# Date 2008-01-16 Time 03:42:36 PST -0800 (1200483756.35 s)
#phil __OFF__

Command line arguments: "../14.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31301
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 14

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 45.9914, 85.5261, 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: (68.4938, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6791 1.95061
Completeness in resolution range: 0.967932
Completeness with d_max=infinity: 0.96488

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6791
                             d_min =   1.9506

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6791 1.95061
Completeness in resolution range: 0.967932
Completeness with d_max=infinity: 0.96488

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6795 -  4.1733 [2137/2161]  1921   216  10.1%
  bin  2:  4.1733 -  3.3251 [2034/2053]  1835   199   9.8%
  bin  3:  3.3251 -  2.9085 [2020/2039]  1818   202  10.0%
  bin  4:  2.9085 -  2.6443 [1987/2017]  1781   206  10.4%
  bin  5:  2.6443 -  2.4557 [2001/2020]  1805   196   9.8%
  bin  6:  2.4557 -  2.3115 [1970/1995]  1774   196   9.9%
  bin  7:  2.3115 -  2.1961 [1958/1986]  1763   195  10.0%
  bin  8:  2.1961 -  2.1008 [1975/2011]  1776   199  10.1%
  bin  9:  2.1008 -  2.0202 [1925/1967]  1729   196  10.2%
  bin 10:  2.0202 -  1.9506 [1582/1989]  1428   154   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_14/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: 0.13 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:
        0.96 -     1.75: 9
        1.75 -     2.54: 104
        2.54 -     3.33: 4025
        3.33 -     4.11: 9752
        4.11 -     4.90: 15341
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  0.963 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.070 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.564 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.570 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.621 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29226 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_14/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_14/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 45.9914 85.5261 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 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4754   r_free= 0.4754   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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: 6.279033                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6795 -  4.6544 0.99   1385  153 0.3845 0.3745      6.5655      6.5584|
|  2:  4.6544 -  3.7140 0.99   1321  150 0.4098 0.3949      6.7987      6.7879|
|  3:  3.7140 -  3.2504 0.99   1310  144 0.4583 0.4469      6.7036      6.7648|
|  4:  3.2504 -  2.9558 0.99   1298  138 0.4609 0.4554      6.5405      6.5272|
|  5:  2.9558 -  2.7454 0.99   1279  145 0.5062 0.4576      6.3757       6.372|
|  6:  2.7454 -  2.5845 0.99   1291  148 0.5067 0.5310      6.2864      6.2328|
|  7:  2.5845 -  2.4557 0.99   1276  141 0.5081 0.5135      6.2435       6.182|
|  8:  2.4557 -  2.3492 0.98   1275  137 0.5236 0.5445      6.1922      6.2188|
|  9:  2.3492 -  2.2591 0.98   1248  144 0.5229 0.5076      6.1192      6.1647|
| 10:  2.2591 -  2.1814 0.99   1281  138 0.5241 0.5219      6.1262      6.1225|
| 11:  2.1814 -  2.1134 0.98   1252  140 0.5072 0.5793      6.0308      6.0656|
| 12:  2.1134 -  2.0532 0.97   1255  140 0.5090 0.5420      5.9706      6.0403|
| 13:  2.0532 -  1.9993 1.00   1251  138 0.5095 0.4854      5.8954      5.8362|
| 14:  1.9993 -  1.9506 0.71    908  103 0.5311 0.5145      5.8575      5.7855|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6795 -  4.6544  1385   153  0.68  35.99   0.82     0.73      77284.85|
|  2:  4.6544 -  3.7140  1321   150  0.68  36.98   0.92     0.80     115090.10|
|  3:  3.7140 -  3.2504  1310   144  0.57  46.68   0.93     0.76     125122.52|
|  4:  3.2504 -  2.9558  1298   138  0.47  54.13   0.95     0.66     113546.94|
|  5:  2.9558 -  2.7454  1279   145  0.39  60.72   0.89     0.57      88514.68|
|  6:  2.7454 -  2.5845  1291   148  0.36  62.54   0.88     0.52      75661.06|
|  7:  2.5845 -  2.4557  1276   141  0.32  66.24   0.93     0.46      70902.02|
|  8:  2.4557 -  2.3492  1275   137  0.29  68.08   0.93     0.44      65543.94|
|  9:  2.3492 -  2.2591  1248   144  0.28  68.83   0.90     0.43      60786.03|
| 10:  2.2591 -  2.1814  1281   138  0.32  66.38   0.97     0.48      52257.73|
| 11:  2.1814 -  2.1134  1252   140  0.30  67.56   0.96     0.47      49804.77|
| 12:  2.1134 -  2.0532  1255   140  0.29  68.16   1.00     0.46      44547.97|
| 13:  2.0532 -  1.9993  1251   138  0.28  69.30   1.00     0.45      39082.27|
| 14:  1.9993 -  1.9506   908   103  0.34  64.49   0.95     0.49      29904.85|
|alpha:            min =        0.43 max =            0.80 mean =         0.55|
|beta:             min =    29904.85 max =       125122.52 mean =     73307.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.34|
|phase err.(test): min =        0.00 max =           89.99 mean =        59.41|
|-----------------------------------------------------------------------------|

============================== 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 = 15.564196             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.434   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.896453              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.841   (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 |  0.963 -  1.357:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.357 -  1.751:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.751 -  2.144:       38 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.144 -  2.538:       66 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.538 -  2.932:     1594 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.932 -  3.325:     2431 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.325 -  3.719:     3888 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.719 -  4.113:     5864 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.113 -  4.506:     6765 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.506 -  4.900:     8576 |
|-----------------------------------------------------------------------------|
|-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 |        0.245 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.104    4.900  0.963 |       1.475 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.201)------------------------------------------|
|    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 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4754   r_free= 0.4754   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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: 6.279033                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4667   r_free= 0.4652   ksol= 0.34   Bsol= 8.66   scale= 0.935    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,1.48,-0.92,0.00,-0.00,-0.00); trace/3= 0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.272846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.900836             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.438   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.439792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.517   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4667      final r-factor (work) = 0.3516          |
| start r-factor (free) = 0.4652      final r-factor (free) = 0.3794          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.5630 = 11.90 * 0.50 * 6.2715 + 1.00 * 0.2447                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.8354 = 11.90 * 0.50 * 6.1653 + 1.00 * 0.1492                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3516      final r-factor (work) = 0.3153          |
| start r-factor (free) = 0.3794      final r-factor (free) = 0.3906          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8830 = 1.44 * 1.00 * 6.1653 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7019 = 1.44 * 1.00 * 6.0278 + 1.00 * 0.0231                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.201)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.44  19.71    None  None   None       |
|    all(noH): 2823   0      0.00    106.44  19.71    None  None   None       |
|    Sol.    : 438    0      2.00    106.44  39.71    None  None   None       |
