Starting phenix.real_space_refine
on Wed Jul  1 23:40:30 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7p14_13155/07_2026/7p14_13155.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.046
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      25      5.16       5
     C    2533      2.51       5
     N     579      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3796
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2706
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 320}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 964
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "A"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 126
          Unusual residues: {'PLC': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
  Time building chain proxies: 1.07, per 1000 atoms: 0.28
  Number of scatterers: 3796
  At special positions: 0
  Unit cell: (96.348, 69.006, 70.308, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P       3     15.00
     O     656      8.00
     N     579      7.00
     C    2533      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B 102 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 110.5 milliseconds
  

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  846

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 2 sheets defined
      67.2% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 36
      removed outlier: 3.515A  pdb=" N   ILE A  15 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ILE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 67
      removed outlier: 3.741A  pdb=" N   VAL A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 86
      removed outlier: 3.762A  pdb=" N   GLY A  86 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 86'
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.530A  pdb=" N   PHE A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 158
      removed outlier: 3.590A  pdb=" N   LEU A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   CYS A 144 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      Proline residue:  A 145  - end of helix
      removed outlier: 3.572A  pdb=" N   LEU A 149 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 190
      removed outlier: 3.504A  pdb=" N   ARG A 187 " --> pdb=" O   GLN A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 5.032A  pdb=" N   LEU A 195 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG A 197 " --> pdb=" O   ASN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 227
      removed outlier: 3.654A  pdb=" N   LEU A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 250
      removed outlier: 3.535A  pdb=" N   VAL A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 3.733A  pdb=" N   PHE A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   PHE A 273 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 4.233A  pdb=" N   GLN A 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 308
    Processing helix  chain 'A' and resid 314 through 343
      removed outlier: 3.616A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 115 through 119
      removed outlier: 3.778A  pdb=" N   TYR B 119 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.725A  pdb=" N   ALA B  55 " --> pdb=" O   TRP B  42 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ARG B  44 " --> pdb=" O   GLY B  53 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   GLY B  53 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    735 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.46

  Time building geometry restraints manager: 0.41 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.32: 545
        1.32 -     1.44: 1168
        1.44 -     1.56: 2136
        1.56 -     1.69: 6
        1.69 -     1.81: 37
  Bond restraints: 3892
  Sorted by residual:
  bond pdb=" N   LYS A 284 "
       pdb=" CA  LYS A 284 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.29e-02 6.01e+03 1.05e+01
  bond pdb=" C3  P5S A 403 "
       pdb=" O16 P5S A 403 "
    ideal  model  delta    sigma   weight residual
    1.405  1.456 -0.051 2.00e-02 2.50e+03 6.38e+00
  bond pdb=" C4  PLC A 402 "
       pdb=" O4P PLC A 402 "
    ideal  model  delta    sigma   weight residual
    1.409  1.456 -0.047 2.00e-02 2.50e+03 5.48e+00
  bond pdb=" C4  PLC A 401 "
       pdb=" O4P PLC A 401 "
    ideal  model  delta    sigma   weight residual
    1.409  1.454 -0.045 2.00e-02 2.50e+03 4.97e+00
  bond pdb=" C1  PLC A 402 "
       pdb=" O3P PLC A 402 "
    ideal  model  delta    sigma   weight residual
    1.410  1.453 -0.043 2.00e-02 2.50e+03 4.69e+00
  ... (remaining 3887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 5177
        2.12 -     4.23: 76
        4.23 -     6.35: 13
        6.35 -     8.47: 2
        8.47 -    10.58: 2
  Bond angle restraints: 5270
  Sorted by residual:
  angle pdb=" O3P PLC A 402 "
        pdb=" P   PLC A 402 "
        pdb=" O4P PLC A 402 "
      ideal   model   delta    sigma   weight residual
