Starting phenix.real_space_refine
on Fri Aug 22 12:59:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x3k_38038/08_2025/8x3k_38038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x3k_38038/08_2025/8x3k_38038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x3k_38038/08_2025/8x3k_38038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x3k_38038/08_2025/8x3k_38038.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x3k_38038/08_2025/8x3k_38038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x3k_38038/08_2025/8x3k_38038.cif"
  }
  resolution = 2.98
  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=  -0.001 sd=   0.120
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: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    1865      2.51       5
     N     434      2.21       5
     O     470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2797
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 2784
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 23, 'TRANS': 349}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'SRO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.93, per 1000 atoms: 0.33
  Number of scatterers: 2797
  At special positions: 0
  Unit cell: (68.968, 54.056, 62.444, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     470      8.00
     N     434      7.00
     C    1865      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.19
  Conformation dependent library (CDL) restraints added in 113.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  670

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      90.3% alpha, 0.0% 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 18 through 41
      removed outlier: 3.918A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 157
      removed outlier: 4.442A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   ALA A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
      removed outlier: 4.131A  pdb=" N   ASN A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ARG A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 178
      removed outlier: 3.889A  pdb=" N   GLY A 165 " --> pdb=" O   PRO A 161 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   PHE A 166 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   CYS A 167 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   MET A 169 " --> pdb=" O   GLY A 165 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 178 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 211
    Processing helix  chain 'A' and resid 213 through 234
      removed outlier: 3.781A  pdb=" N   ASN A 219 " --> pdb=" O   GLU A 215 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 246
      removed outlier: 3.708A  pdb=" N   PHE A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 270
    Processing helix  chain 'A' and resid 284 through 290
    Processing helix  chain 'A' and resid 291 through 323
      Proline residue:  A 313  - end of helix
      Proline residue:  A 316  - end of helix
      removed outlier: 4.069A  pdb=" N   GLU A 321 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 333
    Processing helix  chain 'A' and resid 334 through 356
      removed outlier: 3.799A  pdb=" N   SER A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ILE A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   HIS A 353 " --> pdb=" O   GLY A 349 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 374
    Processing helix  chain 'A' and resid 380 through 384
    Processing helix  chain 'A' and resid 385 through 413
      removed outlier: 3.990A  pdb=" N   SER A 401 " --> pdb=" O   MET A 397 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 418 through 448
      removed outlier: 3.972A  pdb=" N   GLY A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR A 433 " --> pdb=" O   PHE A 429 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 465 through 471

    233 hydrogen bonds defined for protein.
    681 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: 0.34

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 544
        1.33 -     1.45: 629
        1.45 -     1.57: 1644
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 2865
  Sorted by residual:
  bond pdb=" CA  SER A 197 "
       pdb=" C   SER A 197 "
    ideal  model  delta    sigma   weight residual
    1.524  1.488  0.035 1.27e-02 6.20e+03 7.79e+00
  bond pdb=" CA  SRO A 601 "
       pdb=" NZ  SRO A 601 "
    ideal  model  delta    sigma   weight residual
    1.469  1.520 -0.051 2.00e-02 2.50e+03 6.57e+00
  bond pdb=" C   ILE A 301 "
       pdb=" O   ILE A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.029 1.17e-02 7.31e+03 6.15e+00
  bond pdb=" CA  SER A 209 "
       pdb=" C   SER A 209 "
    ideal  model  delta    sigma   weight residual
    1.523  1.489  0.033 1.37e-02 5.33e+03 5.95e+00
  bond pdb=" CA  LYS A 281 "
       pdb=" C   LYS A 281 "
    ideal  model  delta    sigma   weight residual
    1.524  1.493  0.031 1.35e-02 5.49e+03 5.21e+00
  ... (remaining 2860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 3716
        1.80 -     3.59: 139
