# Date 2008-01-16 Time 05:25:01 PST -0800 (1200489901.78 s)
#phil __OFF__

Command line arguments: "../727.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2346
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 727

-------------------------------------------------------------------------------
  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: (70.6012, 45.7567, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.95157
Completeness in resolution range: 0.954211
Completeness with d_max=infinity: 0.951384

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9645
                             d_min =   1.9516

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: (70.6012, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.95157
Completeness in resolution range: 0.954211
Completeness with d_max=infinity: 0.951384

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9649 -  4.1769 [2150/2176]  1939   211   9.8%
  bin  2:  4.1769 -  3.3273 [2078/2098]  1866   212  10.2%
  bin  3:  3.3273 -  2.9102 [2044/2063]  1839   205  10.0%
  bin  4:  2.9102 -  2.6458 [2016/2046]  1818   198   9.8%
  bin  5:  2.6458 -  2.4570 [2028/2047]  1828   200   9.9%
  bin  6:  2.4570 -  2.3127 [2003/2028]  1791   212  10.6%
  bin  7:  2.3127 -  2.1973 [1990/2018]  1798   192   9.6%
  bin  8:  2.1973 -  2.1019 [1982/2018]  1783   199  10.0%
  bin  9:  2.1019 -  2.0212 [1977/2019]  1780   197  10.0%
  bin 10:  2.0212 -  1.9516 [1321/2016]  1188   133  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_727/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:
        1.41 -     2.11: 22
        2.11 -     2.80: 837
        2.80 -     3.50: 4566
        3.50 -     4.20: 9518
        4.20 -     4.90: 13961
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.407 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.771 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.791 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28899 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_727/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_727/model_refine_001.geo

CPU time processing inputs: 9.29


============================ 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 = 70.60125 45.75675 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4784   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.289718                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6592 0.99   1401  159 0.3954 0.4069      6.5932      6.6468|
|  2:  4.6592 -  3.7168 0.99   1345  145 0.4229 0.4267      6.8381      6.7672|
|  3:  3.7168 -  3.2525 0.99   1321  143 0.4552 0.4420      6.7083      6.7876|
|  4:  3.2525 -  2.9576 0.99   1315  157 0.4673 0.4561       6.555      6.5094|
|  5:  2.9576 -  2.7470 0.99   1300  142 0.5053 0.4858      6.3762      6.3715|
|  6:  2.7470 -  2.5859 0.99   1305  143 0.5093 0.5428      6.2926      6.2667|
|  7:  2.5859 -  2.4570 0.99   1303  137 0.5026 0.4951      6.2506      6.2145|
|  8:  2.4570 -  2.3505 0.98   1258  148 0.5143 0.4723       6.171      6.1608|
|  9:  2.3505 -  2.2603 0.98   1297  150 0.5244 0.5587       6.133      6.1742|
| 10:  2.2603 -  2.1825 1.00   1292  139 0.5148 0.5476      6.0924      6.1044|
| 11:  2.1825 -  2.1145 0.98   1271  135 0.5147 0.5319       6.037      6.0645|
| 12:  2.1145 -  2.0542 0.98   1268  143 0.5109 0.5100      5.9646      6.0158|
| 13:  2.0542 -  2.0003 0.98   1266  143 0.5123 0.4934      5.8774      5.8097|
| 14:  2.0003 -  1.9516 0.53    688   75 0.5471 0.4587      5.9022      5.7776|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6592  1401   159  0.66  38.06   0.81     0.72      86257.40|
|  2:  4.6592 -  3.7168  1345   145  0.66  38.36   0.90     0.79     124391.75|
|  3:  3.7168 -  3.2525  1321   143  0.56  47.18   0.92     0.76     129243.94|
|  4:  3.2525 -  2.9576  1315   157  0.45  55.67   0.93     0.64     117872.31|
|  5:  2.9576 -  2.7470  1300   142  0.35  63.88   0.88     0.51      92296.80|
|  6:  2.7470 -  2.5859  1305   143  0.30  67.77   0.89     0.43      83991.84|
|  7:  2.5859 -  2.4570  1303   137  0.30  67.43   0.92     0.42      70979.72|
|  8:  2.4570 -  2.3505  1258   148  0.30  67.29   0.91     0.46      64541.65|
|  9:  2.3505 -  2.2603  1297   150  0.33  65.20   0.91     0.48      55741.48|
| 10:  2.2603 -  2.1825  1292   139  0.33  65.58   0.94     0.50      51941.23|
| 11:  2.1825 -  2.1145  1271   135  0.29  68.10   0.97     0.46      49987.98|
| 12:  2.1145 -  2.0542  1268   143  0.31  66.73   0.99     0.51      44556.82|
| 13:  2.0542 -  2.0003  1266   143  0.37  62.03   0.96     0.60      34731.17|
| 14:  2.0003 -  1.9516   688    75  0.53  50.21   0.96     0.77      21631.23|
|alpha:            min =        0.42 max =            0.79 mean =         0.57|
|beta:             min =    21631.23 max =       129243.94 mean =     75748.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.88|
|phase err.(test): min =        0.00 max =           89.93 mean =        59.14|
|-----------------------------------------------------------------------------|