      93.62  104.20  -10.58 3.00e+00 1.11e-01 1.24e+01
  angle pdb=" O3P PLC A 401 "
        pdb=" P   PLC A 401 "
        pdb=" O4P PLC A 401 "
      ideal   model   delta    sigma   weight residual
      93.62  103.08   -9.46 3.00e+00 1.11e-01 9.94e+00
  angle pdb=" C3  PLC A 401 "
        pdb=" C2  PLC A 401 "
        pdb=" O2  PLC A 401 "
      ideal   model   delta    sigma   weight residual
     107.38  114.66   -7.28 3.00e+00 1.11e-01 5.89e+00
  angle pdb=" CA  LYS A 284 "
        pdb=" CB  LYS A 284 "
        pdb=" CG  LYS A 284 "
      ideal   model   delta    sigma   weight residual
     114.10  118.68   -4.58 2.00e+00 2.50e-01 5.24e+00
  angle pdb=" CA  LEU A 330 "
        pdb=" CB  LEU A 330 "
        pdb=" CG  LEU A 330 "
      ideal   model   delta    sigma   weight residual
     116.30  122.98   -6.68 3.50e+00 8.16e-02 3.65e+00
  ... (remaining 5265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.82: 2014
       22.82 -    45.64: 172
       45.64 -    68.45: 19
       68.45 -    91.27: 9
       91.27 -   114.09: 2
  Dihedral angle restraints: 2216
    sinusoidal: 887
      harmonic: 1329
  Sorted by residual:
  dihedral pdb=" C27 P5S A 403 "
           pdb=" C28 P5S A 403 "
           pdb=" C29 P5S A 403 "
           pdb=" C30 P5S A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -179.38  -65.29 -114.09     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" CA  ILE A 319 "
           pdb=" C   ILE A 319 "
           pdb=" N   PRO A 320 "
           pdb=" CA  PRO A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.33   16.67     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" C41 P5S A 403 "
           pdb=" C42 P5S A 403 "
           pdb=" C43 P5S A 403 "
           pdb=" C44 P5S A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.47   89.64   91.83     1      3.00e+01 1.11e-03 1.10e+01
  ... (remaining 2213 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 508
       0.053 -    0.106: 74
       0.106 -    0.159: 4
       0.159 -    0.213: 0
       0.213 -    0.266: 1
  Chirality restraints: 587
  Sorted by residual:
  chirality pdb=" C2  PLC A 401 "
            pdb=" C1  PLC A 401 "
            pdb=" C3  PLC A 401 "
            pdb=" O2  PLC A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.05   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  PRO A 201 "
            pdb=" N   PRO A 201 "
            pdb=" C   PRO A 201 "
            pdb=" CB  PRO A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  PHE A 276 "
            pdb=" N   PHE A 276 "
            pdb=" C   PHE A 276 "
            pdb=" CB  PHE A 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 584 not shown)

  Planarity restraints: 624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 319 "    0.042 5.00e-02 4.00e+02   6.37e-02 6.49e+00
        pdb=" N   PRO A 320 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 320 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 320 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 200 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A 201 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 201 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 201 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  33 "   -0.005 2.00e-02 2.50e+03   9.48e-03 8.99e-01
        pdb=" C   ASN B  33 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ASN B  33 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ILE B  34 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 621 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1090
        2.82 -     3.34: 3666
        3.34 -     3.86: 5942
        3.86 -     4.38: 7105
        4.38 -     4.90: 12065
  Nonbonded interactions: 29868
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 260 "
            pdb=" NH2 ARG A 264 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   ILE A  16 "
            pdb=" OG1 THR A  20 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OH  TYR A 182 "
            pdb=" O   LEU A 371 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   ILE A 175 "
            pdb=" OG1 THR A 179 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" OH  TYR A 208 "
            pdb=" OH  TYR A 291 "
     model   vdw
     2.419 3.040
  ... (remaining 29863 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.050
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3893  Z= 0.215
  Angle     :  0.638  10.583   5272  Z= 0.288
  Chirality :  0.037   0.266    587
  Planarity :  0.004   0.064    624
  Dihedral  : 16.559 114.091   1367
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.40), residues: 444
  helix:  1.37 (0.31), residues: 257
  sheet:  1.11 (0.70), residues: 52
  loop : -0.55 (0.57), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  51 
 TYR   0.015   0.001   TYR A 340 
 PHE   0.005   0.001   PHE A 225 
 TRP   0.005   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  56 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.21 ( 3892)
