Starting phenix.real_space_refine
on Tue Mar  3 11:23:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ex5_28651/03_2026/8ex5_28651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ex5_28651/03_2026/8ex5_28651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2026/8ex5_28651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2026/8ex5_28651.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2026/8ex5_28651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ex5_28651/03_2026/8ex5_28651.cif"
  }
  resolution = 3.47
  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=   0.018
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      17      5.16       5
     C    2090      2.51       5
     N     524      2.21       5
     O     546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3177
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3177
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 12, 'TRANS': 401}
          Chain breaks: 2
  Time building chain proxies: 0.87, per 1000 atoms: 0.27
  Number of scatterers: 3177
  At special positions: 0
  Unit cell: (70.092, 68.794, 79.827, 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      17     16.00
     O     546      8.00
     N     524      7.00
     C    2090      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: 0.27
  Conformation dependent library (CDL) restraints added in 121.4 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      90.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 3.628A  pdb=" N   ALA A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   VAL A 122 " --> pdb=" O   ASP A 118 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   LEU A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   ASP A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 165
      removed outlier: 3.726A  pdb=" N   ALA A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
      removed outlier: 3.792A  pdb=" N   ARG A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 186
    Processing helix  chain 'A' and resid 193 through 222
      Proline residue:  A 215  - end of helix
      removed outlier: 3.820A  pdb=" N   PHE A 222 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 256
      removed outlier: 4.259A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 265 through 281
      removed outlier: 4.435A  pdb=" N   LEU A 269 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 281 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 312 through 348
      Proline residue:  A 337  - end of helix
    Processing helix  chain 'A' and resid 361 through 392
    Processing helix  chain 'A' and resid 394 through 417
      removed outlier: 3.635A  pdb=" N   LEU A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   CYS A 400 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY A 403 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 438
      removed outlier: 4.295A  pdb=" N   LEU A 435 " --> pdb=" O   VAL A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 450
      removed outlier: 3.583A  pdb=" N   ALA A 444 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 454
      No H-bonds generated for 'chain 'A' and resid 452 through 454'
    Processing helix  chain 'A' and resid 455 through 470
    Processing helix  chain 'A' and resid 474 through 488
    Processing helix  chain 'A' and resid 493 through 538
      removed outlier: 4.238A  pdb=" N   CYS A 508 " --> pdb=" O   ALA A 504 " (cutoff:3.500A)
      Proline residue:  A 509  - end of helix
      removed outlier: 5.161A  pdb=" N   VAL A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   SER A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)

    274 hydrogen bonds defined for protein.
    822 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: 0.50

  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: 968
        1.34 -     1.46: 631
        1.46 -     1.58: 1626
        1.58 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 3251
  Sorted by residual:
  bond pdb=" C   CYS A 508 "
       pdb=" N   PRO A 509 "
    ideal  model  delta    sigma   weight residual
    1.333  1.356 -0.023 1.44e-02 4.82e+03 2.55e+00
  bond pdb=" C   SER A 266 "
       pdb=" N   PRO A 267 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.14e+00
  bond pdb=" N   LYS A 224 "
       pdb=" CA  LYS A 224 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.018 1.29e-02 6.01e+03 2.00e+00
  bond pdb=" CG  LEU A 171 "
       pdb=" CD2 LEU A 171 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.25e+00
  bond pdb=" CB  ILE A 107 "
       pdb=" CG2 ILE A 107 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 9.99e-01
  ... (remaining 3246 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 4132
        1.27 -     2.55: 227
        2.55 -     3.82: 35
        3.82 -     5.10: 16
        5.10 -     6.37: 6
  Bond angle restraints: 4416
  Sorted by residual:
  angle pdb=" N   ILE A 188 "
        pdb=" CA  ILE A 188 "
        pdb=" C   ILE A 188 "
      ideal   model   delta    sigma   weight residual
     108.95  112.36   -3.41 9.80e-01 1.04e+00 1.21e+01