|    Mac.    : 2385   0      0.00    86.44   16.04    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 -  10.644:  940   |   5:    53.218 -  63.862:   85        |
|      1:    10.644 -  21.287:  875   |   6:    63.862 -  74.506:   36        |
|      2:    21.287 -  31.931:  498   |   7:    74.506 -  85.150:   17        |
|      3:    31.931 -  42.575:  243   |   8:    85.150 -  95.793:    3        |
|      4:    42.575 -  53.218:  124   |   9:    95.793 - 106.437:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3153 r_free = 0.3906             target_work(ml) = 6.041         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3151 r_free = 0.3919             target_work(ml) = 6.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3151   r_free= 0.3919   ksol= 0.34   Bsol= 8.66   scale= 1.026    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,1.48,-0.92,0.00,-0.00,-0.00); trace/3= 0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.041435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3124   r_free= 0.3890   ksol= 0.33   Bsol= 34.57   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,0.19,-0.50,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.032242                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.276101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.930   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545880              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.429  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3124      final r-factor (work) = 0.2426          |
| start r-factor (free) = 0.3890      final r-factor (free) = 0.3191          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0880 = 9.28 * 0.50 * 6.0239 + 1.00 * 0.1490                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6407 = 9.28 * 0.50 * 5.9409 + 1.00 * 0.0863                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2426      final r-factor (work) = 0.2203          |
| start r-factor (free) = 0.3191      final r-factor (free) = 0.2906          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2654 = 0.55 * 1.00 * 5.9409 + 1.00 * 0.0223                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1768 = 0.55 * 1.00 * 5.7853 + 1.00 * 0.0187                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.201)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.25  18.45    None  None   None       |
|    all(noH): 2823   0      0.00    101.25  18.45    None  None   None       |
|    Sol.    : 438    0      5.05    101.25  40.49    None  None   None       |
|    Mac.    : 2385   0      0.00    91.05   14.40    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 -  10.125:  996   |   5:    50.626 -  60.752:   77        |
|      1:    10.125 -  20.251:  974   |   6:    60.752 -  70.877:   46        |
|      2:    20.251 -  30.376:  347   |   7:    70.877 -  81.002:   12        |
|      3:    30.376 -  40.501:  211   |   8:    81.002 -  91.128:    4        |
|      4:    40.501 -  50.626:  155   |   9:    91.128 - 101.253:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2203 r_free = 0.2906             target_work(ml) = 5.742         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2200 r_free = 0.2902             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2200   r_free= 0.2902   ksol= 0.33   Bsol= 34.57   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,0.19,-0.50,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.740905                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2203   r_free= 0.2890   ksol= 0.33   Bsol= 36.86   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-0.92,-0.52,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.738734                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.288531              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.122  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.209913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.119   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2203      final r-factor (work) = 0.1660          |
| start r-factor (free) = 0.2890      final r-factor (free) = 0.2213          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3851 = 5.29 * 0.50 * 5.7858 + 1.00 * 0.0859                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9525 = 5.29 * 0.50 * 5.6287 + 1.00 * 0.0687                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1660      final r-factor (work) = 0.1513          |
| start r-factor (free) = 0.2213      final r-factor (free) = 0.2036          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2060 = 0.21 * 1.00 * 5.6287 + 1.00 * 0.0245                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1504 = 0.21 * 1.00 * 5.4423 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.201)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.78   17.35    None  None   None       |
|    all(noH): 2823   0      0.00    94.78   17.35    None  None   None       |
|    Sol.    : 438    0      5.04    94.78   40.31    None  None   None       |
|    Mac.    : 2385   0      0.00    87.59   13.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.478:  889   |   5:    47.389 -  56.867:  111        |
|      1:     9.478 -  18.956: 1224   |   6:    56.867 -  66.345:   44        |
|      2:    18.956 -  28.434:  236   |   7:    66.345 -  75.823:   24        |
|      3:    28.434 -  37.911:  159   |   8:    75.823 -  85.300:    2        |
|      4:    37.911 -  47.389:  132   |   9:    85.300 -  94.778:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1513 r_free = 0.2036             target_work(ml) = 5.396         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1508 r_free = 0.2027             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1508   r_free= 0.2027   ksol= 0.33   Bsol= 36.86   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-0.92,-0.52,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.393532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1505   r_free= 0.2014   ksol= 0.32   Bsol= 36.86   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.08,-1.17,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.390159                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.790044              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.975  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.255726              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.161  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1505      final r-factor (work) = 0.1332          |
| start r-factor (free) = 0.2014      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9449 = 1.79 * 0.50 * 5.4481 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8303 = 1.79 * 0.50 * 5.3405 + 1.00 * 0.0504                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1332      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1778      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3737 = 0.26 * 1.00 * 5.3405 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3530 = 0.26 * 1.00 * 5.2582 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.201)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    89.71   17.30    None  None   None       |
|    all(noH): 2823   0      0.78    89.71   17.30    None  None   None       |
|    Sol.    : 438    0      3.26    89.71   41.34    None  None   None       |
|    Mac.    : 2385   0      0.78    87.44   12.88    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:     0.778 -   9.671:  972   |   5:    45.244 -  54.137:  102        |
|      1:     9.671 -  18.565: 1146   |   6:    54.137 -  63.030:   75        |
|      2:    18.565 -  27.458:  231   |   7:    63.030 -  71.923:   30        |
|      3:    27.458 -  36.351:  127   |   8:    71.923 -  80.817:   12        |
|      4:    36.351 -  45.244:  124   |   9:    80.817 -  89.710:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1732             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1284 r_free = 0.1728             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1728   ksol= 0.32   Bsol= 36.86   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.08,-1.17,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.243541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1728   ksol= 0.32   Bsol= 36.86   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.23,-1.20,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.243061                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.852146              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.255  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.375711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.283  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9193 = 1.85 * 0.50 * 5.2576 + 1.00 * 0.0504                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8763 = 1.85 * 0.50 * 5.2053 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9640 = 0.38 * 1.00 * 5.2053 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9524 = 0.38 * 1.00 * 5.1734 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.201)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.58    88.78   17.21    None  None   None       |