  covalent geometry    : angle       0.63844 /  0.29 ( 5270)
  SS BOND              : bond        0.00002 /  0.00 (    1)
  SS BOND              : angle       0.41090 /  0.23 (    2)
  hydrogen bonds       : bond        0.24301 / 15.74 (  256)
  hydrogen bonds       : angle       7.43826 /  5.47 (  735)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  139 THR cc_start: 0.9153 (m) cc_final: 0.8884 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0528
  time to fit residues: 4.9149
Evaluate side-chains
  63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 150 GLN
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.166303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.134320 restraints weight = 4398.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.137691 restraints weight = 2912.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.139970 restraints weight = 2220.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141567 restraints weight = 1852.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.142436 restraints weight = 1644.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3893  Z= 0.147
  Angle     :  0.594   9.679   5272  Z= 0.298
  Chirality :  0.039   0.130    587
  Planarity :  0.004   0.039    624
  Dihedral  : 11.989  74.189    572
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.05 %
    Favored  : 91.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.40), residues: 444
  helix:  2.38 (0.29), residues: 265
  sheet:  0.34 (0.69), residues: 57
  loop : -0.43 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 366 
 TYR   0.015   0.001   TYR A 291 
 PHE   0.033   0.002   PHE A  94 
 TRP   0.008   0.001   TRP A  93 
 HIS   0.002   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.15 ( 3892)
  covalent geometry    : angle       0.59361 /  0.30 ( 5270)
  SS BOND              : bond        0.00017 /  0.01 (    1)
  SS BOND              : angle       0.11744 /  0.07 (    2)
  hydrogen bonds       : bond        0.04653 /  2.93 (  256)
  hydrogen bonds       : angle       4.37580 /  3.24 (  735)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   50 CYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7488 (m)
REVERT: A  130 ASP cc_start: 0.8964 (t0) cc_final: 0.8739 (t70)
REVERT: A  139 THR cc_start: 0.9127 (m) cc_final: 0.8813 (p)
REVERT: B  127 GLN cc_start: 0.8490 (tp40) cc_final: 0.8227 (tp-100)
  outliers start: 4
  outliers final: 1
  residues processed: 72
  average time/residue: 0.0388
  time to fit residues: 3.7412
Evaluate side-chains
  66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue   83 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  82 HIS
A 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.164940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.132414 restraints weight = 4400.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.135649 restraints weight = 2944.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.138176 restraints weight = 2273.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.139662 restraints weight = 1901.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.140595 restraints weight = 1693.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3893  Z= 0.149
  Angle     :  0.559   9.322   5272  Z= 0.279
  Chirality :  0.039   0.188    587
  Planarity :  0.003   0.042    624
  Dihedral  : 10.583  74.358    572
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.32 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.39), residues: 444
  helix:  2.75 (0.29), residues: 264
  sheet:  0.97 (0.69), residues: 52
  loop : -0.66 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.028   0.001   TYR A 343 
 PHE   0.022   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A 245 
 HIS   0.001   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 3892)
  covalent geometry    : angle       0.55903 /  0.28 ( 5270)
  SS BOND              : bond        0.00093 /  0.05 (    1)
  SS BOND              : angle       0.18106 /  0.10 (    2)
  hydrogen bonds       : bond        0.04105 /  2.60 (  256)
  hydrogen bonds       : angle       4.08336 /  2.99 (  735)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A    7 ASN cc_start: 0.8902 (t0) cc_final: 0.8658 (m-40)
REVERT: A  130 ASP cc_start: 0.8962 (t0) cc_final: 0.8655 (t0)
REVERT: A  258 SER cc_start: 0.8874 (t) cc_final: 0.8592 (p)
REVERT: B  121 TYR cc_start: 0.7307 (p90) cc_final: 0.5874 (p90)
REVERT: B  127 GLN cc_start: 0.8529 (tp40) cc_final: 0.8274 (tp-100)
  outliers start: 7
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0451
  time to fit residues: 4.5706
Evaluate side-chains
  75 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.170105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.138925 restraints weight = 4445.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.142220 restraints weight = 2988.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.144228 restraints weight = 2301.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.145870 restraints weight = 1940.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.147138 restraints weight = 1707.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3893  Z= 0.150
