
   4_occ:  0.1095 0.1516   5.111311e+00   5.347440e+00
   5_bss:  0.1095 0.1515   5.111254e+00   5.347280e+00
   5_xyz:  0.1056 0.1504   5.090697e+00   5.341090e+00
   5_adp:  0.1051 0.1517   5.091976e+00   5.347541e+00
   5_occ:  0.1051 0.1516   5.091879e+00   5.347451e+00
   5_bss:  0.1050 0.1516   5.091811e+00   5.347259e+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:  0.320  20.000  -0.907   0.184  -1.386   0.000  -0.000  -0.000
   1_xyz:  0.320  20.000  -0.907   0.184  -1.386   0.000  -0.000  -0.000
   1_adp:  0.320  20.000  -0.907   0.184  -1.386   0.000  -0.000  -0.000
   1_occ:  0.320  20.000  -0.907   0.184  -1.386   0.000  -0.000  -0.000
   2_bss:  0.319  36.373  -2.558  -1.987  -1.701  -0.000  -0.000  -0.000
   2_xyz:  0.319  36.373  -2.558  -1.987  -1.701  -0.000  -0.000  -0.000
   2_adp:  0.319  36.373  -2.558  -1.987  -1.701  -0.000  -0.000  -0.000
   2_occ:  0.319  36.373  -2.558  -1.987  -1.701  -0.000  -0.000  -0.000
   3_bss:  0.319  37.682  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   3_xyz:  0.319  37.682  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   3_adp:  0.319  37.682  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   3_occ:  0.319  37.682  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   4_bss:  0.320  40.761  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   4_xyz:  0.320  40.761  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   4_adp:  0.320  40.761  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   4_occ:  0.320  40.761  -2.908  -2.407  -1.462  -0.000  -0.000  -0.000
   5_bss:  0.321  41.263  -2.804  -2.327  -1.247  -0.000  -0.000  -0.000
   5_xyz:  0.321  41.263  -2.804  -2.327  -1.247  -0.000  -0.000  -0.000
   5_adp:  0.321  41.263  -2.804  -2.327  -1.247  -0.000  -0.000  -0.000
   5_occ:  0.321  41.263  -2.804  -2.327  -1.247  -0.000  -0.000  -0.000
   5_bss:  0.322  42.923  -2.611  -2.158  -1.037  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  34.516 0.7109  0.9101    32947.360
   1_bss:  33.265 0.7232  0.9004    29308.272
   1_xyz:  19.083 0.8718  1.0225    10591.820
   1_adp:  20.204 0.8605  1.0157    11432.755
   1_occ:  20.180 0.8607  1.0157    11394.028
   2_bss:  19.765 0.8644  0.9712    10994.597
   2_xyz:  15.325 0.9036  0.9916     7106.452
   2_adp:  14.234 0.9131  0.9950     6560.057
   2_occ:  14.226 0.9132  0.9949     6546.185
   3_bss:  14.181 0.9135  0.9887     6504.115
   3_xyz:  13.131 0.9215  0.9917     5748.149
   3_adp:  13.079 0.9221  0.9876     5717.619
   3_occ:  13.082 0.9220  0.9875     5719.954
   4_bss:  13.070 0.9221  0.9878     5712.825
   4_xyz:  13.133 0.9219  0.9866     5798.845
   4_adp:  13.116 0.9221  0.9823     5797.693
   4_occ:  13.119 0.9221  0.9823     5800.614
   5_bss:  13.118 0.9221  0.9872     5799.807
   5_xyz:  12.996 0.9230  0.9875     5732.305
   5_adp:  13.112 0.9221  0.9813     5786.051
   5_occ:  13.111 0.9221  0.9812     5785.619
   5_bss:  13.107 0.9221  0.9876     5784.875
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7095e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7095e-01
   1_xyz:   1.066  0.008  0.074 14.929  0.005  4.108   6.8552e-02
   1_adp:   1.066  0.008  0.074 14.929  0.005  4.108   6.8552e-02
