Starting phenix.real_space_refine
on Fri Oct 10 10:43:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qct_18335/10_2025/8qct_18335_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qct_18335/10_2025/8qct_18335.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qct_18335/10_2025/8qct_18335_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qct_18335/10_2025/8qct_18335_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qct_18335/10_2025/8qct_18335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qct_18335/10_2025/8qct_18335.map"
  }
  resolution = 2.6
  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=   0.000 sd=   0.005
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      18      5.16       5
     C    2167      2.51       5
     N     505      2.21       5
     O     569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3259
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3252
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 17, 'TRANS': 400}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'CHT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.09, per 1000 atoms: 0.33
  Number of scatterers: 3259
  At special positions: 0
  Unit cell: (81.366, 56.154, 65.322, 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      18     16.00
     O     569      8.00
     N     505      7.00
     C    2167      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: 0.28
  Conformation dependent library (CDL) restraints added in 158.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      85.6% 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 105 through 127
      removed outlier: 4.093A  pdb=" N   VAL A 109 " --> pdb=" O   PRO A 105 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 131 through 140
    Processing helix  chain 'A' and resid 142 through 171
      removed outlier: 3.712A  pdb=" N   ILE A 146 " --> pdb=" O   THR A 142 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TYR A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR A 157 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
      removed outlier: 5.022A  pdb=" N   PHE A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 172 through 193
      removed outlier: 3.647A  pdb=" N   THR A 176 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY A 193 " --> pdb=" O   TRP A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 215
      removed outlier: 3.803A  pdb=" N   VAL A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 4.190A  pdb=" N   ARG A 223 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 260
      removed outlier: 3.614A  pdb=" N   ASN A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN A 246 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 266 through 296
    Processing helix  chain 'A' and resid 305 through 314
    Processing helix  chain 'A' and resid 320 through 329
    Processing helix  chain 'A' and resid 331 through 363
      removed outlier: 5.124A  pdb=" N   ASN A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   GLN A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 388
    Processing helix  chain 'A' and resid 397 through 420
    Processing helix  chain 'A' and resid 421 through 423
      No H-bonds generated for 'chain 'A' and resid 421 through 423'
    Processing helix  chain 'A' and resid 424 through 440
      removed outlier: 3.615A  pdb=" N   VAL A 428 " --> pdb=" O   TYR A 424 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE A 438 " --> pdb=" O   VAL A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 450
      removed outlier: 3.564A  pdb=" N   PHE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 489
      removed outlier: 3.556A  pdb=" N   SER A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 510
      removed outlier: 3.614A  pdb=" N   GLY A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)

    252 hydrogen bonds defined for protein.
    756 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: 0.41

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 967
        1.34 -     1.46: 779
        1.46 -     1.58: 1566
        1.58 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 3340
  Sorted by residual:
  bond pdb=" N   GLU A 233 "
       pdb=" CA  GLU A 233 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.031 1.33e-02 5.65e+03 5.56e+00
  bond pdb=" CG  ASN A 265 "
       pdb=" ND2 ASN A 265 "
    ideal  model  delta    sigma   weight residual
    1.328  1.351 -0.023 2.10e-02 2.27e+03 1.20e+00
  bond pdb=" C   LEU A 220 "
       pdb=" N   PRO A 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.348 -0.013 1.51e-02 4.39e+03 7.94e-01
  bond pdb=" C   TYR A 455 "
       pdb=" N   PRO A 456 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.80e-01
  bond pdb=" CB  GLU A 298 "
       pdb=" CG  GLU A 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.21e-01
  ... (remaining 3335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 4393
        1.11 -     2.21: 121
        2.21 -     3.32: 29
        3.32 -     4.43: 7
        4.43 -     5.54: 6
  Bond angle restraints: 4556
  Sorted by residual:
  angle pdb=" CB  GLU A 298 "
        pdb=" CG  GLU A 298 "
        pdb=" CD  GLU A 298 "
      ideal   model   delta    sigma   weight residual
     112.60  116.60   -4.00 1.70e+00 3.46e-01 5.55e+00
  angle pdb=" CA  TYR A 117 "
        pdb=" CB  TYR A 117 "
        pdb=" CG  TYR A 117 "
      ideal   model   delta    sigma   weight residual
     113.90  117.89   -3.99 1.80e+00 3.09e-01 4.91e+00
  angle pdb=" N   PRO A 256 "
        pdb=" CA  PRO A 256 "
        pdb=" C   PRO A 256 "
      ideal   model   delta    sigma   weight residual
     110.70  113.40   -2.70 1.22e+00 6.72e-01 4.91e+00