  angle pdb=" N   VAL A 431 "
        pdb=" CA  VAL A 431 "
        pdb=" C   VAL A 431 "
      ideal   model   delta    sigma   weight residual
     112.80  108.88    3.92 1.15e+00 7.56e-01 1.16e+01
  angle pdb=" C   PHE A 177 "
        pdb=" N   TRP A 178 "
        pdb=" CA  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     120.31  115.32    4.99 1.52e+00 4.33e-01 1.08e+01
  angle pdb=" N   TRP A 178 "
        pdb=" CA  TRP A 178 "
        pdb=" CB  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     110.28  115.08   -4.80 1.55e+00 4.16e-01 9.58e+00
  angle pdb=" CA  TRP A 178 "
        pdb=" CB  TRP A 178 "
        pdb=" CG  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     113.60  119.39   -5.79 1.90e+00 2.77e-01 9.28e+00
  ... (remaining 4411 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 1714
       15.94 -    31.88: 125
       31.88 -    47.82: 26
       47.82 -    63.75: 6
       63.75 -    79.69: 1
  Dihedral angle restraints: 1872
    sinusoidal: 692
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CA  THR A 223 "
           pdb=" C   THR A 223 "
           pdb=" N   LYS A 224 "
           pdb=" CA  LYS A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.37  -23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  GLU A 207 "
           pdb=" C   GLU A 207 "
           pdb=" N   ALA A 208 "
           pdb=" CA  ALA A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.16   17.84     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  LEU A 221 "
           pdb=" C   LEU A 221 "
           pdb=" N   PHE A 222 "
           pdb=" CA  PHE A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.50  -17.50     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 1869 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 313
       0.031 -    0.061: 146
       0.061 -    0.092: 39
       0.092 -    0.123: 18
       0.123 -    0.153: 5
  Chirality restraints: 521
  Sorted by residual:
  chirality pdb=" CA  GLU A 207 "
            pdb=" N   GLU A 207 "
            pdb=" C   GLU A 207 "
            pdb=" CB  GLU A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  PRO A 267 "
            pdb=" N   PRO A 267 "
            pdb=" C   PRO A 267 "
            pdb=" CB  PRO A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  SER A 475 "
            pdb=" N   SER A 475 "
            pdb=" C   SER A 475 "
            pdb=" CB  SER A 475 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 518 not shown)

  Planarity restraints: 539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 178 "    0.025 2.00e-02 2.50e+03   2.10e-02 1.10e+01
        pdb=" CG  TRP A 178 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 178 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 178 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 178 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 178 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 178 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 508 "   -0.033 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 509 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 509 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 509 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 223 "   -0.007 2.00e-02 2.50e+03   1.45e-02 2.09e+00
        pdb=" C   THR A 223 "    0.025 2.00e-02 2.50e+03
        pdb=" O   THR A 223 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 224 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 536 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 52
        2.69 -     3.24: 3428
        3.24 -     3.80: 5240
        3.80 -     4.35: 6680
        4.35 -     4.90: 11130
  Nonbonded interactions: 26530
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 186 "
            pdb=" O   LEU A 263 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   GLY A 206 "
            pdb=" OG  SER A 209 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD1 ASP A 118 "
            pdb=" OG  SER A 266 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   MET A 404 "
            pdb=" OG  SER A 407 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" NH1 ARG A 167 "
            pdb=" OG1 THR A 216 "
     model   vdw
     2.368 3.120
  ... (remaining 26525 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:             3.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.170
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3251  Z= 0.207
  Angle     :  0.714   6.370   4416  Z= 0.423
  Chirality :  0.041   0.153    521
  Planarity :  0.005   0.051    539
  Dihedral  : 12.108  79.692   1116
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.42), residues: 408
  helix:  1.13 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -2.78 (0.82), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 264 
 TYR   0.018   0.002   TYR A 426 
 PHE   0.023   0.002   PHE A 465 
 TRP   0.058   0.003   TRP A 178 
 HIS   0.001   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3251)
  covalent geometry    : angle       0.71382 ( 4416)
