# Date 2008-01-16 Time 04:26:53 PST -0800 (1200486413.34 s)
#phil __OFF__

Command line arguments: "../318.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1351
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 318

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.1647, 88.5498, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9516 1.97089
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928345

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9516
                             d_min =   1.9709

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9516 1.97089
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928345

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9520 -  4.2174 [2207/2235]  1985   222  10.1%
  bin  2:  4.2174 -  3.3599 [2127/2146]  1911   216  10.2%
  bin  3:  3.3599 -  2.9389 [2095/2115]  1893   202   9.6%
  bin  4:  2.9389 -  2.6719 [2078/2103]  1866   212  10.2%
  bin  5:  2.6719 -  2.4813 [2053/2073]  1843   210  10.2%
  bin  6:  2.4813 -  2.3356 [2039/2086]  1837   202   9.9%
  bin  7:  2.3356 -  2.2190 [2048/2081]  1852   196   9.6%
  bin  8:  2.2190 -  2.1227 [2050/2084]  1835   215  10.5%
  bin  9:  2.1227 -  2.0412 [2010/2051]  1816   194   9.7%
  bin 10:  2.0412 -  1.9709 [ 882/2063]   792    90  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_318/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.33 -     2.04: 14
        2.04 -     2.76: 387
        2.76 -     3.47: 4552
        3.47 -     4.19: 9301
        4.19 -     4.90: 13893
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.330 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.440 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.537 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.603 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.698 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28142 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_318/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_318/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.16465 88.54975 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 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4128   r_free= 0.4083   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.212623                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9520 -  4.7039 0.99   1437  158 0.3196 0.3255      6.4644      6.4273|
|  2:  4.7039 -  3.7531 0.99   1389  155 0.3384 0.3493      6.6665      6.7374|
|  3:  3.7531 -  3.2844 0.99   1341  153 0.3875 0.3443      6.5829      6.5371|
|  4:  3.2844 -  2.9867 0.99   1358  140 0.3973 0.4273        6.42       6.452|
|  5:  2.9867 -  2.7741 0.99   1325  154 0.4342 0.3977      6.2844      6.2925|
|  6:  2.7741 -  2.6114 0.98   1322  147 0.4465 0.4765      6.2067      6.1488|
|  7:  2.6114 -  2.4813 0.99   1326  155 0.4385 0.3837      6.1621      6.0384|
|  8:  2.4813 -  2.3737 0.98   1334  143 0.4643 0.4323      6.1197      6.0962|
|  9:  2.3737 -  2.2827 0.98   1308  142 0.4611 0.4480      6.0719      6.1309|
| 10:  2.2827 -  2.2041 0.98   1320  142 0.4801 0.5049      6.0591      6.0359|
| 11:  2.2041 -  2.1354 0.99   1301  156 0.4733 0.4647      5.9699      5.9702|
| 12:  2.1354 -  2.0745 0.98   1322  143 0.4735 0.4775      5.9171      5.9355|
| 13:  2.0745 -  2.0201 0.89   1182  121 0.4788 0.4962      5.8442      5.8316|
| 14:  2.0201 -  1.9709 0.28    365   50 0.4428 0.3948       5.834      5.6645|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9520 -  4.7039  1437   158  0.76  28.67   0.84     0.78      51593.64|
|  2:  4.7039 -  3.7531  1389   155  0.77  29.07   0.94     0.86      75674.63|
|  3:  3.7531 -  3.2844  1341   153  0.69  36.25   0.92     0.85      80499.04|
|  4:  3.2844 -  2.9867  1358   140  0.61  42.55   0.93     0.78      72800.90|
|  5:  2.9867 -  2.7741  1325   154  0.55  47.91   0.93     0.72      58926.29|
|  6:  2.7741 -  2.6114  1322   147  0.54  48.92   0.92     0.71      51190.14|
|  7:  2.6114 -  2.4813  1326   155  0.56  47.15   0.95     0.74      43939.26|
|  8:  2.4813 -  2.3737  1334   143  0.56  47.43   0.94     0.76      38641.91|
|  9:  2.3737 -  2.2827  1308   142  0.56  47.60   0.96     0.76      36386.12|
| 10:  2.2827 -  2.2041  1320   142  0.53  50.27   0.95     0.71      34786.41|
| 11:  2.2041 -  2.1354  1301   156  0.47  54.35   0.94     0.70      37452.13|
| 12:  2.1354 -  2.0745  1322   143  0.44  57.22   0.98     0.67      35520.44|
| 13:  2.0745 -  2.0201  1182   121  0.43  57.46   0.94     0.67      31645.91|
| 14:  2.0201 -  1.9709   365    50  0.50  51.96   1.03     0.66      23283.70|
|alpha:            min =        0.66 max =            0.86 mean =         0.75|
|beta:             min =    23283.70 max =        80499.04 mean =     49729.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           90.00 mean =        45.59|
|phase err.(test): min =        0.00 max =           89.99 mean =        45.51|
|-----------------------------------------------------------------------------|