   1_occ:   1.066  0.008  0.074 14.929  0.005  4.108   6.8552e-02
   2_bss:   1.066  0.008  0.074 14.929  0.005  4.108   6.8552e-02
   2_xyz:   0.902  0.004  0.066 14.452  0.004  4.112   4.8549e-02
   2_adp:   0.902  0.004  0.066 14.452  0.004  4.112   4.8549e-02
   2_occ:   0.902  0.004  0.066 14.452  0.004  4.112   4.8549e-02
   3_bss:   0.902  0.004  0.066 14.452  0.004  4.112   4.8549e-02
   3_xyz:   0.966  0.006  0.072 14.778  0.004  4.111   5.6497e-02
   3_adp:   0.966  0.006  0.072 14.778  0.004  4.111   5.6497e-02
   3_occ:   0.966  0.006  0.072 14.778  0.004  4.111   5.6497e-02
   4_bss:   0.966  0.006  0.072 14.778  0.004  4.111   5.6497e-02
   4_xyz:   0.869  0.005  0.066 14.416  0.004  4.111   4.7916e-02
   4_adp:   0.869  0.005  0.066 14.416  0.004  4.111   4.7916e-02
   4_occ:   0.869  0.005  0.066 14.416  0.004  4.111   4.7916e-02
   5_bss:   0.869  0.005  0.066 14.416  0.004  4.111   4.7916e-02
   5_xyz:   0.998  0.006  0.075 14.726  0.004  4.111   5.9262e-02
   5_adp:   0.998  0.006  0.075 14.726  0.004  4.111   5.9262e-02
   5_occ:   0.998  0.006  0.075 14.726  0.004  4.111   5.9262e-02
   5_bss:   0.998  0.006  0.075 14.726  0.004  4.111   5.9262e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.618   2.3824e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.618   2.3824e-01
   1_xyz:   7.112  0.057  0.277 89.154  0.045  2.189   7.1558e-02
   1_adp:   7.112  0.057  0.277 89.154  0.045  2.189   7.1558e-02
   1_occ:   7.112  0.057  0.277 89.154  0.045  2.189   7.1558e-02
   2_bss:   7.112  0.057  0.277 89.154  0.045  2.189   7.1558e-02
   2_xyz:   6.767  0.039  0.186 82.504  0.045  2.379   3.5323e-02
   2_adp:   6.767  0.039  0.186 82.504  0.045  2.379   3.5323e-02
   2_occ:   6.767  0.039  0.186 82.504  0.045  2.379   3.5323e-02
   3_bss:   6.767  0.039  0.186 82.504  0.045  2.379   3.5323e-02
   3_xyz:   6.304  0.042  0.231 84.614  0.038  2.312   4.0356e-02
   3_adp:   6.304  0.042  0.231 84.614  0.038  2.312   4.0356e-02
   3_occ:   6.304  0.042  0.231 84.614  0.038  2.312   4.0356e-02
   4_bss:   6.304  0.042  0.231 84.614  0.038  2.312   4.0356e-02
   4_xyz:   5.906  0.040  0.202 83.369  0.040  2.369   3.4473e-02
   4_adp:   5.906  0.040  0.202 83.369  0.040  2.369   3.4473e-02
   4_occ:   5.906  0.040  0.202 83.369  0.040  2.369   3.4473e-02
   5_bss:   5.906  0.040  0.202 83.369  0.040  2.369   3.4473e-02
   5_xyz:   6.318  0.044  0.242 84.017  0.038  2.284   4.3023e-02
   5_adp:   6.318  0.044  0.242 84.017  0.038  2.284   4.3023e-02
   5_occ:   6.318  0.044  0.242 84.017  0.038  2.284   4.3023e-02
   5_bss:   6.318  0.044  0.242 84.017  0.038  2.284   4.3023e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  74.44   0.00  17.30  72.31   0.00  13.23  74.44   7.46  39.49
   1_occ:  74.44   0.00  17.30  72.31   0.00  13.23  74.44   7.46  39.49
   2_bss:  74.44   0.00  17.30  72.31   0.00  13.23  74.44   7.46  39.49
   2_xyz:  74.44   0.00  17.30  72.31   0.00  13.23  74.44   7.46  39.49
   2_adp:  74.81   1.68  16.68  74.81   1.68  12.99  73.19   6.66  36.75
   2_occ:  74.81   1.68  16.68  74.81   1.68  12.99  73.19   6.66  36.75
   3_bss:  74.81   1.68  16.68  74.81   1.68  12.99  73.19   6.66  36.75
   3_xyz:  74.81   1.68  16.68  74.81   1.68  12.99  73.19   6.66  36.75