  angle pdb=" CA  PRO A 256 "
        pdb=" C   PRO A 256 "
        pdb=" N   PRO A 257 "
      ideal   model   delta    sigma   weight residual
     117.93  120.23   -2.30 1.20e+00 6.94e-01 3.66e+00
  angle pdb=" CA  GLY A 219 "
        pdb=" C   GLY A 219 "
        pdb=" N   LEU A 220 "
      ideal   model   delta    sigma   weight residual
     118.41  116.05    2.36 1.29e+00 6.01e-01 3.34e+00
  ... (remaining 4551 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 1691
       17.44 -    34.89: 171
       34.89 -    52.33: 48
       52.33 -    69.77: 11
       69.77 -    87.22: 3
  Dihedral angle restraints: 1924
    sinusoidal: 721
      harmonic: 1203
  Sorted by residual:
  dihedral pdb=" CA  TYR A 117 "
           pdb=" C   TYR A 117 "
           pdb=" N   SER A 118 "
           pdb=" CA  SER A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.09   15.91     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  GLU A 459 "
           pdb=" CB  GLU A 459 "
           pdb=" CG  GLU A 459 "
           pdb=" CD  GLU A 459 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.35  -59.65     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LEU A 173 "
           pdb=" CA  LEU A 173 "
           pdb=" CB  LEU A 173 "
           pdb=" CG  LEU A 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.25   57.25     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 1921 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 360
       0.029 -    0.059: 126
       0.059 -    0.088: 40
       0.088 -    0.118: 17
       0.118 -    0.147: 1
  Chirality restraints: 544
  Sorted by residual:
  chirality pdb=" CA  GLU A 233 "
            pdb=" N   GLU A 233 "
            pdb=" C   GLU A 233 "
            pdb=" CB  GLU A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.42e-01
  chirality pdb=" CA  LEU A 220 "
            pdb=" N   LEU A 220 "
            pdb=" C   LEU A 220 "
            pdb=" CB  LEU A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.12 2.00e-01 2.50e+01 3.33e-01
  chirality pdb=" CA  PRO A 221 "
            pdb=" N   PRO A 221 "
            pdb=" C   PRO A 221 "
            pdb=" CB  PRO A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.19e-01
  ... (remaining 541 not shown)

  Planarity restraints: 552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 104 "   -0.034 5.00e-02 4.00e+02   5.18e-02 4.30e+00
        pdb=" N   PRO A 105 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 162 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.64e+00
        pdb=" N   PRO A 163 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 163 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 163 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 303 "    0.019 5.00e-02 4.00e+02   2.94e-02 1.39e+00
        pdb=" N   PRO A 304 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 304 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 304 "    0.016 5.00e-02 4.00e+02
  ... (remaining 549 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 288
        2.74 -     3.28: 3401
        3.28 -     3.82: 5718
        3.82 -     4.36: 6918
        4.36 -     4.90: 11519
  Nonbonded interactions: 27844
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 415 "
            pdb=" OG1 THR A 419 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER A 350 "
            pdb=" OE1 GLN A 481 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OD2 ASP A 169 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OH  TYR A 128 "
            pdb=" OG1 THR A 203 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   THR A 263 "
            pdb=" OG1 THR A 263 "
     model   vdw
     2.326 3.040
  ... (remaining 27839 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:             0.190
  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:                    0.010
  Process input model:                     5.150
  Find NCS groups from input model:        0.010
  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:6.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
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      :  0.003   0.032   3340  Z= 0.120
  Angle     :  0.494   5.535   4556  Z= 0.268
  Chirality :  0.036   0.147    544
  Planarity :  0.004   0.052    552
  Dihedral  : 15.836  87.215   1158
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.75 %
    Favored  : 78.25 %
  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:  0.55 (0.40), residues: 416
  helix:  1.04 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -2.24 (0.61), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 423 
 TYR   0.018   0.001   TYR A 117 
 PHE   0.010   0.001   PHE A 114 
 TRP   0.004   0.001   TRP A 148 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3340)
  covalent geometry    : angle       0.49444 ( 4556)
  hydrogen bonds       : bond        0.20073 (  252)
  hydrogen bonds       : angle       7.25046 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.6626
  time to fit residues: 27.8067
Evaluate side-chains
  39 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
A 273 ASN
A 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.133230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.105047 restraints weight = 3860.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 1.72
r_work: 0.2940 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3340  Z= 0.169
  Angle     :  0.577   6.146   4556  Z= 0.308
  Chirality :  0.040   0.169    544
  Planarity :  0.005   0.050    552
  Dihedral  :  4.540  31.528    450
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.64 %
    Favored  : 79.38 %
  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 aren not related in a simple way.