        3.59 -     5.39: 27
        5.39 -     7.18: 10
        7.18 -     8.98: 4
  Bond angle restraints: 3896
  Sorted by residual:
  angle pdb=" N   VAL A 427 "
        pdb=" CA  VAL A 427 "
        pdb=" C   VAL A 427 "
      ideal   model   delta    sigma   weight residual
     111.00  106.06    4.94 1.09e+00 8.42e-01 2.05e+01
  angle pdb=" N   ARG A 274 "
        pdb=" CA  ARG A 274 "
        pdb=" C   ARG A 274 "
      ideal   model   delta    sigma   weight residual
     109.95  116.99   -7.04 1.59e+00 3.96e-01 1.96e+01
  angle pdb=" N   VAL A 417 "
        pdb=" CA  VAL A 417 "
        pdb=" C   VAL A 417 "
      ideal   model   delta    sigma   weight residual
     108.12  102.08    6.04 1.44e+00 4.82e-01 1.76e+01
  angle pdb=" N   ILE A 405 "
        pdb=" CA  ILE A 405 "
        pdb=" C   ILE A 405 "
      ideal   model   delta    sigma   weight residual
     111.44  106.40    5.04 1.34e+00 5.57e-01 1.41e+01
  angle pdb=" N   SER A 199 "
        pdb=" CA  SER A 199 "
        pdb=" C   SER A 199 "
      ideal   model   delta    sigma   weight residual
     111.82  116.09   -4.27 1.16e+00 7.43e-01 1.36e+01
  ... (remaining 3891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.76: 1437
       12.76 -    25.52: 160
       25.52 -    38.28: 56
       38.28 -    51.04: 17
       51.04 -    63.81: 7
  Dihedral angle restraints: 1677
    sinusoidal: 625
      harmonic: 1052
  Sorted by residual:
  dihedral pdb=" CA  TYR A 422 "
           pdb=" C   TYR A 422 "
           pdb=" N   ALA A 423 "
           pdb=" CA  ALA A 423 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ASN A 146 "
           pdb=" CB  ASN A 146 "
           pdb=" CG  ASN A 146 "
           pdb=" OD1 ASN A 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -176.19  -63.81     2      2.00e+01 2.50e-03 9.66e+00
  dihedral pdb=" CA  ASP A 213 "
           pdb=" CB  ASP A 213 "
           pdb=" CG  ASP A 213 "
           pdb=" OD1 ASP A 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.99   52.99     1      2.00e+01 2.50e-03 9.55e+00
  ... (remaining 1674 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 250
       0.030 -    0.059: 131
       0.059 -    0.089: 52
       0.089 -    0.119: 24
       0.119 -    0.149: 8
  Chirality restraints: 465
  Sorted by residual:
  chirality pdb=" CA  PRO A 159 "
            pdb=" N   PRO A 159 "
            pdb=" C   PRO A 159 "
            pdb=" CB  PRO A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  PHE A 348 "
            pdb=" N   PHE A 348 "
            pdb=" C   PHE A 348 "
            pdb=" CB  PHE A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CA  SER A 199 "
            pdb=" N   SER A 199 "
            pdb=" C   SER A 199 "
            pdb=" CB  SER A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 462 not shown)

  Planarity restraints: 476
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 164 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.34e+00
        pdb=" C   ALA A 164 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ALA A 164 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY A 165 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 235 "    0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO A 236 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 236 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 236 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 404 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.17e+00
        pdb=" C   PRO A 404 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PRO A 404 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE A 405 "    0.009 2.00e-02 2.50e+03
  ... (remaining 473 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 641
        2.77 -     3.30: 2781
        3.30 -     3.84: 4751
        3.84 -     4.37: 5519
        4.37 -     4.90: 9726
  Nonbonded interactions: 23418
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 301 "
            pdb=" ND2 ASN A 305 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" O   THR A 212 "
            pdb=" OG1 THR A 212 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   PRO A 336 "
            pdb=" OG  SER A 340 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" NH2 ARG A  19 "
            pdb=" OE1 GLU A 216 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" OE1 GLU A 215 "
            pdb=" ND1 HIS A 353 "
     model   vdw
     2.481 3.120
  ... (remaining 23413 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             1.030
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.230
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:6.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
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      :  0.008   0.058   2865  Z= 0.386
  Angle     :  0.905   8.976   3896  Z= 0.521
  Chirality :  0.046   0.149    465
  Planarity :  0.005   0.037    476
  Dihedral  : 13.537  63.806   1007
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.77 %
    Favored  : 83.89 %
  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 aren not related in a simple way.