|    all(noH): 2823   0      0.58    88.78   17.21    None  None   None       |
|    Sol.    : 438    0      4.70    88.78   41.56    None  None   None       |
|    Mac.    : 2385   0      0.58    88.50   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.581 -   9.401:  916   |   5:    44.682 -  53.503:  104        |
|      1:     9.401 -  18.222: 1190   |   6:    53.503 -  62.323:   70        |
|      2:    18.222 -  27.042:  248   |   7:    62.323 -  71.143:   38        |
|      3:    27.042 -  35.862:  120   |   8:    71.143 -  79.964:   12        |
|      4:    35.862 -  44.682:  116   |   9:    79.964 -  88.784:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1161 r_free = 0.1629             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1628             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1628   ksol= 0.32   Bsol= 36.86   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.23,-1.20,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169152                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6795 -  4.6544 0.99   1385  153 0.1032 0.1321      5.4149       5.563|
|  2:  4.6544 -  3.7140 0.99   1321  150 0.0866 0.1177      5.4595      5.6525|
|  3:  3.7140 -  3.2504 0.99   1310  144 0.1127 0.1505       5.523       5.835|
|  4:  3.2504 -  2.9558 0.99   1298  138 0.1252 0.1717      5.4762      5.6645|
|  5:  2.9558 -  2.7454 0.99   1279  145 0.1385 0.1749      5.3458      5.5238|
|  6:  2.7454 -  2.5845 0.99   1291  148 0.1258 0.1817      5.2216      5.4523|
|  7:  2.5845 -  2.4557 0.99   1276  141 0.1277 0.1713      5.1695      5.3732|
|  8:  2.4557 -  2.3492 0.98   1275  137 0.1248 0.1671      5.1147      5.3488|
|  9:  2.3492 -  2.2591 0.98   1248  144 0.1217 0.1841      5.0543      5.3064|
| 10:  2.2591 -  2.1814 0.99   1281  138 0.1140 0.1784       4.979      5.2127|
| 11:  2.1814 -  2.1134 0.98   1252  140 0.1149 0.1898      4.9546      5.2886|
| 12:  2.1134 -  2.0532 0.97   1255  140 0.1229 0.1659      4.9298      5.2043|
| 13:  2.0532 -  1.9993 1.00   1251  138 0.1153 0.1976      4.8313      5.1202|
| 14:  1.9993 -  1.9506 0.71    908  103 0.1067 0.1720      4.6934      4.9443|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6795 -  4.6544  1385   153  0.94   9.54   0.99     0.96       7586.70|
|  2:  4.6544 -  3.7140  1321   150  0.95   8.29   1.04     1.02       9446.68|
|  3:  3.7140 -  3.2504  1310   144  0.93  11.72   1.05     1.04      11049.29|
|  4:  3.2504 -  2.9558  1298   138  0.92  13.63   1.02     1.02      10403.78|
|  5:  2.9558 -  2.7454  1279   145  0.90  15.58   1.01     0.99       8219.46|
|  6:  2.7454 -  2.5845  1291   148  0.90  15.69   0.99     0.97       6897.11|
|  7:  2.5845 -  2.4557  1276   141  0.90  16.17   1.00     0.96       6282.31|
|  8:  2.4557 -  2.3492  1275   137  0.91  15.21   1.01     1.00       5553.83|
|  9:  2.3492 -  2.2591  1248   144  0.91  15.57   1.02     0.99       5134.16|
| 10:  2.2591 -  2.1814  1281   138  0.90  15.84   1.01     0.97       4491.27|
| 11:  2.1814 -  2.1134  1252   140  0.90  16.56   1.01     0.99       4625.19|
| 12:  2.1134 -  2.0532  1255   140  0.90  16.47   1.03     1.01       4300.36|
| 13:  2.0532 -  1.9993  1251   138  0.90  16.32   1.02     1.01       3638.24|
| 14:  1.9993 -  1.9506   908   103  0.91  14.85   1.00     0.97       2704.89|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2704.89 max =        11049.29 mean =      6570.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.32|
|phase err.(test): min =        0.00 max =           89.89 mean =        13.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1627   ksol= 0.32   Bsol= 36.84   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.27,-1.15,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1627   ksol= 0.32   Bsol= 36.84   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.27,-1.15,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168518                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6795 -  4.6544 0.99   1385  153 0.1022 0.1306      5.3974      5.5504|
|  2:  4.6544 -  3.7140 0.99   1321  150 0.0886 0.1184      5.4694      5.6698|
|  3:  3.7140 -  3.2504 0.99   1310  144 0.1135 0.1498      5.5296      5.8327|
|  4:  3.2504 -  2.9558 0.99   1298  138 0.1254 0.1710      5.4765      5.6669|
|  5:  2.9558 -  2.7454 0.99   1279  145 0.1380 0.1741       5.347      5.5226|
|  6:  2.7454 -  2.5845 0.99   1291  148 0.1261 0.1818      5.2221       5.452|
|  7:  2.5845 -  2.4557 0.99   1276  141 0.1277 0.1721      5.1695      5.3786|
|  8:  2.4557 -  2.3492 0.98   1275  137 0.1244 0.1658       5.113      5.3431|
|  9:  2.3492 -  2.2591 0.98   1248  144 0.1215 0.1844      5.0519      5.3069|
| 10:  2.2591 -  2.1814 0.99   1281  138 0.1139 0.1786      4.9778      5.2144|
| 11:  2.1814 -  2.1134 0.98   1252  140 0.1148 0.1887      4.9531      5.2839|
| 12:  2.1134 -  2.0532 0.97   1255  140 0.1225 0.1652      4.9275      5.2021|
| 13:  2.0532 -  1.9993 1.00   1251  138 0.1155 0.1975      4.8305      5.1187|
| 14:  1.9993 -  1.9506 0.71    908  103 0.1066 0.1717      4.6946      4.9465|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6795 -  4.6544  1385   153  0.94   9.17   0.99     0.96       7266.88|
|  2:  4.6544 -  3.7140  1321   150  0.95   8.27   1.04     1.03       9425.73|
|  3:  3.7140 -  3.2504  1310   144  0.93  11.82   1.05     1.04      11260.47|
|  4:  3.2504 -  2.9558  1298   138  0.92  13.70   1.02     1.01      10445.54|
|  5:  2.9558 -  2.7454  1279   145  0.90  15.63   1.01     0.98       8251.01|
|  6:  2.7454 -  2.5845  1291   148  0.90  15.75   0.99     0.97       6930.23|
|  7:  2.5845 -  2.4557  1276   141  0.90  16.22   1.00     0.96       6295.59|
|  8:  2.4557 -  2.3492  1275   137  0.91  15.19   1.01     1.00       5545.07|
|  9:  2.3492 -  2.2591  1248   144  0.91  15.56   1.02     0.99       5119.32|
| 10:  2.2591 -  2.1814  1281   138  0.90  15.81   1.01     0.97       4476.06|
| 11:  2.1814 -  2.1134  1252   140  0.90  16.54   1.01     0.99       4615.04|
| 12:  2.1134 -  2.0532  1255   140  0.90  16.41   1.03     1.01       4276.96|
| 13:  2.0532 -  1.9993  1251   138  0.90  16.32   1.02     1.01       3631.04|
| 14:  1.9993 -  1.9506   908   103  0.91  14.90   1.00     0.97       2717.81|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2717.81 max =        11260.47 mean =      6563.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.31|
|phase err.(test): min =        0.00 max =           89.50 mean =        13.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.201)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.56    88.76   17.20    None  None   None       |
|    all(noH): 2823   0      0.56    88.76   17.20    None  None   None       |
|    Sol.    : 438    0      4.69    88.76   41.55    None  None   None       |
|    Mac.    : 2385   0      0.56    88.48   12.72    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:     0.562 -   9.383:  916   |   5:    44.664 -  53.484:  104        |
|      1:     9.383 -  18.203: 1190   |   6:    53.484 -  62.304:   70        |
|      2:    18.203 -  27.023:  248   |   7:    62.304 -  71.124:   38        |
|      3:    27.023 -  35.843:  120   |   8:    71.124 -  79.945:   12        |
|      4:    35.843 -  44.664:  116   |   9:    79.945 -  88.765:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.411 - 5.159
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 314
   mapped sites are within: 0.763 - 5.159

peak=    8.182 closest distance to " O   HOH Z 178 " =    1.147
peak=    7.021 closest distance to " O   HOH Z 385 " =    1.243
peak=    6.799 closest distance to " O   HOH Z 142 " =    2.022
peak=    6.500 closest distance to " O   HOH Z 130 " =    1.244
peak=    6.438 closest distance to " O   HOH Z 416 " =    1.664
peak=    6.411 closest distance to " O   HOH Z 375 " =    1.768
peak=    6.333 closest distance to " O   HOH Z  37 " =    1.551