   3_adp:  82.48   1.04  17.01  82.48   1.04  12.97  75.57   6.35  38.97
   3_occ:  82.48   1.04  17.01  82.48   1.04  12.97  75.57   6.35  38.97
   4_bss:  82.48   1.04  17.01  82.48   1.04  12.97  75.57   6.35  38.97
   4_xyz:  82.48   1.04  17.01  82.48   1.04  12.97  75.57   6.35  38.97
   4_adp:  83.66   1.29  16.80  83.66   1.29  12.84  76.22   6.32  38.39
   4_occ:  83.66   1.29  16.80  83.66   1.29  12.84  76.22   6.32  38.39
   5_bss:  83.66   1.29  16.80  83.66   1.29  12.84  76.22   6.32  38.39
   5_xyz:  83.66   1.29  16.80  83.66   1.29  12.84  76.22   6.32  38.39
   5_adp:  86.69   0.54  16.85  86.69   0.54  12.74  78.36   6.11  39.21
   5_occ:  86.69   0.54  16.85  86.69   0.54  12.74  78.36   6.11  39.21
   5_bss:  86.68   0.52  16.83  86.68   0.52  12.73  78.34   6.10  39.20
------------------------------------------------------------------------
 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:    1.188    0.008    0.333
   1_adp:    1.188    0.008    0.333
   1_occ:    1.188    0.008    0.333
   2_bss:    1.188    0.008    0.333
   2_xyz:    0.925    0.018    0.378
   2_adp:    0.925    0.018    0.378
   2_occ:    0.925    0.018    0.378
   3_bss:    0.925    0.018    0.378
   3_xyz:    0.973    0.025    0.421
   3_adp:    0.973    0.025    0.421
   3_occ:    0.973    0.025    0.421
   4_bss:    0.973    0.025    0.421
   4_xyz:    1.045    0.040    0.429
   4_adp:    1.045    0.040    0.429
   4_occ:    1.045    0.040    0.429
   5_bss:    1.045    0.040    0.429
   5_xyz:    1.062    0.073    0.436
   5_adp:    1.062    0.073    0.436
   5_occ:    1.062    0.073    0.436
   5_bss:    1.062    0.073    0.436
------------------------------------------------------------------------

CPU time actual refinement: 326.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_279/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_279/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_279/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_279/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_279/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.59 
  Macro-tasks:
    bulk solvent and scale       = 43.14  
    individual site refinement   = 132.83 
    weights calculation          = 29.33  
    collect and process          = 6.59   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.99 
  Micro-tasks:
    mask                            = 1.25   
    f_calc                          = 101.82 
    alpha_beta                      = 8.56   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 110.57 
    fmodel                         = 6.93   
    r_factors                      = 0.26   
    phase_errors                   = 10.84  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 241.70 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.631 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    634 calls, 101.45 s
gradients_fft:          579 calls,  97.02 s

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

# Date 2008-01-16 Time 04:26:47 PST -0800 (1200486407.80 s)
Start R-work = 0.3469, R-free = 0.3442 (no bulk solvent and anisotropic scale)
Final R-work = 0.1307, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.3335, R-free = 0.3294
Final R-work = 0.1050, R-free = 0.1516