============================== 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 = 11.327699             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.555   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.267042              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.044   (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 |  1.407 -  1.756:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.756 -  2.106:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.106 -  2.455:       45 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.455 -  2.804:      792 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.804 -  3.153:     2126 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.153 -  3.503:     2440 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.503 -  3.852:     4671 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.852 -  4.201:     4847 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.201 -  4.551:     6294 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7667 |
|-----------------------------------------------------------------------------|
|-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 |        0.193 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.407 |       0.678 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.422)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4784   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.289718                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4685   r_free= 0.4675   ksol= 0.34   Bsol= 28.25   scale= 0.915   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,1.85,0.73,0.00,0.00,0.00); trace/3= -0.20                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.285189                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.318546              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.444   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.608786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.903   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4685      final r-factor (work) = 0.4019          |
| start r-factor (free) = 0.4675      final r-factor (free) = 0.4336          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.4653 = 9.32 * 0.50 * 6.2825 + 1.00 * 0.1933                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0580 = 9.32 * 0.50 * 6.2123 + 1.00 * 0.1132                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4019      final r-factor (work) = 0.3693          |
| start r-factor (free) = 0.4336      final r-factor (free) = 0.4439          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0004 = 1.61 * 1.00 * 6.2123 + 1.00 * 0.0062                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9158 = 1.61 * 1.00 * 6.1496 + 1.00 * 0.0224                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.422)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.12  19.30    None  None   None       |
|    all(noH): 2823   0      0.00    123.12  19.30    None  None   None       |
|    Sol.    : 438    0      0.00    123.12  33.61    None  None   None       |
|    Mac.    : 2385   0      0.00    104.59  16.67    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 -  12.313: 1080   |   5:    61.562 -  73.875:   35        |
|      1:    12.313 -  24.625:  951   |   6:    73.875 -  86.187:   10        |
|      2:    24.625 -  36.937:  442   |   7:    86.187 -  98.500:    2        |
|      3:    36.937 -  49.250:  216   |   8:    98.500 - 110.812:    2        |
|      4:    49.250 -  61.562:   84   |   9:   110.812 - 123.125:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3693 r_free = 0.4439             target_work(ml) = 6.157         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3689 r_free = 0.4439             target_work(ml) = 6.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3689   r_free= 0.4439   ksol= 0.34   Bsol= 28.25   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,1.85,0.73,0.00,0.00,0.00); trace/3= -0.20                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.155779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3687   r_free= 0.4436   ksol= 0.36   Bsol= 53.51   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,1.16,0.56,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.158602                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.441319              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.981  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.936030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.897  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3687      final r-factor (work) = 0.3272          |
| start r-factor (free) = 0.4436      final r-factor (free) = 0.4036          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.0800 = 8.44 * 0.50 * 6.1523 + 1.00 * 0.1132                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8856 = 8.44 * 0.50 * 6.1145 + 1.00 * 0.0786                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3272      final r-factor (work) = 0.3180          |
| start r-factor (free) = 0.4036      final r-factor (free) = 0.3991          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7455 = 0.94 * 1.00 * 6.1145 + 1.00 * 0.0221                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6922 = 0.94 * 1.00 * 6.0639 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.422)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.17  18.93    None  None   None       |
|    all(noH): 2823   0      0.00    126.17  18.93    None  None   None       |
|    Sol.    : 438    0      0.00    126.17  32.83    None  None   None       |
|    Mac.    : 2385   0      0.00    106.87  16.38    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 -  12.617: 1163   |   5:    63.084 -  75.700:   24        |
|      1:    12.617 -  25.234:  929   |   6:    75.700 -  88.317:    7        |
|      2:    25.234 -  37.850:  442   |   7:    88.317 - 100.934:    1        |
|      3:    37.850 -  50.467:  186   |   8:   100.934 - 113.551:    2        |
|      4:    50.467 -  63.084:   68   |   9:   113.551 - 126.167:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3180 r_free = 0.3991             target_work(ml) = 6.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3179 r_free = 0.3996             target_work(ml) = 6.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3179   r_free= 0.3996   ksol= 0.36   Bsol= 53.51   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,1.16,0.56,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.057458                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3183   r_free= 0.3996   ksol= 0.36   Bsol= 61.48   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,0.55,0.71,0.00,0.00,0.00); trace/3= 0.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.057972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.921151             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.900  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.566261              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.491  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3183      final r-factor (work) = 0.2593          |
| start r-factor (free) = 0.3996      final r-factor (free) = 0.3346          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.1978 = 10.92 * 0.50 * 6.0652 + 1.00 * 0.0786                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.7992 = 10.92 * 0.50 * 5.9871 + 1.00 * 0.1061                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2593      final r-factor (work) = 0.2334          |
| start r-factor (free) = 0.3346      final r-factor (free) = 0.3224          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.3807 = 2.57 * 1.00 * 5.9871 + 1.00 * 0.0162                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.9965 = 2.57 * 1.00 * 5.8356 + 1.00 * 0.0207                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.422)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    132.59  19.31    None  None   None       |
|    all(noH): 2823   0      0.00    132.59  19.31    None  None   None       |
|    Sol.    : 438    0      0.66    132.59  43.02    None  None   None       |
|    Mac.    : 2385   0      0.00    120.35  14.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  13.259: 1389   |   5:    66.294 -  79.553:   52        |
|      1:    13.259 -  26.518:  781   |   6:    79.553 -  92.812:   19        |
|      2:    26.518 -  39.777:  283   |   7:    92.812 - 106.071:    3        |
|      3:    39.777 -  53.036:  186   |   8:   106.071 - 119.330:    1        |
|      4:    53.036 -  66.294:  107   |   9:   119.330 - 132.589:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2334 r_free = 0.3224             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2330 r_free = 0.3231             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2330   r_free= 0.3231   ksol= 0.36   Bsol= 61.48   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,0.55,0.71,0.00,0.00,0.00); trace/3= 0.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.811081                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2332   r_free= 0.3216   ksol= 0.34   Bsol= 57.46   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,-0.40,0.24,-0.00,0.00,0.00); trace/3= -0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.808405                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.349659              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.099   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.703327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.692  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2332      final r-factor (work) = 0.2031          |
| start r-factor (free) = 0.3216      final r-factor (free) = 0.2798          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8794 = 3.35 * 0.50 * 5.8354 + 1.00 * 0.1061                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6958 = 3.35 * 0.50 * 5.7568 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2031      final r-factor (work) = 0.1916          |
| start r-factor (free) = 0.2798      final r-factor (free) = 0.2599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0698 = 0.70 * 1.00 * 5.7568 + 1.00 * 0.0208                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9960 = 0.70 * 1.00 * 5.6607 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.422)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    129.73  18.29    None  None   None       |