peak=    6.226 closest distance to " O   HOH Z 236 " =    1.727
peak=    6.188 closest distance to " NE2 GLN A  11 " =    1.283
peak=    6.111 closest distance to " O   HOH Z 112 " =    1.774
peak=    5.822 closest distance to " CB  ARG A 275 " =    0.979
peak=    5.627 closest distance to " O   HOH Z 126 " =    2.053
peak=    5.622 closest distance to " O   HOH Z 193 " =    1.743
peak=    5.616 closest distance to " O   HOH Z 117 " =    1.401
peak=    5.479 closest distance to " O   HOH Z  65 " =    1.182
peak=    5.462 closest distance to " CG  PRO A  54 " =    1.312
peak=    5.386 closest distance to " NH2 ARG A  56 " =    2.033
peak=    5.364 closest distance to " O   HOH Z 124 " =    1.539
peak=    5.271 closest distance to " O   HOH Z 431 " =    1.304
peak=    5.231 closest distance to " O   HOH Z  52 " =    2.288
peak=    4.996 closest distance to " CG  PRO A 213 " =    1.337
peak=    4.983 closest distance to " O   HOH Z 287 " =    1.729
peak=    4.877 closest distance to " O   HOH Z 417 " =    1.692
peak=    4.864 closest distance to " O   HOH Z 213 " =    1.784
peak=    4.831 closest distance to " O   HOH Z 371 " =    2.003
peak=    4.763 closest distance to " O   HOH Z  78 " =    1.671
peak=    4.757 closest distance to " O   HOH Z 380 " =    1.740
peak=    4.730 closest distance to " NZ  LYS A 117 " =    2.990
peak=    4.691 closest distance to " O   HOH Z  24 " =    1.723
peak=    4.665 closest distance to " CB  PRO A  54 " =    1.004
peak=    4.663 closest distance to " CA  TYR A  30 " =    0.996
peak=    4.650 closest distance to " O   HOH Z 272 " =    1.811
peak=    4.572 closest distance to " O   HOH Z  92 " =    1.393
peak=    4.511 closest distance to " O   HOH Z  69 " =    1.128
peak=    4.483 closest distance to " CB  ASN A 148 " =    1.350
peak=    4.478 closest distance to " O   HOH Z 427 " =    2.256
peak=    4.453 closest distance to " O   HOH Z 371 " =    1.948
peak=    4.442 closest distance to " O   HOH Z 126 " =    1.472
peak=    4.397 closest distance to " O   HOH Z 232 " =    2.351
peak=    4.356 closest distance to " O   HOH Z  57 " =    2.334
peak=    4.339 closest distance to " O   HOH Z  97 " =    1.987
peak=    4.326 closest distance to " CB  SER A   3 " =    1.216
peak=    4.320 closest distance to " O   HOH Z 403 " =    1.843
peak=    4.314 closest distance to " O   SER A  87 " =    2.425
peak=    4.303 closest distance to " O   HOH Z 414 " =    1.324
peak=    4.287 closest distance to " O   HOH Z 427 " =    1.112
peak=    4.284 closest distance to " O   HOH Z 130 " =    2.250
peak=    4.264 closest distance to " CB  SER A  63 " =    1.238
peak=    4.250 closest distance to " CB  GLN A 223 " =    1.539
peak=    4.208 closest distance to " O   HOH Z 106 " =    2.552
peak=    4.194 closest distance to " O   HOH Z 423 " =    1.527
peak=    4.193 closest distance to " O   HOH Z 394 " =    1.607
peak=    4.183 closest distance to " O   HOH Z 166 " =    1.627
peak=    4.146 closest distance to " O   HOH Z 425 " =    1.975
peak=    4.112 closest distance to " O   HOH Z  49 " =    1.142
peak=    4.100 closest distance to " CG  GLN A  11 " =    2.054
peak=    4.098 closest distance to " O   HOH Z  11 " =    1.404
peak=    4.096 closest distance to " O   HOH Z  93 " =    2.060
peak=    4.095 closest distance to " O   HOH Z 298 " =    1.830
peak=    4.075 closest distance to " CG  PRO A  90 " =    1.217
peak=    4.067 closest distance to " O   HOH Z 132 " =    1.138
peak=    4.021 closest distance to " O   HOH Z 368 " =    3.568
peak=    4.018 closest distance to " O   HOH Z  61 " =    1.538
peak=    4.011 closest distance to " CB  THR A  31 " =    1.663
peak=    4.006 closest distance to " O   HOH Z 128 " =    1.986
peak=    3.981 closest distance to " O   HOH Z  44 " =    1.841
peak=    3.981 closest distance to " CE  LYS A 119 " =    1.190
peak=    3.978 closest distance to " CG  PRO A 243 " =    1.138
peak=    3.975 closest distance to " O   HOH Z 222 " =    2.370
peak=    3.975 closest distance to " O   HOH Z 425 " =    1.385
peak=    3.972 closest distance to " O   HOH Z 419 " =    2.056
peak=    3.966 closest distance to " CB  GLN A 183 " =    1.147
peak=    3.966 closest distance to " CB  GLU A 128 " =    1.093
peak=    3.965 closest distance to " CG2 VAL A 257 " =    0.931
peak=    3.960 closest distance to " O   HOH Z 227 " =    1.911
peak=    3.957 closest distance to " O   HOH Z 234 " =    3.417
peak=    3.953 closest distance to " O   HOH Z 211 " =    1.134
peak=    3.940 closest distance to " O   HOH Z  66 " =    2.133
peak=    3.935 closest distance to " CB  GLU A 152 " =    1.299
peak=    3.930 closest distance to " OG BSER A 164 " =    2.081
peak=    3.922 closest distance to " CG AARG A 275 " =    1.239
peak=    3.915 closest distance to " O   HOH Z  63 " =    1.569
peak=    3.891 closest distance to " O   HOH Z  32 " =    1.793
peak=    3.886 closest distance to " O   HOH Z 352 " =    1.315
peak=    3.886 closest distance to " O   HOH Z 146 " =    1.668
peak=    3.882 closest distance to " NH1BARG A 145 " =    1.355
peak=    3.879 closest distance to " CG  TRP A 179 " =    2.199
peak=    3.878 closest distance to " O   HOH Z   6 " =    2.182
peak=    3.878 closest distance to " O   HOH Z 289 " =    1.678
peak=    3.868 closest distance to " O   HOH Z  50 " =    1.727
peak=    3.840 closest distance to " CA  ALA A 299 " =    0.953
peak=    3.840 closest distance to " O   HOH Z 245 " =    1.331
peak=    3.829 closest distance to " O   HOH Z 378 " =    0.991
peak=    3.816 closest distance to " O   HOH Z 406 " =    1.484
peak=    3.808 closest distance to " O   HOH Z  69 " =    2.040
peak=    3.802 closest distance to " OE1 GLN A  55 " =    1.376
peak=    3.799 closest distance to " O   HOH Z 316 " =    2.985
peak=    3.795 closest distance to " O   HOH Z 250 " =    1.465
peak=    3.773 closest distance to " O   HOH Z 305 " =    3.559
peak=    3.758 closest distance to " CD  GLN A 194 " =    1.495
peak=    3.741 closest distance to " CB  ALA A 114 " =    1.437
peak=    3.737 closest distance to " O   HOH Z 434 " =    1.249
peak=    3.734 closest distance to " O   HOH Z 365 " =    1.634
peak=    3.727 closest distance to " CB  GLU A 277 " =    1.091
peak=    3.718 closest distance to " CB  ALA A   1 " =    1.063
peak=    3.717 closest distance to " O   HOH Z 130 " =    2.044
peak=    3.701 closest distance to " O   HOH Z 175 " =    1.957
peak=    3.684 closest distance to " O   HOH Z 212 " =    1.616
peak=    3.679 closest distance to " O   HOH Z  47 " =    1.575
peak=    3.673 closest distance to " O   HOH Z 302 " =    1.357
peak=    3.670 closest distance to " OD1 ASN A  69 " =    2.433
peak=    3.631 closest distance to " CB  VAL A 202 " =    1.593
peak=    3.629 closest distance to " O   HOH Z 257 " =    2.066
peak=    3.618 closest distance to " C   PRO A 198 " =    1.622
peak=    3.613 closest distance to " O   HOH Z 365 " =    2.462
peak=    3.601 closest distance to " O   HOH Z 104 " =    1.212
peak=    3.600 closest distance to " O   HOH Z 423 " =    1.920
peak=    3.599 closest distance to " O   HOH Z 189 " =    1.821
peak=    3.596 closest distance to " O   HOH Z 145 " =    1.243
peak=    3.596 closest distance to " O   HOH Z 327 " =    1.780
peak=    3.595 closest distance to " O   HOH Z 189 " =    1.812
peak=    3.594 closest distance to " O  BHOH Z  74 " =    1.353
peak=    3.593 closest distance to " O   HOH Z 326 " =    1.829
peak=    3.593 closest distance to " OG BSER A  99 " =    2.274
peak=    3.591 closest distance to " O   ALA A   1 " =    1.508
peak=    3.586 closest distance to " CB  SER A  26 " =    1.617
peak=    3.583 closest distance to " O   HOH Z 183 " =    1.835
peak=    3.582 closest distance to " O   HOH Z 299 " =    2.481
peak=    3.579 closest distance to " CG1 ILE A 120 " =    1.471
peak=    3.572 closest distance to " O   HOH Z 393 " =    1.484
peak=    3.571 closest distance to " O   HOH Z  43 " =    1.005
peak=    3.569 closest distance to " O   HOH Z 385 " =    3.568
peak=    3.558 closest distance to " CG  MET A 185 " =    1.464
peak=    3.543 closest distance to " O   HOH Z 345 " =    3.043
peak=    3.539 closest distance to " CB  TYR A 169 " =    0.778
peak=    3.534 closest distance to " CG  GLU A 277 " =    1.922
peak=    3.530 closest distance to " CB  TRP A 179 " =    1.115
peak=    3.527 closest distance to " N   TYR A  15 " =    1.171
peak=    3.517 closest distance to " ND2 ASN A 110 " =    1.858
peak=    3.515 closest distance to " O   HOH Z  43 " =    2.497