============================== 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 = 8.638342              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.357   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.213438              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.828   (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 |  1.330 -  1.687:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.687 -  2.044:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.044 -  2.401:       17 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.401 -  2.758:      370 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.758 -  3.115:     2253 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.115 -  3.472:     2299 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.472 -  3.829:     4316 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.829 -  4.186:     4985 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.186 -  4.543:     6254 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.543 -  4.900:     7639 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.330 |       0.533 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    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 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4128   r_free= 0.4083   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.212623                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4011   r_free= 0.3941   ksol= 0.31   Bsol= 41.16   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-2.33,5.40,-0.00,0.00,0.00); trace/3= 0.43                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.196421                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.376473              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.031   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.692627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.525   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4011      final r-factor (work) = 0.2555          |
| start r-factor (free) = 0.3941      final r-factor (free) = 0.2825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0398 = 7.38 * 0.50 * 6.1960 + 1.00 * 0.1875                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1866 = 7.38 * 0.50 * 5.9815 + 1.00 * 0.1253                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2555      final r-factor (work) = 0.2343          |
| start r-factor (free) = 0.2825      final r-factor (free) = 0.2904          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1498 = 0.69 * 1.00 * 5.9815 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0326 = 0.69 * 1.00 * 5.7695 + 1.00 * 0.0365                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.51  17.17    None  None   None       |
|    all(noH): 2823   0      0.00    122.51  17.17    None  None   None       |
|    Sol.    : 438    0      5.32    64.78   38.32    None  None   None       |
|    Mac.    : 2385   0      0.00    122.51  13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.251: 1250   |   5:    61.254 -  73.505:    6        |
|      1:    12.251 -  24.502: 1033   |   6:    73.505 -  85.755:    0        |
|      2:    24.502 -  36.752:  236   |   7:    85.755 -  98.006:    0        |
|      3:    36.752 -  49.003:  206   |   8:    98.006 - 110.257:    0        |
|      4:    49.003 -  61.254:   91   |   9:   110.257 - 122.508:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2343 r_free = 0.2904             target_work(ml) = 5.779         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2340 r_free = 0.2906             target_work(ml) = 5.779         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2340   r_free= 0.2906   ksol= 0.31   Bsol= 41.16   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-2.33,5.40,-0.00,0.00,0.00); trace/3= 0.43                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.779040                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2302   r_free= 0.2880   ksol= 0.33   Bsol= 60.53   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.34,1.48,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.772155                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.724495              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.459   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.476273              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.184   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2302      final r-factor (work) = 0.1753          |
| start r-factor (free) = 0.2880      final r-factor (free) = 0.2231          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9900 = 2.72 * 0.50 * 5.7734 + 1.00 * 0.1253                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7732 = 2.72 * 0.50 * 5.6631 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1753      final r-factor (work) = 0.1634          |
| start r-factor (free) = 0.2231      final r-factor (free) = 0.2132          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7170 = 0.48 * 1.00 * 5.6631 + 1.00 * 0.0198                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6254 = 0.48 * 1.00 * 5.4899 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.77   17.68    None  None   None       |
|    all(noH): 2823   0      0.00    78.77   17.68    None  None   None       |
|    Sol.    : 438    0      5.85    78.77   41.65    None  None   None       |
|    Mac.    : 2385   0      0.00    74.06   13.28    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 -   7.877:  571   |   5:    39.384 -  47.261:  113        |
|      1:     7.877 -  15.754: 1256   |   6:    47.261 -  55.138:   87        |
|      2:    15.754 -  23.630:  423   |   7:    55.138 -  63.014:   82        |
|      3:    23.630 -  31.507:  155   |   8:    63.014 -  70.891:   28        |
|      4:    31.507 -  39.384:   99   |   9:    70.891 -  78.768:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1634 r_free = 0.2132             target_work(ml) = 5.467         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1633 r_free = 0.2133             target_work(ml) = 5.467         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1633   r_free= 0.2133   ksol= 0.33   Bsol= 60.53   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.34,1.48,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.467221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1635   r_free= 0.2125   ksol= 0.33   Bsol= 63.89   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-2.07,0.43,-0.00,0.00,0.00); trace/3= -1.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.466901                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.761023              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.177  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.520960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.405  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1635      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.2125      final r-factor (free) = 0.1850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8934 = 1.76 * 0.50 * 5.4908 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8007 = 1.76 * 0.50 * 5.3928 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1850      final r-factor (free) = 0.1815          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8202 = 0.52 * 1.00 * 5.3928 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7741 = 0.52 * 1.00 * 5.3046 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.67   17.58    None  None   None       |
|    all(noH): 2823   0      0.00    82.67   17.58    None  None   None       |
|    Sol.    : 438    0      5.10    82.67   42.21    None  None   None       |
|    Mac.    : 2385   0      0.00    80.27   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.267:  655   |   5:    41.335 -  49.602:   94        |
|      1:     8.267 -  16.534: 1308   |   6:    49.602 -  57.869:  100        |
|      2:    16.534 -  24.801:  333   |   7:    57.869 -  66.137:   62        |
|      3:    24.801 -  33.068:  136   |   8:    66.137 -  74.404:   24        |
|      4:    33.068 -  41.335:  100   |   9:    74.404 -  82.671:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1815             target_work(ml) = 5.296         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1330 r_free = 0.1815             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1815   ksol= 0.33   Bsol= 63.89   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-2.07,0.43,-0.00,0.00,0.00); trace/3= -1.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.295461                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1815   ksol= 0.33   Bsol= 65.62   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.04,-0.07,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.295628                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.169340              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.819  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.329410              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.909  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1815      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4589 = 3.17 * 0.50 * 5.3049 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3828 = 3.17 * 0.50 * 5.2450 + 1.00 * 0.0712                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1665      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7383 = 0.33 * 1.00 * 5.2450 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7201 = 0.33 * 1.00 * 5.1926 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.31   17.15    None  None   None       |