  Angle     :  0.550   8.585   5272  Z= 0.274
  Chirality :  0.039   0.197    587
  Planarity :  0.003   0.030    624
  Dihedral  :  9.947  74.242    572
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.59 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.40), residues: 444
  helix:  2.93 (0.29), residues: 264
  sheet:  0.97 (0.68), residues: 52
  loop : -0.64 (0.59), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.016   0.001   TYR A 343 
 PHE   0.018   0.001   PHE A 199 
 TRP   0.007   0.001   TRP A 245 
 HIS   0.001   0.000   HIS A 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.15 ( 3892)
  covalent geometry    : angle       0.55054 /  0.27 ( 5270)
  SS BOND              : bond        0.00071 /  0.04 (    1)
  SS BOND              : angle       0.19095 /  0.11 (    2)
  hydrogen bonds       : bond        0.03774 /  2.40 (  256)
  hydrogen bonds       : angle       3.94241 /  2.88 (  735)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8877 (t0) cc_final: 0.8508 (t0)
REVERT: A  258 SER cc_start: 0.8874 (t) cc_final: 0.8636 (p)
REVERT: B  127 GLN cc_start: 0.8387 (tp40) cc_final: 0.8135 (tp-100)
  outliers start: 8
  outliers final: 5
  residues processed: 73
  average time/residue: 0.0347
  time to fit residues: 3.4065
Evaluate side-chains
  70 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 8 optimal weight:    0.0970
   chunk 10 optimal weight:    0.2980
   chunk 33 optimal weight:    8.9990
   chunk 5 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.3978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.170526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.139866 restraints weight = 4387.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.143274 restraints weight = 2923.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.145344 restraints weight = 2226.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.147036 restraints weight = 1868.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.147412 restraints weight = 1655.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3893  Z= 0.118
  Angle     :  0.527   8.167   5272  Z= 0.261
  Chirality :  0.038   0.197    587
  Planarity :  0.003   0.027    624
  Dihedral  :  9.175  73.290    572
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.09 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.73 (0.40), residues: 444
  helix:  3.11 (0.29), residues: 264
  sheet:  0.35 (0.68), residues: 57
  loop : -0.48 (0.60), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.013   0.001   TYR A 343 
 PHE   0.017   0.001   PHE A   8 
 TRP   0.008   0.001   TRP A 245 
 HIS   0.001   0.000   HIS A 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 3892)
  covalent geometry    : angle       0.52697 /  0.26 ( 5270)
  SS BOND              : bond        0.00079 /  0.04 (    1)
  SS BOND              : angle       0.13339 /  0.07 (    2)
  hydrogen bonds       : bond        0.03464 /  2.20 (  256)
  hydrogen bonds       : angle       3.79112 /  2.76 (  735)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8663 (t0) cc_final: 0.8279 (t0)
REVERT: A  258 SER cc_start: 0.8831 (t) cc_final: 0.8623 (p)
REVERT: A  264 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7484 (ttm170)
REVERT: A  265 LEU cc_start: 0.8571 (tp) cc_final: 0.8329 (tt)
REVERT: B  127 GLN cc_start: 0.8342 (tp40) cc_final: 0.8100 (tp-100)
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0490
  time to fit residues: 4.8719
Evaluate side-chains
  76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ASN
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.170160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.139225 restraints weight = 4439.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.142608 restraints weight = 2965.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.144966 restraints weight = 2259.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.146256 restraints weight = 1875.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.147470 restraints weight = 1673.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3893  Z= 0.137
  Angle     :  0.544   8.092   5272  Z= 0.270
  Chirality :  0.038   0.201    587
  Planarity :  0.003   0.024    624
  Dihedral  :  8.920  73.234    572
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.11 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.40), residues: 444
  helix:  3.04 (0.29), residues: 264
  sheet:  0.96 (0.68), residues: 52
  loop : -0.70 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.013   0.001   TYR B 121 
 PHE   0.019   0.001   PHE A   8 
 TRP   0.007   0.001   TRP A 245 
 HIS   0.001   0.000   HIS A 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 3892)
  covalent geometry    : angle       0.54372 /  0.27 ( 5270)
  SS BOND              : bond        0.00095 /  0.05 (    1)