  whole:  1.78 (0.43), residues: 416
  helix:  1.88 (0.29), residues: 337
  sheet:  None (None), residues: 0
  loop : -1.99 (0.72), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 423 
 TYR   0.023   0.002   TYR A 117 
 PHE   0.017   0.002   PHE A 114 
 TRP   0.007   0.001   TRP A 201 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3340)
  covalent geometry    : angle       0.57687 ( 4556)
  hydrogen bonds       : bond        0.05330 (  252)
  hydrogen bonds       : angle       4.86898 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 ASP cc_start: 0.7322 (t0) cc_final: 0.7043 (t0)
REVERT: A  423 ARG cc_start: 0.7652 (mmt-90) cc_final: 0.7305 (mmt180)
  outliers start: 7
  outliers final: 4
  residues processed: 47
  average time/residue: 0.5517
  time to fit residues: 26.6754
Evaluate side-chains
  47 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  326 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.104283 restraints weight = 3833.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.52
r_work: 0.2991 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3340  Z= 0.136
  Angle     :  0.527   6.065   4556  Z= 0.280
  Chirality :  0.038   0.164    544
  Planarity :  0.004   0.047    552
  Dihedral  :  4.481  30.510    450
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.80 %
    Favored  : 78.53 %
  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:  2.04 (0.43), residues: 416
  helix:  2.04 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.85 (0.75), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 423 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.014   0.002   PHE A 114 
 TRP   0.007   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3340)
  covalent geometry    : angle       0.52666 ( 4556)
  hydrogen bonds       : bond        0.04595 (  252)
  hydrogen bonds       : angle       4.54498 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 ASP cc_start: 0.8408 (m-30) cc_final: 0.8165 (m-30)
REVERT: A  196 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7376 (mt0)
REVERT: A  266 ASP cc_start: 0.7295 (t0) cc_final: 0.6805 (t0)
REVERT: A  298 GLU cc_start: 0.7348 (tp30) cc_final: 0.7130 (tp30)
REVERT: A  400 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.6888 (tm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 52
  average time/residue: 0.5397
  time to fit residues: 28.9533
Evaluate side-chains
  46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  426 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.8384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.107505 restraints weight = 3848.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.50
r_work: 0.3039 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3340  Z= 0.133
  Angle     :  0.526   6.117   4556  Z= 0.279
  Chirality :  0.038   0.167    544
  Planarity :  0.004   0.043    552
  Dihedral  :  4.466  30.517    450
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.36 %
    Favored  : 78.81 %
  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:  2.16 (0.43), residues: 416
  helix:  2.14 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.86 (0.75), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 423 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.014   0.002   PHE A 114 
 TRP   0.007   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3340)
  covalent geometry    : angle       0.52580 ( 4556)
  hydrogen bonds       : bond        0.04380 (  252)
  hydrogen bonds       : angle       4.41870 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7279 (mt0)
REVERT: A  266 ASP cc_start: 0.7370 (t0) cc_final: 0.6764 (t0)
REVERT: A  301 ARG cc_start: 0.7026 (ttm110) cc_final: 0.6352 (mtp180)
REVERT: A  326 ARG cc_start: 0.6783 (ptm160) cc_final: 0.5896 (mtt180)
REVERT: A  400 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.6888 (tm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 50
  average time/residue: 0.4457
  time to fit residues: 23.1372
Evaluate side-chains
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  419 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.135192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105744 restraints weight = 3795.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.50
r_work: 0.2998 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3340  Z= 0.130
  Angle     :  0.520   6.177   4556  Z= 0.277
  Chirality :  0.038   0.168    544
  Planarity :  0.004   0.042    552
  Dihedral  :  4.437  30.194    450
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.08 %
    Favored  : 78.81 %
  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:  2.27 (0.43), residues: 416
  helix:  2.28 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.86 (0.72), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 423 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.014   0.002   PHE A 114 
 TRP   0.007   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3340)
  covalent geometry    : angle       0.52045 ( 4556)
  hydrogen bonds       : bond        0.04250 (  252)
  hydrogen bonds       : angle       4.35178 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7251 (mt0)
REVERT: A  266 ASP cc_start: 0.7406 (t0) cc_final: 0.6852 (t0)
REVERT: A  301 ARG cc_start: 0.7039 (ttm110) cc_final: 0.6355 (mtp180)
REVERT: A  326 ARG cc_start: 0.6738 (ptm160) cc_final: 0.5860 (mtt180)
REVERT: A  400 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6854 (tm-30)
REVERT: A  512 LYS cc_start: 0.6624 (mmtt) cc_final: 0.6157 (pptt)
  outliers start: 11
  outliers final: 5
  residues processed: 48
  average time/residue: 0.4751
  time to fit residues: 23.5601
Evaluate side-chains
  49 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  426 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.137465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.108790 restraints weight = 3787.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.48