|    all(noH): 2823   0      0.00    83.31   17.15    None  None   None       |
|    Sol.    : 438    0      0.00    83.31   41.08    None  None   None       |
|    Mac.    : 2385   0      1.10    81.02   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.331:  675   |   5:    41.653 -  49.983:   94        |
|      1:     8.331 -  16.661: 1327   |   6:    49.983 -  58.314:   94        |
|      2:    16.661 -  24.992:  313   |   7:    58.314 -  66.644:   52        |
|      3:    24.992 -  33.322:  133   |   8:    66.644 -  74.975:   20        |
|      4:    33.322 -  41.653:  104   |   9:    74.975 -  83.305:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1632             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1632             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1632   ksol= 0.33   Bsol= 65.62   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.04,-0.07,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183347                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1631   ksol= 0.33   Bsol= 65.62   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.85,-0.09,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183451                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.728535              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.200  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.525430              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.277  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1558 = 2.73 * 0.50 * 5.1930 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1370 = 2.73 * 0.50 * 5.1775 + 1.00 * 0.0735                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7300 = 0.53 * 1.00 * 5.1775 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7275 = 0.53 * 1.00 * 5.1719 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.18   16.99    None  None   None       |
|    all(noH): 2823   0      0.00    89.18   16.99    None  None   None       |
|    Sol.    : 438    0      0.00    89.18   40.99    None  None   None       |
|    Mac.    : 2385   0      0.67    86.06   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.918:  873   |   5:    44.592 -  53.510:   94        |
|      1:     8.918 -  17.837: 1222   |   6:    53.510 -  62.428:   75        |
|      2:    17.837 -  26.755:  258   |   7:    62.428 -  71.346:   36        |
|      3:    26.755 -  35.673:  128   |   8:    71.346 -  80.265:   15        |
|      4:    35.673 -  44.592:  115   |   9:    80.265 -  89.183:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1624             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1625             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1625   ksol= 0.33   Bsol= 65.62   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.85,-0.09,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174141                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9520 -  4.7039 0.99   1437  158 0.0986 0.1331      5.4005      5.5731|
|  2:  4.7039 -  3.7531 0.99   1389  155 0.0844 0.1088      5.4365      5.6321|
|  3:  3.7531 -  3.2844 0.99   1341  153 0.1091 0.1540      5.4931      5.8343|
|  4:  3.2844 -  2.9867 0.99   1358  140 0.1264 0.1619      5.4615      5.6321|
|  5:  2.9867 -  2.7741 0.99   1325  154 0.1338 0.1614      5.3434      5.5223|
|  6:  2.7741 -  2.6114 0.98   1322  147 0.1270 0.2106      5.2376      5.5364|
|  7:  2.6114 -  2.4813 0.99   1326  155 0.1300 0.1803      5.2067       5.383|
|  8:  2.4813 -  2.3737 0.98   1334  143 0.1210 0.1728      5.1289      5.3486|
|  9:  2.3737 -  2.2827 0.98   1308  142 0.1189 0.1932       5.051      5.3938|
| 10:  2.2827 -  2.2041 0.98   1320  142 0.1147 0.1775      4.9626      5.1754|
| 11:  2.2041 -  2.1354 0.99   1301  156 0.1174 0.1877       4.932      5.3121|
| 12:  2.1354 -  2.0745 0.98   1322  143 0.1168 0.1650      4.9029      5.1162|
| 13:  2.0745 -  2.0201 0.89   1182  121 0.1069 0.1753      4.7677       4.991|
| 14:  2.0201 -  1.9709 0.28    365   50 0.0879 0.1694      4.6136      4.9453|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9520 -  4.7039  1437   158  0.94   9.56   0.97     0.94       7702.53|
|  2:  4.7039 -  3.7531  1389   155  0.95   8.20   1.01     0.99       9281.94|
|  3:  3.7531 -  3.2844  1341   153  0.93  11.75   1.02     1.02      10730.55|
|  4:  3.2844 -  2.9867  1358   140  0.92  14.02   1.01     1.00      10407.57|
|  5:  2.9867 -  2.7741  1325   154  0.90  16.50   0.99     0.97       8829.12|
|  6:  2.7741 -  2.6114  1322   147  0.89  17.23   0.97     0.94       7544.28|
|  7:  2.6114 -  2.4813  1326   155  0.89  16.81   0.98     0.94       6921.76|
|  8:  2.4813 -  2.3737  1334   143  0.90  16.85   0.99     0.96       6271.92|
|  9:  2.3737 -  2.2827  1308   142  0.90  16.74   0.99     0.95       5356.06|
| 10:  2.2827 -  2.2041  1320   142  0.90  16.00   0.99     0.94       4503.81|
| 11:  2.2041 -  2.1354  1301   156  0.90  16.71   0.99     0.95       4429.53|
| 12:  2.1354 -  2.0745  1322   143  0.90  16.70   1.00     0.99       4242.79|
| 13:  2.0745 -  2.0201  1182   121  0.90  16.28   0.97     0.95       3346.38|
| 14:  2.0201 -  1.9709   365    50  0.93  12.70   0.96     0.93       2321.49|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2321.49 max =        10730.55 mean =      6853.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.75|
|phase err.(test): min =        0.00 max =           89.92 mean =        14.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1624   ksol= 0.32   Bsol= 59.13   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-1.63,0.07,-0.00,0.00,0.00); trace/3= -1.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174353                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1624   ksol= 0.32   Bsol= 59.13   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-1.63,0.07,-0.00,0.00,0.00); trace/3= -1.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174353                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9520 -  4.7039 0.99   1437  158 0.0983 0.1328      5.3976      5.5708|
|  2:  4.7039 -  3.7531 0.99   1389  155 0.0840 0.1084      5.4341      5.6293|
|  3:  3.7531 -  3.2844 0.99   1341  153 0.1090 0.1542       5.492       5.836|
|  4:  3.2844 -  2.9867 0.99   1358  140 0.1266 0.1624      5.4632      5.6339|
|  5:  2.9867 -  2.7741 0.99   1325  154 0.1341 0.1617      5.3455       5.524|
|  6:  2.7741 -  2.6114 0.98   1322  147 0.1271 0.2110      5.2395      5.5391|
|  7:  2.6114 -  2.4813 0.99   1326  155 0.1301 0.1804      5.2082      5.3836|
|  8:  2.4813 -  2.3737 0.98   1334  143 0.1211 0.1730      5.1298      5.3497|
|  9:  2.3737 -  2.2827 0.98   1308  142 0.1190 0.1930      5.0514      5.3938|
| 10:  2.2827 -  2.2041 0.98   1320  142 0.1147 0.1774       4.963      5.1754|
| 11:  2.2041 -  2.1354 0.99   1301  156 0.1174 0.1876      4.9321      5.3122|
| 12:  2.1354 -  2.0745 0.98   1322  143 0.1168 0.1651      4.9031      5.1162|
| 13:  2.0745 -  2.0201 0.89   1182  121 0.1069 0.1755       4.768      4.9916|
| 14:  2.0201 -  1.9709 0.28    365   50 0.0879 0.1692      4.6147      4.9449|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9520 -  4.7039  1437   158  0.94   9.54   0.97     0.95       7663.21|
|  2:  4.7039 -  3.7531  1389   155  0.95   8.18   1.01     1.00       9251.73|
|  3:  3.7531 -  3.2844  1341   153  0.93  11.74   1.03     1.02      10713.84|
|  4:  3.2844 -  2.9867  1358   140  0.92  14.07   1.01     1.00      10447.05|
|  5:  2.9867 -  2.7741  1325   154  0.90  16.55   1.00     0.97       8872.51|
|  6:  2.7741 -  2.6114  1322   147  0.89  17.28   0.98     0.95       7578.02|
|  7:  2.6114 -  2.4813  1326   155  0.89  16.84   0.99     0.95       6943.76|
|  8:  2.4813 -  2.3737  1334   143  0.90  16.87   1.00     0.96       6284.50|
|  9:  2.3737 -  2.2827  1308   142  0.90  16.74   1.00     0.95       5358.91|
| 10:  2.2827 -  2.2041  1320   142  0.90  15.99   1.00     0.95       4503.61|
| 11:  2.2041 -  2.1354  1301   156  0.90  16.71   1.00     0.96       4427.15|
| 12:  2.1354 -  2.0745  1322   143  0.90  16.71   1.01     1.00       4245.56|
| 13:  2.0745 -  2.0201  1182   121  0.90  16.29   0.99     0.96       3348.02|
| 14:  2.0201 -  1.9709   365    50  0.93  12.71   0.98     0.94       2323.59|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2323.59 max =        10713.84 mean =      6858.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.76|
|phase err.(test): min =        0.00 max =           89.91 mean =        14.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.19   17.00    None  None   None       |
|    all(noH): 2823   0      0.00    89.19   17.00    None  None   None       |
|    Sol.    : 438    0      0.00    89.19   40.99    None  None   None       |
|    Mac.    : 2385   0      0.67    86.07   12.59    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:     0.003 -   8.921:  873   |   5:    44.594 -  53.513:   94        |
|      1:     8.921 -  17.840: 1222   |   6:    53.513 -  62.431:   75        |
|      2:    17.840 -  26.758:  258   |   7:    62.431 -  71.349:   36        |
|      3:    26.758 -  35.676:  128   |   8:    71.349 -  80.268:   15        |
|      4:    35.676 -  44.594:  115   |   9:    80.268 -  89.186:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 4.911
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 289 from: 294
   mapped sites are within: 0.705 - 4.911

