Starting phenix.real_space_refine
on Fri Aug 22 13:57:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qsm_18636/08_2025/8qsm_18636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qsm_18636/08_2025/8qsm_18636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qsm_18636/08_2025/8qsm_18636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qsm_18636/08_2025/8qsm_18636.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qsm_18636/08_2025/8qsm_18636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qsm_18636/08_2025/8qsm_18636.map"
  }
  resolution = 3.69
  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=   0.013
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      20      5.16       5
     C    2377      2.51       5
     N     573      2.21       5
     O     609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3579
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3579
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 18, 'TRANS': 445}
          Chain breaks: 3
  Time building chain proxies: 0.82, per 1000 atoms: 0.23
  Number of scatterers: 3579
  At special positions: 0
  Unit cell: (80.465, 70.015, 65.835, 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      20     16.00
     O     609      8.00
     N     573      7.00
     C    2377      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: 0.21
  Conformation dependent library (CDL) restraints added in 103.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  846

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      83.4% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 57
      removed outlier: 4.287A  pdb=" N   ASN A  57 " --> pdb=" O   GLY A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 65
    Processing helix  chain 'A' and resid 70 through 98
      removed outlier: 3.899A  pdb=" N   SER A  89 " --> pdb=" O   THR A  85 " (cutoff:3.500A)
      Proline residue:  A  90  - end of helix
    Processing helix  chain 'A' and resid 102 through 118
    Processing helix  chain 'A' and resid 156 through 183
      removed outlier: 4.226A  pdb=" N   THR A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 3.629A  pdb=" N   VAL A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 218
      removed outlier: 3.818A  pdb=" N   THR A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ALA A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 246
      removed outlier: 3.931A  pdb=" N   GLY A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR A 226 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      Proline residue:  A 229  - end of helix
      removed outlier: 3.638A  pdb=" N   VAL A 246 " --> pdb=" O   CYS A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 273
    Processing helix  chain 'A' and resid 297 through 305
      removed outlier: 3.954A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY A 305 " --> pdb=" O   MET A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 347
      removed outlier: 3.942A  pdb=" N   VAL A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
      Proline residue:  A 323  - end of helix
      Proline residue:  A 330  - end of helix
      removed outlier: 3.691A  pdb=" N   VAL A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 349
      No H-bonds generated for 'chain 'A' and resid 348 through 349'
    Processing helix  chain 'A' and resid 365 through 366
      No H-bonds generated for 'chain 'A' and resid 365 through 366'
    Processing helix  chain 'A' and resid 367 through 396
      removed outlier: 3.958A  pdb=" N   ASP A 373 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 374 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
      Proline residue:  A 382  - end of helix
      removed outlier: 5.109A  pdb=" N   ASP A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      Proline residue:  A 390  - end of helix
    Processing helix  chain 'A' and resid 400 through 431
      removed outlier: 3.528A  pdb=" N   LYS A 431 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 453
      removed outlier: 4.034A  pdb=" N   TRP A 453 " --> pdb=" O   SER A 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 450 through 453'
    Processing helix  chain 'A' and resid 454 through 468
    Processing helix  chain 'A' and resid 468 through 479
    Processing helix  chain 'A' and resid 484 through 510
    Processing helix  chain 'A' and resid 531 through 560
      removed outlier: 3.573A  pdb=" N   HIS A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439

    281 hydrogen bonds defined for protein.