  hydrogen bonds       : bond        0.09494 (  274)
  hydrogen bonds       : angle       5.54775 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  182 THR cc_start: 0.7787 (m) cc_final: 0.6251 (t)
REVERT: A  447 LEU cc_start: 0.8555 (tt) cc_final: 0.8258 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0498
  time to fit residues: 2.6032
Evaluate side-chains
  35 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.234858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.212992 restraints weight = 3675.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.4333 rms_B_bonded: 1.55
r_work: 0.4184 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3251  Z= 0.173
  Angle     :  0.614   6.275   4416  Z= 0.331
  Chirality :  0.042   0.155    521
  Planarity :  0.005   0.050    539
  Dihedral  :  5.008  20.854    444
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  7.46 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.41), residues: 408
  helix:  1.42 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -2.68 (0.77), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 264 
 TYR   0.015   0.002   TYR A 426 
 PHE   0.014   0.002   PHE A 327 
 TRP   0.037   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3251)
  covalent geometry    : angle       0.61352 ( 4416)
  hydrogen bonds       : bond        0.05293 (  274)
  hydrogen bonds       : angle       4.68541 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8046 (m) cc_final: 0.6363 (t)
REVERT: A  264 ARG cc_start: 0.4554 (mtp85) cc_final: 0.3537 (mtp-110)
REVERT: A  447 LEU cc_start: 0.8597 (tt) cc_final: 0.8324 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0570
  time to fit residues: 2.8968
Evaluate side-chains
  40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.235627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.213803 restraints weight = 3696.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.4354 rms_B_bonded: 1.52
r_work: 0.4177 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3251  Z= 0.163
  Angle     :  0.578   6.215   4416  Z= 0.312
  Chirality :  0.042   0.142    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.856  21.066    444
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.45 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.41), residues: 408
  helix:  1.55 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.60 (0.81), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.015   0.002   TYR A 426 
 PHE   0.014   0.002   PHE A 327 
 TRP   0.030   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 3251)
  covalent geometry    : angle       0.57787 ( 4416)
  hydrogen bonds       : bond        0.05056 (  274)
  hydrogen bonds       : angle       4.49124 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8060 (m) cc_final: 0.6336 (t)
REVERT: A  264 ARG cc_start: 0.4510 (mtp85) cc_final: 0.3346 (mtp-110)
REVERT: A  447 LEU cc_start: 0.8579 (tt) cc_final: 0.8299 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 43
  average time/residue: 0.0444
  time to fit residues: 2.5531
Evaluate side-chains
  40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0020
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.237020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.215087 restraints weight = 3696.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.4369 rms_B_bonded: 1.55
r_work: 0.4208 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3251  Z= 0.151
  Angle     :  0.555   6.406   4416  Z= 0.298
  Chirality :  0.041   0.139    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.742  20.825    444
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 11.34 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.42), residues: 408
  helix:  1.74 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.43 (0.82), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.016   0.002   TYR A 426 
 PHE   0.013   0.001   PHE A 327 
 TRP   0.024   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3251)
  covalent geometry    : angle       0.55457 ( 4416)
  hydrogen bonds       : bond        0.04802 (  274)
  hydrogen bonds       : angle       4.35692 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8031 (m) cc_final: 0.6349 (t)
REVERT: A  264 ARG cc_start: 0.4589 (mtp85) cc_final: 0.3254 (mtp-110)
REVERT: A  447 LEU cc_start: 0.8562 (tt) cc_final: 0.8286 (tp)
  outliers start: 4
  outliers final: 3
  residues processed: 42
  average time/residue: 0.0592
  time to fit residues: 3.1834
Evaluate side-chains
  42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  248 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.235341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.213402 restraints weight = 3638.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 1.53
r_work: 0.4144 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3251  Z= 0.164
  Angle     :  0.572   6.243   4416  Z= 0.308
  Chirality :  0.041   0.139    521
  Planarity :  0.004   0.050    539
  Dihedral  :  4.778  21.023    444
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.24 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.41), residues: 408