peak=    6.305 closest distance to " O  BHOH Z  74 " =    1.150
peak=    5.446 closest distance to " CG  PRO A  54 " =    1.353
peak=    5.086 closest distance to " CB  ARG A 275 " =    0.948
peak=    5.042 closest distance to " O   HOH Z 113 " =    2.079
peak=    4.938 closest distance to " CB  GLN A 223 " =    1.482
peak=    4.910 closest distance to " NE2 GLN A  11 " =    1.147
peak=    4.894 closest distance to " O   HOH Z 369 " =    2.200
peak=    4.711 closest distance to " O   HOH Z 403 " =    1.828
peak=    4.684 closest distance to " O   HOH Z 142 " =    1.690
peak=    4.683 closest distance to " CZ  PHE A 218 " =    1.212
peak=    4.577 closest distance to " O   HOH Z 248 " =    1.431
peak=    4.569 closest distance to " CB  ARG A 190 " =    1.595
peak=    4.551 closest distance to " O   HOH Z 287 " =    1.913
peak=    4.497 closest distance to " O   SER A  87 " =    2.288
peak=    4.485 closest distance to " CB  SER A  63 " =    1.094
peak=    4.477 closest distance to " CB  GLN A 183 " =    1.215
peak=    4.476 closest distance to " CB  ARG A  79 " =    1.505
peak=    4.385 closest distance to " CB  GLU A 277 " =    3.656
peak=    4.383 closest distance to " O   HOH Z 126 " =    1.862
peak=    4.362 closest distance to " CD2 TRP A 179 " =    1.256
peak=    4.325 closest distance to " ND2 ASN A 187 " =    1.590
peak=    4.313 closest distance to " O   HOH Z  19 " =    2.036
peak=    4.275 closest distance to " O   HOH Z 232 " =    2.500
peak=    4.270 closest distance to " O   HOH Z 402 " =    1.384
peak=    4.204 closest distance to " CZ3 TRP A 266 " =    1.090
peak=    4.200 closest distance to " O   HOH Z 188 " =    2.673
peak=    4.194 closest distance to " O   HOH Z  15 " =    2.175
peak=    4.166 closest distance to " CG  PRO A  90 " =    1.209
peak=    4.156 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.152 closest distance to " ND2 ASN A 249 " =    0.920
peak=    4.148 closest distance to " CB  PRO A  54 " =    0.936
peak=    4.121 closest distance to " CG  GLN A  58 " =    1.010
peak=    4.114 closest distance to " CB  ASN A 148 " =    1.481
peak=    4.107 closest distance to " CB  VAL A 265 " =    1.301
peak=    4.078 closest distance to " O   HOH Z 427 " =    3.078
peak=    4.074 closest distance to " CB  GLU A 152 " =    1.191
peak=    4.063 closest distance to " CB  PRO A  90 " =    1.158
peak=    4.056 closest distance to " O   HOH Z 298 " =    1.931
peak=    4.048 closest distance to " O   HOH Z 126 " =    1.584
peak=    4.024 closest distance to " O   HOH Z  78 " =    1.730
peak=    4.014 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.011 closest distance to " CA  ARG A  36 " =    1.066
peak=    3.978 closest distance to " CB  VAL A 202 " =    1.534
peak=    3.952 closest distance to " CE  LYS A  76 " =    0.939
peak=    3.948 closest distance to " O   HOH Z 180 " =    2.148
peak=    3.942 closest distance to " CG  ARG A  66 " =    2.405
peak=    3.931 closest distance to " O   HOH Z 261 " =    2.329
peak=    3.922 closest distance to " O   HOH Z 251 " =    1.591
peak=    3.903 closest distance to " O   HOH Z  63 " =    1.984
peak=    3.902 closest distance to " O   PRO A 198 " =    1.561
peak=    3.895 closest distance to " O   HOH Z  49 " =    1.066
peak=    3.889 closest distance to " O  BHOH Z 338 " =    2.194
peak=    3.887 closest distance to " O   HOH Z  76 " =    1.117
peak=    3.879 closest distance to " O   HOH Z 112 " =    1.058
peak=    3.864 closest distance to " O   HOH Z 227 " =    1.561
peak=    3.862 closest distance to " O   HOH Z 234 " =    3.624
peak=    3.856 closest distance to " O   HOH Z 346 " =    1.624
peak=    3.849 closest distance to " O   HOH Z 313 " =    2.054
peak=    3.848 closest distance to " O   HOH Z 368 " =    2.183
peak=    3.837 closest distance to " O   HOH Z 406 " =    1.669
peak=    3.835 closest distance to " CB  ASN A 142 " =    1.065
peak=    3.829 closest distance to " O   HOH Z 199 " =    1.650
peak=    3.823 closest distance to " NZ  LYS A 117 " =    3.063
peak=    3.813 closest distance to " CA  ARG A 195 " =    1.270
peak=    3.807 closest distance to " O   HOH Z 303 " =    2.237
peak=    3.806 closest distance to " CD  ARG A 269 " =    0.967
peak=    3.800 closest distance to " O   HOH Z 412 " =    3.979
peak=    3.788 closest distance to " CB  TYR A 169 " =    0.756
peak=    3.780 closest distance to " CG  PRO A 243 " =    1.076
peak=    3.780 closest distance to " CA  VAL A 125 " =    1.098
peak=    3.779 closest distance to " O   HOH Z 425 " =    1.327
peak=    3.774 closest distance to " O   HOH Z  40 " =    1.866
peak=    3.767 closest distance to " O   ASN A  74 " =    1.357
peak=    3.766 closest distance to " O   HOH Z 368 " =    3.622
peak=    3.759 closest distance to " O   HOH Z 188 " =    1.479
peak=    3.755 closest distance to " CB  ARG A  79 " =    0.894
peak=    3.750 closest distance to " CD  LYS A  76 " =    1.915
peak=    3.750 closest distance to " O   HOH Z 250 " =    1.402
peak=    3.746 closest distance to " CG AARG A 275 " =    1.203
peak=    3.739 closest distance to " NH1AARG A 145 " =    1.388
peak=    3.739 closest distance to " CZ  PHE A  38 " =    1.167
peak=    3.737 closest distance to " O   HOH Z 392 " =    2.581
peak=    3.734 closest distance to " O   HOH Z 359 " =    1.675
peak=    3.726 closest distance to " O   HOH Z 265 " =    2.052
peak=    3.723 closest distance to " CG2 ILE A 120 " =    1.303
peak=    3.710 closest distance to " CB  ASN A  39 " =    0.850
peak=    3.689 closest distance to " O   HOH Z 203 " =    1.529
peak=    3.686 closest distance to " CG2AVAL A 121 " =    2.226
peak=    3.679 closest distance to " O   HOH Z 214 " =    1.627
peak=    3.667 closest distance to " CA  ALA A  51 " =    0.945
peak=    3.663 closest distance to " O   HOH Z  61 " =    1.756
peak=    3.663 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.661 closest distance to " O   HOH Z 365 " =    2.809
peak=    3.649 closest distance to " O   THR A 182 " =    1.500
peak=    3.649 closest distance to " O   HOH Z 132 " =    2.804
peak=    3.643 closest distance to " CG2 VAL A 257 " =    0.764
peak=    3.641 closest distance to " O   HOH Z 417 " =    3.362
peak=    3.639 closest distance to " CD1 LEU A  96 " =    0.722
peak=    3.621 closest distance to " O   HOH Z  78 " =    2.058
peak=    3.617 closest distance to " CD  ARG A 159 " =    0.726
peak=    3.614 closest distance to " CB  SER A  26 " =    1.883
peak=    3.612 closest distance to " CB  ASN A 215 " =    1.169
peak=    3.608 closest distance to " O   HOH Z 299 " =    4.431
peak=    3.605 closest distance to " CA  ALA A 160 " =    0.992
peak=    3.602 closest distance to " O   HOH Z 394 " =    3.749
peak=    3.601 closest distance to " CG  MET A 185 " =    1.160
peak=    3.580 closest distance to " O   HOH Z 117 " =    1.967
peak=    3.579 closest distance to " O   HOH Z 280 " =    2.914
peak=    3.575 closest distance to " O   HOH Z  80 " =    1.738
peak=    3.574 closest distance to " N   ASN A  39 " =    1.255
peak=    3.572 closest distance to " O   HOH Z 126 " =    1.831
peak=    3.570 closest distance to " CB  TRP A 266 " =    1.065
peak=    3.563 closest distance to " NH2AARG A 275 " =    3.482
peak=    3.562 closest distance to " O   HOH Z 214 " =    2.805
peak=    3.558 closest distance to " CG2AVAL A  72 " =    1.830
peak=    3.557 closest distance to " CD  LYS A 166 " =    1.276
peak=    3.552 closest distance to " O   HOH Z 380 " =    2.110
peak=    3.545 closest distance to " O   HOH Z  43 " =    2.115
peak=    3.543 closest distance to " O   HOH Z 158 " =    3.008
peak=    3.541 closest distance to " CB  ASN A 110 " =    1.119
peak=    3.532 closest distance to " O   HOH Z 353 " =    2.661
peak=    3.530 closest distance to " CA  ASP A 162 " =    1.041
peak=    3.527 closest distance to " O   HOH Z 327 " =    1.520
peak=    3.522 closest distance to " O   HOH Z 423 " =    1.948
peak=    3.521 closest distance to " O   HOH Z   1 " =    1.974
peak=    3.515 closest distance to " O   HOH Z 193 " =    1.323
peak=    3.514 closest distance to " O   HOH Z 357 " =    2.148
peak=    3.511 closest distance to " CA  ALA A 154 " =    1.042
peak=    3.510 closest distance to " CB  PHE A 204 " =    0.814
peak=    3.507 closest distance to " CA  MET A 105 " =    1.008
peak=    3.504 closest distance to " CB  ASP A 298 " =    1.151
peak=    3.504 closest distance to " CB  TRP A 179 " =    1.437
peak=    3.501 closest distance to " O   HOH Z 166 " =    4.087
peak=    3.501 closest distance to " CB  GLU A 128 " =    0.998
peak=    3.498 closest distance to " CB  ASN A 285 " =    1.029
peak=    3.498 closest distance to " O   HOH Z  97 " =    2.135
peak=    3.497 closest distance to " O   HOH Z 285 " =    2.269
peak=    3.495 closest distance to " OG BSER A 164 " =    2.346
peak=    3.490 closest distance to " CD1 ILE A 199 " =    1.188
peak=    3.487 closest distance to " OG ASER A 258 " =    3.077
peak=    3.485 closest distance to " O   HOH Z 148 " =    3.492
peak=    3.476 closest distance to " O   HOH Z 325 " =    2.426
peak=    3.474 closest distance to " CB  THR A  31 " =    1.652
peak=    3.472 closest distance to " O   HOH Z  35 " =    2.506
peak=    3.460 closest distance to " O   HOH Z 305 " =    3.578