peak=    3.513 closest distance to " N   ALA A   1 " =    3.015
peak=    3.507 closest distance to " N   PHE A 130 " =    1.213
peak=    3.501 closest distance to " O   HOH Z 116 " =    2.354
peak=    3.495 closest distance to " O   HOH Z 389 " =    1.348
peak=    3.494 closest distance to " O   HOH Z 145 " =    2.320
peak=    3.485 closest distance to " O   HOH Z 173 " =    2.024
peak=    3.484 closest distance to " O   HOH Z 218 " =    2.154
peak=    3.479 closest distance to " N   GLU A   2 " =    1.319
peak=    3.475 closest distance to " O   HOH Z 313 " =    1.687
peak=    3.474 closest distance to " O   HOH Z 148 " =    1.683
peak=    3.472 closest distance to " O   HOH Z  28 " =    1.391
peak=    3.470 closest distance to " O   GLY A 147 " =    1.528
peak=    3.468 closest distance to " CB  SER A 276 " =    1.380
peak=    3.468 closest distance to " CA  ALA A  21 " =    1.214
peak=    3.451 closest distance to " CB  GLN A 278 " =    0.794
peak=    3.451 closest distance to " O   HOH Z 176 " =    1.770
peak=    3.447 closest distance to " ND2 ASN A 187 " =    1.475
peak=    3.445 closest distance to " CB  PHE A 130 " =    0.997
peak=    3.443 closest distance to " OG BSER A 210 " =    1.395
peak=    3.441 closest distance to " O   PRO A 198 " =    1.272
peak=    3.440 closest distance to " O   HOH Z 365 " =    1.708
peak=    3.437 closest distance to " CH2 TRP A  92 " =    2.074
peak=    3.430 closest distance to " O   HOH Z 111 " =    1.597
peak=    3.427 closest distance to " O   HOH Z 412 " =    1.681
peak=    3.427 closest distance to " CB  VAL A 265 " =    1.330
peak=    3.426 closest distance to " CG  LYS A 166 " =    1.507
peak=    3.423 closest distance to " O   HOH Z 424 " =    2.764
peak=    3.422 closest distance to " O   HOH Z 255 " =    1.795
peak=    3.420 closest distance to " O   HOH Z 139 " =    1.206
peak=    3.418 closest distance to " O   HOH Z 234 " =    1.945
peak=    3.417 closest distance to " O   HOH Z 368 " =    1.969
peak=    3.417 closest distance to " O   HOH Z 222 " =    1.242
peak=    3.416 closest distance to " O   HOH Z 207 " =    2.010
peak=    3.412 closest distance to " CB  TRP A 266 " =    1.214
peak=    3.407 closest distance to " O   HOH Z 188 " =    2.387
peak=    3.404 closest distance to " O   HOH Z 203 " =    1.583
peak=    3.401 closest distance to " CB  ARG A  79 " =    1.441
peak=    3.400 closest distance to " O   HOH Z 128 " =    1.953
peak=    3.393 closest distance to " O   HOH Z 128 " =    2.780
peak=    3.391 closest distance to " CG1 ILE A  33 " =    1.206
peak=    3.389 closest distance to " CA  PHE A 283 " =    1.302
peak=    3.388 closest distance to " O   HOH Z   9 " =    2.153
peak=    3.385 closest distance to " CB  ARG A 139 " =    1.037
peak=    3.384 closest distance to " CA  ASN A 215 " =    0.989
peak=    3.383 closest distance to " O   HOH Z 166 " =    1.842
peak=    3.381 closest distance to " OG1 THR A 246 " =    1.255
peak=    3.380 closest distance to " CB  SER A 216 " =    0.763
peak=    3.376 closest distance to " O   HOH Z 411 " =    3.659
peak=    3.373 closest distance to " CA  ASN A 127 " =    0.964
peak=    3.373 closest distance to " O   HOH Z 257 " =    1.265
peak=    3.368 closest distance to " CG  PRO A 198 " =    1.298
peak=    3.368 closest distance to " CG2 THR A 221 " =    1.316
peak=    3.367 closest distance to " O   HOH Z 413 " =    1.705
peak=    3.364 closest distance to " O   HOH Z 214 " =    2.304
peak=    3.361 closest distance to " CG  LEU A 101 " =    1.058
peak=    3.360 closest distance to " O   HOH Z 368 " =    2.595
peak=    3.358 closest distance to " NH1 ARG A  14 " =    1.112
peak=    3.354 closest distance to " O   HOH Z   7 " =    1.350
peak=    3.350 closest distance to " N   HIS A  86 " =    1.581
peak=    3.349 closest distance to " CA  ALA A 291 " =    0.900
peak=    3.342 closest distance to " O   HOH Z 144 " =    1.960
peak=    3.338 closest distance to " O   HOH Z 419 " =    1.538
peak=    3.337 closest distance to " O   HOH Z  51 " =    1.850
peak=    3.334 closest distance to " O   HOH Z 422 " =    2.595
peak=    3.332 closest distance to " CG  GLN A  77 " =    0.994
peak=    3.327 closest distance to " O   HOH Z 244 " =    1.842
peak=    3.327 closest distance to " O   HOH Z 362 " =    1.853
peak=    3.318 closest distance to " O   HOH Z 158 " =    1.361
peak=    3.316 closest distance to " NH2BARG A 145 " =    1.718
peak=    3.315 closest distance to " N   SER A  97 " =    0.934
peak=    3.310 closest distance to " O   HOH Z  43 " =    1.483
peak=    3.308 closest distance to " O   HOH Z  88 " =    2.583
peak=    3.304 closest distance to " CA  ALA A  84 " =    1.291
peak=    3.304 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.300 closest distance to " CG2 VAL A 232 " =    0.963
peak=    3.299 closest distance to " CB  ASN A 187 " =    1.122
peak=    3.296 closest distance to " O   HOH Z  44 " =    2.862
peak=    3.295 closest distance to " N   ALA A 256 " =    1.613
peak=    3.295 closest distance to " O   HOH Z 435 " =    1.825
peak=    3.292 closest distance to " CG  LYS A  76 " =    1.595
peak=    3.291 closest distance to " CD  LYS A 166 " =    1.356
peak=    3.291 closest distance to " O   HOH Z 109 " =    2.378
peak=    3.290 closest distance to " CG2 THR A 294 " =    1.653
peak=    3.288 closest distance to " O   HOH Z 108 " =    2.028
peak=    3.287 closest distance to " CE3 TRP A  85 " =    1.028
peak=    3.280 closest distance to " CG  LEU A 167 " =    1.264
peak=    3.280 closest distance to " O   HOH Z 227 " =    2.058
peak=    3.280 closest distance to " O   HOH Z  61 " =    1.714
peak=    3.278 closest distance to " O  BHOH Z  74 " =    1.458
peak=    3.278 closest distance to " O   HOH Z 291 " =    1.775
peak=    3.277 closest distance to " CB  ASN A 215 " =    0.986
peak=    3.277 closest distance to " NZ  LYS A 119 " =    2.573
peak=    3.275 closest distance to " O   HOH Z 153 " =    3.367
peak=    3.273 closest distance to " O   HOH Z 155 " =    1.725
peak=    3.272 closest distance to " CA  LEU A 101 " =    1.387
peak=    3.269 closest distance to " O   HOH Z 123 " =    1.282
peak=    3.267 closest distance to " O   HOH Z 194 " =    1.773
peak=    3.261 closest distance to " O   HOH Z 119 " =    4.306
peak=    3.256 closest distance to " CE BLYS A 290 " =    0.841
peak=    3.255 closest distance to " O   HOH Z   1 " =    1.691
peak=    3.253 closest distance to " CB  GLU A 277 " =    3.399
peak=    3.248 closest distance to " CA  ARG A 195 " =    1.517
peak=    3.248 closest distance to " O   HOH Z  64 " =    1.974
peak=    3.242 closest distance to " O   HOH Z 411 " =    1.581
peak=    3.238 closest distance to " O   HOH Z  59 " =    1.399
peak=    3.238 closest distance to " O   HOH Z 162 " =    2.142
peak=    3.237 closest distance to " O   HOH Z 222 " =    2.160
peak=    3.236 closest distance to " O   HOH Z 437 " =    1.734
peak=    3.236 closest distance to " CB  THR A 157 " =    0.988
peak=    3.231 closest distance to " CB  MET A 188 " =    1.546
peak=    3.230 closest distance to " CB  ALA A  21 " =    1.840
peak=    3.229 closest distance to " O   HOH Z 181 " =    2.153
peak=    3.228 closest distance to " CE  LYS A 166 " =    1.849
peak=    3.224 closest distance to " O   HOH Z 154 " =    1.847
peak=    3.223 closest distance to " O   HOH Z 419 " =    1.795
peak=    3.216 closest distance to " CB  ALA A  34 " =    1.102
peak=    3.216 closest distance to " OD1BASN A 224 " =    2.184
peak=    3.215 closest distance to " O   HOH Z 357 " =    1.729
peak=    3.215 closest distance to " O   HOH Z 365 " =    5.159
peak=    3.213 closest distance to " O   HOH Z  88 " =    2.567
peak=    3.212 closest distance to " O   HOH Z   1 " =    1.472
peak=    3.211 closest distance to " CB  HIS A 108 " =    0.868
peak=    3.208 closest distance to " CB  GLU A 175 " =    0.940
peak=    3.202 closest distance to " O   HOH Z 261 " =    2.003
peak=    3.201 closest distance to " O   HOH Z 344 " =    3.111
peak=    3.199 closest distance to " O   HOH Z 423 " =    2.031
peak=    3.196 closest distance to " CZ  PHE A  38 " =    1.249
peak=    3.195 closest distance to " O   HOH Z   9 " =    0.929
peak=    3.189 closest distance to " O   HOH Z  39 " =    1.122
peak=    3.189 closest distance to " O   HOH Z  88 " =    3.214
peak=    3.188 closest distance to " OG BSER A  99 " =    2.644
peak=    3.186 closest distance to " O   HOH Z 408 " =    1.487
peak=    3.181 closest distance to " O   HOH Z 104 " =    1.492
peak=    3.181 closest distance to " O   HOH Z 410 " =    1.709