  SS BOND              : angle       0.19904 /  0.11 (    2)
  hydrogen bonds       : bond        0.03534 /  2.25 (  256)
  hydrogen bonds       : angle       3.78043 /  2.75 (  735)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8682 (t0) cc_final: 0.8304 (t0)
REVERT: A  199 PHE cc_start: 0.7783 (t80) cc_final: 0.7539 (t80)
REVERT: A  258 SER cc_start: 0.8829 (t) cc_final: 0.8611 (p)
REVERT: A  264 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7609 (ttm170)
REVERT: A  265 LEU cc_start: 0.8604 (tp) cc_final: 0.8363 (tt)
REVERT: B  127 GLN cc_start: 0.8348 (tp40) cc_final: 0.8083 (tp-100)
  outliers start: 10
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0537
  time to fit residues: 5.2231
Evaluate side-chains
  75 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.166103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134158 restraints weight = 4543.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.137315 restraints weight = 3028.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.139897 restraints weight = 2324.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.141286 restraints weight = 1942.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.142421 restraints weight = 1721.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3893  Z= 0.141
  Angle     :  0.555   8.067   5272  Z= 0.276
  Chirality :  0.039   0.210    587
  Planarity :  0.003   0.025    624
  Dihedral  :  8.785  73.523    572
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.61 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.40), residues: 444
  helix:  3.09 (0.29), residues: 263
  sheet:  0.93 (0.67), residues: 52
  loop : -0.72 (0.57), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  97 
 TYR   0.013   0.001   TYR B 121 
 PHE   0.015   0.001   PHE A 104 
 TRP   0.015   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 3892)
  covalent geometry    : angle       0.55534 /  0.28 ( 5270)
  SS BOND              : bond        0.00090 /  0.05 (    1)
  SS BOND              : angle       0.19905 /  0.11 (    2)
  hydrogen bonds       : bond        0.03526 /  2.26 (  256)
  hydrogen bonds       : angle       3.79220 /  2.75 (  735)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8688 (t0) cc_final: 0.8302 (t0)
REVERT: A  199 PHE cc_start: 0.7806 (t80) cc_final: 0.7351 (t80)
REVERT: A  258 SER cc_start: 0.8862 (t) cc_final: 0.8604 (p)
REVERT: A  264 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7702 (ttm170)
REVERT: B  127 GLN cc_start: 0.8375 (tp40) cc_final: 0.8107 (tp-100)
  outliers start: 10
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0454
  time to fit residues: 4.5181
Evaluate side-chains
  74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.166032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134734 restraints weight = 4475.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.137842 restraints weight = 2981.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.140329 restraints weight = 2296.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.141428 restraints weight = 1909.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.142478 restraints weight = 1718.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3893  Z= 0.150
  Angle     :  0.560   8.201   5272  Z= 0.278
  Chirality :  0.039   0.217    587
  Planarity :  0.003   0.026    624
  Dihedral  :  8.767  74.137    572
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.11 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.40), residues: 444
  helix:  3.01 (0.29), residues: 263
  sheet:  0.92 (0.67), residues: 52
  loop : -0.69 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  97 
 TYR   0.013   0.001   TYR B 121 
 PHE   0.015   0.001   PHE A 104 
 TRP   0.010   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 3892)
  covalent geometry    : angle       0.55975 /  0.28 ( 5270)
  SS BOND              : bond        0.00072 /  0.04 (    1)
  SS BOND              : angle       0.17868 /  0.10 (    2)
  hydrogen bonds       : bond        0.03606 /  2.33 (  256)
  hydrogen bonds       : angle       3.81202 /  2.75 (  735)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8691 (t0) cc_final: 0.8280 (t0)
REVERT: A  199 PHE cc_start: 0.7867 (t80) cc_final: 0.7409 (t80)
REVERT: A  258 SER cc_start: 0.8865 (t) cc_final: 0.8618 (p)
REVERT: A  265 LEU cc_start: 0.8709 (tp) cc_final: 0.8463 (tt)
REVERT: B  127 GLN cc_start: 0.8380 (tp40) cc_final: 0.8108 (tp-100)
  outliers start: 10
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0521
  time to fit residues: 5.0728
Evaluate side-chains
  74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.166377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.135145 restraints weight = 4454.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.138360 restraints weight = 2974.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.140651 restraints weight = 2276.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141926 restraints weight = 1912.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.143043 restraints weight = 1713.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3893  Z= 0.152