peak=    3.457 closest distance to " O   HOH Z 130 " =    2.828
peak=    3.457 closest distance to " O   ALA A 165 " =    1.534
peak=    3.457 closest distance to " N   PHE A 130 " =    1.301
peak=    3.454 closest distance to " O   HOH Z 361 " =    2.483
peak=    3.444 closest distance to " CB  PRO A 198 " =    1.327
peak=    3.443 closest distance to " O   HOH Z 422 " =    2.620
peak=    3.441 closest distance to " CA  THR A 264 " =    0.924
peak=    3.440 closest distance to " CA  ALA A 100 " =    0.929
peak=    3.435 closest distance to " CA  ASN A 215 " =    0.989
peak=    3.435 closest distance to " CG  GLN A  11 " =    1.850
peak=    3.434 closest distance to " O   HOH Z  59 " =    2.242
peak=    3.429 closest distance to " CG2 ILE A  20 " =    1.307
peak=    3.427 closest distance to " CG1 ILE A  49 " =    1.495
peak=    3.425 closest distance to " N   TYR A 116 " =    1.591
peak=    3.420 closest distance to " CA  ILE A 234 " =    0.982
peak=    3.418 closest distance to " CB  LYS A 117 " =    1.144
peak=    3.416 closest distance to " CA  ASP A 124 " =    0.769
peak=    3.413 closest distance to " CD  PRO A  54 " =    1.021
peak=    3.412 closest distance to " CB  SER A   3 " =    1.335
peak=    3.411 closest distance to " CG  PRO A 198 " =    1.314
peak=    3.409 closest distance to " CB  ASN A 148 " =    1.967
peak=    3.409 closest distance to " CG  GLN A  55 " =    2.509
peak=    3.405 closest distance to " CA  TYR A 116 " =    1.389
peak=    3.405 closest distance to " OG  SER A  22 " =    2.582
peak=    3.404 closest distance to " O   HOH Z 209 " =    2.228
peak=    3.402 closest distance to " O   THR A 220 " =    1.239
peak=    3.401 closest distance to " CG  LEU A 167 " =    1.291
peak=    3.400 closest distance to " CB  LEU A 228 " =    1.060
peak=    3.397 closest distance to " CE1 TYR A 186 " =    1.260
peak=    3.396 closest distance to " CB  GLN A  88 " =    1.183
peak=    3.394 closest distance to " O   HOH Z  88 " =    2.688
peak=    3.386 closest distance to " O   HOH Z 246 " =    1.314
peak=    3.385 closest distance to " OD1 ASN A  69 " =    2.460
peak=    3.382 closest distance to " CB  SER A  62 " =    0.776
peak=    3.378 closest distance to " CA  ASN A 127 " =    1.259
peak=    3.368 closest distance to " O   HOH Z 393 " =    3.003
peak=    3.364 closest distance to " O   HOH Z 290 " =    1.107
peak=    3.362 closest distance to " O   HOH Z 213 " =    1.939
peak=    3.361 closest distance to " O   HOH Z 193 " =    1.866
peak=    3.361 closest distance to " CA  ASP A 140 " =    1.363
peak=    3.357 closest distance to " O   HOH Z 345 " =    4.101
peak=    3.356 closest distance to " O   HOH Z   3 " =    1.820
peak=    3.355 closest distance to " O   HOH Z  94 " =    2.748
peak=    3.354 closest distance to " CA  ILE A 106 " =    0.841
peak=    3.353 closest distance to " CG  GLU A  37 " =    0.981
peak=    3.351 closest distance to " O   HOH Z 438 " =    2.882
peak=    3.349 closest distance to " CD  ARG A  66 " =    2.493
peak=    3.345 closest distance to " O   HOH Z 298 " =    2.407
peak=    3.345 closest distance to " CE  LYS A 119 " =    1.146
peak=    3.340 closest distance to " CB  GLN A  89 " =    1.361
peak=    3.339 closest distance to " O   HOH Z  62 " =    2.249
peak=    3.338 closest distance to " O   HOH Z  88 " =    3.117
peak=    3.335 closest distance to " N   ASP A 162 " =    1.212
peak=    3.333 closest distance to " O   HOH Z 291 " =    1.435
peak=    3.333 closest distance to " CB  LEU A  83 " =    0.705
peak=    3.332 closest distance to " O   HOH Z  85 " =    1.781
peak=    3.326 closest distance to " NE2 GLN A  77 " =    3.202
peak=    3.326 closest distance to " O   HOH Z 193 " =    1.463
peak=    3.319 closest distance to " CB  ARG A 102 " =    0.745
peak=    3.314 closest distance to " N   ARG A 156 " =    1.390
peak=    3.311 closest distance to " O   HOH Z 419 " =    2.085
peak=    3.311 closest distance to " O   HOH Z  54 " =    1.688
peak=    3.310 closest distance to " CE3 TRP A 150 " =    1.126
peak=    3.303 closest distance to " CA  ASN A 217 " =    1.130
peak=    3.302 closest distance to " NH2BARG A 145 " =    2.129
peak=    3.297 closest distance to " CB  ALA A 227 " =    1.267
peak=    3.294 closest distance to " CA  GLN A  94 " =    0.773
peak=    3.294 closest distance to " O   HOH Z  85 " =    1.308
peak=    3.291 closest distance to " O   HOH Z 173 " =    1.846
peak=    3.291 closest distance to " CG1 VAL A 153 " =    1.048
peak=    3.284 closest distance to " N   GLY A 111 " =    1.215
peak=    3.283 closest distance to " O   HOH Z  48 " =    1.577
peak=    3.273 closest distance to " OD2 ASP A 286 " =    3.259
peak=    3.271 closest distance to " CB  ASP A 140 " =    1.250
peak=    3.270 closest distance to " CG BARG A 275 " =    1.427
peak=    3.268 closest distance to " CA  SER A  87 " =    0.993
peak=    3.268 closest distance to " CA  ALA A 158 " =    1.309
peak=    3.264 closest distance to " O   HOH Z 128 " =    2.413
peak=    3.261 closest distance to " OG BSER A 134 " =    2.808
peak=    3.260 closest distance to " O   HOH Z 117 " =    1.065
peak=    3.256 closest distance to " OE2 GLU A  53 " =    2.009
peak=    3.254 closest distance to " O   HOH Z 156 " =    3.158
peak=    3.253 closest distance to " NE2 HIS A 207 " =    1.133
peak=    3.251 closest distance to " O   HOH Z 198 " =    1.545
peak=    3.249 closest distance to " O   SER A 164 " =    1.213
peak=    3.248 closest distance to " O   HOH Z 128 " =    2.032
peak=    3.240 closest distance to " O   HOH Z 371 " =    2.837
peak=    3.239 closest distance to " CB  SER A 141 " =    1.094
peak=    3.239 closest distance to " O   TYR A 116 " =    1.437
peak=    3.237 closest distance to " O   HOH Z 368 " =    4.309
peak=    3.235 closest distance to " O   HOH Z 117 " =    2.138
peak=    3.235 closest distance to " CG2 VAL A 197 " =    1.102
peak=    3.234 closest distance to " O   ALA A 158 " =    1.159
peak=    3.229 closest distance to " OG BSER A  99 " =    2.350
peak=    3.225 closest distance to " CA  SER A  32 " =    1.718
peak=    3.222 closest distance to " O   HOH Z 141 " =    1.560
peak=    3.221 closest distance to " O   HOH Z  10 " =    1.746
peak=    3.220 closest distance to " O   HOH Z 172 " =    3.843
peak=    3.218 closest distance to " O   HOH Z 383 " =    1.931
peak=    3.215 closest distance to " CE1 HIS A  81 " =    1.370
peak=    3.215 closest distance to " CB  ARG A 139 " =    1.065
peak=    3.214 closest distance to " O   HOH Z  83 " =    1.572
peak=    3.212 closest distance to " O   HOH Z   1 " =    2.190
peak=    3.210 closest distance to " CB  ALA A 291 " =    1.030
peak=    3.209 closest distance to " CA  ASP A 149 " =    1.257
peak=    3.209 closest distance to " O   HOH Z 258 " =    1.485
peak=    3.200 closest distance to " O   HOH Z  47 " =    1.808
peak=    3.198 closest distance to " CB  SER A  62 " =    1.105
peak=    3.196 closest distance to " CB  ALA A   1 " =    4.911
peak=    3.195 closest distance to " N   CYS A 260 " =    0.881
peak=    3.192 closest distance to " O   PHE A 192 " =    1.451
peak=    3.191 closest distance to " CA  ARG A 102 " =    1.071
peak=    3.189 closest distance to " O   LEU A 228 " =    1.817
peak=    3.183 closest distance to " CG2 ILE A 239 " =    0.821
peak=    3.180 closest distance to " CA  ALA A 233 " =    1.506
peak=    3.180 closest distance to " CB  ARG A 156 " =    1.210
peak=    3.180 closest distance to " O   ASP A 124 " =    1.299
peak=    3.180 closest distance to " CB  SER A  99 " =    1.344
peak=    3.173 closest distance to " CG  ARG A 138 " =    1.325
peak=    3.167 closest distance to " CB  TYR A 116 " =    0.731
peak=    3.161 closest distance to " CB  ASP A 191 " =    1.190
peak=    3.161 closest distance to " O   HOH Z 132 " =    2.609
peak=    3.160 closest distance to " O   HOH Z  88 " =    1.714
peak=    3.158 closest distance to " O   HOH Z 272 " =    1.760
peak=    3.156 closest distance to " O   HOH Z 285 " =    1.987
peak=    3.156 closest distance to " CA  ALA A 129 " =    1.465
peak=    3.153 closest distance to " O   HOH Z 350 " =    1.916
peak=    3.152 closest distance to " O   HOH Z  44 " =    1.934
peak=    3.129 closest distance to " CD2 TYR A 186 " =    1.078
peak=    3.126 closest distance to " O   HOH Z 162 " =    2.030
peak=    3.125 closest distance to " O   HOH Z 389 " =    1.759
peak=    3.120 closest distance to " CG2 THR A 221 " =    1.107
peak=    3.118 closest distance to " CB  LEU A 300 " =    0.966
peak=    3.117 closest distance to " O   HOH Z 345 " =    3.188
peak=    3.104 closest distance to " O   HOH Z 258 " =    1.140
peak=    3.092 closest distance to " CB  ARG A 156 " =    1.031
peak=    3.090 closest distance to " CB  ALA A 100 " =    1.130
peak=    3.087 closest distance to " OH  TYR A 116 " =    1.126
peak=    3.084 closest distance to " O   HOH Z 421 " =    1.885
peak=    3.072 closest distance to " O   HOH Z 183 " =    1.795
peak=    3.069 closest distance to " OG  SER A  62 " =    2.778
peak=    3.053 closest distance to " CB  PHE A 283 " =    0.725
peak=    3.047 closest distance to " CB  SER A 210 " =    0.758
peak=    3.045 closest distance to " NE2 GLN A  58 " =    4.719