|    all(noH): 2823   0      0.00    129.73  18.29    None  None   None       |
|    Sol.    : 438    0      3.71    129.73  44.47    None  None   None       |
|    Mac.    : 2385   0      0.00    118.54  13.48    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 -  12.973: 1529   |   5:    64.866 -  77.839:   63        |
|      1:    12.973 -  25.946:  686   |   6:    77.839 -  90.812:   17        |
|      2:    25.946 -  38.919:  240   |   7:    90.812 - 103.785:    4        |
|      3:    38.919 -  51.892:  180   |   8:   103.785 - 116.758:    1        |
|      4:    51.892 -  64.866:  101   |   9:   116.758 - 129.731:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1916 r_free = 0.2599             target_work(ml) = 5.626         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1913 r_free = 0.2592             target_work(ml) = 5.625         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1913   r_free= 0.2592   ksol= 0.34   Bsol= 57.46   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,-0.40,0.24,-0.00,0.00,0.00); trace/3= -0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.625336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1914   r_free= 0.2583   ksol= 0.32   Bsol= 45.69   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.99,-0.14,-0.00,-0.00,-0.00); trace/3= -0.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.624317                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.034251              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.391  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.015384              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.059  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1914      final r-factor (work) = 0.1582          |
| start r-factor (free) = 0.2583      final r-factor (free) = 0.2145          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6426 = 3.03 * 0.50 * 5.6611 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4647 = 3.03 * 0.50 * 5.5431 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1582      final r-factor (work) = 0.1446          |
| start r-factor (free) = 0.2145      final r-factor (free) = 0.2029          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.7290 = 3.02 * 1.00 * 5.5431 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3223 = 3.02 * 1.00 * 5.4083 + 1.00 * 0.0143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.422)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.26  18.01    None  None   None       |
|    all(noH): 2823   0      0.00    124.26  18.01    None  None   None       |
|    Sol.    : 438    0      4.71    124.26  47.97    None  None   None       |
|    Mac.    : 2385   0      0.00    122.90  12.51    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 -  12.426: 1612   |   5:    62.131 -  74.557:   77        |
|      1:    12.426 -  24.852:  669   |   6:    74.557 -  86.983:   40        |
|      2:    24.852 -  37.279:  164   |   7:    86.983 -  99.409:   15        |
|      3:    37.279 -  49.705:  115   |   8:    99.409 - 111.836:    2        |
|      4:    49.705 -  62.131:  127   |   9:   111.836 - 124.262:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1446 r_free = 0.2029             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1445 r_free = 0.2026             target_work(ml) = 5.376         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1445   r_free= 0.2026   ksol= 0.32   Bsol= 45.69   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.99,-0.14,-0.00,-0.00,-0.00); trace/3= -0.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.376138                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6592 0.99   1401  159 0.1063 0.1455      5.4815      5.6948|
|  2:  4.6592 -  3.7168 0.99   1345  145 0.1011 0.1394      5.6075      5.8486|
|  3:  3.7168 -  3.2525 0.99   1321  143 0.1366 0.1800      5.6907      5.9896|
|  4:  3.2525 -  2.9576 0.99   1315  157 0.1564 0.2151      5.6924      5.8897|
|  5:  2.9576 -  2.7470 0.99   1300  142 0.1682 0.2341      5.5386      5.7793|
|  6:  2.7470 -  2.5859 0.99   1305  143 0.1606 0.2225      5.4478      5.5964|
|  7:  2.5859 -  2.4570 0.99   1303  137 0.1606 0.2180      5.3728      5.5988|
|  8:  2.4570 -  2.3505 0.98   1258  148 0.1627 0.2428      5.3327      5.6104|
|  9:  2.3505 -  2.2603 0.98   1297  150 0.1650 0.2468      5.3116      5.5492|
| 10:  2.2603 -  2.1825 1.00   1292  139 0.1508 0.2245      5.2187      5.4374|
| 11:  2.1825 -  2.1145 0.98   1271  135 0.1513 0.2389      5.1933      5.5275|
| 12:  2.1145 -  2.0542 0.98   1268  143 0.1459 0.2019      5.1087      5.3459|
| 13:  2.0542 -  2.0003 0.98   1266  143 0.1583 0.2381      5.0539      5.3224|
| 14:  2.0003 -  1.9516 0.53    688   75 0.1605 0.2063      4.9844      5.1806|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6592  1401   159  0.92  11.61   0.98     0.96      10108.90|
|  2:  4.6592 -  3.7168  1345   145  0.94  10.56   1.05     1.02      13079.89|
|  3:  3.7168 -  3.2525  1321   143  0.90  15.31   1.07     1.07      15933.44|
|  4:  3.2525 -  2.9576  1315   157  0.88  18.77   1.05     1.02      17443.94|
|  5:  2.9576 -  2.7470  1300   142  0.86  20.86   1.02     0.98      13210.53|
|  6:  2.7470 -  2.5859  1305   143  0.86  20.91   1.01     0.97      11467.33|
|  7:  2.5859 -  2.4570  1303   137  0.85  21.12   1.03     0.98      10082.54|
|  8:  2.4570 -  2.3505  1258   148  0.84  22.11   1.01     0.97       9380.80|
|  9:  2.3505 -  2.2603  1297   150  0.85  21.89   1.02     0.97       9040.33|
| 10:  2.2603 -  2.1825  1292   139  0.85  21.72   1.02     0.96       7756.59|
| 11:  2.1825 -  2.1145  1271   135  0.84  22.15   1.03     0.96       7477.63|
| 12:  2.1145 -  2.0542  1268   143  0.86  21.31   1.03     0.99       6663.66|
| 13:  2.0542 -  2.0003  1266   143  0.84  22.55   1.02     0.99       5824.65|
| 14:  2.0003 -  1.9516   688    75  0.85  21.79   1.02     0.97       4726.87|
|alpha:            min =        0.96 max =            1.07 mean =         0.99|
|beta:             min =     4726.87 max =        17443.94 mean =     10388.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.98 mean =        19.30|
|phase err.(test): min =        0.00 max =           89.37 mean =        18.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1449   r_free= 0.2024   ksol= 0.31   Bsol= 45.69   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,-1.39,-0.41,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.374836                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1449   r_free= 0.2024   ksol= 0.31   Bsol= 45.69   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,-1.39,-0.41,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.374836                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6592 0.99   1401  159 0.1066 0.1434      5.4701      5.6751|
|  2:  4.6592 -  3.7168 0.99   1345  145 0.1022 0.1386      5.6084      5.8415|
|  3:  3.7168 -  3.2525 0.99   1321  143 0.1372 0.1803      5.6912      5.9884|
|  4:  3.2525 -  2.9576 0.99   1315  157 0.1566 0.2163      5.6924      5.8911|
|  5:  2.9576 -  2.7470 0.99   1300  142 0.1684 0.2333      5.5379       5.778|
|  6:  2.7470 -  2.5859 0.99   1305  143 0.1602 0.2224      5.4464      5.5969|
|  7:  2.5859 -  2.4570 0.99   1303  137 0.1607 0.2174      5.3728      5.5981|
|  8:  2.4570 -  2.3505 0.98   1258  148 0.1622 0.2435      5.3318      5.6119|
|  9:  2.3505 -  2.2603 0.98   1297  150 0.1646 0.2463      5.3107      5.5467|
| 10:  2.2603 -  2.1825 1.00   1292  139 0.1506 0.2251      5.2183      5.4383|
| 11:  2.1825 -  2.1145 0.98   1271  135 0.1511 0.2390      5.1928      5.5287|
| 12:  2.1145 -  2.0542 0.98   1268  143 0.1456 0.2012       5.108      5.3452|
| 13:  2.0542 -  2.0003 0.98   1266  143 0.1583 0.2378      5.0533      5.3212|
| 14:  2.0003 -  1.9516 0.53    688   75 0.1606 0.2060      4.9832      5.1791|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6592  1401   159  0.92  11.34   0.97     0.96       9667.89|
|  2:  4.6592 -  3.7168  1345   145  0.94  10.38   1.04     1.02      12763.51|
|  3:  3.7168 -  3.2525  1321   143  0.90  15.24   1.06     1.06      15814.88|
|  4:  3.2525 -  2.9576  1315   157  0.88  18.73   1.04     1.01      17388.66|
|  5:  2.9576 -  2.7470  1300   142  0.86  20.83   1.01     0.98      13206.28|
|  6:  2.7470 -  2.5859  1305   143  0.86  20.89   1.00     0.96      11463.22|
|  7:  2.5859 -  2.4570  1303   137  0.85  21.10   1.02     0.97      10075.44|
|  8:  2.4570 -  2.3505  1258   148  0.84  22.12   1.00     0.95       9392.30|
|  9:  2.3505 -  2.2603  1297   150  0.85  21.89   1.01     0.96       9038.66|
| 10:  2.2603 -  2.1825  1292   139  0.85  21.72   1.01     0.95       7760.51|
| 11:  2.1825 -  2.1145  1271   135  0.84  22.13   1.02     0.95       7478.37|
| 12:  2.1145 -  2.0542  1268   143  0.86  21.31   1.01     0.98       6657.67|
| 13:  2.0542 -  2.0003  1266   143  0.84  22.52   1.00     0.97       5812.53|
| 14:  2.0003 -  1.9516   688    75  0.85  21.72   1.00     0.96       4704.52|
|alpha:            min =        0.95 max =            1.06 mean =         0.98|
|beta:             min =     4704.52 max =        17388.66 mean =     10313.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.86 mean =        19.25|
|phase err.(test): min =        0.00 max =           89.59 mean =        18.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.422)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.26  18.01    None  None   None       |
|    all(noH): 2823   0      0.00    124.26  18.01    None  None   None       |
|    Sol.    : 438    0      4.72    124.26  47.97    None  None   None       |
|    Mac.    : 2385   0      0.00    122.91  12.51    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 -  12.429: 1612   |   5:    62.134 -  74.560:   77        |
|      1:    12.429 -  24.855:  669   |   6:    74.560 -  86.986:   40        |
|      2:    24.855 -  37.282:  164   |   7:    86.986 -  99.412:   15        |
|      3:    37.282 -  49.708:  115   |   8:    99.412 - 111.839:    2        |
|      4:    49.708 -  62.134:  127   |   9:   111.839 - 124.265:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.731 - 5.741
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 342
   mapped sites are within: 0.731 - 5.741