    837 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: 0.45

  Time building geometry restraints manager: 0.29 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: 1081
        1.34 -     1.46: 817
        1.46 -     1.58: 1743
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 3672
  Sorted by residual:
  bond pdb=" CB  PRO A 399 "
       pdb=" CG  PRO A 399 "
    ideal  model  delta    sigma   weight residual
    1.492  1.537 -0.045 5.00e-02 4.00e+02 8.11e-01
  bond pdb=" CA  ILE A 329 "
       pdb=" C   ILE A 329 "
    ideal  model  delta    sigma   weight residual
    1.523  1.531 -0.008 9.20e-03 1.18e+04 7.12e-01
  bond pdb=" C   VAL A 246 "
       pdb=" O   VAL A 246 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.19e-02 7.06e+03 6.67e-01
  bond pdb=" CB  PRO A 306 "
       pdb=" CG  PRO A 306 "
    ideal  model  delta    sigma   weight residual
    1.492  1.524 -0.032 5.00e-02 4.00e+02 4.05e-01
  bond pdb=" N   VAL A 322 "
       pdb=" CA  VAL A 322 "
    ideal  model  delta    sigma   weight residual
    1.463  1.470 -0.007 1.18e-02 7.18e+03 4.00e-01
  ... (remaining 3667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 4860
        1.18 -     2.36: 89
        2.36 -     3.55: 23
        3.55 -     4.73: 7
        4.73 -     5.91: 6
  Bond angle restraints: 4985
  Sorted by residual:
  angle pdb=" C   PHE A 247 "
        pdb=" N   ILE A 248 "
        pdb=" CA  ILE A 248 "
      ideal   model   delta    sigma   weight residual
     121.97  125.78   -3.81 1.80e+00 3.09e-01 4.48e+00
  angle pdb=" N   ILE A 466 "
        pdb=" CA  ILE A 466 "
        pdb=" C   ILE A 466 "
      ideal   model   delta    sigma   weight residual
     113.00  110.27    2.73 1.30e+00 5.92e-01 4.42e+00
  angle pdb=" N   GLU A 309 "
        pdb=" CA  GLU A 309 "
        pdb=" C   GLU A 309 "
      ideal   model   delta    sigma   weight residual
     110.80  115.23   -4.43 2.13e+00 2.20e-01 4.32e+00
  angle pdb=" C   THR A 308 "
        pdb=" N   GLU A 309 "
        pdb=" CA  GLU A 309 "
      ideal   model   delta    sigma   weight residual
     121.54  125.26   -3.72 1.91e+00 2.74e-01 3.79e+00
  angle pdb=" N   ALA A 468 "
        pdb=" CA  ALA A 468 "
        pdb=" C   ALA A 468 "
      ideal   model   delta    sigma   weight residual
     111.02  113.92   -2.90 1.52e+00 4.33e-01 3.64e+00
  ... (remaining 4980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.62: 1970
       14.62 -    29.24: 99
       29.24 -    43.87: 29
       43.87 -    58.49: 8
       58.49 -    73.11: 2
  Dihedral angle restraints: 2108
    sinusoidal: 785
      harmonic: 1323
  Sorted by residual:
  dihedral pdb=" CA  THR A 308 "
           pdb=" C   THR A 308 "
           pdb=" N   GLU A 309 "
           pdb=" CA  GLU A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.82  -16.18     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  ARG A  33 "
           pdb=" CB  ARG A  33 "
           pdb=" CG  ARG A  33 "
           pdb=" CD  ARG A  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.47   55.47     3      1.50e+01 4.44e-03 9.35e+00
  dihedral pdb=" CA  ARG A 104 "
           pdb=" CB  ARG A 104 "
           pdb=" CG  ARG A 104 "
           pdb=" CD  ARG A 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  127.75   52.25     3      1.50e+01 4.44e-03 9.10e+00
  ... (remaining 2105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 389
       0.025 -    0.050: 100
       0.050 -    0.075: 55
       0.075 -    0.101: 24
       0.101 -    0.126: 6
  Chirality restraints: 574
  Sorted by residual:
  chirality pdb=" CA  THR A 176 "
            pdb=" N   THR A 176 "
            pdb=" C   THR A 176 "
            pdb=" CB  THR A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  ILE A 439 "
            pdb=" N   ILE A 439 "
            pdb=" C   ILE A 439 "
            pdb=" CB  ILE A 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  chirality pdb=" CA  ILE A 435 "
            pdb=" N   ILE A 435 "
            pdb=" C   ILE A 435 "
            pdb=" CB  ILE A 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.12e-01
  ... (remaining 571 not shown)

  Planarity restraints: 611
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 238 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   VAL A 238 "    0.027 2.00e-02 2.50e+03
        pdb=" O   VAL A 238 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   VAL A 239 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 239 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.44e+00
        pdb=" C   VAL A 239 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   VAL A 239 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE A 240 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 237 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   PHE A 237 "    0.026 2.00e-02 2.50e+03
        pdb=" O   PHE A 237 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   VAL A 238 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 608 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 887
        2.80 -     3.32: 3828
        3.32 -     3.85: 5935
        3.85 -     4.37: 6627
        4.37 -     4.90: 11289
  Nonbonded interactions: 28566
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 264 "
            pdb=" OG  SER A 267 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ILE A 461 "
            pdb=" OG  SER A 464 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   GLY A 499 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   LYS A 262 "
            pdb=" OG1 THR A 265 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   CYS A 242 "
            pdb=" OG  SER A 245 "
     model   vdw
     2.326 3.040
  ... (remaining 28561 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:                     4.250