peak=    3.181 closest distance to " O   HOH Z 283 " =    2.243
peak=    3.179 closest distance to " OG  SER A  62 " =    2.767
peak=    3.177 closest distance to " O   HOH Z  85 " =    1.428
peak=    3.174 closest distance to " CB  ALA A  84 " =    1.622
peak=    3.166 closest distance to " O   HOH Z 388 " =    1.930
peak=    3.166 closest distance to " NE2 GLN A  58 " =    3.845
peak=    3.157 closest distance to " O   HOH Z  58 " =    1.578
peak=    3.157 closest distance to " O   HOH Z 303 " =    1.677
peak=    3.155 closest distance to " CG2 ILE A  20 " =    1.196
peak=    3.152 closest distance to " O   HOH Z 218 " =    1.973
peak=    3.143 closest distance to " O   HOH Z  80 " =    2.029
peak=    3.139 closest distance to " CE  MET A  93 " =    1.473
peak=    3.139 closest distance to " CB  ARG A 190 " =    1.831
peak=    3.136 closest distance to " O   HOH Z  94 " =    1.826
peak=    3.129 closest distance to " ND2 ASN A 249 " =    0.895
peak=    3.128 closest distance to " O   HOH Z 379 " =    1.452
peak=    3.125 closest distance to " CB  ARG A 102 " =    0.806
peak=    3.122 closest distance to " O   HOH Z 435 " =    1.430
peak=    3.121 closest distance to " O   HOH Z  85 " =    1.927
peak=    3.116 closest distance to " O   HOH Z 156 " =    2.745
peak=    3.115 closest distance to " CD BLYS A 290 " =    1.234
peak=    3.110 closest distance to " CB  GLN A  88 " =    1.308
peak=    3.109 closest distance to " NH2AARG A 190 " =    1.846
peak=    3.107 closest distance to " CD2 TRP A 179 " =    1.246
peak=    3.105 closest distance to " CA  ALA A 233 " =    0.909
peak=    3.103 closest distance to " NH1AARG A 145 " =    1.107
peak=    3.099 closest distance to " CD1 ILE A 263 " =    1.497
peak=    3.093 closest distance to " O   HOH Z 247 " =    1.172
peak=    3.087 closest distance to " O   HOH Z   1 " =    4.260
peak=    3.083 closest distance to " O   HOH Z   3 " =    2.280
peak=    3.080 closest distance to " OG BSER A 258 " =    2.969
peak=    3.075 closest distance to " CA  ILE A  20 " =    0.795
peak=    3.065 closest distance to " O   HOH Z 145 " =    1.783
peak=    3.059 closest distance to " CG  LYS A 119 " =    1.073
peak=    3.044 closest distance to " O   HOH Z 412 " =    1.959
peak=    3.040 closest distance to " CA  ASP A 140 " =    1.466
peak=    3.016 closest distance to " O   HOH Z 346 " =    1.455

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.307 - 5.204
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 199
   mapped sites are within: 0.760 - 5.204

peak=   -5.018 closest distance to " O   HOH Z 385 " =    0.985
peak=   -4.694 closest distance to " O   PRO A 198 " =    1.223
peak=   -4.683 closest distance to " O   HOH Z 290 " =    1.075
peak=   -4.367 closest distance to " OG BSER A 134 " =    1.395
peak=   -4.348 closest distance to " OD2 ASP A 191 " =    1.378
peak=   -4.345 closest distance to " CG2 ILE A  20 " =    2.814
peak=   -4.331 closest distance to " CD  ARG A 156 " =    2.083
peak=   -4.282 closest distance to " N   GLN A  58 " =    1.800
peak=   -4.257 closest distance to " O   SER A 135 " =    1.539
peak=   -4.211 closest distance to " O   SER A  95 " =    1.322
peak=   -4.181 closest distance to " O   HOH Z 372 " =    2.592
peak=   -4.173 closest distance to " O   VAL A  67 " =    2.649
peak=   -4.060 closest distance to " O   HOH Z  65 " =    0.855
peak=   -4.023 closest distance to " O   ALA A 161 " =    1.732
peak=   -3.989 closest distance to " O   HOH Z 198 " =    1.646
peak=   -3.954 closest distance to " O   HOH Z  13 " =    1.568
peak=   -3.928 closest distance to " C   HIS A 108 " =    1.231
peak=   -3.914 closest distance to " CD2 LEU A 237 " =    2.270
peak=   -3.914 closest distance to " OG  SER A   3 " =    1.486
peak=   -3.908 closest distance to " O   HOH Z  60 " =    1.592
peak=   -3.900 closest distance to " OXT GLY A 302 " =    2.797
peak=   -3.883 closest distance to " CA  GLY A  98 " =    1.784
peak=   -3.872 closest distance to " CE  LYS A  76 " =    2.936
peak=   -3.867 closest distance to " O   HOH Z 407 " =    2.573
peak=   -3.853 closest distance to " CB  ALA A 291 " =    2.082
peak=   -3.838 closest distance to " O   HOH Z 250 " =    1.294
peak=   -3.820 closest distance to " O   HOH Z 429 " =    1.930
peak=   -3.807 closest distance to " CD1 LEU A 255 " =    2.818
peak=   -3.793 closest distance to " CB  GLN A  55 " =    1.356
peak=   -3.777 closest distance to " OD2 ASP A 171 " =    1.953
peak=   -3.760 closest distance to " OG  SER A 245 " =    1.341
peak=   -3.751 closest distance to " CZ  PHE A  59 " =    1.298
peak=   -3.727 closest distance to " CA  GLY A 133 " =    2.062
peak=   -3.712 closest distance to " CA  GLY A  23 " =    1.655
peak=   -3.710 closest distance to " O   SER A  22 " =    2.319
peak=   -3.710 closest distance to " O   HOH Z  79 " =    1.218
peak=   -3.675 closest distance to " OG  SER A  97 " =    2.135
peak=   -3.674 closest distance to " O   HOH Z 388 " =    1.945
peak=   -3.655 closest distance to " OD2 ASP A  50 " =    1.540
peak=   -3.645 closest distance to " O   HOH Z 435 " =    2.960
peak=   -3.633 closest distance to " CZ  PHE A  38 " =    2.705
peak=   -3.631 closest distance to " O   HOH Z 313 " =    1.635
peak=   -3.616 closest distance to " CG  PHE A 283 " =    2.599
peak=   -3.616 closest distance to " CD  GLN A  88 " =    0.904
peak=   -3.614 closest distance to " CD1 ILE A 239 " =    2.331
peak=   -3.606 closest distance to " CD  ARG A  14 " =    3.080
peak=   -3.596 closest distance to " C   ASN A 285 " =    2.046
peak=   -3.595 closest distance to " O   HOH Z 351 " =    1.613
peak=   -3.592 closest distance to " O   HOH Z 185 " =    1.945
peak=   -3.584 closest distance to " O   HOH Z 412 " =    5.204
peak=   -3.580 closest distance to " ND2 ASN A 209 " =    1.927
peak=   -3.576 closest distance to " O   HOH Z 130 " =    2.213
peak=   -3.574 closest distance to " O   HOH Z  69 " =    1.791
peak=   -3.574 closest distance to " O   HOH Z 263 " =    3.071
peak=   -3.573 closest distance to " O   HOH Z 131 " =    4.089
peak=   -3.562 closest distance to " OG  SER A  97 " =    1.539
peak=   -3.562 closest distance to " O   SER A   3 " =    1.127
peak=   -3.560 closest distance to " O   HOH Z 423 " =    2.537
peak=   -3.560 closest distance to " N   GLN A 122 " =    1.356
peak=   -3.558 closest distance to " O   ILE A  49 " =    1.574
peak=   -3.553 closest distance to " O   HOH Z 234 " =    3.802
peak=   -3.550 closest distance to " O   HOH Z 103 " =    1.749
peak=   -3.548 closest distance to " O   HOH Z 147 " =    1.374
peak=   -3.544 closest distance to " CZ3 TRP A 123 " =    1.684
peak=   -3.535 closest distance to " CG  MET A  93 " =    2.250
peak=   -3.518 closest distance to " O   HOH Z  88 " =    1.634
peak=   -3.517 closest distance to " OG  SER A  63 " =    1.378
peak=   -3.516 closest distance to " OD1 ASN A 148 " =    1.591
peak=   -3.515 closest distance to " O   ALA A 180 " =    1.027
peak=   -3.513 closest distance to " O   HOH Z  11 " =    1.787
peak=   -3.492 closest distance to " O   PRO A 198 " =    1.144
peak=   -3.491 closest distance to " CG  GLN A  58 " =    1.313
peak=   -3.481 closest distance to " CG1 VAL A 112 " =    2.925
peak=   -3.473 closest distance to " O   PHE A 218 " =    1.427
peak=   -3.473 closest distance to " CB  PHE A 192 " =    1.790
peak=   -3.466 closest distance to " O   ALA A  10 " =    1.802
peak=   -3.455 closest distance to " N   ALA A 248 " =    1.648
peak=   -3.452 closest distance to " C   ILE A 239 " =    2.042
peak=   -3.452 closest distance to " O   HOH Z 422 " =    1.363
peak=   -3.449 closest distance to " O   VAL A 189 " =    2.407
peak=   -3.447 closest distance to " O   HOH Z 387 " =    2.327
peak=   -3.445 closest distance to " OG  SER A  87 " =    1.252
peak=   -3.444 closest distance to " CB  SER A 210 " =    1.296
peak=   -3.439 closest distance to " O   HOH Z 100 " =    1.246
peak=   -3.438 closest distance to " CB  ALA A 114 " =    2.454
peak=   -3.437 closest distance to " C   ALA A 158 " =    1.496
peak=   -3.428 closest distance to " N   THR A 157 " =    1.444
peak=   -3.421 closest distance to " O   HOH Z 211 " =    1.768
peak=   -3.421 closest distance to " O   HOH Z 427 " =    1.756
peak=   -3.413 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.407 closest distance to " O   ASP A 231 " =    2.403
peak=   -3.401 closest distance to " O   HOH Z  28 " =    2.135
peak=   -3.396 closest distance to " CG1 VAL A 230 " =    1.883
peak=   -3.391 closest distance to " OG  SER A  87 " =    1.899
peak=   -3.389 closest distance to " CA  GLY A 203 " =    2.382