peak=    9.041 closest distance to " O   HOH Z 399 " =    1.066
peak=    8.360 closest distance to " O   HOH Z 390 " =    1.434
peak=    7.328 closest distance to " O   HOH Z 138 " =    1.050
peak=    6.517 closest distance to " O   HOH Z 289 " =    1.764
peak=    6.207 closest distance to " O   HOH Z  65 " =    1.795
peak=    6.108 closest distance to " O   HOH Z 431 " =    1.882
peak=    6.041 closest distance to " O   HOH Z 130 " =    1.123
peak=    5.848 closest distance to " O   SER A  62 " =    0.989
peak=    5.818 closest distance to " O   HOH Z 159 " =    1.028
peak=    5.757 closest distance to " O   HOH Z 385 " =    1.731
peak=    5.752 closest distance to " O   HOH Z 205 " =    1.088
peak=    5.742 closest distance to " O   HOH Z  61 " =    1.358
peak=    5.652 closest distance to " OD1 ASN A  45 " =    1.187
peak=    5.595 closest distance to " O   HOH Z 245 " =    1.383
peak=    5.290 closest distance to " NE2 GLN A  11 " =    1.552
peak=    5.254 closest distance to " O   HOH Z  29 " =    1.373
peak=    5.217 closest distance to " CG  PRO A  90 " =    1.101
peak=    5.185 closest distance to " O   HOH Z  97 " =    1.710
peak=    5.137 closest distance to " NH2 ARG A  56 " =    2.192
peak=    5.135 closest distance to " O   HOH Z 350 " =    1.273
peak=    5.092 closest distance to " O   HOH Z 222 " =    1.497
peak=    5.064 closest distance to " O   HOH Z 244 " =    1.366
peak=    5.049 closest distance to " O   HOH Z 403 " =    1.675
peak=    5.046 closest distance to " O   HOH Z 416 " =    1.497
peak=    5.035 closest distance to " O   HOH Z 117 " =    1.229
peak=    5.022 closest distance to " O   ASN A 285 " =    0.897
peak=    5.021 closest distance to " O   HOH Z 214 " =    1.883
peak=    4.990 closest distance to " O   HOH Z 424 " =    1.365
peak=    4.961 closest distance to " O   HOH Z 278 " =    1.404
peak=    4.953 closest distance to " O   HOH Z 120 " =    1.085
peak=    4.929 closest distance to " O   HOH Z 381 " =    1.108
peak=    4.885 closest distance to " O   HOH Z 287 " =    1.788
peak=    4.869 closest distance to " O   PRO A 198 " =    1.265
peak=    4.848 closest distance to " NZ BLYS A 290 " =    1.153
peak=    4.815 closest distance to " O   HOH Z 363 " =    1.370
peak=    4.809 closest distance to " O   HOH Z 258 " =    1.311
peak=    4.787 closest distance to " O   HOH Z  78 " =    1.898
peak=    4.759 closest distance to " O   HOH Z  59 " =    1.490
peak=    4.720 closest distance to " O   HOH Z 427 " =    1.932
peak=    4.720 closest distance to " O   HOH Z 358 " =    1.406
peak=    4.714 closest distance to " OD1 ASP A 286 " =    1.046
peak=    4.697 closest distance to " O   HOH Z 133 " =    1.574
peak=    4.694 closest distance to " O   HOH Z 415 " =    1.117
peak=    4.688 closest distance to " O   HOH Z 427 " =    1.371
peak=    4.682 closest distance to " O   HOH Z 400 " =    0.864
peak=    4.679 closest distance to " O   HOH Z   7 " =    2.041
peak=    4.653 closest distance to " O   HOH Z  54 " =    1.362
peak=    4.565 closest distance to " O   HOH Z  53 " =    2.267
peak=    4.539 closest distance to " O   HOH Z 302 " =    1.542
peak=    4.497 closest distance to " O   HOH Z 375 " =    1.053
peak=    4.483 closest distance to " O   HOH Z 276 " =    1.648
peak=    4.483 closest distance to " OG BSER A  12 " =    1.141
peak=    4.462 closest distance to " NZ  LYS A 117 " =    1.228
peak=    4.430 closest distance to " O   HOH Z 139 " =    1.799
peak=    4.406 closest distance to " O   HOH Z 105 " =    1.413
peak=    4.405 closest distance to " N   ASN A 285 " =    0.815
peak=    4.394 closest distance to " CD1 PHE A 283 " =    0.917
peak=    4.391 closest distance to " O   HOH Z 383 " =    1.181
peak=    4.390 closest distance to " CG  PRO A 198 " =    1.391
peak=    4.360 closest distance to " O   HOH Z 417 " =    1.889
peak=    4.347 closest distance to " CB  SER A 216 " =    1.030
peak=    4.337 closest distance to " CB  PRO A  54 " =    1.120
peak=    4.299 closest distance to " CB  ARG A 275 " =    1.250
peak=    4.297 closest distance to " O   HOH Z  28 " =    1.803
peak=    4.286 closest distance to " O   HOH Z 352 " =    1.657
peak=    4.284 closest distance to " O   HOH Z  46 " =    1.097
peak=    4.277 closest distance to " N   GLN A 278 " =    1.108
peak=    4.272 closest distance to " O   HOH Z 144 " =    1.917
peak=    4.261 closest distance to " OG ASER A 258 " =    2.977
peak=    4.239 closest distance to " O   HOH Z  63 " =    2.001
peak=    4.238 closest distance to " O   HOH Z  57 " =    1.185
peak=    4.212 closest distance to " N   GLU A   2 " =    1.401
peak=    4.200 closest distance to " N   SER A  63 " =    0.790
peak=    4.195 closest distance to " O   ALA A 165 " =    1.261
peak=    4.182 closest distance to " O   HOH Z  69 " =    2.278
peak=    4.164 closest distance to " O   HOH Z 250 " =    2.028
peak=    4.137 closest distance to " O   HOH Z 414 " =    1.664
peak=    4.130 closest distance to " O   HOH Z 402 " =    1.480
peak=    4.129 closest distance to " O   HOH Z 246 " =    1.531
peak=    4.101 closest distance to " O   HOH Z 259 " =    1.986
peak=    4.049 closest distance to " O   HOH Z 103 " =    0.933
peak=    4.043 closest distance to " N   GLN A  73 " =    1.418
peak=    4.042 closest distance to " O   HOH Z 311 " =    1.569
peak=    4.039 closest distance to " CG  PRO A 213 " =    1.282
peak=    4.023 closest distance to " O   HOH Z 124 " =    1.676
peak=    4.013 closest distance to " CB  TRP A 179 " =    1.421
peak=    4.007 closest distance to " O   HOH Z 293 " =    1.239
peak=    3.976 closest distance to " O   HOH Z 133 " =    2.374
peak=    3.939 closest distance to " O   ASP A 286 " =    2.336
peak=    3.919 closest distance to " O   HOH Z 380 " =    2.152
peak=    3.907 closest distance to " CG2 VAL A 257 " =    1.071
peak=    3.904 closest distance to " CG  LEU A 167 " =    1.230
peak=    3.886 closest distance to " O   HOH Z 215 " =    1.625
peak=    3.876 closest distance to " O   SER A  87 " =    2.270
peak=    3.874 closest distance to " OE1 GLN A  58 " =    5.453
peak=    3.859 closest distance to " CA  ARG A  36 " =    1.232
peak=    3.858 closest distance to " O   HOH Z 431 " =    1.036
peak=    3.856 closest distance to " CB  ARG A  79 " =    1.021
peak=    3.838 closest distance to " CG  PRO A  54 " =    1.237
peak=    3.838 closest distance to " NH2 ARG A 269 " =    0.751
peak=    3.827 closest distance to " O   HOH Z 132 " =    1.239
peak=    3.827 closest distance to " CA  ASN A 284 " =    0.932
peak=    3.820 closest distance to " N   GLY A 287 " =    0.872
peak=    3.810 closest distance to " OG BSER A 258 " =    1.114
peak=    3.810 closest distance to " OE1 GLU A   2 " =    1.929
peak=    3.809 closest distance to " O   HOH Z 217 " =    2.651
peak=    3.793 closest distance to " CA  SER A  62 " =    1.146
peak=    3.787 closest distance to " O   HOH Z 135 " =    1.728
peak=    3.776 closest distance to " O   HOH Z  88 " =    3.176
peak=    3.775 closest distance to " CA  TYR A  30 " =    1.048
peak=    3.764 closest distance to " CZ  PHE A  16 " =    0.965
peak=    3.762 closest distance to " O   HOH Z 272 " =    1.733
peak=    3.760 closest distance to " O   HOH Z 134 " =    1.567
peak=    3.757 closest distance to " O   HOH Z 298 " =    1.932