  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:    6.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
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      :  0.002   0.045   3672  Z= 0.114
  Angle     :  0.482   5.910   4985  Z= 0.259
  Chirality :  0.034   0.126    574
  Planarity :  0.004   0.029    611
  Dihedral  : 10.371  73.110   1262
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  :  6.17 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.41), residues: 456
  helix:  2.29 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop : -1.69 (0.60), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 192 
 TYR   0.006   0.001   TYR A  52 
 PHE   0.009   0.001   PHE A 198 
 TRP   0.004   0.001   TRP A 332 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 3672)
  covalent geometry    : angle       0.48155 ( 4985)
  hydrogen bonds       : bond        0.10547 (  281)
  hydrogen bonds       : angle       5.39646 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6378 (mtm-85)
REVERT: A   47 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8512 (tm-30)
REVERT: A   91 PHE cc_start: 0.8867 (m-80) cc_final: 0.8633 (m-10)
REVERT: A  198 PHE cc_start: 0.9093 (t80) cc_final: 0.8810 (t80)
REVERT: A  200 TRP cc_start: 0.9106 (t60) cc_final: 0.8447 (t60)
REVERT: A  313 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8762 (mm-30)
REVERT: A  342 TYR cc_start: 0.8881 (m-10) cc_final: 0.8544 (m-80)
REVERT: A  369 LEU cc_start: 0.8694 (mt) cc_final: 0.8279 (mt)
REVERT: A  427 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8142 (mt)
REVERT: A  451 LEU cc_start: 0.9317 (tp) cc_final: 0.9072 (mp)
REVERT: A  454 GLN cc_start: 0.8734 (tp40) cc_final: 0.8242 (tp40)
REVERT: A  457 GLN cc_start: 0.7944 (pt0) cc_final: 0.6272 (pt0)
REVERT: A  474 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: A  535 TYR cc_start: 0.8767 (t80) cc_final: 0.8253 (t80)
  outliers start: 14
  outliers final: 3
  residues processed: 181
  average time/residue: 0.0594
  time to fit residues: 13.1179
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  427 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0470
   chunk 37 optimal weight:    0.0040
   overall best weight:    0.3690

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

Flipped N/Q/H residues before XYZ refinement:
A 345 GLN
A 521 HIS
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.097897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.083586 restraints weight = 13621.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.085893 restraints weight = 7811.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.087510 restraints weight = 5210.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.088633 restraints weight = 3837.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.089410 restraints weight = 3046.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3672  Z= 0.146
  Angle     :  0.727  10.170   4985  Z= 0.342
  Chirality :  0.040   0.161    574
  Planarity :  0.005   0.053    611
  Dihedral  :  5.718  54.617    502
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.23 %
    Favored  : 78.28 %
  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:  2.28 (0.40), residues: 456
  helix:  2.31 (0.27), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.85 (0.58), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 192 
 TYR   0.014   0.002   TYR A 444 
 PHE   0.034   0.002   PHE A 417 
 TRP   0.025   0.001   TRP A  69 
 HIS   0.002   0.001   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3672)
  covalent geometry    : angle       0.72678 ( 4985)
  hydrogen bonds       : bond        0.04398 (  281)
  hydrogen bonds       : angle       3.97143 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6537 (ptp-170)
REVERT: A   69 TRP cc_start: 0.7132 (m100) cc_final: 0.6774 (m100)
REVERT: A   91 PHE cc_start: 0.8861 (m-80) cc_final: 0.8618 (m-10)
REVERT: A  200 TRP cc_start: 0.9105 (t60) cc_final: 0.8478 (t60)
REVERT: A  235 LEU cc_start: 0.9533 (mt) cc_final: 0.8966 (tp)
REVERT: A  301 MET cc_start: 0.5909 (tpt) cc_final: 0.5688 (tmm)
REVERT: A  331 TYR cc_start: 0.8994 (t80) cc_final: 0.8529 (t80)
REVERT: A  369 LEU cc_start: 0.8979 (mt) cc_final: 0.8508 (mt)
REVERT: A  427 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8447 (mt)
REVERT: A  451 LEU cc_start: 0.9303 (tp) cc_final: 0.9065 (mp)
REVERT: A  535 TYR cc_start: 0.8883 (t80) cc_final: 0.8449 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 119
  average time/residue: 0.0359
  time to fit residues: 5.8094
Evaluate side-chains
  102 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  532 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   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 = 0.3858 r_free = 0.3858 target = 0.097078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.083311 restraints weight = 13399.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.085436 restraints weight = 7837.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.086883 restraints weight = 5365.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.087848 restraints weight = 4063.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.088583 restraints weight = 3332.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.4090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3672  Z= 0.138
  Angle     :  0.706  10.958   4985  Z= 0.330
  Chirality :  0.040   0.174    574
  Planarity :  0.005   0.055    611
  Dihedral  :  5.760  54.771    500
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 20.64 %
    Favored  : 73.99 %
  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:  1.98 (0.40), residues: 456
  helix:  2.03 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop : -1.88 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 192 