peak=   -3.389 closest distance to " CD  GLU A 236 " =    1.021
peak=   -3.374 closest distance to " O   HOH Z 298 " =    1.262
peak=   -3.374 closest distance to " O   PHE A  59 " =    2.141
peak=   -3.369 closest distance to " O   THR A 235 " =    1.412
peak=   -3.357 closest distance to " NH2 ARG A  79 " =    1.993
peak=   -3.354 closest distance to " O   HOH Z 193 " =    1.540
peak=   -3.354 closest distance to " CB  ALA A  43 " =    2.156
peak=   -3.352 closest distance to " O   ALA A  51 " =    1.106
peak=   -3.343 closest distance to " O   HOH Z 137 " =    1.469
peak=   -3.341 closest distance to " NE  ARG A  36 " =    1.851
peak=   -3.338 closest distance to " CB  TYR A  15 " =    2.091
peak=   -3.336 closest distance to " CG  GLU A 152 " =    1.121
peak=   -3.334 closest distance to " O   HOH Z 438 " =    0.931
peak=   -3.330 closest distance to " O   PRO A 163 " =    1.078
peak=   -3.327 closest distance to " CB  PHE A  38 " =    2.780
peak=   -3.327 closest distance to " N   VAL A  72 " =    1.603
peak=   -3.325 closest distance to " ND2 ASN A  45 " =    1.094
peak=   -3.325 closest distance to " O   HOH Z 298 " =    2.484
peak=   -3.319 closest distance to " CB  ASN A  39 " =    2.243
peak=   -3.318 closest distance to " O   HOH Z 165 " =    2.298
peak=   -3.308 closest distance to " OD1 ASP A 171 " =    1.551
peak=   -3.308 closest distance to " CD2 TYR A 293 " =    1.874
peak=   -3.295 closest distance to " OE1 GLN A 205 " =    1.162
peak=   -3.295 closest distance to " O   HOH Z 377 " =    0.786
peak=   -3.293 closest distance to " O   HOH Z 421 " =    2.658
peak=   -3.293 closest distance to " CE  MET A 105 " =    2.389
peak=   -3.292 closest distance to " OG1 THR A  82 " =    1.769
peak=   -3.289 closest distance to " O   TRP A  70 " =    1.420
peak=   -3.287 closest distance to " O   HOH Z  97 " =    1.242
peak=   -3.286 closest distance to " CG  GLN A  11 " =    2.026
peak=   -3.281 closest distance to " C   ALA A 114 " =    2.105
peak=   -3.281 closest distance to " ND2 ASN A  39 " =    1.284
peak=   -3.280 closest distance to " O   HOH Z 213 " =    1.301
peak=   -3.277 closest distance to " O   HOH Z 406 " =    1.163
peak=   -3.276 closest distance to " O   HOH Z 266 " =    4.636
peak=   -3.272 closest distance to " O   HOH Z 314 " =    1.598
peak=   -3.270 closest distance to " O   ARG A 219 " =    1.801
peak=   -3.266 closest distance to " CG  LEU A  83 " =    2.041
peak=   -3.258 closest distance to " CE2 TYR A  30 " =    2.730
peak=   -3.251 closest distance to " O   HOH Z 337 " =    1.539
peak=   -3.251 closest distance to " OE1 GLN A 183 " =    1.323
peak=   -3.247 closest distance to " O   HOH Z 134 " =    3.226
peak=   -3.246 closest distance to " CB  ASP A 132 " =    2.369
peak=   -3.243 closest distance to " CG  GLN A 223 " =    1.379
peak=   -3.240 closest distance to " O   HOH Z 385 " =    2.228
peak=   -3.238 closest distance to " C   GLN A 205 " =    1.892
peak=   -3.236 closest distance to " OE1 GLU A 277 " =    2.160
peak=   -3.232 closest distance to " O   GLN A 240 " =    1.845
peak=   -3.232 closest distance to " O   ILE A 120 " =    1.521
peak=   -3.229 closest distance to " O   HOH Z 231 " =    2.121
peak=   -3.227 closest distance to " CG  MET A 105 " =    0.831
peak=   -3.226 closest distance to " CG  ARG A 219 " =    1.953
peak=   -3.226 closest distance to " CG  ASP A 231 " =    0.760
peak=   -3.221 closest distance to " O   HOH Z 236 " =    2.106
peak=   -3.216 closest distance to " NH2 ARG A  66 " =    4.822
peak=   -3.215 closest distance to " C   ASP A 124 " =    1.962
peak=   -3.211 closest distance to " O   HOH Z 359 " =    3.344
peak=   -3.210 closest distance to " O   HOH Z 198 " =    1.607
peak=   -3.209 closest distance to " O   HOH Z 142 " =    0.801
peak=   -3.206 closest distance to " CB  ALA A   7 " =    1.903
peak=   -3.204 closest distance to " N   TYR A 169 " =    1.046
peak=   -3.200 closest distance to " NE2 GLN A 278 " =    1.675
peak=   -3.198 closest distance to " OD2 ASP A 270 " =    1.281
peak=   -3.198 closest distance to " O   LEU A 300 " =    2.448
peak=   -3.193 closest distance to " N   ALA A 226 " =    1.936
peak=   -3.193 closest distance to " NH1 ARG A  56 " =    2.321
peak=   -3.189 closest distance to " O   VAL A 174 " =    2.171
peak=   -3.187 closest distance to " CG2 THR A 178 " =    1.828
peak=   -3.186 closest distance to " O   HOH Z 377 " =    1.072
peak=   -3.184 closest distance to " O   ASP A 162 " =    2.118
peak=   -3.182 closest distance to " N   SER A 276 " =    1.091
peak=   -3.179 closest distance to " CG2 ILE A  49 " =    2.675
peak=   -3.175 closest distance to " CD1 ILE A 151 " =    2.325
peak=   -3.174 closest distance to " CB  ASP A  27 " =    2.250
peak=   -3.172 closest distance to " O   HOH Z 256 " =    1.278
peak=   -3.165 closest distance to " OG ASER A 134 " =    1.201
peak=   -3.160 closest distance to " O   HOH Z  90 " =    2.355
peak=   -3.160 closest distance to " O   HOH Z 231 " =    1.541
peak=   -3.160 closest distance to " OG1 THR A 246 " =    1.360
peak=   -3.157 closest distance to " NE2 GLN A  55 " =    0.816
peak=   -3.156 closest distance to " NH1BARG A 145 " =    3.441
peak=   -3.153 closest distance to " O   HOH Z 385 " =    1.723
peak=   -3.142 closest distance to " O   HOH Z 351 " =    1.705
peak=   -3.135 closest distance to " CG  ARG A 219 " =    2.307
peak=   -3.131 closest distance to " CB  ALA A  51 " =    1.858
peak=   -3.127 closest distance to " O   HOH Z 389 " =    1.289
peak=   -3.121 closest distance to " OG  SER A  22 " =    4.335
peak=   -3.115 closest distance to " O   HOH Z 348 " =    2.194
peak=   -3.114 closest distance to " O   TRP A  92 " =    1.610
peak=   -3.108 closest distance to " O   HOH Z 197 " =    2.899
peak=   -3.108 closest distance to " O   HOH Z  60 " =    2.067
peak=   -3.104 closest distance to " O   HOH Z  88 " =    1.967
peak=   -3.100 closest distance to " OD1 ASN A 170 " =    2.340
peak=   -3.087 closest distance to " OG BSER A 134 " =    1.630
peak=   -3.076 closest distance to " O   HOH Z 122 " =    1.985
peak=   -3.065 closest distance to " CG BARG A 275 " =    0.947
peak=   -3.059 closest distance to " ND2 ASN A  45 " =    1.574
peak=   -3.055 closest distance to " O   HOH Z 211 " =    1.388
peak=   -3.040 closest distance to " CG  GLN A 278 " =    1.862
peak=   -3.034 closest distance to " CG  GLN A  58 " =    0.938

================= 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    :  0.4754 0.4754   6.279033e+00   6.276303e+00
   1_bss:  0.4667 0.4652   6.272846e+00   6.260744e+00
   1_xyz:  0.3516 0.3794   6.092675e+00   6.141873e+00
   1_adp:  0.3153 0.3906   6.041074e+00   6.163182e+00
   1_occ:  0.3151 0.3919   6.041435e+00   6.164417e+00
   2_bss:  0.3124 0.3890   6.032242e+00   6.158609e+00
   2_xyz:  0.2426 0.3191   5.821626e+00   6.003551e+00
   2_adp:  0.2203 0.2906   5.742301e+00   5.932552e+00
   2_occ:  0.2200 0.2902   5.740905e+00   5.931368e+00
   3_bss:  0.2203 0.2890   5.738734e+00   5.928407e+00
   3_xyz:  0.1660 0.2213   5.486681e+00   5.704491e+00
   3_adp:  0.1513 0.2036   5.396140e+00   5.618455e+00
   3_occ:  0.1508 0.2027   5.393532e+00   5.615446e+00
   4_bss:  0.1505 0.2014   5.390159e+00   5.611713e+00
   4_xyz:  0.1332 0.1778   5.275348e+00   5.488704e+00
   4_adp:  0.1285 0.1732   5.244258e+00   5.459929e+00
   4_occ:  0.1284 0.1728   5.243541e+00   5.458653e+00
   5_bss:  0.1283 0.1728   5.243061e+00   5.458248e+00
   5_xyz:  0.1181 0.1645   5.181331e+00   5.413015e+00
   5_adp:  0.1161 0.1629   5.169539e+00   5.405170e+00
   5_occ:  0.1160 0.1628   5.169152e+00   5.404584e+00
   5_bss:  0.1163 0.1627   5.168518e+00   5.404476e+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   8.660  -0.198   1.481  -0.923   0.000  -0.000  -0.000
   1_xyz:  0.342   8.660  -0.198   1.481  -0.923   0.000  -0.000  -0.000
   1_adp:  0.342   8.660  -0.198   1.481  -0.923   0.000  -0.000  -0.000
   1_occ:  0.342   8.660  -0.198   1.481  -0.923   0.000  -0.000  -0.000
   2_bss:  0.331  34.573  -1.229   0.189  -0.497   0.000  -0.000  -0.000
   2_xyz:  0.331  34.573  -1.229   0.189  -0.497   0.000  -0.000  -0.000
   2_adp:  0.331  34.573  -1.229   0.189  -0.497   0.000  -0.000  -0.000
   2_occ:  0.331  34.573  -1.229   0.189  -0.497   0.000  -0.000  -0.000
   3_bss:  0.331  36.856  -1.745  -0.916  -0.517  -0.000  -0.000  -0.000
   3_xyz:  0.331  36.856  -1.745  -0.916  -0.517  -0.000  -0.000  -0.000
   3_adp:  0.331  36.856  -1.745  -0.916  -0.517  -0.000  -0.000  -0.000