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.763 - 5.923
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 200
   mapped sites are within: 0.763 - 5.923

peak=   -5.119 closest distance to " CD  ARG A  14 " =    3.369
peak=   -4.900 closest distance to " CG  GLN A  58 " =    0.978
peak=   -4.662 closest distance to " CG2 ILE A  20 " =    3.005
peak=   -4.647 closest distance to " O   HOH Z 193 " =    1.001
peak=   -4.565 closest distance to " O   PRO A 198 " =    1.302
peak=   -4.468 closest distance to " O   HOH Z 211 " =    1.048
peak=   -4.449 closest distance to " CG2 ILE A  49 " =    2.820
peak=   -4.411 closest distance to " CB  PRO A 243 " =    2.755
peak=   -4.309 closest distance to " O   VAL A  67 " =    2.754
peak=   -4.303 closest distance to " CD2 TYR A 293 " =    1.944
peak=   -4.288 closest distance to " C   HIS A 108 " =    1.113
peak=   -4.280 closest distance to " OG BSER A 134 " =    1.214
peak=   -4.255 closest distance to " CG1 VAL A 112 " =    2.717
peak=   -4.194 closest distance to " O   HOH Z 377 " =    2.146
peak=   -4.157 closest distance to " O   HOH Z 278 " =    1.020
peak=   -4.139 closest distance to " CE2 PHE A  61 " =    2.683
peak=   -4.071 closest distance to " O   HOH Z 198 " =    1.270
peak=   -4.050 closest distance to " CE  MET A 105 " =    2.563
peak=   -3.970 closest distance to " OE1 GLN A 223 " =    2.210
peak=   -3.964 closest distance to " O   HOH Z 231 " =    2.311
peak=   -3.937 closest distance to " CA  GLY A 241 " =    2.448
peak=   -3.925 closest distance to " O   HOH Z 267 " =    5.654
peak=   -3.920 closest distance to " CD  ARG A 156 " =    2.172
peak=   -3.912 closest distance to " CB  PHE A 192 " =    2.033
peak=   -3.908 closest distance to " NE2 GLN A  11 " =    1.664
peak=   -3.878 closest distance to " O   PRO A 163 " =    2.018
peak=   -3.877 closest distance to " OXT GLY A 302 " =    2.981
peak=   -3.799 closest distance to " O   HOH Z 102 " =    1.524
peak=   -3.795 closest distance to " N   ALA A  43 " =    2.605
peak=   -3.791 closest distance to " CG1 VAL A 250 " =    2.625
peak=   -3.785 closest distance to " O   SER A 210 " =    1.937
peak=   -3.768 closest distance to " CA  ASP A 298 " =    1.081
peak=   -3.763 closest distance to " O   HOH Z 394 " =    1.519
peak=   -3.754 closest distance to " O   HOH Z 166 " =    1.853
peak=   -3.750 closest distance to " CB  ALA A  43 " =    2.566
peak=   -3.747 closest distance to " O   HOH Z  73 " =    2.574
peak=   -3.747 closest distance to " O   HOH Z 216 " =    1.109
peak=   -3.746 closest distance to " ND2 ASN A  45 " =    2.043
peak=   -3.729 closest distance to " O   HOH Z 348 " =    2.155
peak=   -3.712 closest distance to " CD1 LEU A 101 " =    2.379
peak=   -3.706 closest distance to " O   HOH Z 196 " =    1.964
peak=   -3.694 closest distance to " CB  ASN A  39 " =    2.328
peak=   -3.688 closest distance to " CD2 HIS A 207 " =    2.189
peak=   -3.688 closest distance to " OG  SER A  97 " =    2.295
peak=   -3.658 closest distance to " CB  TRP A  85 " =    2.602
peak=   -3.657 closest distance to " CE3 TRP A 150 " =    2.357
peak=   -3.656 closest distance to " CE BMET A  47 " =    1.484
peak=   -3.651 closest distance to " O   HOH Z 113 " =    1.484
peak=   -3.637 closest distance to " CZ  TYR A 169 " =    1.838
peak=   -3.637 closest distance to " CG  ARG A 269 " =    2.214
peak=   -3.636 closest distance to " CB  ASP A 132 " =    2.335
peak=   -3.632 closest distance to " O   HOH Z 185 " =    2.309
peak=   -3.629 closest distance to " CH2 TRP A 179 " =    1.292
peak=   -3.623 closest distance to " O   HOH Z 131 " =    4.088
peak=   -3.619 closest distance to " ND2 ASN A 249 " =    2.297
peak=   -3.610 closest distance to " O   HOH Z 290 " =    1.063
peak=   -3.608 closest distance to " O   HOH Z 252 " =    3.942
peak=   -3.606 closest distance to " O   HOH Z 174 " =    2.562
peak=   -3.591 closest distance to " CG1 VAL A 112 " =    2.585
peak=   -3.571 closest distance to " O   HOH Z 374 " =    1.872
peak=   -3.570 closest distance to " O   HOH Z   6 " =    2.159
peak=   -3.566 closest distance to " OD1 ASP A 171 " =    1.617
peak=   -3.565 closest distance to " NE2 GLN A 278 " =    1.579
peak=   -3.556 closest distance to " CG  ARG A  66 " =    2.479
peak=   -3.554 closest distance to " O   ALA A  10 " =    1.797
peak=   -3.539 closest distance to " O   VAL A 189 " =    1.747
peak=   -3.537 closest distance to " C   ASN A 285 " =    2.268
peak=   -3.512 closest distance to " CZ3 TRP A 274 " =    2.374
peak=   -3.509 closest distance to " O   VAL A 174 " =    2.254
peak=   -3.509 closest distance to " N   THR A  52 " =    1.679
peak=   -3.504 closest distance to " O   HOH Z 357 " =    2.275
peak=   -3.499 closest distance to " O   HOH Z  13 " =    1.915
peak=   -3.492 closest distance to " O   HOH Z 116 " =    1.527
peak=   -3.488 closest distance to " OD2 ASP A 191 " =    1.441
peak=   -3.485 closest distance to " O   HOH Z   9 " =    1.987
peak=   -3.481 closest distance to " CD2 PHE A  61 " =    2.257
peak=   -3.478 closest distance to " O   HOH Z 165 " =    2.062
peak=   -3.474 closest distance to " O   HOH Z  69 " =    2.043
peak=   -3.474 closest distance to " CB  HIS A  86 " =    1.163
peak=   -3.472 closest distance to " O   HOH Z 285 " =    1.581
peak=   -3.470 closest distance to " CD  GLN A 223 " =    1.712
peak=   -3.466 closest distance to " CD1 ILE A 199 " =    2.437
peak=   -3.464 closest distance to " CA  GLY A 241 " =    3.314
peak=   -3.454 closest distance to " O   HOH Z 171 " =    2.245
peak=   -3.452 closest distance to " O   HOH Z 123 " =    2.462
peak=   -3.448 closest distance to " CG2 VAL A 189 " =    2.085
peak=   -3.444 closest distance to " O   HOH Z 351 " =    1.684
peak=   -3.442 closest distance to " CZ  ARG A 259 " =    0.966
peak=   -3.434 closest distance to " CG2AVAL A  72 " =    2.752
peak=   -3.430 closest distance to " OE2 GLU A 152 " =    1.371
peak=   -3.429 closest distance to " O   HOH Z 275 " =    1.450
peak=   -3.426 closest distance to " O   HOH Z 149 " =    1.989
peak=   -3.423 closest distance to " N   ALA A 248 " =    1.586
peak=   -3.411 closest distance to " OD2 ASP A 171 " =    2.481
peak=   -3.408 closest distance to " O   ALA A  34 " =    2.494
peak=   -3.402 closest distance to " O   HOH Z  68 " =    1.345
peak=   -3.401 closest distance to " CB  ALA A 248 " =    2.199
peak=   -3.393 closest distance to " O   HOH Z 106 " =    1.824