  whole: -2.22 (0.39), residues: 369
  helix: -1.07 (0.27), residues: 297
  sheet:  None (None), residues: 0
  loop : -2.46 (0.62), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 217 
 TYR   0.018   0.002   TYR A 422 
 PHE   0.015   0.002   PHE A 348 
 TRP   0.006   0.001   TRP A 318 
 HIS   0.003   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 ( 2865)
  covalent geometry    : angle       0.90468 ( 3896)
  hydrogen bonds       : bond        0.15004 (  233)
  hydrogen bonds       : angle       7.30361 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.8060 (mt) cc_final: 0.7827 (mp)
REVERT: A  166 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6340 (t80)
REVERT: A  310 MET cc_start: 0.8148 (mtt) cc_final: 0.7878 (mtp)
REVERT: A  453 MET cc_start: 0.7412 (mmp) cc_final: 0.6925 (mmp)
  outliers start: 4
  outliers final: 1
  residues processed: 54
  average time/residue: 0.3910
  time to fit residues: 21.9015
Evaluate side-chains
  46 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 PHE
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 146 ASN
A 346 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.149370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.130175 restraints weight = 3262.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.13
r_work: 0.3492 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2865  Z= 0.171
  Angle     :  0.653   7.397   3896  Z= 0.331
  Chirality :  0.042   0.126    465
  Planarity :  0.005   0.037    476
  Dihedral  :  6.694  61.456    397
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 17.11 %
    Favored  : 78.86 %
  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 aren not related in a simple way.
  whole: -0.13 (0.43), residues: 369
  helix:  0.40 (0.29), residues: 306
  sheet:  None (None), residues: 0
  loop : -2.12 (0.65), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.015   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 238 
 TRP   0.006   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 2865)
  covalent geometry    : angle       0.65277 ( 3896)
  hydrogen bonds       : bond        0.05075 (  233)
  hydrogen bonds       : angle       5.27340 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.8146 (mt) cc_final: 0.7901 (mp)
REVERT: A  181 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.6640 (p)
REVERT: A  310 MET cc_start: 0.8297 (mtt) cc_final: 0.8096 (mtp)
REVERT: A  453 MET cc_start: 0.7733 (mmp) cc_final: 0.7248 (mmp)
  outliers start: 12
  outliers final: 6
  residues processed: 49
  average time/residue: 0.4177
  time to fit residues: 21.2527
Evaluate side-chains
  51 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  431 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.153497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.133400 restraints weight = 3209.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.16
r_work: 0.3494 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2865  Z= 0.167
  Angle     :  0.623   6.772   3896  Z= 0.314
  Chirality :  0.042   0.126    465
  Planarity :  0.005   0.037    476
  Dihedral  :  6.492  67.202    395
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 17.79 %
    Favored  : 77.85 %
  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 aren not related in a simple way.
  whole:  0.70 (0.43), residues: 369
  helix:  0.90 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -1.58 (0.68), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.013   0.001   PHE A 238 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 2865)
  covalent geometry    : angle       0.62279 ( 3896)
  hydrogen bonds       : bond        0.04815 (  233)
  hydrogen bonds       : angle       4.97683 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.8045 (mt) cc_final: 0.7768 (mp)
REVERT: A  181 SER cc_start: 0.7165 (OUTLIER) cc_final: 0.6449 (p)
REVERT: A  233 LEU cc_start: 0.7803 (tt) cc_final: 0.7578 (tp)
REVERT: A  310 MET cc_start: 0.8114 (mtt) cc_final: 0.7892 (mtp)
REVERT: A  453 MET cc_start: 0.7643 (mmp) cc_final: 0.7173 (mmp)
  outliers start: 13
  outliers final: 6
  residues processed: 51
  average time/residue: 0.4336
  time to fit residues: 22.8681
Evaluate side-chains
  52 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  166 PHE
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.155596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.135125 restraints weight = 3192.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.18
r_work: 0.3541 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2865  Z= 0.154
  Angle     :  0.607   6.849   3896  Z= 0.304
  Chirality :  0.041   0.126    465
  Planarity :  0.005   0.034    476
  Dihedral  :  6.482  68.856    395
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.13 %
    Favored  : 76.17 %
  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 aren not related in a simple way.
  whole:  1.13 (0.44), residues: 369
  helix:  1.16 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.24 (0.68), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.015   0.001   TYR A 422 
 PHE   0.013   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 2865)
  covalent geometry    : angle       0.60687 ( 3896)
  hydrogen bonds       : bond        0.04543 (  233)
  hydrogen bonds       : angle       4.80586 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.8034 (mt) cc_final: 0.7765 (mp)
REVERT: A  181 SER cc_start: 0.7094 (OUTLIER) cc_final: 0.6312 (p)
REVERT: A  233 LEU cc_start: 0.7719 (tt) cc_final: 0.7508 (tp)
REVERT: A  310 MET cc_start: 0.8078 (mtt) cc_final: 0.7856 (mtp)
REVERT: A  453 MET cc_start: 0.7532 (mmp) cc_final: 0.7065 (mmp)
  outliers start: 14
  outliers final: 8
  residues processed: 51
  average time/residue: 0.3874
  time to fit residues: 20.5468
Evaluate side-chains
  53 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0570
   chunk 33 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.157138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.137241 restraints weight = 3187.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.18
r_work: 0.3548 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2865  Z= 0.154
  Angle     :  0.603   6.852   3896  Z= 0.302
  Chirality :  0.042   0.161    465
  Planarity :  0.005   0.033    476
  Dihedral  :  6.502  69.948    395
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 18.12 %
    Favored  : 76.17 %
  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 aren not related in a simple way.