   3_occ:  0.331  36.856  -1.745  -0.916  -0.517  -0.000  -0.000  -0.000
   4_bss:  0.322  36.856  -2.664  -2.081  -1.166  -0.000  -0.000  -0.000
   4_xyz:  0.322  36.856  -2.664  -2.081  -1.166  -0.000  -0.000  -0.000
   4_adp:  0.322  36.856  -2.664  -2.081  -1.166  -0.000  -0.000  -0.000
   4_occ:  0.322  36.856  -2.664  -2.081  -1.166  -0.000  -0.000  -0.000
   5_bss:  0.317  36.856  -2.798  -2.229  -1.199  -0.000  -0.000  -0.000
   5_xyz:  0.317  36.856  -2.798  -2.229  -1.199  -0.000  -0.000  -0.000
   5_adp:  0.317  36.856  -2.798  -2.229  -1.199  -0.000  -0.000  -0.000
   5_occ:  0.317  36.856  -2.798  -2.229  -1.199  -0.000  -0.000  -0.000
   5_bss:  0.317  36.838  -2.787  -2.271  -1.145  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.347 0.4022  0.5549    73298.288
   1_bss:  58.045 0.4172  0.5781    69262.593
   1_xyz:  40.998 0.6316  0.8460    41539.700
   1_adp:  42.978 0.6070  0.8224    45110.232
   1_occ:  43.107 0.6054  0.8193    45360.891
   2_bss:  42.496 0.6123  0.8143    44055.891
   2_xyz:  32.836 0.7249  0.9508    26742.858
   2_adp:  29.009 0.7687  0.9800    22025.881
   2_occ:  28.941 0.7694  0.9800    21914.653
   3_bss:  28.751 0.7713  0.9626    21614.415
   3_xyz:  21.452 0.8473  1.0149    12545.447
   3_adp:  19.094 0.8707  1.0209    10489.884
   3_occ:  19.017 0.8713  1.0209    10388.321
   4_bss:  18.873 0.8724  0.9873    10224.413
   4_xyz:  16.076 0.8977  0.9993     7822.652
   4_adp:  15.397 0.9038  0.9986     7410.450
   4_occ:  15.384 0.9039  0.9985     7385.645
   5_bss:  15.371 0.9040  0.9946     7374.190
   5_xyz:  14.501 0.9110  0.9975     6673.535
   5_adp:  14.292 0.9129  0.9940     6581.293
   5_occ:  14.284 0.9130  0.9939     6569.436
   5_bss:  14.272 0.9130  0.9935     6562.157
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.104   2.4467e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.104   2.4467e-01
   1_xyz:   1.599  0.013  0.107 15.510  0.007  4.101   1.4921e-01
   1_adp:   1.599  0.013  0.107 15.510  0.007  4.101   1.4921e-01
   1_occ:   1.599  0.013  0.107 15.510  0.007  4.101   1.4921e-01
   2_bss:   1.599  0.013  0.107 15.510  0.007  4.101   1.4921e-01
   2_xyz:   1.264  0.008  0.089 14.984  0.005  4.109   8.6285e-02
   2_adp:   1.264  0.008  0.089 14.984  0.005  4.109   8.6285e-02
   2_occ:   1.264  0.008  0.089 14.984  0.005  4.109   8.6285e-02
   3_bss:   1.264  0.008  0.089 14.984  0.005  4.109   8.6285e-02
   3_xyz:   1.098  0.008  0.074 14.806  0.004  4.108   6.8680e-02
   3_adp:   1.098  0.008  0.074 14.806  0.004  4.108   6.8680e-02
   3_occ:   1.098  0.008  0.074 14.806  0.004  4.108   6.8680e-02
   4_bss:   1.098  0.008  0.074 14.806  0.004  4.108   6.8680e-02
   4_xyz:   0.904  0.005  0.063 14.484  0.004  4.106   5.0433e-02
   4_adp:   0.904  0.005  0.063 14.484  0.004  4.106   5.0433e-02
   4_occ:   0.904  0.005  0.063 14.484  0.004  4.106   5.0433e-02
   5_bss:   0.904  0.005  0.063 14.484  0.004  4.106   5.0433e-02
   5_xyz:   0.960  0.005  0.067 14.597  0.004  4.105   5.5773e-02
   5_adp:   0.960  0.005  0.067 14.597  0.004  4.105   5.5773e-02
   5_occ:   0.960  0.005  0.067 14.597  0.004  4.105   5.5773e-02
   5_bss:   0.960  0.005  0.067 14.597  0.004  4.105   5.5773e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.963   2.4122e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.963   2.4122e-01
   1_xyz:  10.700  0.088  0.393 76.235  0.059  1.779   1.0617e-01
   1_adp:  10.700  0.088  0.393 76.235  0.059  1.779   1.0617e-01
   1_occ:  10.700  0.088  0.393 76.235  0.059  1.779   1.0617e-01
   2_bss:  10.700  0.088  0.393 76.235  0.059  1.779   1.0617e-01
   2_xyz:   8.944  0.047  0.320 75.010  0.028  2.160   7.7249e-02
   2_adp:   8.944  0.047  0.320 75.010  0.028  2.160   7.7249e-02
   2_occ:   8.944  0.047  0.320 75.010  0.028  2.160   7.7249e-02
   3_bss:   8.944  0.047  0.320 75.010  0.028  2.160   7.7249e-02
   3_xyz:   8.829  0.048  0.234 80.333  0.031  2.254   6.8965e-02
   3_adp:   8.829  0.048  0.234 80.333  0.031  2.254   6.8965e-02
   3_occ:   8.829  0.048  0.234 80.333  0.031  2.254   6.8965e-02
   4_bss:   8.829  0.048  0.234 80.333  0.031  2.254   6.8965e-02
   4_xyz:   7.521  0.045  0.194 82.844  0.037  2.329   3.4287e-02
   4_adp:   7.521  0.045  0.194 82.844  0.037  2.329   3.4287e-02
   4_occ:   7.521  0.045  0.194 82.844  0.037  2.329   3.4287e-02
   5_bss:   7.521  0.045  0.194 82.844  0.037  2.329   3.4287e-02
   5_xyz:   7.556  0.043  0.199 85.388  0.039  2.293   4.4165e-02
   5_adp:   7.556  0.043  0.199 85.388  0.039  2.293   4.4165e-02
   5_occ:   7.556  0.043  0.199 85.388  0.039  2.293   4.4165e-02
   5_bss:   7.556  0.043  0.199 85.388  0.039  2.293   4.4165e-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: 106.44   0.00  19.71  86.44   0.00  16.04 106.44   2.00  39.71
   1_occ: 106.44   0.00  19.71  86.44   0.00  16.04 106.44   2.00  39.71
   2_bss: 106.44   0.00  19.71  86.44   0.00  16.04 106.44   2.00  39.71
   2_xyz: 106.44   0.00  19.71  86.44   0.00  16.04 106.44   2.00  39.71
   2_adp: 101.25   0.00  18.45  91.05   0.00  14.40 101.25   5.05  40.49
   2_occ: 101.25   0.00  18.45  91.05   0.00  14.40 101.25   5.05  40.49
   3_bss: 101.25   0.00  18.45  91.05   0.00  14.40 101.25   5.05  40.49
   3_xyz: 101.25   0.00  18.45  91.05   0.00  14.40 101.25   5.05  40.49
   3_adp:  94.78   0.00  17.35  87.59   0.00  13.13  94.78   5.04  40.31
   3_occ:  94.78   0.00  17.35  87.59   0.00  13.13  94.78   5.04  40.31
   4_bss:  94.78   0.00  17.35  87.59   0.00  13.13  94.78   5.04  40.31
   4_xyz:  94.78   0.00  17.35  87.59   0.00  13.13  94.78   5.04  40.31
   4_adp:  89.71   0.78  17.30  87.44   0.78  12.88  89.71   3.26  41.34
   4_occ:  89.71   0.78  17.30  87.44   0.78  12.88  89.71   3.26  41.34
   5_bss:  89.71   0.78  17.30  87.44   0.78  12.88  89.71   3.26  41.34
   5_xyz:  89.71   0.78  17.30  87.44   0.78  12.88  89.71   3.26  41.34
   5_adp:  88.78   0.58  17.21  88.50   0.58  12.74  88.78   4.70  41.56
   5_occ:  88.78   0.58  17.21  88.50   0.58  12.74  88.78   4.70  41.56
   5_bss:  88.76   0.56  17.20  88.48   0.56  12.72  88.76   4.69  41.55
------------------------------------------------------------------------
 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:    2.908    0.009    0.405
   1_adp:    2.908    0.009    0.405
   1_occ:    2.908    0.009    0.405
   2_bss:    2.908    0.009    0.405
   2_xyz:    2.885    0.066    0.595
   2_adp:    2.885    0.066    0.595
   2_occ:    2.885    0.066    0.595
   3_bss:    2.885    0.066    0.595
   3_xyz:    2.641    0.070    0.730
   3_adp:    2.641    0.070    0.730
   3_occ:    2.641    0.070    0.730
   4_bss:    2.641    0.070    0.730
   4_xyz:    2.507    0.057    0.765
   4_adp:    2.507    0.057    0.765
   4_occ:    2.507    0.057    0.765
   5_bss:    2.507    0.057    0.765
   5_xyz:    2.349    0.109    0.792
   5_adp:    2.349    0.109    0.792
   5_occ:    2.349    0.109    0.792
   5_bss:    2.349    0.109    0.792
------------------------------------------------------------------------

CPU time actual refinement: 350.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_14/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_14/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_14/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_14/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_14/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.81 
  Macro-tasks:
    bulk solvent and scale       = 45.18  
    individual site refinement   = 141.92 
    weights calculation          = 30.85  
    collect and process          = 6.53   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 224.59 
  Micro-tasks:
    mask                            = 2.34   
    f_calc                          = 111.89 
    alpha_beta                      = 8.08   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 120.00 
    fmodel                         = 7.40   
    r_factors                      = 0.23   
    phase_errors                   = 10.55  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 261.89 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.976 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    649 calls, 111.62 s
gradients_fft:          594 calls, 106.97 s

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

# Date 2008-01-16 Time 03:48:40 PST -0800 (1200484120.45 s)
Start R-work = 0.4754, R-free = 0.4754 (no bulk solvent and anisotropic scale)
Final R-work = 0.1414, R-free = 0.1806 (no bulk solvent and anisotropic scale)

Start R-work = 0.4667, R-free = 0.4652
Final R-work = 0.1163, R-free = 0.1627