 TYR   0.019   0.002   TYR A 335 
 PHE   0.045   0.002   PHE A 372 
 TRP   0.008   0.001   TRP A  69 
 HIS   0.003   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3672)
  covalent geometry    : angle       0.70589 ( 4985)
  hydrogen bonds       : bond        0.04198 (  281)
  hydrogen bonds       : angle       3.98172 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6517 (ptp-170)
REVERT: A   91 PHE cc_start: 0.8844 (m-80) cc_final: 0.8641 (m-10)
REVERT: A  200 TRP cc_start: 0.9162 (t60) cc_final: 0.8465 (t60)
REVERT: A  301 MET cc_start: 0.6146 (tpt) cc_final: 0.5926 (tmm)
REVERT: A  307 PHE cc_start: 0.3912 (OUTLIER) cc_final: 0.3639 (m-80)
REVERT: A  310 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: A  331 TYR cc_start: 0.8930 (t80) cc_final: 0.8602 (t80)
REVERT: A  369 LEU cc_start: 0.9123 (mt) cc_final: 0.8775 (mt)
REVERT: A  454 GLN cc_start: 0.8770 (tp40) cc_final: 0.8251 (tp40)
REVERT: A  474 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8199 (mt-10)
REVERT: A  535 TYR cc_start: 0.8815 (t80) cc_final: 0.8462 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 115
  average time/residue: 0.0355
  time to fit residues: 5.6071
Evaluate side-chains
  108 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  532 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 33 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 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 = 0.3843 r_free = 0.3843 target = 0.096067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.082604 restraints weight = 13685.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.084764 restraints weight = 8006.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.086299 restraints weight = 5436.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.087180 restraints weight = 4041.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.087967 restraints weight = 3336.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3672  Z= 0.143
  Angle     :  0.686  10.899   4985  Z= 0.332
  Chirality :  0.041   0.156    574
  Planarity :  0.005   0.046    611
  Dihedral  :  5.698  54.570    498
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 22.25 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.40), residues: 456
  helix:  2.04 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.83 (0.65), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  48 
 TYR   0.017   0.002   TYR A 215 
 PHE   0.053   0.002   PHE A 372 
 TRP   0.006   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3672)
  covalent geometry    : angle       0.68578 ( 4985)
  hydrogen bonds       : bond        0.04131 (  281)
  hydrogen bonds       : angle       3.90186 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6473 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9208 (t60) cc_final: 0.8445 (t60)
REVERT: A  213 ILE cc_start: 0.9320 (mm) cc_final: 0.9117 (tp)
REVERT: A  220 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7462 (m)
REVERT: A  307 PHE cc_start: 0.4053 (OUTLIER) cc_final: 0.3784 (m-80)
REVERT: A  331 TYR cc_start: 0.9004 (t80) cc_final: 0.8700 (t80)
REVERT: A  535 TYR cc_start: 0.8828 (t80) cc_final: 0.8469 (t80)
  outliers start: 22
  outliers final: 11
  residues processed: 112
  average time/residue: 0.0436
  time to fit residues: 6.5530
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  484 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    0.2980
   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 454 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 = 0.3830 r_free = 0.3830 target = 0.095582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.081215 restraints weight = 13620.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.083458 restraints weight = 7902.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.084987 restraints weight = 5331.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.086034 restraints weight = 3984.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.086848 restraints weight = 3234.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3672  Z= 0.131
  Angle     :  0.711  11.188   4985  Z= 0.333
  Chirality :  0.041   0.186    574
  Planarity :  0.005   0.044    611
  Dihedral  :  5.776  54.784    498
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 23.32 %
    Favored  : 71.05 %
  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:  1.94 (0.40), residues: 456
  helix:  2.01 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -2.05 (0.67), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  48 
 TYR   0.018   0.001   TYR A 444 
 PHE   0.051   0.002   PHE A 372 
 TRP   0.006   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3672)
  covalent geometry    : angle       0.71141 ( 4985)
  hydrogen bonds       : bond        0.04076 (  281)
  hydrogen bonds       : angle       3.73579 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6503 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9205 (t60) cc_final: 0.8427 (t60)
REVERT: A  220 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7361 (m)
REVERT: A  457 GLN cc_start: 0.8298 (pm20) cc_final: 0.7776 (pm20)
REVERT: A  474 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8268 (mt-10)
REVERT: A  535 TYR cc_start: 0.8871 (t80) cc_final: 0.8522 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 109
  average time/residue: 0.0433
  time to fit residues: 6.2613
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  484 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0030
   chunk 1 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
A 203 ASN