  whole:  1.37 (0.44), residues: 369
  helix:  1.29 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.01 (0.71), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2865)
  covalent geometry    : angle       0.60337 ( 3896)
  hydrogen bonds       : bond        0.04524 (  233)
  hydrogen bonds       : angle       4.76268 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.063 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.8125 (mt) cc_final: 0.7867 (mp)
REVERT: A  181 SER cc_start: 0.7535 (OUTLIER) cc_final: 0.6735 (p)
REVERT: A  233 LEU cc_start: 0.7813 (tt) cc_final: 0.7543 (mt)
REVERT: A  310 MET cc_start: 0.8202 (mtt) cc_final: 0.7985 (mtp)
REVERT: A  453 MET cc_start: 0.7482 (mmp) cc_final: 0.6978 (mmp)
  outliers start: 17
  outliers final: 10
  residues processed: 51
  average time/residue: 0.3820
  time to fit residues: 20.1491
Evaluate side-chains
  55 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.157611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.137644 restraints weight = 3211.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 2.19
r_work: 0.3555 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2865  Z= 0.152
  Angle     :  0.601   6.836   3896  Z= 0.301
  Chirality :  0.042   0.144    465
  Planarity :  0.005   0.033    476
  Dihedral  :  6.536  71.125    395
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.80 %
    Favored  : 75.50 %
  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 aren not related in a simple way.
  whole:  1.52 (0.44), residues: 369
  helix:  1.40 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -0.91 (0.74), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 471 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2865)
  covalent geometry    : angle       0.60059 ( 3896)
  hydrogen bonds       : bond        0.04451 (  233)
  hydrogen bonds       : angle       4.71822 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.8078 (mt) cc_final: 0.7817 (mp)
REVERT: A  169 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6644 (ttm)
REVERT: A  181 SER cc_start: 0.7472 (OUTLIER) cc_final: 0.6710 (p)
REVERT: A  233 LEU cc_start: 0.7738 (tt) cc_final: 0.7485 (mt)
REVERT: A  310 MET cc_start: 0.8162 (mtt) cc_final: 0.7921 (mtp)
REVERT: A  397 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7679 (mtm)
  outliers start: 14
  outliers final: 9
  residues processed: 52
  average time/residue: 0.3766
  time to fit residues: 20.2789
Evaluate side-chains
  58 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0870
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.156775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.136294 restraints weight = 3153.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.16
r_work: 0.3558 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2865  Z= 0.152
  Angle     :  0.606   6.829   3896  Z= 0.303
  Chirality :  0.042   0.132    465
  Planarity :  0.005   0.034    476
  Dihedral  :  6.645  73.672    395
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 21.14 %
    Favored  : 74.50 %
  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 aren not related in a simple way.
  whole:  1.64 (0.44), residues: 369
  helix:  1.49 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -0.89 (0.74), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 471 
 TYR   0.015   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2865)
  covalent geometry    : angle       0.60643 ( 3896)
  hydrogen bonds       : bond        0.04453 (  233)
  hydrogen bonds       : angle       4.69519 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7981 (mt) cc_final: 0.7712 (mp)
REVERT: A  169 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6597 (ttm)
REVERT: A  181 SER cc_start: 0.7193 (OUTLIER) cc_final: 0.6443 (p)
REVERT: A  233 LEU cc_start: 0.7634 (tt) cc_final: 0.7400 (mt)
REVERT: A  310 MET cc_start: 0.8101 (mtt) cc_final: 0.7852 (mtp)
  outliers start: 13
  outliers final: 7
  residues processed: 50
  average time/residue: 0.4142
  time to fit residues: 21.4782
Evaluate side-chains
  53 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.157704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.137466 restraints weight = 3279.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.20
r_work: 0.3542 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2865  Z= 0.164
  Angle     :  0.621   6.999   3896  Z= 0.310
  Chirality :  0.043   0.145    465
  Planarity :  0.005   0.034    476
  Dihedral  :  6.649  73.801    395
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 20.47 %
    Favored  : 74.50 %
  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 aren not related in a simple way.