  helix:  1.68 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -2.09 (0.84), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.017   0.002   TYR A 426 
 PHE   0.014   0.002   PHE A 327 
 TRP   0.026   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3251)
  covalent geometry    : angle       0.57249 ( 4416)
  hydrogen bonds       : bond        0.04925 (  274)
  hydrogen bonds       : angle       4.37680 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8094 (m) cc_final: 0.6438 (t)
REVERT: A  264 ARG cc_start: 0.4605 (mtp85) cc_final: 0.3161 (mtp-110)
REVERT: A  447 LEU cc_start: 0.8612 (tt) cc_final: 0.8351 (tp)
  outliers start: 4
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0489
  time to fit residues: 2.7509
Evaluate side-chains
  43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  385 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 36 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.235976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.214022 restraints weight = 3587.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.4366 rms_B_bonded: 1.53
r_work: 0.4182 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3251  Z= 0.148
  Angle     :  0.545   5.978   4416  Z= 0.293
  Chirality :  0.040   0.139    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.681  20.432    444
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.54 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.42), residues: 408
  helix:  1.86 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.20 (0.84), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.017   0.002   TYR A 426 
 PHE   0.013   0.001   PHE A 327 
 TRP   0.026   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3251)
  covalent geometry    : angle       0.54520 ( 4416)
  hydrogen bonds       : bond        0.04688 (  274)
  hydrogen bonds       : angle       4.27984 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8042 (m) cc_final: 0.6362 (t)
REVERT: A  264 ARG cc_start: 0.4668 (mtp85) cc_final: 0.3277 (mtm180)
REVERT: A  439 ASN cc_start: 0.7224 (p0) cc_final: 0.6592 (m-40)
REVERT: A  447 LEU cc_start: 0.8576 (tt) cc_final: 0.8301 (tp)
REVERT: A  517 MET cc_start: 0.4525 (ttt) cc_final: 0.4219 (ttm)
  outliers start: 5
  outliers final: 4
  residues processed: 44
  average time/residue: 0.0519
  time to fit residues: 2.9856
Evaluate side-chains
  40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  385 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    0.0050
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 22 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.236857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.214596 restraints weight = 3687.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.4363 rms_B_bonded: 1.57
r_work: 0.4162 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3251  Z= 0.150
  Angle     :  0.555   6.213   4416  Z= 0.296
  Chirality :  0.041   0.137    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.682  19.983    444
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.24 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.42), residues: 408
  helix:  1.82 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -2.05 (0.86), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.016   0.001   TYR A 426 
 PHE   0.014   0.001   PHE A 327 
 TRP   0.026   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3251)
  covalent geometry    : angle       0.55487 ( 4416)
  hydrogen bonds       : bond        0.04698 (  274)
  hydrogen bonds       : angle       4.27879 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8078 (m) cc_final: 0.6426 (t)
REVERT: A  264 ARG cc_start: 0.4827 (mtp85) cc_final: 0.3350 (mtm180)
REVERT: A  439 ASN cc_start: 0.7251 (p0) cc_final: 0.6708 (m-40)
REVERT: A  447 LEU cc_start: 0.8574 (tt) cc_final: 0.8308 (tp)
REVERT: A  517 MET cc_start: 0.4520 (ttt) cc_final: 0.4189 (ttm)
REVERT: A  535 GLN cc_start: 0.5523 (mt0) cc_final: 0.5218 (mt0)
  outliers start: 6
  outliers final: 4
  residues processed: 43
  average time/residue: 0.0453
  time to fit residues: 2.5856
Evaluate side-chains
  39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  248 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 29 optimal weight:    0.1980
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0270
   chunk 31 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.238988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.216756 restraints weight = 3701.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.4387 rms_B_bonded: 1.58
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
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   0.032   3251  Z= 0.136
  Angle     :  0.533   6.230   4416  Z= 0.284
  Chirality :  0.040   0.136    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.507  19.455    444
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.84 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.42), residues: 408