r_work: 0.3011 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3340  Z= 0.124
  Angle     :  0.508   6.151   4556  Z= 0.271
  Chirality :  0.037   0.166    544
  Planarity :  0.004   0.040    552
  Dihedral  :  4.401  29.963    450
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.08 %
    Favored  : 78.81 %
  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:  2.37 (0.43), residues: 416
  helix:  2.36 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.85 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 423 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.013   0.001   PHE A 114 
 TRP   0.007   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3340)
  covalent geometry    : angle       0.50833 ( 4556)
  hydrogen bonds       : bond        0.04114 (  252)
  hydrogen bonds       : angle       4.28553 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7182 (mt0)
REVERT: A  266 ASP cc_start: 0.7422 (t0) cc_final: 0.6810 (t0)
REVERT: A  301 ARG cc_start: 0.6855 (ttm110) cc_final: 0.6428 (mtp180)
REVERT: A  326 ARG cc_start: 0.6658 (ptm160) cc_final: 0.5938 (mtt180)
REVERT: A  364 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6924 (pp20)
REVERT: A  398 TYR cc_start: 0.7993 (m-80) cc_final: 0.7790 (m-80)
REVERT: A  400 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.6876 (tm-30)
REVERT: A  512 LYS cc_start: 0.6643 (mmtt) cc_final: 0.6198 (pptt)
  outliers start: 11
  outliers final: 5
  residues processed: 50
  average time/residue: 0.4499
  time to fit residues: 23.3363
Evaluate side-chains
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  364 GLU
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  426 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.107905 restraints weight = 3887.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 1.50
r_work: 0.3002 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3340  Z= 0.134
  Angle     :  0.520   6.121   4556  Z= 0.278
  Chirality :  0.038   0.170    544
  Planarity :  0.004   0.039    552
  Dihedral  :  4.436  30.229    450
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.08 %
    Favored  : 78.81 %
  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:  2.35 (0.43), residues: 416
  helix:  2.35 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.84 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 423 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.015   0.002   PHE A 114 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3340)
  covalent geometry    : angle       0.52048 ( 4556)
  hydrogen bonds       : bond        0.04230 (  252)
  hydrogen bonds       : angle       4.30871 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7235 (mt0)
REVERT: A  266 ASP cc_start: 0.7373 (t0) cc_final: 0.6778 (t0)
REVERT: A  326 ARG cc_start: 0.6661 (ptm160) cc_final: 0.5947 (mtt180)
REVERT: A  364 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6964 (pp20)
REVERT: A  400 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.6867 (tm-30)
REVERT: A  512 LYS cc_start: 0.6649 (mmtt) cc_final: 0.6207 (pptt)
  outliers start: 11
  outliers final: 6
  residues processed: 47
  average time/residue: 0.4138
  time to fit residues: 20.1452
Evaluate side-chains
  51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  364 GLU
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  515 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.107186 restraints weight = 3931.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.54
r_work: 0.3011 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3340  Z= 0.127
  Angle     :  0.516   6.233   4556  Z= 0.275
  Chirality :  0.038   0.167    544
  Planarity :  0.004   0.038    552
  Dihedral  :  4.415  29.953    450
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.36 %
    Favored  : 78.81 %
  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:  2.39 (0.43), residues: 416
  helix:  2.30 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.78 (0.75), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 301 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.014   0.002   PHE A 114 
 TRP   0.007   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3340)
  covalent geometry    : angle       0.51595 ( 4556)
  hydrogen bonds       : bond        0.04102 (  252)
  hydrogen bonds       : angle       4.27155 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7232 (mt0)
REVERT: A  201 TRP cc_start: 0.7710 (m100) cc_final: 0.5577 (p-90)
REVERT: A  266 ASP cc_start: 0.7387 (t0) cc_final: 0.6754 (t0)
REVERT: A  301 ARG cc_start: 0.7051 (ttm110) cc_final: 0.6351 (mtp180)
REVERT: A  326 ARG cc_start: 0.6637 (ptm160) cc_final: 0.5925 (mtt180)
REVERT: A  364 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6954 (pp20)
REVERT: A  400 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.6903 (tm-30)
REVERT: A  512 LYS cc_start: 0.6471 (mmtt) cc_final: 0.6126 (pptt)
  outliers start: 10
  outliers final: 6
  residues processed: 46
  average time/residue: 0.4425
  time to fit residues: 21.0639
Evaluate side-chains
  50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  364 GLU
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  515 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.136412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.106731 restraints weight = 3837.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.51
r_work: 0.3042 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3340  Z= 0.128
  Angle     :  0.518   6.140   4556  Z= 0.276
  Chirality :  0.038   0.167    544
  Planarity :  0.004   0.038    552
  Dihedral  :  4.419  30.089    450
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.36 %
    Favored  : 79.10 %
  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 aren not related in a simple way.