peak=   -3.386 closest distance to " CE2 TYR A  30 " =    2.752
peak=   -3.373 closest distance to " O   HOH Z 407 " =    2.818
peak=   -3.368 closest distance to " O   HOH Z 128 " =    2.710
peak=   -3.365 closest distance to " CB  ALA A  10 " =    2.332
peak=   -3.363 closest distance to " O   HOH Z  64 " =    1.294
peak=   -3.356 closest distance to " O   ALA A 292 " =    2.238
peak=   -3.354 closest distance to " CG1AVAL A  41 " =    2.608
peak=   -3.353 closest distance to " O   HOH Z 154 " =    1.868
peak=   -3.351 closest distance to " O   HOH Z 110 " =    1.404
peak=   -3.350 closest distance to " O   HOH Z 359 " =    2.982
peak=   -3.345 closest distance to " O   TRP A  92 " =    1.946
peak=   -3.338 closest distance to " CG  PHE A 283 " =    2.578
peak=   -3.335 closest distance to " CD  GLN A  88 " =    0.913
peak=   -3.335 closest distance to " O   HOH Z 281 " =    2.635
peak=   -3.333 closest distance to " O  BHOH Z  74 " =    0.763
peak=   -3.332 closest distance to " CD2 TYR A 247 " =    2.493
peak=   -3.332 closest distance to " O   HOH Z 236 " =    1.536
peak=   -3.322 closest distance to " C   LEU A 143 " =    1.026
peak=   -3.315 closest distance to " O   ASN A 252 " =    1.295
peak=   -3.307 closest distance to " O   HOH Z 156 " =    3.468
peak=   -3.307 closest distance to " O   HOH Z 177 " =    1.717
peak=   -3.305 closest distance to " CD  ARG A  79 " =    1.206
peak=   -3.304 closest distance to " O   VAL A 257 " =    1.371
peak=   -3.303 closest distance to " CD1 LEU A 255 " =    2.797
peak=   -3.301 closest distance to " CZ  TYR A 172 " =    1.900
peak=   -3.300 closest distance to " NE  ARG A 156 " =    1.962
peak=   -3.293 closest distance to " O   HOH Z 395 " =    5.185
peak=   -3.291 closest distance to " OG BSER A 134 " =    1.877
peak=   -3.291 closest distance to " O   HOH Z  63 " =    1.508
peak=   -3.290 closest distance to " CA  GLY A 203 " =    2.467
peak=   -3.289 closest distance to " CG  GLU A 277 " =    1.329
peak=   -3.283 closest distance to " O   HOH Z 368 " =    1.817
peak=   -3.283 closest distance to " O   HOH Z  38 " =    1.717
peak=   -3.282 closest distance to " O   ILE A 263 " =    2.217
peak=   -3.278 closest distance to " OE1 GLN A 183 " =    1.610
peak=   -3.277 closest distance to " OD1 ASN A 249 " =    2.500
peak=   -3.276 closest distance to " O   HOH Z  10 " =    1.495
peak=   -3.271 closest distance to " CG  TRP A 266 " =    1.991
peak=   -3.270 closest distance to " O   ILE A 106 " =    1.892
peak=   -3.269 closest distance to " O   HOH Z 252 " =    3.845
peak=   -3.264 closest distance to " O   HOH Z  60 " =    2.054
peak=   -3.258 closest distance to " O   HOH Z 421 " =    3.470
peak=   -3.255 closest distance to " O   HOH Z   6 " =    1.390
peak=   -3.243 closest distance to " NH2 ARG A  79 " =    1.645
peak=   -3.242 closest distance to " O   HOH Z 264 " =    1.631
peak=   -3.239 closest distance to " CZ  ARG A 156 " =    2.799
peak=   -3.239 closest distance to " CG  ASN A 148 " =    2.309
peak=   -3.237 closest distance to " O   PHE A 218 " =    1.575
peak=   -3.235 closest distance to " O   HOH Z 313 " =    1.870
peak=   -3.223 closest distance to " CD2 PHE A 225 " =    1.229
peak=   -3.221 closest distance to " CB  ALA A 291 " =    2.250
peak=   -3.221 closest distance to " NH2 ARG A 159 " =    2.280
peak=   -3.216 closest distance to " O   HOH Z 246 " =    1.015
peak=   -3.210 closest distance to " ND2 ASN A  45 " =    1.268
peak=   -3.209 closest distance to " CD  PRO A 243 " =    1.993
peak=   -3.205 closest distance to " CB  PHE A  16 " =    2.501
peak=   -3.202 closest distance to " ND2 ASN A  60 " =    1.407
peak=   -3.198 closest distance to " O   TYR A 186 " =    1.730
peak=   -3.194 closest distance to " O   HOH Z 393 " =    1.238
peak=   -3.190 closest distance to " N   ALA A 226 " =    1.888
peak=   -3.189 closest distance to " CG2 THR A 182 " =    2.261
peak=   -3.184 closest distance to " N   GLY A 196 " =    1.721
peak=   -3.177 closest distance to " CD1 TRP A  70 " =    1.088
peak=   -3.177 closest distance to " CG  GLU A  53 " =    1.616
peak=   -3.176 closest distance to " CZ  PHE A  38 " =    2.054
peak=   -3.173 closest distance to " ND2 ASN A 187 " =    1.660
peak=   -3.172 closest distance to " CG  LEU A  83 " =    2.072
peak=   -3.168 closest distance to " O   SER A 276 " =    1.657
peak=   -3.166 closest distance to " O   HOH Z 174 " =    3.712
peak=   -3.159 closest distance to " O   HOH Z 389 " =    1.500
peak=   -3.158 closest distance to " CG1 VAL A 265 " =    2.702
peak=   -3.157 closest distance to " OD1 ASN A 301 " =    1.944
peak=   -3.151 closest distance to " CB  SER A 245 " =    2.205
peak=   -3.149 closest distance to " O   HOH Z  89 " =    2.721
peak=   -3.144 closest distance to " OE1 GLN A  88 " =    1.105
peak=   -3.142 closest distance to " O   HOH Z  43 " =    1.471
peak=   -3.142 closest distance to " O   HOH Z 126 " =    1.775
peak=   -3.136 closest distance to " CD  PRO A 213 " =    2.186
peak=   -3.129 closest distance to " O   ALA A 161 " =    1.778
peak=   -3.127 closest distance to " CE1 TYR A 172 " =    1.965
peak=   -3.125 closest distance to " O   HOH Z 122 " =    1.545
peak=   -3.125 closest distance to " O   ALA A 227 " =    1.426
peak=   -3.124 closest distance to " CB  ASP A 132 " =    2.358
peak=   -3.112 closest distance to " CB  ALA A 291 " =    2.003
peak=   -3.109 closest distance to " O   HOH Z  52 " =    1.822
peak=   -3.108 closest distance to " CA  GLY A 133 " =    2.293
peak=   -3.102 closest distance to " CG2 ILE A 263 " =    2.046
peak=   -3.097 closest distance to " O   HOH Z 428 " =    2.932
peak=   -3.093 closest distance to " O   HOH Z  28 " =    2.149
peak=   -3.092 closest distance to " O   GLU A 152 " =    1.423
peak=   -3.091 closest distance to " O   HOH Z 166 " =    1.891
peak=   -3.084 closest distance to " O   HOH Z  37 " =    1.746
peak=   -3.079 closest distance to " CA  GLY A  57 " =    2.196
peak=   -3.079 closest distance to " NE2 GLN A  88 " =    1.814
peak=   -3.077 closest distance to " O   HOH Z 154 " =    1.728
peak=   -3.073 closest distance to " O   HOH Z  69 " =    1.250
peak=   -3.070 closest distance to " O   HOH Z 318 " =    1.900
peak=   -3.063 closest distance to " O   HOH Z 362 " =    5.923
peak=   -3.037 closest distance to " CB  ASN A  45 " =    2.045
peak=   -3.035 closest distance to " O   HOH Z 150 " =    1.944
peak=   -3.009 closest distance to " CA  SER A  62 " =    2.523