peak=    3.751 closest distance to " N   ARG A 156 " =    1.282
peak=    3.749 closest distance to " NH2 ARG A  36 " =    0.975
peak=    3.746 closest distance to " O   HOH Z   5 " =    1.324
peak=    3.733 closest distance to " O   HOH Z 109 " =    1.494
peak=    3.723 closest distance to " O   HOH Z 389 " =    1.582
peak=    3.719 closest distance to " CB  GLN A 183 " =    1.050
peak=    3.714 closest distance to " CB  ASP A 124 " =    1.059
peak=    3.711 closest distance to " O   HOH Z 392 " =    1.331
peak=    3.709 closest distance to " CB  SER A   3 " =    1.361
peak=    3.706 closest distance to " CE  LYS A  48 " =    1.001
peak=    3.694 closest distance to " CB  ALA A 104 " =    1.299
peak=    3.683 closest distance to " O   HOH Z 269 " =    3.327
peak=    3.682 closest distance to " O   HOH Z 211 " =    1.681
peak=    3.676 closest distance to " CE  MET A  93 " =    1.474
peak=    3.674 closest distance to " CA  ALA A  21 " =    1.248
peak=    3.670 closest distance to " CD  ARG A 138 " =    0.920
peak=    3.666 closest distance to " CG1BVAL A 121 " =    1.820
peak=    3.650 closest distance to " O   HOH Z 405 " =    1.804
peak=    3.649 closest distance to " O   HOH Z 182 " =    1.193
peak=    3.638 closest distance to " CB  SER A  63 " =    1.546
peak=    3.638 closest distance to " NE AARG A 275 " =    1.408
peak=    3.636 closest distance to " CB  ASN A 148 " =    1.465
peak=    3.635 closest distance to " O   HOH Z   9 " =    0.934
peak=    3.635 closest distance to " NH1 ARG A  36 " =    0.993
peak=    3.631 closest distance to " CB  GLN A 223 " =    1.584
peak=    3.627 closest distance to " CB  GLU A 128 " =    1.068
peak=    3.625 closest distance to " N   SER A 210 " =    1.071
peak=    3.621 closest distance to " O   HOH Z  32 " =    2.000
peak=    3.616 closest distance to " O   HOH Z  88 " =    2.680
peak=    3.596 closest distance to " CA  PRO A  54 " =    1.013
peak=    3.591 closest distance to " CG  TRP A 179 " =    2.250
peak=    3.590 closest distance to " O   HOH Z 368 " =    1.591
peak=    3.588 closest distance to " O   HOH Z 110 " =    1.381
peak=    3.586 closest distance to " O   HOH Z 139 " =    5.480
peak=    3.583 closest distance to " CG  PRO A 243 " =    1.160
peak=    3.575 closest distance to " O   HOH Z 128 " =    2.252
peak=    3.571 closest distance to " O   HOH Z 384 " =    1.683
peak=    3.570 closest distance to " O   HOH Z   6 " =    1.842
peak=    3.567 closest distance to " O   HOH Z 351 " =    0.968
peak=    3.563 closest distance to " O   HOH Z 371 " =    3.240
peak=    3.558 closest distance to " CG BARG A 102 " =    0.941
peak=    3.554 closest distance to " O   HOH Z 347 " =    1.002
peak=    3.544 closest distance to " O   HOH Z 158 " =    1.418
peak=    3.542 closest distance to " CB  ASP A 132 " =    3.686
peak=    3.540 closest distance to " O   HOH Z 369 " =    1.660
peak=    3.540 closest distance to " CA  ALA A 160 " =    0.770
peak=    3.540 closest distance to " CB  VAL A 202 " =    1.707
peak=    3.534 closest distance to " O   HOH Z  63 " =    1.896
peak=    3.534 closest distance to " O   HOH Z 371 " =    2.166
peak=    3.533 closest distance to " O   HOH Z 269 " =    1.175
peak=    3.532 closest distance to " O   HOH Z 166 " =    1.447
peak=    3.531 closest distance to " O   HOH Z 344 " =    1.176
peak=    3.529 closest distance to " CB  GLU A 277 " =    1.093
peak=    3.529 closest distance to " O   HOH Z 155 " =    2.148
peak=    3.526 closest distance to " CG2 THR A 279 " =    1.082
peak=    3.523 closest distance to " O   HOH Z 261 " =    2.105
peak=    3.520 closest distance to " O   HOH Z 426 " =    1.174
peak=    3.520 closest distance to " O   HOH Z 116 " =    5.741
peak=    3.507 closest distance to " O   HOH Z 207 " =    2.266
peak=    3.491 closest distance to " O   HOH Z  11 " =    1.148
peak=    3.490 closest distance to " CB  MET A  47 " =    1.063
peak=    3.484 closest distance to " CB  SER A 276 " =    1.248
peak=    3.483 closest distance to " O   HOH Z 411 " =    3.323
peak=    3.481 closest distance to " O   HOH Z 119 " =    1.376
peak=    3.479 closest distance to " CG  LEU A 297 " =    0.968
peak=    3.479 closest distance to " C   ASN A 215 " =    1.278
peak=    3.474 closest distance to " CE AMET A  47 " =    1.197
peak=    3.473 closest distance to " C   GLN A  73 " =    0.968
peak=    3.472 closest distance to " O   HOH Z 167 " =    1.391
peak=    3.471 closest distance to " CB  MET A 105 " =    1.258
peak=    3.468 closest distance to " O   HOH Z 239 " =    1.518
peak=    3.468 closest distance to " CB  PHE A  16 " =    0.993
peak=    3.467 closest distance to " O   HOH Z 384 " =    1.534
peak=    3.463 closest distance to " O   HOH Z 412 " =    1.893
peak=    3.462 closest distance to " O   HOH Z  39 " =    1.245
peak=    3.460 closest distance to " O   HOH Z 264 " =    0.973
peak=    3.458 closest distance to " CD2 LEU A 300 " =    1.154
peak=    3.457 closest distance to " O   HOH Z  89 " =    1.505
peak=    3.451 closest distance to " CE1 TYR A  68 " =    1.087
peak=    3.450 closest distance to " O   HOH Z 282 " =    1.667
peak=    3.445 closest distance to " CA  ASN A 127 " =    1.021
peak=    3.445 closest distance to " O   HOH Z 359 " =    1.444
peak=    3.438 closest distance to " O   HOH Z 185 " =    1.453
peak=    3.430 closest distance to " NZ  LYS A  76 " =    1.256
peak=    3.423 closest distance to " CA  LEU A 282 " =    1.050
peak=    3.413 closest distance to " N   CYS A 260 " =    1.095
peak=    3.404 closest distance to " OD1 ASP A  50 " =    0.992
peak=    3.400 closest distance to " O   HOH Z  76 " =    1.008
peak=    3.396 closest distance to " O   HOH Z 235 " =    1.137
peak=    3.395 closest distance to " CB  LYS A 290 " =    1.506
peak=    3.393 closest distance to " CG2 THR A  29 " =    1.285
peak=    3.392 closest distance to " O   HOH Z  65 " =    1.516
peak=    3.385 closest distance to " CG  GLN A  88 " =    1.006
peak=    3.379 closest distance to " O   HOH Z 161 " =    1.007
peak=    3.378 closest distance to " CB  GLN A  89 " =    1.203
peak=    3.374 closest distance to " O   HOH Z 332 " =    1.290
peak=    3.373 closest distance to " O   HOH Z 363 " =    2.962
peak=    3.371 closest distance to " O   HOH Z 145 " =    1.868
peak=    3.368 closest distance to " O   HOH Z 233 " =    1.329
peak=    3.368 closest distance to " O   HOH Z 112 " =    1.440
peak=    3.366 closest distance to " CE AMET A  47 " =    1.356
peak=    3.358 closest distance to " O   HOH Z 271 " =    1.851
peak=    3.356 closest distance to " O   HOH Z 193 " =    1.563
peak=    3.353 closest distance to " CB  ASN A  60 " =    0.857
peak=    3.349 closest distance to " CB  TYR A 116 " =    1.136
peak=    3.347 closest distance to " CD1 PHE A 130 " =    0.919
peak=    3.346 closest distance to " O   HOH Z 364 " =    1.276
peak=    3.343 closest distance to " O   HOH Z 143 " =    0.965
peak=    3.336 closest distance to " CA  ASN A 217 " =    1.161
peak=    3.334 closest distance to " O   HOH Z 313 " =    1.819
peak=    3.334 closest distance to " O   HOH Z 124 " =    4.299
peak=    3.333 closest distance to " O   GLY A 302 " =    1.519
peak=    3.332 closest distance to " CG  GLN A  77 " =    2.067