  helix:  1.99 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.50 (0.94), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.016   0.001   TYR A 426 
 PHE   0.013   0.001   PHE A 327 
 TRP   0.026   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3251)
  covalent geometry    : angle       0.53257 ( 4416)
  hydrogen bonds       : bond        0.04387 (  274)
  hydrogen bonds       : angle       4.16102 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  182 THR cc_start: 0.7932 (m) cc_final: 0.6447 (t)
REVERT: A  264 ARG cc_start: 0.4518 (mtp85) cc_final: 0.3380 (mtm180)
REVERT: A  447 LEU cc_start: 0.8488 (tt) cc_final: 0.8213 (tp)
REVERT: A  517 MET cc_start: 0.4875 (ttt) cc_final: 0.4572 (ttm)
  outliers start: 5
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0484
  time to fit residues: 2.6780
Evaluate side-chains
  40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  454 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0370
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0470
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.240124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.217601 restraints weight = 3718.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.4393 rms_B_bonded: 1.59
r_work: 0.4213 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3251  Z= 0.132
  Angle     :  0.531   6.183   4416  Z= 0.283
  Chirality :  0.040   0.133    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.470  19.236    444
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.13 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.42), residues: 408
  helix:  2.07 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.41 (0.95), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.014   0.001   TYR A 426 
 PHE   0.012   0.001   PHE A 327 
 TRP   0.026   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3251)
  covalent geometry    : angle       0.53110 ( 4416)
  hydrogen bonds       : bond        0.04297 (  274)
  hydrogen bonds       : angle       4.11987 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  182 THR cc_start: 0.7988 (m) cc_final: 0.6285 (t)
REVERT: A  264 ARG cc_start: 0.4755 (mtp85) cc_final: 0.3313 (mtm180)
REVERT: A  447 LEU cc_start: 0.8503 (tt) cc_final: 0.8240 (tp)
REVERT: A  517 MET cc_start: 0.4554 (ttt) cc_final: 0.4210 (ttm)
  outliers start: 4
  outliers final: 3
  residues processed: 40
  average time/residue: 0.0474
  time to fit residues: 2.5492
Evaluate side-chains
  38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0770
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.236017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.213964 restraints weight = 3572.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.4376 rms_B_bonded: 1.54
r_work: 0.4210 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3251  Z= 0.151
  Angle     :  0.560   6.258   4416  Z= 0.300
  Chirality :  0.041   0.169    521
  Planarity :  0.004   0.050    539
  Dihedral  :  4.504  18.974    444
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 14.03 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.42), residues: 408
  helix:  2.04 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -1.57 (0.89), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.015   0.001   TYR A 426 
 PHE   0.019   0.002   PHE A 465 
 TRP   0.027   0.002   TRP A 178 
 HIS   0.001   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3251)
  covalent geometry    : angle       0.55967 ( 4416)
  hydrogen bonds       : bond        0.04567 (  274)
  hydrogen bonds       : angle       4.21847 (  822)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  182 THR cc_start: 0.8010 (m) cc_final: 0.6387 (t)
REVERT: A  264 ARG cc_start: 0.4790 (mtp85) cc_final: 0.3341 (mtm180)
REVERT: A  517 MET cc_start: 0.4603 (ttt) cc_final: 0.4284 (ttm)
  outliers start: 3
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0466
  time to fit residues: 2.2841
Evaluate side-chains
  36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.236854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.214547 restraints weight = 3705.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.4365 rms_B_bonded: 1.54
r_work: 0.4177 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3251  Z= 0.159
  Angle     :  0.571   6.353   4416  Z= 0.306
  Chirality :  0.041   0.155    521
  Planarity :  0.004   0.049    539
  Dihedral  :  4.568  17.834    444
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 15.22 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.42), residues: 408
  helix:  1.92 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -1.53 (0.88), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.015   0.002   TYR A 426 
 PHE   0.018   0.002   PHE A 465 
 TRP   0.027   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3251)
  covalent geometry    : angle       0.57069 ( 4416)
  hydrogen bonds       : bond        0.04740 (  274)
  hydrogen bonds       : angle       4.34240 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 910.63 seconds
wall clock time: 16 minutes 16.67 seconds (976.67 seconds total)