  Angle     :  0.576   8.192   5272  Z= 0.285
  Chirality :  0.039   0.215    587
  Planarity :  0.003   0.034    624
  Dihedral  :  8.716  74.804    572
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.37 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.40), residues: 444
  helix:  2.86 (0.29), residues: 268
  sheet:  0.88 (0.67), residues: 52
  loop : -0.90 (0.58), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  97 
 TYR   0.031   0.001   TYR A 343 
 PHE   0.016   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.15 ( 3892)
  covalent geometry    : angle       0.57574 /  0.29 ( 5270)
  SS BOND              : bond        0.00070 /  0.04 (    1)
  SS BOND              : angle       0.17245 /  0.09 (    2)
  hydrogen bonds       : bond        0.03629 /  2.36 (  256)
  hydrogen bonds       : angle       3.81924 /  2.76 (  735)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8672 (t0) cc_final: 0.8254 (t0)
REVERT: A  199 PHE cc_start: 0.7700 (t80) cc_final: 0.7204 (t80)
REVERT: B  127 GLN cc_start: 0.8366 (tp40) cc_final: 0.8074 (tp-100)
  outliers start: 11
  outliers final: 9
  residues processed: 77
  average time/residue: 0.0423
  time to fit residues: 4.3237
Evaluate side-chains
  72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0670
   overall best weight:    0.5118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.169919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.138423 restraints weight = 4476.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.141690 restraints weight = 3005.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.144018 restraints weight = 2299.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.145448 restraints weight = 1933.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.146341 restraints weight = 1723.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3893  Z= 0.130
  Angle     :  0.567   8.236   5272  Z= 0.283
  Chirality :  0.039   0.215    587
  Planarity :  0.003   0.029    624
  Dihedral  :  8.527  74.613    572
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.38 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.40), residues: 444
  helix:  3.02 (0.30), residues: 262
  sheet:  0.39 (0.65), residues: 57
  loop : -0.65 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 264 
 TYR   0.029   0.001   TYR A 340 
 PHE   0.017   0.001   PHE A 104 
 TRP   0.014   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 ( 3892)
  covalent geometry    : angle       0.56711 /  0.28 ( 5270)
  SS BOND              : bond        0.00068 /  0.04 (    1)
  SS BOND              : angle       0.13473 /  0.07 (    2)
  hydrogen bonds       : bond        0.03502 /  2.28 (  256)
  hydrogen bonds       : angle       3.81025 /  2.76 (  735)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7913 (tmm) cc_final: 0.7624 (tmm)
REVERT: A  130 ASP cc_start: 0.8618 (t0) cc_final: 0.8199 (t0)
REVERT: A  199 PHE cc_start: 0.7672 (t80) cc_final: 0.7167 (t80)
REVERT: B  127 GLN cc_start: 0.8383 (tp40) cc_final: 0.8085 (tp-100)
  outliers start: 8
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0500
  time to fit residues: 4.7371
Evaluate side-chains
  71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.168603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.136710 restraints weight = 4473.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.140097 restraints weight = 3002.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.142447 restraints weight = 2300.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.143838 restraints weight = 1929.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.144733 restraints weight = 1725.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3893  Z= 0.151
  Angle     :  0.582   8.410   5272  Z= 0.290
  Chirality :  0.040   0.221    587
  Planarity :  0.003   0.034    624
  Dihedral  :  8.471  75.155    572
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.13 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.40), residues: 444
  helix:  2.95 (0.29), residues: 262
  sheet:  0.39 (0.65), residues: 57
  loop : -0.61 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 264 
 TYR   0.040   0.002   TYR A 340 
 PHE   0.017   0.001   PHE A 104 
 TRP   0.011   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  56 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 ( 3892)
  covalent geometry    : angle       0.58221 /  0.29 ( 5270)
  SS BOND              : bond        0.00078 /  0.04 (    1)
  SS BOND              : angle       0.20457 /  0.11 (    2)
  hydrogen bonds       : bond        0.03609 /  2.36 (  256)
  hydrogen bonds       : angle       3.86640 /  2.80 (  735)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 682.67 seconds
wall clock time: 12 minutes 25.05 seconds (745.05 seconds total)