peak=    3.332 closest distance to " CD2 LEU A  25 " =    1.175
peak=    3.331 closest distance to " NE BARG A 275 " =    1.124
peak=    3.325 closest distance to " N   TYR A  15 " =    1.166
peak=    3.324 closest distance to " CG AARG A 275 " =    1.174
peak=    3.323 closest distance to " OG  SER A  62 " =    3.467
peak=    3.317 closest distance to " CB  ALA A 233 " =    1.497
peak=    3.314 closest distance to " O   HOH Z 434 " =    1.428
peak=    3.310 closest distance to " O   VAL A  72 " =    1.100
peak=    3.309 closest distance to " O   HOH Z 152 " =    2.188
peak=    3.308 closest distance to " O   HOH Z 186 " =    1.328
peak=    3.305 closest distance to " O   HOH Z 393 " =    1.417
peak=    3.303 closest distance to " OE1 GLN A 240 " =    1.802
peak=    3.297 closest distance to " CA  SER A  12 " =    1.661
peak=    3.297 closest distance to " O   HOH Z 137 " =    1.174
peak=    3.296 closest distance to " CD1 LEU A 228 " =    1.769
peak=    3.295 closest distance to " O   HOH Z 353 " =    1.904
peak=    3.293 closest distance to " NE2 GLN A  73 " =    1.339
peak=    3.293 closest distance to " NZ  LYS A 119 " =    1.668
peak=    3.290 closest distance to " CG  ASN A  60 " =    0.967
peak=    3.285 closest distance to " CG2 THR A 221 " =    1.254
peak=    3.283 closest distance to " O   HOH Z 334 " =    1.838
peak=    3.280 closest distance to " O   HOH Z 325 " =    1.967
peak=    3.280 closest distance to " O   HOH Z 326 " =    1.490
peak=    3.278 closest distance to " O   HOH Z 193 " =    1.468
peak=    3.277 closest distance to " O   HOH Z 108 " =    1.528
peak=    3.275 closest distance to " O   HOH Z  11 " =    1.751
peak=    3.275 closest distance to " O   HOH Z  68 " =    1.810
peak=    3.273 closest distance to " O   HOH Z 422 " =    2.774
peak=    3.270 closest distance to " O   HOH Z 180 " =    2.188
peak=    3.269 closest distance to " OE1 GLN A  88 " =    0.954
peak=    3.267 closest distance to " O   HOH Z 409 " =    1.875
peak=    3.267 closest distance to " CB  GLN A  11 " =    1.477
peak=    3.265 closest distance to " CD  ARG A 195 " =    3.414
peak=    3.265 closest distance to " CB  PHE A 225 " =    1.491
peak=    3.264 closest distance to " CG  ARG A  66 " =    2.607
peak=    3.262 closest distance to " O   HOH Z 139 " =    2.762
peak=    3.261 closest distance to " N   TRP A  85 " =    1.168
peak=    3.261 closest distance to " CA  THR A 264 " =    0.731
peak=    3.259 closest distance to " O   HOH Z  44 " =    2.999
peak=    3.255 closest distance to " O   HOH Z 248 " =    1.930
peak=    3.252 closest distance to " CA  ARG A 195 " =    1.331
peak=    3.249 closest distance to " O   HOH Z 361 " =    1.330
peak=    3.241 closest distance to " CB  THR A 235 " =    1.143
peak=    3.239 closest distance to " O   HOH Z 164 " =    1.714
peak=    3.236 closest distance to " CD1 TRP A 179 " =    0.945
peak=    3.236 closest distance to " OE2 GLU A   2 " =    1.902
peak=    3.234 closest distance to " CB  ASP A 107 " =    1.069
peak=    3.230 closest distance to " OG ASER A 134 " =    1.373
peak=    3.230 closest distance to " CB  GLU A 152 " =    1.321
peak=    3.228 closest distance to " CA  ALA A 295 " =    1.055
peak=    3.216 closest distance to " CG2 ILE A 151 " =    1.500
peak=    3.212 closest distance to " NH1AARG A 145 " =    1.090
peak=    3.212 closest distance to " O   HOH Z 112 " =    2.519
peak=    3.207 closest distance to " CG1 VAL A 232 " =    1.477
peak=    3.206 closest distance to " O   HOH Z 361 " =    2.599
peak=    3.204 closest distance to " O   HOH Z 395 " =    3.023
peak=    3.201 closest distance to " NH2 ARG A 219 " =    1.720
peak=    3.198 closest distance to " O   HOH Z 140 " =    1.970
peak=    3.197 closest distance to " O   HOH Z 394 " =    1.858
peak=    3.194 closest distance to " CA  ALA A 299 " =    0.967
peak=    3.192 closest distance to " CE2 PHE A  16 " =    0.822
peak=    3.190 closest distance to " N   LYS A 119 " =    0.909
peak=    3.186 closest distance to " CB  ALA A   1 " =    1.074
peak=    3.184 closest distance to " O   HOH Z 425 " =    2.532
peak=    3.180 closest distance to " N   ASP A 286 " =    0.884
peak=    3.179 closest distance to " CA  ILE A 234 " =    1.326
peak=    3.177 closest distance to " CG2 THR A   4 " =    0.896
peak=    3.175 closest distance to " CA  GLU A 152 " =    1.022
peak=    3.174 closest distance to " O   HOH Z 124 " =    1.955
peak=    3.171 closest distance to " O   HOH Z 383 " =    3.024
peak=    3.168 closest distance to " O   HOH Z 135 " =    1.922
peak=    3.168 closest distance to " N   GLY A 136 " =    1.161
peak=    3.167 closest distance to " CB  CYS A 168 " =    1.286
peak=    3.164 closest distance to " CB  SER A  26 " =    1.490
peak=    3.160 closest distance to " CB  PHE A  61 " =    1.210
peak=    3.159 closest distance to " N   ALA A 100 " =    0.789
peak=    3.157 closest distance to " CG2 THR A 294 " =    1.093
peak=    3.154 closest distance to " O   HOH Z 368 " =    3.803
peak=    3.154 closest distance to " ND2 ASN A 285 " =    0.796
peak=    3.153 closest distance to " CB  TRP A 266 " =    1.031
peak=    3.152 closest distance to " C   SER A 135 " =    0.884
peak=    3.150 closest distance to " O   HOH Z 130 " =    2.427
peak=    3.148 closest distance to " NH2 ARG A 269 " =    1.295
peak=    3.145 closest distance to " O   HOH Z 185 " =    1.654
peak=    3.142 closest distance to " O   HOH Z 151 " =    1.787
peak=    3.139 closest distance to " O   HOH Z  92 " =    1.272
peak=    3.138 closest distance to " O   HOH Z 277 " =    2.394
peak=    3.127 closest distance to " CB  ALA A  10 " =    1.078
peak=    3.127 closest distance to " O   HOH Z  30 " =    1.592
peak=    3.125 closest distance to " O   HOH Z 230 " =    1.442
peak=    3.125 closest distance to " O   HOH Z 158 " =    2.485
peak=    3.117 closest distance to " OD2 ASP A 140 " =    1.071
peak=    3.117 closest distance to " OD2 ASP A 286 " =    2.439
peak=    3.115 closest distance to " O   HOH Z 365 " =    2.865
peak=    3.113 closest distance to " O   HOH Z   7 " =    2.961
peak=    3.112 closest distance to " O   HOH Z 137 " =    1.806
peak=    3.112 closest distance to " CG2 THR A 251 " =    1.704
peak=    3.109 closest distance to " O   HOH Z  25 " =    1.381
peak=    3.106 closest distance to " OD1 ASP A 298 " =    2.293
peak=    3.104 closest distance to " N   ALA A   1 " =    1.489
peak=    3.098 closest distance to " CZ3 TRP A 123 " =    1.272
peak=    3.094 closest distance to " O   HOH Z 172 " =    2.177
peak=    3.092 closest distance to " NE2 GLN A  55 " =    1.106
peak=    3.089 closest distance to " NE1 TRP A  85 " =    0.966
peak=    3.088 closest distance to " CB  MET A  47 " =    1.288
peak=    3.084 closest distance to " NE2 GLN A  89 " =    1.220
peak=    3.081 closest distance to " O   HOH Z 291 " =    1.586
peak=    3.081 closest distance to " NH2AARG A 275 " =    3.916
peak=    3.080 closest distance to " O   HOH Z  44 " =    1.561
peak=    3.080 closest distance to " SD  MET A 105 " =    1.041
peak=    3.073 closest distance to " C   THR A  18 " =    1.147
peak=    3.058 closest distance to " O   GLU A   2 " =    0.816
peak=    3.047 closest distance to " O   HOH Z 334 " =    2.608
peak=    3.037 closest distance to " O   ALA A 242 " =    0.858