================= 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    :  0.4128 0.4083   6.212623e+00   6.197325e+00
   1_bss:  0.4011 0.3941   6.196421e+00   6.178584e+00
   1_xyz:  0.2555 0.2825   5.825876e+00   5.916358e+00
   1_adp:  0.2343 0.2904   5.779031e+00   5.938156e+00
   1_occ:  0.2340 0.2906   5.779040e+00   5.939629e+00
   2_bss:  0.2302 0.2880   5.772155e+00   5.936874e+00
   2_xyz:  0.1753 0.2231   5.527495e+00   5.710160e+00
   2_adp:  0.1634 0.2132   5.467473e+00   5.663949e+00
   2_occ:  0.1633 0.2133   5.467221e+00   5.664033e+00
   3_bss:  0.1635 0.2125   5.466901e+00   5.662838e+00
   3_xyz:  0.1383 0.1850   5.322436e+00   5.536050e+00
   3_adp:  0.1331 0.1815   5.295534e+00   5.515036e+00
   3_occ:  0.1330 0.1815   5.295461e+00   5.515214e+00
   4_bss:  0.1331 0.1815   5.295628e+00   5.514033e+00
   4_xyz:  0.1182 0.1665   5.198496e+00   5.436589e+00
   4_adp:  0.1163 0.1632   5.183830e+00   5.419668e+00
   4_occ:  0.1162 0.1632   5.183347e+00   5.419332e+00
   5_bss:  0.1161 0.1631   5.183451e+00   5.419524e+00
   5_xyz:  0.1143 0.1623   5.174648e+00   5.414263e+00
   5_adp:  0.1139 0.1624   5.174079e+00   5.416032e+00
   5_occ:  0.1138 0.1625   5.174141e+00   5.416267e+00
   5_bss:  0.1137 0.1624   5.174353e+00   5.416624e+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:  0.310  41.159  -1.777  -2.327   5.397  -0.000   0.000   0.000
   1_xyz:  0.310  41.159  -1.777  -2.327   5.397  -0.000   0.000   0.000
   1_adp:  0.310  41.159  -1.777  -2.327   5.397  -0.000   0.000   0.000
   1_occ:  0.310  41.159  -1.777  -2.327   5.397  -0.000   0.000   0.000
   2_bss:  0.332  60.530  -2.924  -2.339   1.484  -0.000   0.000   0.000
   2_xyz:  0.332  60.530  -2.924  -2.339   1.484  -0.000   0.000   0.000
   2_adp:  0.332  60.530  -2.924  -2.339   1.484  -0.000   0.000   0.000
   2_occ:  0.332  60.530  -2.924  -2.339   1.484  -0.000   0.000   0.000
   3_bss:  0.332  63.892  -3.029  -2.070   0.435  -0.000   0.000   0.000
   3_xyz:  0.332  63.892  -3.029  -2.070   0.435  -0.000   0.000   0.000
   3_adp:  0.332  63.892  -3.029  -2.070   0.435  -0.000   0.000   0.000
   3_occ:  0.332  63.892  -3.029  -2.070   0.435  -0.000   0.000   0.000
   4_bss:  0.330  65.616  -3.023  -2.043  -0.070  -0.000  -0.000  -0.000
   4_xyz:  0.330  65.616  -3.023  -2.043  -0.070  -0.000  -0.000  -0.000
   4_adp:  0.330  65.616  -3.023  -2.043  -0.070  -0.000  -0.000  -0.000
   4_occ:  0.330  65.616  -3.023  -2.043  -0.070  -0.000  -0.000  -0.000
   5_bss:  0.332  65.616  -2.758  -1.854  -0.090  -0.000  -0.000  -0.000
   5_xyz:  0.332  65.616  -2.758  -1.854  -0.090  -0.000  -0.000  -0.000
   5_adp:  0.332  65.616  -2.758  -1.854  -0.090  -0.000  -0.000  -0.000
   5_occ:  0.332  65.616  -2.758  -1.854  -0.090  -0.000  -0.000  -0.000
   5_bss:  0.324  59.125  -2.524  -1.633   0.072  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.583 0.5769  0.7470    49725.530
   1_bss:  44.151 0.5930  0.7841    46299.333
   1_xyz:  28.623 0.7738  0.9690    21129.823
   1_adp:  29.692 0.7613  0.9601    22353.385
   1_occ:  29.764 0.7605  0.9593    22442.696
   2_bss:  29.296 0.7657  0.9116    22047.506
   2_xyz:  21.673 0.8453  0.9678    12692.272
   2_adp:  20.317 0.8590  0.9695    11611.106
   2_occ:  20.319 0.8590  0.9695    11609.728
   3_bss:  20.229 0.8599  0.9603    11563.599
   3_xyz:  17.356 0.8860  0.9755     8749.029
   3_adp:  16.826 0.8911  0.9686     8399.617
   3_occ:  16.829 0.8911  0.9686     8403.116
   4_bss:  16.808 0.8913  0.9634     8396.067
   4_xyz:  15.190 0.9050  0.9713     7101.984
   4_adp:  14.814 0.9083  0.9659     6910.540
   4_occ:  14.808 0.9083  0.9659     6903.088
   5_bss:  14.809 0.9084  0.9710     6907.742
   5_xyz:  14.674 0.9096  0.9715     6837.728
   5_adp:  14.690 0.9095  0.9644     6850.705
   5_occ:  14.696 0.9095  0.9642     6852.748
   5_bss:  14.709 0.9094  0.9711     6857.710
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.8750e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.8750e-01
   1_xyz:   1.407  0.012  0.086 15.365  0.006  4.114   1.2529e-01
   1_adp:   1.407  0.012  0.086 15.365  0.006  4.114   1.2529e-01
   1_occ:   1.407  0.012  0.086 15.365  0.006  4.114   1.2529e-01
   2_bss:   1.407  0.012  0.086 15.365  0.006  4.114   1.2529e-01
   2_xyz:   1.011  0.007  0.075 14.701  0.004  4.126   5.8684e-02
   2_adp:   1.011  0.007  0.075 14.701  0.004  4.126   5.8684e-02
   2_occ:   1.011  0.007  0.075 14.701  0.004  4.126   5.8684e-02
   3_bss:   1.011  0.007  0.075 14.701  0.004  4.126   5.8684e-02
   3_xyz:   0.939  0.006  0.068 14.525  0.003  4.123   5.2336e-02
   3_adp:   0.939  0.006  0.068 14.525  0.003  4.123   5.2336e-02
   3_occ:   0.939  0.006  0.068 14.525  0.003  4.123   5.2336e-02
   4_bss:   0.939  0.006  0.068 14.525  0.003  4.123   5.2336e-02
   4_xyz:   1.114  0.009  0.083 14.795  0.004  4.133   7.1163e-02
   4_adp:   1.114  0.009  0.083 14.795  0.004  4.133   7.1163e-02
   4_occ:   1.114  0.009  0.083 14.795  0.004  4.133   7.1163e-02
   5_bss:   1.114  0.009  0.083 14.795  0.004  4.133   7.1163e-02
   5_xyz:   1.120  0.010  0.084 14.767  0.004  4.113   7.3465e-02
   5_adp:   1.120  0.010  0.084 14.767  0.004  4.113   7.3465e-02
   5_occ:   1.120  0.010  0.084 14.767  0.004  4.113   7.3465e-02
   5_bss:   1.120  0.010  0.084 14.767  0.004  4.113   7.3465e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.330   2.4342e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.330   2.4342e-01
   1_xyz:  10.321  0.094  0.353 82.606  0.047  2.095   2.8541e-01
   1_adp:  10.321  0.094  0.353 82.606  0.047  2.095   2.8541e-01
   1_occ:  10.321  0.094  0.353 82.606  0.047  2.095   2.8541e-01
   2_bss:  10.321  0.094  0.353 82.606  0.047  2.095   2.8541e-01
   2_xyz:   6.611  0.039  0.224 81.934  0.046  2.317   4.8058e-02
   2_adp:   6.611  0.039  0.224 81.934  0.046  2.317   4.8058e-02
   2_occ:   6.611  0.039  0.224 81.934  0.046  2.317   4.8058e-02
   3_bss:   6.611  0.039  0.224 81.934  0.046  2.317   4.8058e-02
   3_xyz:   6.192  0.040  0.216 82.535  0.034  2.278   4.0356e-02
   3_adp:   6.192  0.040  0.216 82.535  0.034  2.278   4.0356e-02
   3_occ:   6.192  0.040  0.216 82.535  0.034  2.278   4.0356e-02
   4_bss:   6.192  0.040  0.216 82.535  0.034  2.278   4.0356e-02
   4_xyz:   7.959  0.064  0.291 83.910  0.036  2.256   5.2073e-02
   4_adp:   7.959  0.064  0.291 83.910  0.036  2.256   5.2073e-02
   4_occ:   7.959  0.064  0.291 83.910  0.036  2.256   5.2073e-02
   5_bss:   7.959  0.064  0.291 83.910  0.036  2.256   5.2073e-02
   5_xyz:   7.862  0.058  0.296 83.574  0.038  2.287   5.1066e-02
   5_adp:   7.862  0.058  0.296 83.574  0.038  2.287   5.1066e-02
   5_occ:   7.862  0.058  0.296 83.574  0.038  2.287   5.1066e-02
   5_bss:   7.862  0.058  0.296 83.574  0.038  2.287   5.1066e-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: 122.51   0.00  17.17 122.51   0.00  13.29  64.78   5.32  38.32
   1_occ: 122.51   0.00  17.17 122.51   0.00  13.29  64.78   5.32  38.32
   2_bss: 122.51   0.00  17.17 122.51   0.00  13.29  64.78   5.32  38.32
   2_xyz: 122.51   0.00  17.17 122.51   0.00  13.29  64.78   5.32  38.32
   2_adp:  78.77   0.00  17.68  74.06   0.00  13.28  78.77   5.85  41.65
   2_occ:  78.77   0.00  17.68  74.06   0.00  13.28  78.77   5.85  41.65
   3_bss:  78.77   0.00  17.68  74.06   0.00  13.28  78.77   5.85  41.65
   3_xyz:  78.77   0.00  17.68  74.06   0.00  13.28  78.77   5.85  41.65
   3_adp:  82.67   0.00  17.58  80.27   0.00  13.05  82.67   5.10  42.21
   3_occ:  82.67   0.00  17.58  80.27   0.00  13.05  82.67   5.10  42.21
   4_bss:  82.67   0.00  17.58  80.27   0.00  13.05  82.67   5.10  42.21
   4_xyz:  82.67   0.00  17.58  80.27   0.00  13.05  82.67   5.10  42.21
   4_adp:  83.31   0.00  17.15  81.02   1.10  12.75  83.31   0.00  41.08
   4_occ:  83.31   0.00  17.15  81.02   1.10  12.75  83.31   0.00  41.08
   5_bss:  83.31   0.00  17.15  81.02   1.10  12.75  83.31   0.00  41.08
   5_xyz:  83.31   0.00  17.15  81.02   1.10  12.75  83.31   0.00  41.08
   5_adp:  89.18   0.00  16.99  86.06   0.67  12.59  89.18   0.00  40.99
   5_occ:  89.18   0.00  16.99  86.06   0.67  12.59  89.18   0.00  40.99
   5_bss:  89.19   0.00  17.00  86.07   0.67  12.59  89.19   0.00  40.99
------------------------------------------------------------------------
 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:    1.843    0.017    0.396
   1_adp:    1.843    0.017    0.396
   1_occ:    1.843    0.017    0.396
   2_bss:    1.843    0.017    0.396
   2_xyz:    1.381    0.025    0.474
   2_adp:    1.381    0.025    0.474
   2_occ:    1.381    0.025    0.474
   3_bss:    1.381    0.025    0.474
   3_xyz:    1.211    0.040    0.543
   3_adp:    1.211    0.040    0.543
   3_occ:    1.211    0.040    0.543
   4_bss:    1.211    0.040    0.543
   4_xyz:    1.190    0.043    0.580
   4_adp:    1.190    0.043    0.580
   4_occ:    1.190    0.043    0.580
   5_bss:    1.190    0.043    0.580
   5_xyz:    1.192    0.056    0.581
   5_adp:    1.192    0.056    0.581
   5_occ:    1.192    0.056    0.581
   5_bss:    1.192    0.056    0.581
------------------------------------------------------------------------

CPU time actual refinement: 317.14


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_318/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_318/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_318/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_318/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_318/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.99 
  Macro-tasks:
    bulk solvent and scale       = 37.33  
    individual site refinement   = 127.85 
    weights calculation          = 29.68  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 201.53 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 100.51 
    alpha_beta                      = 8.26   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 108.39 
    fmodel                         = 5.97   
    r_factors                      = 0.19   
    phase_errors                   = 11.05  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 237.52 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.578 micro seconds
Total CPU time: 5.51 minutes
from_scatterers_fft:    620 calls, 100.24 s
gradients_fft:          565 calls,  95.48 s

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

# Date 2008-01-16 Time 04:32:22 PST -0800 (1200486742.89 s)
Start R-work = 0.4128, R-free = 0.4083 (no bulk solvent and anisotropic scale)
Final R-work = 0.1364, R-free = 0.1796 (no bulk solvent and anisotropic scale)

Start R-work = 0.4011, R-free = 0.3941
Final R-work = 0.1137, R-free = 0.1624