  whole:  2.39 (0.43), residues: 416
  helix:  2.31 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.84 (0.74), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 301 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.014   0.002   PHE A 114 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3340)
  covalent geometry    : angle       0.51778 ( 4556)
  hydrogen bonds       : bond        0.04107 (  252)
  hydrogen bonds       : angle       4.26138 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7324 (mt0)
REVERT: A  201 TRP cc_start: 0.7713 (m100) cc_final: 0.5573 (p-90)
REVERT: A  266 ASP cc_start: 0.7368 (t0) cc_final: 0.6718 (t0)
REVERT: A  301 ARG cc_start: 0.6973 (ttm110) cc_final: 0.6352 (mtp180)
REVERT: A  326 ARG cc_start: 0.6635 (ptm160) cc_final: 0.5929 (mtt180)
REVERT: A  400 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.6884 (tm-30)
REVERT: A  512 LYS cc_start: 0.6462 (mmtt) cc_final: 0.6151 (pptt)
  outliers start: 9
  outliers final: 6
  residues processed: 46
  average time/residue: 0.4611
  time to fit residues: 21.9913
Evaluate side-chains
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  515 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.137271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.108414 restraints weight = 3799.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.48
r_work: 0.3014 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3340  Z= 0.132
  Angle     :  0.525   6.171   4556  Z= 0.280
  Chirality :  0.038   0.169    544
  Planarity :  0.004   0.037    552
  Dihedral  :  4.438  30.323    450
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.64 %
    Favored  : 79.10 %
  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 aren not related in a simple way.
  whole:  2.33 (0.43), residues: 416
  helix:  2.28 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.91 (0.74), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 301 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.015   0.002   PHE A 114 
 TRP   0.007   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3340)
  covalent geometry    : angle       0.52510 ( 4556)
  hydrogen bonds       : bond        0.04154 (  252)
  hydrogen bonds       : angle       4.28232 (  756)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7296 (mt0)
REVERT: A  201 TRP cc_start: 0.7748 (m100) cc_final: 0.5628 (p-90)
REVERT: A  266 ASP cc_start: 0.7423 (t0) cc_final: 0.6770 (t0)
REVERT: A  326 ARG cc_start: 0.6651 (ptm160) cc_final: 0.5952 (mtt180)
REVERT: A  400 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.6909 (tm-30)
REVERT: A  512 LYS cc_start: 0.6436 (mmtt) cc_final: 0.6116 (pptt)
  outliers start: 8
  outliers final: 6
  residues processed: 44
  average time/residue: 0.5011
  time to fit residues: 22.8743
Evaluate side-chains
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  515 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.136607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.107322 restraints weight = 3870.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.51
r_work: 0.3008 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3340  Z= 0.132
  Angle     :  0.534   6.206   4556  Z= 0.283
  Chirality :  0.038   0.169    544
  Planarity :  0.005   0.049    552
  Dihedral  :  4.447  30.414    450
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.36 %
    Favored  : 78.81 %
  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:  2.36 (0.43), residues: 416
  helix:  2.36 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.93 (0.70), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 301 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.015   0.002   PHE A 114 
 TRP   0.007   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3340)
  covalent geometry    : angle       0.53351 ( 4556)
  hydrogen bonds       : bond        0.04127 (  252)
  hydrogen bonds       : angle       4.27207 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1210.24 seconds
wall clock time: 21 minutes 24.95 seconds (1284.95 seconds total)