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.714 - 5.537
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 188
   mapped sites are within: 0.714 - 5.537

peak=   -5.227 closest distance to " O   SER A  62 " =    0.999
peak=   -4.615 closest distance to " O   HOH Z 381 " =    0.960
peak=   -4.249 closest distance to " CB  ASP A  27 " =    2.518
peak=   -4.246 closest distance to " O   PRO A 198 " =    1.230
peak=   -4.242 closest distance to " O   HOH Z  60 " =    1.730
peak=   -4.241 closest distance to " N   GLN A  58 " =    1.264
peak=   -4.210 closest distance to " OG  SER A  97 " =    2.175
peak=   -4.182 closest distance to " O   ASP A 191 " =    1.944
peak=   -4.158 closest distance to " O   HOH Z  24 " =    1.178
peak=   -4.112 closest distance to " O   HOH Z  77 " =    1.679
peak=   -4.105 closest distance to " ND2 ASN A 209 " =    1.691
peak=   -4.100 closest distance to " CB  ALA A 248 " =    1.871
peak=   -4.068 closest distance to " O   HOH Z 377 " =    1.821
peak=   -4.062 closest distance to " CG  MET A 105 " =    0.868
peak=   -4.061 closest distance to " O   HOH Z 242 " =    1.584
peak=   -4.042 closest distance to " CD  ARG A  14 " =    2.885
peak=   -4.032 closest distance to " CA  GLY A 133 " =    1.860
peak=   -4.011 closest distance to " O   HOH Z 140 " =    4.512
peak=   -3.989 closest distance to " O   HOH Z 185 " =    2.066
peak=   -3.985 closest distance to " O   HOH Z  88 " =    1.716
peak=   -3.918 closest distance to " CA  ASN A 127 " =    1.323
peak=   -3.910 closest distance to " C   SER A  63 " =    1.063
peak=   -3.881 closest distance to " O   PHE A 218 " =    1.193
peak=   -3.877 closest distance to " O   ASN A 301 " =    1.446
peak=   -3.855 closest distance to " N   LEU A 282 " =    2.381
peak=   -3.847 closest distance to " O   HOH Z  39 " =    1.451
peak=   -3.839 closest distance to " O   ALA A  51 " =    1.302
peak=   -3.819 closest distance to " O   HOH Z 404 " =    1.120
peak=   -3.804 closest distance to " NE1 TRP A 179 " =    1.248
peak=   -3.801 closest distance to " OG ASER A 134 " =    1.012
peak=   -3.800 closest distance to " O   HOH Z  50 " =    1.643
peak=   -3.774 closest distance to " O   HOH Z  14 " =    1.347
peak=   -3.771 closest distance to " O   HOH Z 132 " =    0.714
peak=   -3.758 closest distance to " CG  GLU A 152 " =    2.715
peak=   -3.756 closest distance to " O   HOH Z 409 " =    3.137
peak=   -3.748 closest distance to " CZ  ARG A  36 " =    1.468
peak=   -3.747 closest distance to " O   HOH Z 198 " =    2.314
peak=   -3.722 closest distance to " CG  PRO A 163 " =    2.496
peak=   -3.721 closest distance to " O   HOH Z  52 " =    1.216
peak=   -3.707 closest distance to " O   HOH Z 415 " =    1.062
peak=   -3.705 closest distance to " O   HOH Z 266 " =    4.257
peak=   -3.703 closest distance to " CB  CYS A 201 " =    1.958
peak=   -3.702 closest distance to " O   HOH Z 163 " =    1.728
peak=   -3.700 closest distance to " CG  GLN A  88 " =    0.905
peak=   -3.690 closest distance to " CG1BVAL A  72 " =    1.862
peak=   -3.685 closest distance to " CE1 PHE A  16 " =    1.289
peak=   -3.677 closest distance to " O   HOH Z  65 " =    0.854
peak=   -3.663 closest distance to " OD2 ASP A 140 " =    1.360
peak=   -3.648 closest distance to " O   HOH Z  73 " =    1.534
peak=   -3.641 closest distance to " O   HOH Z 290 " =    1.124
peak=   -3.635 closest distance to " O   HOH Z 234 " =    4.676
peak=   -3.628 closest distance to " CB  ALA A 291 " =    2.045
peak=   -3.616 closest distance to " N   THR A 157 " =    1.553
peak=   -3.598 closest distance to " O   HOH Z 399 " =    1.604
peak=   -3.590 closest distance to " CG1BVAL A  72 " =    4.640
peak=   -3.581 closest distance to " CD2 LEU A 237 " =    2.613
peak=   -3.571 closest distance to " O   HOH Z   1 " =    3.706
peak=   -3.559 closest distance to " CD2 TRP A 179 " =    1.462
peak=   -3.550 closest distance to " CG  ASN A  60 " =    1.209
peak=   -3.549 closest distance to " CD2 TYR A 293 " =    1.922
peak=   -3.539 closest distance to " O   HOH Z 426 " =    1.471
peak=   -3.537 closest distance to " O   HOH Z 236 " =    2.255
peak=   -3.519 closest distance to " OG1 THR A 246 " =    1.517
peak=   -3.518 closest distance to " O   THR A  29 " =    1.823
peak=   -3.518 closest distance to " C   HIS A 108 " =    1.194
peak=   -3.509 closest distance to " CA  LEU A 143 " =    1.110
peak=   -3.502 closest distance to " NE2 GLN A 223 " =    1.452
peak=   -3.474 closest distance to " CB  ALA A 227 " =    2.222
peak=   -3.473 closest distance to " O   HOH Z 264 " =    1.097
peak=   -3.471 closest distance to " N   GLN A  58 " =    1.994
peak=   -3.471 closest distance to " N   ASN A  60 " =    1.189
peak=   -3.470 closest distance to " C   ASN A 285 " =    0.965
peak=   -3.464 closest distance to " O   ILE A  49 " =    1.587
peak=   -3.453 closest distance to " C   GLN A 205 " =    1.984
peak=   -3.443 closest distance to " O   HOH Z  93 " =    1.556
peak=   -3.437 closest distance to " O   SER A 146 " =    1.186
peak=   -3.436 closest distance to " O   HOH Z   4 " =    1.071
peak=   -3.433 closest distance to " CD  PRO A 198 " =    1.387
peak=   -3.429 closest distance to " O   SER A 245 " =    1.297
peak=   -3.427 closest distance to " O   ASN A 215 " =    1.709
peak=   -3.425 closest distance to " O   HOH Z 425 " =    0.893
peak=   -3.420 closest distance to " ND2 ASN A  60 " =    1.308
peak=   -3.415 closest distance to " CA  GLY A  98 " =    1.815
peak=   -3.405 closest distance to " O   LYS A  76 " =    1.083
peak=   -3.402 closest distance to " O   ALA A   1 " =    1.194
peak=   -3.396 closest distance to " OE2 GLU A 175 " =    1.249
peak=   -3.395 closest distance to " CG1 ILE A 234 " =    2.018
peak=   -3.386 closest distance to " CG  GLN A  73 " =    1.321
peak=   -3.382 closest distance to " O   HOH Z 231 " =    1.783
peak=   -3.372 closest distance to " OG BSER A 134 " =    1.547
peak=   -3.368 closest distance to " O   HOH Z 278 " =    1.379
peak=   -3.362 closest distance to " O   HOH Z 150 " =    2.634
peak=   -3.361 closest distance to " N   LYS A 119 " =    0.941
peak=   -3.360 closest distance to " O   SER A  22 " =    2.649
peak=   -3.355 closest distance to " O   HOH Z 137 " =    1.385
peak=   -3.355 closest distance to " O   HOH Z 135 " =    0.840
peak=   -3.355 closest distance to " O   HOH Z 109 " =    3.796
peak=   -3.353 closest distance to " CG BLYS A 290 " =    0.933
peak=   -3.347 closest distance to " CG  GLU A 277 " =    1.441
peak=   -3.346 closest distance to " O   GLN A 194 " =    1.191
peak=   -3.344 closest distance to " CD  GLN A  77 " =    1.201
peak=   -3.344 closest distance to " OG1 THR A 178 " =    1.005
peak=   -3.341 closest distance to " O   LYS A 119 " =    0.806
peak=   -3.340 closest distance to " O   HOH Z 197 " =    3.554
peak=   -3.337 closest distance to " O   HOH Z 410 " =    2.365
peak=   -3.337 closest distance to " O   HOH Z 313 " =    1.486
peak=   -3.333 closest distance to " O   HOH Z 126 " =    1.701
peak=   -3.329 closest distance to " CZ  PHE A  59 " =    1.501
peak=   -3.320 closest distance to " O   HOH Z 347 " =    1.029
peak=   -3.318 closest distance to " O   HOH Z 438 " =    1.034
peak=   -3.303 closest distance to " O   TRP A  70 " =    1.410
peak=   -3.302 closest distance to " O   GLY A  80 " =    2.555
peak=   -3.302 closest distance to " O   HOH Z 399 " =    0.754
peak=   -3.298 closest distance to " CB  VAL A 125 " =    1.456
peak=   -3.298 closest distance to " O   VAL A 189 " =    2.514
peak=   -3.288 closest distance to " OD1 ASN A 249 " =    1.515
peak=   -3.284 closest distance to " O   HOH Z 323 " =    1.959
peak=   -3.280 closest distance to " CG  LYS A 193 " =    2.379
peak=   -3.280 closest distance to " CD2 TYR A 116 " =    2.207
peak=   -3.274 closest distance to " CG2 THR A 221 " =    2.259
peak=   -3.273 closest distance to " N   HIS A 115 " =    1.991
peak=   -3.271 closest distance to " CB  ALA A 244 " =    2.181
peak=   -3.265 closest distance to " O   HOH Z 397 " =    1.602
peak=   -3.264 closest distance to " OG  SER A  32 " =    0.729
peak=   -3.264 closest distance to " OG  SER A   3 " =    1.088
peak=   -3.261 closest distance to " CD1 LEU A  96 " =    2.098
peak=   -3.256 closest distance to " O   SER A   3 " =    1.110
peak=   -3.246 closest distance to " O   HOH Z 359 " =    1.543
peak=   -3.244 closest distance to " CB  TRP A  85 " =    1.936
peak=   -3.242 closest distance to " CG2 THR A 294 " =    2.568
peak=   -3.237 closest distance to " CB  ASN A 285 " =    1.984
peak=   -3.237 closest distance to " CG  ASP A 140 " =    1.047
peak=   -3.236 closest distance to " CB  PRO A  90 " =    1.440
peak=   -3.234 closest distance to " N   GLN A  88 " =    1.602
peak=   -3.233 closest distance to " NE2 GLN A  55 " =    0.724
peak=   -3.231 closest distance to " CD1 LEU A   5 " =    2.398
peak=   -3.231 closest distance to " O   HOH Z 385 " =    2.400
peak=   -3.230 closest distance to " O   ALA A 158 " =    2.320
peak=   -3.228 closest distance to " O   GLY A  98 " =    2.139
peak=   -3.225 closest distance to " CB  ILE A 199 " =    2.613
peak=   -3.214 closest distance to " OD1 ASN A 301 " =    1.930
peak=   -3.212 closest distance to " CA  HIS A  86 " =    2.015
peak=   -3.210 closest distance to " O   ASP A 253 " =    1.460
peak=   -3.204 closest distance to " N   ASP A 171 " =    2.526
peak=   -3.204 closest distance to " NH2AARG A 275 " =    5.537
peak=   -3.203 closest distance to " O   HOH Z 159 " =    1.397
peak=   -3.202 closest distance to " ND2 ASN A 285 " =    2.073
peak=   -3.193 closest distance to " CB  TYR A  15 " =    2.056
peak=   -3.191 closest distance to " O   PRO A 198 " =    1.246
peak=   -3.191 closest distance to " O   HOH Z 377 " =    1.297
peak=   -3.191 closest distance to " O   HOH Z  75 " =    1.699
peak=   -3.190 closest distance to " CD2 LEU A 297 " =    1.321
peak=   -3.188 closest distance to " O   HOH Z 333 " =    1.540
peak=   -3.188 closest distance to " NH1 ARG A  56 " =    2.472
peak=   -3.184 closest distance to " O   HOH Z 246 " =    2.000
peak=   -3.182 closest distance to " O   HOH Z 336 " =    5.361
peak=   -3.177 closest distance to " O   HOH Z 435 " =    2.423
peak=   -3.172 closest distance to " ND2 ASN A  60 " =    4.146
peak=   -3.172 closest distance to " O   HOH Z 174 " =    3.190
peak=   -3.171 closest distance to " O   HOH Z  68 " =    1.441
peak=   -3.171 closest distance to " NH2 ARG A  79 " =    1.790
peak=   -3.167 closest distance to " O   HOH Z 274 " =    3.128
peak=   -3.167 closest distance to " CG  ARG A 139 " =    1.235
peak=   -3.166 closest distance to " O   HOH Z 413 " =    4.553
peak=   -3.161 closest distance to " OG  SER A 245 " =    1.500
peak=   -3.157 closest distance to " O   HOH Z 244 " =    1.456
peak=   -3.156 closest distance to " C   ASN A 285 " =    1.047
peak=   -3.154 closest distance to " N   ASN A 285 " =    1.046
peak=   -3.154 closest distance to " O   HOH Z 114 " =    4.713
peak=   -3.152 closest distance to " O   HOH Z 166 " =    1.016
peak=   -3.148 closest distance to " O   HOH Z 139 " =    2.328
peak=   -3.144 closest distance to " OG1 THR A 294 " =    2.335
peak=   -3.144 closest distance to " O   HOH Z 393 " =    3.460
peak=   -3.133 closest distance to " CB  LYS A 289 " =    2.412
peak=   -3.129 closest distance to " O   HOH Z 401 " =    1.116
peak=   -3.124 closest distance to " CA  GLY A 211 " =    1.423
peak=   -3.120 closest distance to " O   HOH Z 220 " =    1.425
peak=   -3.113 closest distance to " O   HOH Z 388 " =    2.068
peak=   -3.103 closest distance to " O   ASP A 272 " =    1.084
peak=   -3.097 closest distance to " O   HOH Z 300 " =    1.401
peak=   -3.089 closest distance to " O   HOH Z 179 " =    1.291
peak=   -3.076 closest distance to " O   HOH Z 292 " =    3.534
peak=   -3.065 closest distance to " O   HOH Z  97 " =    0.984
peak=   -3.061 closest distance to " N   LYS A 166 " =    1.721
peak=   -3.055 closest distance to " NH1 ARG A  36 " =    2.003
peak=   -3.049 closest distance to " O   HOH Z 125 " =    3.099
peak=   -3.021 closest distance to " O   SER A  62 " =    1.312
peak=   -2.940 closest distance to " CA  SER A  63 " =    0.868