  whole:  1.65 (0.44), residues: 369
  helix:  1.49 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -0.91 (0.73), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 471 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.014   0.001   PHE A 348 
 TRP   0.004   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 2865)
  covalent geometry    : angle       0.62103 ( 3896)
  hydrogen bonds       : bond        0.04555 (  233)
  hydrogen bonds       : angle       4.71565 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7963 (mt) cc_final: 0.7670 (mp)
REVERT: A  181 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.6770 (p)
REVERT: A  233 LEU cc_start: 0.7671 (tt) cc_final: 0.7430 (mt)
  outliers start: 15
  outliers final: 9
  residues processed: 51
  average time/residue: 0.4051
  time to fit residues: 21.4141
Evaluate side-chains
  54 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 0 optimal weight:    0.4980
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.156426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.136076 restraints weight = 3200.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.13
r_work: 0.3549 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2865  Z= 0.162
  Angle     :  0.629   7.837   3896  Z= 0.313
  Chirality :  0.043   0.168    465
  Planarity :  0.005   0.035    476
  Dihedral  :  6.709  74.543    395
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 21.81 %
    Favored  : 74.16 %
  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 aren not related in a simple way.
  whole:  1.71 (0.44), residues: 369
  helix:  1.53 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -0.89 (0.73), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 471 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 2865)
  covalent geometry    : angle       0.62933 ( 3896)
  hydrogen bonds       : bond        0.04521 (  233)
  hydrogen bonds       : angle       4.67906 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.8014 (mt) cc_final: 0.7731 (mp)
REVERT: A  181 SER cc_start: 0.7435 (OUTLIER) cc_final: 0.6710 (p)
REVERT: A  233 LEU cc_start: 0.7776 (tt) cc_final: 0.7543 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 51
  average time/residue: 0.3751
  time to fit residues: 19.8604
Evaluate side-chains
  54 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0170
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.159923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.140068 restraints weight = 3223.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 2.16
r_work: 0.3582 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2865  Z= 0.148
  Angle     :  0.616   7.779   3896  Z= 0.306
  Chirality :  0.042   0.169    465
  Planarity :  0.005   0.034    476
  Dihedral  :  6.736  75.322    395
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.82 %
    Favored  : 74.50 %
  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 aren not related in a simple way.
  whole:  1.85 (0.44), residues: 369
  helix:  1.62 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -0.80 (0.74), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 471 
 TYR   0.014   0.001   TYR A 422 
 PHE   0.011   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.001   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 2865)
  covalent geometry    : angle       0.61619 ( 3896)
  hydrogen bonds       : bond        0.04327 (  233)
  hydrogen bonds       : angle       4.61136 (  681)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  151 LEU cc_start: 0.7933 (mt) cc_final: 0.7651 (mp)
REVERT: A  233 LEU cc_start: 0.7628 (tt) cc_final: 0.7411 (mt)
REVERT: A  312 GLU cc_start: 0.8080 (tt0) cc_final: 0.7855 (tt0)
REVERT: A  397 MET cc_start: 0.8010 (ttt) cc_final: 0.7717 (mtm)
REVERT: A  453 MET cc_start: 0.7614 (mmp) cc_final: 0.7155 (mmp)
  outliers start: 8
  outliers final: 8
  residues processed: 51
  average time/residue: 0.4125
  time to fit residues: 21.8037
Evaluate side-chains
  53 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 30 optimal weight:    0.2980
   chunk 2 optimal weight:    0.0170
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0570
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.162927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.143405 restraints weight = 3131.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.12
r_work: 0.3629 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2865  Z= 0.133
  Angle     :  0.603   8.094   3896  Z= 0.299
  Chirality :  0.041   0.142    465
  Planarity :  0.005   0.035    476
  Dihedral  :  6.744  76.051    395
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 23.83 %
    Favored  : 74.50 %
  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 aren not related in a simple way.
  whole:  2.07 (0.44), residues: 369
  helix:  1.71 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.42 (0.77), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.013   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 393 
 TRP   0.005   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2865)
  covalent geometry    : angle       0.60301 ( 3896)
  hydrogen bonds       : bond        0.04040 (  233)
  hydrogen bonds       : angle       4.53147 (  681)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1035.70 seconds
wall clock time: 18 minutes 20.50 seconds (1100.50 seconds total)