================= 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    :  0.4780 0.4784   6.289718e+00   6.285078e+00
   1_bss:  0.4685 0.4675   6.285189e+00   6.273628e+00
   1_xyz:  0.4019 0.4336   6.192171e+00   6.234071e+00
   1_adp:  0.3693 0.4439   6.156534e+00   6.241276e+00
   1_occ:  0.3689 0.4439   6.155779e+00   6.240701e+00
   2_bss:  0.3687 0.4436   6.158602e+00   6.241531e+00
   2_xyz:  0.3272 0.4036   6.071677e+00   6.192966e+00
   2_adp:  0.3180 0.3991   6.057339e+00   6.183551e+00
   2_occ:  0.3179 0.3996   6.057458e+00   6.184105e+00
   3_bss:  0.3183 0.3996   6.057972e+00   6.184447e+00
   3_xyz:  0.2593 0.3346   5.880986e+00   6.048793e+00
   3_adp:  0.2334 0.3224   5.811022e+00   6.014493e+00
   3_occ:  0.2330 0.3231   5.811081e+00   6.015552e+00
   4_bss:  0.2332 0.3216   5.808405e+00   6.012584e+00
   4_xyz:  0.2031 0.2798   5.682310e+00   5.900926e+00
   4_adp:  0.1916 0.2599   5.626469e+00   5.844273e+00
   4_occ:  0.1913 0.2592   5.625336e+00   5.843113e+00
   5_bss:  0.1914 0.2583   5.624317e+00   5.841695e+00
   5_xyz:  0.1582 0.2145   5.443300e+00   5.675565e+00
   5_adp:  0.1446 0.2029   5.376965e+00   5.617362e+00
   5_occ:  0.1445 0.2026   5.376138e+00   5.615890e+00
   5_bss:  0.1449 0.2024   5.374836e+00   5.613560e+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:  0.342  28.252  -3.170   1.848   0.735   0.000   0.000   0.000
   1_xyz:  0.342  28.252  -3.170   1.848   0.735   0.000   0.000   0.000
   1_adp:  0.342  28.252  -3.170   1.848   0.735   0.000   0.000   0.000
   1_occ:  0.342  28.252  -3.170   1.848   0.735   0.000   0.000   0.000
   2_bss:  0.360  53.514  -0.862   1.155   0.559   0.000   0.000   0.000
   2_xyz:  0.360  53.514  -0.862   1.155   0.559   0.000   0.000   0.000
   2_adp:  0.360  53.514  -0.862   1.155   0.559   0.000   0.000   0.000
   2_occ:  0.360  53.514  -0.862   1.155   0.559   0.000   0.000   0.000
   3_bss:  0.358  61.481  -0.185   0.547   0.714   0.000   0.000   0.000
   3_xyz:  0.358  61.481  -0.185   0.547   0.714   0.000   0.000   0.000
   3_adp:  0.358  61.481  -0.185   0.547   0.714   0.000   0.000   0.000
   3_occ:  0.358  61.481  -0.185   0.547   0.714   0.000   0.000   0.000
   4_bss:  0.341  57.459  -0.150  -0.399   0.238  -0.000   0.000   0.000
   4_xyz:  0.341  57.459  -0.150  -0.399   0.238  -0.000   0.000   0.000
   4_adp:  0.341  57.459  -0.150  -0.399   0.238  -0.000   0.000   0.000
   4_occ:  0.341  57.459  -0.150  -0.399   0.238  -0.000   0.000   0.000
   5_bss:  0.321  45.689  -0.663  -0.987  -0.143  -0.000  -0.000  -0.000
   5_xyz:  0.321  45.689  -0.663  -0.987  -0.143  -0.000  -0.000  -0.000
   5_adp:  0.321  45.689  -0.663  -0.987  -0.143  -0.000  -0.000  -0.000
   5_occ:  0.321  45.689  -0.663  -0.987  -0.143  -0.000  -0.000  -0.000
   5_bss:  0.311  45.692  -0.835  -1.387  -0.408  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.902 0.4084  0.5697    75750.391
   1_bss:  57.685 0.4228  0.5886    71978.452
   1_xyz:  51.355 0.5025  0.6829    58383.804
   1_adp:  52.705 0.4851  0.6612    60561.854
   1_occ:  52.679 0.4855  0.6607    60480.231
   2_bss:  52.717 0.4851  0.6741    60790.740
   2_xyz:  46.843 0.5583  0.7752    49599.958
   2_adp:  45.568 0.5743  0.7877    47969.116
   2_occ:  45.616 0.5738  0.7865    48029.914
   3_bss:  45.574 0.5741  0.7886    47889.289
   3_xyz:  35.443 0.6955  0.9335    30598.736
   3_adp:  33.076 0.7230  0.9385    27653.247
   3_occ:  33.135 0.7223  0.9367    27684.438
   4_bss:  32.958 0.7240  0.9233    27319.709
   4_xyz:  27.965 0.7793  0.9716    20201.964
   4_adp:  25.474 0.8068  0.9802    17467.061
   4_occ:  25.434 0.8072  0.9801    17399.451
   5_bss:  25.381 0.8075  0.9618    17260.311
   5_xyz:  20.826 0.8530  0.9925    11754.050
   5_adp:  19.239 0.8690  0.9874    10419.051
   5_occ:  19.215 0.8692  0.9875    10390.323
   5_bss:  19.161 0.8696  0.9780    10315.852
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.9335e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.9335e-01
   1_xyz:   1.488  0.011  0.098 15.730  0.005  4.104   1.1323e-01
   1_adp:   1.488  0.011  0.098 15.730  0.005  4.104   1.1323e-01
   1_occ:   1.488  0.011  0.098 15.730  0.005  4.104   1.1323e-01
   2_bss:   1.488  0.011  0.098 15.730  0.005  4.104   1.1323e-01
   2_xyz:   1.142  0.008  0.082 14.702  0.005  4.104   7.8589e-02
   2_adp:   1.142  0.008  0.082 14.702  0.005  4.104   7.8589e-02
   2_occ:   1.142  0.008  0.082 14.702  0.005  4.104   7.8589e-02
   3_bss:   1.142  0.008  0.082 14.702  0.005  4.104   7.8589e-02
   3_xyz:   1.368  0.011  0.089 15.269  0.006  4.102   1.0607e-01
   3_adp:   1.368  0.011  0.089 15.269  0.006  4.102   1.0607e-01
   3_occ:   1.368  0.011  0.089 15.269  0.006  4.102   1.0607e-01
   4_bss:   1.368  0.011  0.089 15.269  0.006  4.102   1.0607e-01
   4_xyz:   0.919  0.006  0.063 14.415  0.003  4.111   5.4072e-02
   4_adp:   0.919  0.006  0.063 14.415  0.003  4.111   5.4072e-02
   4_occ:   0.919  0.006  0.063 14.415  0.003  4.111   5.4072e-02
   5_bss:   0.919  0.006  0.063 14.415  0.003  4.111   5.4072e-02
   5_xyz:   0.945  0.005  0.067 14.582  0.004  4.106   5.5113e-02
   5_adp:   0.945  0.005  0.067 14.582  0.004  4.106   5.5113e-02
   5_occ:   0.945  0.005  0.067 14.582  0.004  4.106   5.5113e-02
   5_bss:   0.945  0.005  0.067 14.582  0.004  4.106   5.5113e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.407   2.3827e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.407   2.3827e-01
   1_xyz:   9.466  0.107  0.412 87.673  0.046  1.934   7.8208e-02
   1_adp:   9.466  0.107  0.412 87.673  0.046  1.934   7.8208e-02
   1_occ:   9.466  0.107  0.412 87.673  0.046  1.934   7.8208e-02
   2_bss:   9.466  0.107  0.412 87.673  0.046  1.934   7.8208e-02
   2_xyz:   8.293  0.077  0.266 78.932  0.048  2.218   8.6082e-02
   2_adp:   8.293  0.077  0.266 78.932  0.048  2.218   8.6082e-02
   2_occ:   8.293  0.077  0.266 78.932  0.048  2.218   8.6082e-02
   3_bss:   8.293  0.077  0.266 78.932  0.048  2.218   8.6082e-02
   3_xyz:   9.414  0.055  0.348 78.798  0.057  2.176   1.4973e-01
   3_adp:   9.414  0.055  0.348 78.798  0.057  2.176   1.4973e-01
   3_occ:   9.414  0.055  0.348 78.798  0.057  2.176   1.4973e-01
   4_bss:   9.414  0.055  0.348 78.798  0.057  2.176   1.4973e-01
   4_xyz:   6.333  0.048  0.179 76.755  0.017  2.319   4.8923e-02
   4_adp:   6.333  0.048  0.179 76.755  0.017  2.319   4.8923e-02
   4_occ:   6.333  0.048  0.179 76.755  0.017  2.319   4.8923e-02
   5_bss:   6.333  0.048  0.179 76.755  0.017  2.319   4.8923e-02
   5_xyz:   7.065  0.035  0.230 78.315  0.030  2.290   3.9168e-02
   5_adp:   7.065  0.035  0.230 78.315  0.030  2.290   3.9168e-02
   5_occ:   7.065  0.035  0.230 78.315  0.030  2.290   3.9168e-02
   5_bss:   7.065  0.035  0.230 78.315  0.030  2.290   3.9168e-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: 123.12   0.00  19.30 104.59   0.00  16.67 123.12   0.00  33.61
   1_occ: 123.12   0.00  19.30 104.59   0.00  16.67 123.12   0.00  33.61
   2_bss: 123.12   0.00  19.30 104.59   0.00  16.67 123.12   0.00  33.61
   2_xyz: 123.12   0.00  19.30 104.59   0.00  16.67 123.12   0.00  33.61
   2_adp: 126.17   0.00  18.93 106.87   0.00  16.38 126.17   0.00  32.83
   2_occ: 126.17   0.00  18.93 106.87   0.00  16.38 126.17   0.00  32.83
   3_bss: 126.17   0.00  18.93 106.87   0.00  16.38 126.17   0.00  32.83
   3_xyz: 126.17   0.00  18.93 106.87   0.00  16.38 126.17   0.00  32.83
   3_adp: 132.59   0.00  19.31 120.35   0.00  14.95 132.59   0.66  43.02
   3_occ: 132.59   0.00  19.31 120.35   0.00  14.95 132.59   0.66  43.02
   4_bss: 132.59   0.00  19.31 120.35   0.00  14.95 132.59   0.66  43.02
   4_xyz: 132.59   0.00  19.31 120.35   0.00  14.95 132.59   0.66  43.02
   4_adp: 129.73   0.00  18.29 118.54   0.00  13.48 129.73   3.71  44.47
   4_occ: 129.73   0.00  18.29 118.54   0.00  13.48 129.73   3.71  44.47
   5_bss: 129.73   0.00  18.29 118.54   0.00  13.48 129.73   3.71  44.47
   5_xyz: 129.73   0.00  18.29 118.54   0.00  13.48 129.73   3.71  44.47
   5_adp: 124.26   0.00  18.01 122.90   0.00  12.51 124.26   4.71  47.97
   5_occ: 124.26   0.00  18.01 122.90   0.00  12.51 124.26   4.71  47.97
   5_bss: 124.26   0.00  18.01 122.91   0.00  12.51 124.26   4.72  47.97
------------------------------------------------------------------------
 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:    1.791    0.017    0.280
   1_adp:    1.791    0.017    0.280
   1_occ:    1.791    0.017    0.280
   2_bss:    1.791    0.017    0.280
   2_xyz:    1.486    0.037    0.426
   2_adp:    1.486    0.037    0.426
   2_occ:    1.486    0.037    0.426
   3_bss:    1.486    0.037    0.426
   3_xyz:    1.628    0.072    0.680
   3_adp:    1.628    0.072    0.680
   3_occ:    1.628    0.072    0.680
   4_bss:    1.628    0.072    0.680
   4_xyz:    1.589    0.066    0.735
   4_adp:    1.589    0.066    0.735
   4_occ:    1.589    0.066    0.735
   5_bss:    1.589    0.066    0.735
   5_xyz:    1.616    0.025    0.835
   5_adp:    1.616    0.025    0.835
   5_occ:    1.616    0.025    0.835
   5_bss:    1.616    0.025    0.835
------------------------------------------------------------------------

CPU time actual refinement: 349.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_727/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_727/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_727/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_727/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_727/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.33 
  Macro-tasks:
    bulk solvent and scale       = 38.69  
    individual site refinement   = 149.10 
    weights calculation          = 30.09  
    collect and process          = 6.51   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 224.49 
  Micro-tasks:
    mask                            = 3.07   
    f_calc                          = 115.45 
    alpha_beta                      = 8.12   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 122.83 
    fmodel                         = 6.45   
    r_factors                      = 0.17   
    phase_errors                   = 10.04  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 267.54 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.017 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    619 calls, 115.13 s
gradients_fft:          564 calls, 110.21 s

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

# Date 2008-01-16 Time 05:31:05 PST -0800 (1200490265.18 s)
Start R-work = 0.4780, R-free = 0.4784 (no bulk solvent and anisotropic scale)
Final R-work = 0.1601, R-free = 0.2155 (no bulk solvent and anisotropic scale)

Start R-work = 0.4685, R-free = 0.4675
Final R-work = 0.1449, R-free = 0.2024