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.095567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.082096 restraints weight = 13566.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.084245 restraints weight = 7806.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.085731 restraints weight = 5274.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.086799 restraints weight = 3947.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.087600 restraints weight = 3168.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3672  Z= 0.128
  Angle     :  0.715  10.345   4985  Z= 0.337
  Chirality :  0.041   0.235    574
  Planarity :  0.004   0.045    611
  Dihedral  :  5.823  57.548    498
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 26.01 %
    Favored  : 69.71 %
  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:  1.99 (0.40), residues: 456
  helix:  2.05 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -2.05 (0.67), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  48 
 TYR   0.013   0.001   TYR A 477 
 PHE   0.061   0.001   PHE A 372 
 TRP   0.009   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3672)
  covalent geometry    : angle       0.71463 ( 4985)
  hydrogen bonds       : bond        0.04098 (  281)
  hydrogen bonds       : angle       3.68521 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6448 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9177 (t60) cc_final: 0.8489 (t60)
REVERT: A  220 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7397 (m)
REVERT: A  331 TYR cc_start: 0.9048 (t80) cc_final: 0.8628 (t80)
REVERT: A  535 TYR cc_start: 0.8816 (t80) cc_final: 0.8460 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0437
  time to fit residues: 6.2293
Evaluate side-chains
  107 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 182 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 = 0.3811 r_free = 0.3811 target = 0.094148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.080606 restraints weight = 13931.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.082875 restraints weight = 7920.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.084346 restraints weight = 5280.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.085476 restraints weight = 3911.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.085992 restraints weight = 3101.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.5238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3672  Z= 0.148
  Angle     :  0.772  13.043   4985  Z= 0.358
  Chirality :  0.042   0.168    574
  Planarity :  0.004   0.047    611
  Dihedral  :  5.413  59.351    496
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 26.81 %
    Favored  : 68.90 %
  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:  2.03 (0.41), residues: 456
  helix:  2.09 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -2.11 (0.67), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  48 
 TYR   0.014   0.001   TYR A 477 
 PHE   0.057   0.002   PHE A 372 
 TRP   0.006   0.001   TRP A  94 
 HIS   0.001   0.000   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3672)
  covalent geometry    : angle       0.77186 ( 4985)
  hydrogen bonds       : bond        0.04140 (  281)
  hydrogen bonds       : angle       3.77251 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6422 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9204 (t60) cc_final: 0.8511 (t60)
REVERT: A  331 TYR cc_start: 0.9124 (t80) cc_final: 0.8710 (t80)
REVERT: A  474 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8262 (mt-10)
REVERT: A  535 TYR cc_start: 0.8950 (t80) cc_final: 0.8654 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0402
  time to fit residues: 5.8521
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  484 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0060
   chunk 15 optimal weight:    0.0570
   chunk 22 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4714

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

Flipped N/Q/H residues before XYZ refinement:
** A 454 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 = 0.3828 r_free = 0.3828 target = 0.095737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.081089 restraints weight = 13460.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.083083 restraints weight = 7762.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.084710 restraints weight = 5501.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.085809 restraints weight = 4102.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.086681 restraints weight = 3318.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.5430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3672  Z= 0.138
  Angle     :  0.866  16.007   4985  Z= 0.382
  Chirality :  0.045   0.291    574
  Planarity :  0.004   0.047    611
  Dihedral  :  5.416  59.264    496
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 28.42 %
    Favored  : 68.10 %
  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:  1.93 (0.41), residues: 456
  helix:  2.01 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.96 (0.66), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  48 
 TYR   0.017   0.001   TYR A 215 
 PHE   0.059   0.002   PHE A 372 
 TRP   0.005   0.001   TRP A 517 
 HIS   0.001   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3672)
  covalent geometry    : angle       0.86586 ( 4985)
  hydrogen bonds       : bond        0.04208 (  281)
  hydrogen bonds       : angle       3.77144 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6427 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9145 (t60) cc_final: 0.8497 (t60)
REVERT: A  331 TYR cc_start: 0.9104 (t80) cc_final: 0.8747 (t80)
REVERT: A  371 MET cc_start: 0.8825 (ptp) cc_final: 0.8508 (mpp)
REVERT: A  474 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8213 (mt-10)
REVERT: A  535 TYR cc_start: 0.8951 (t80) cc_final: 0.8698 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0507
  time to fit residues: 7.3869
Evaluate side-chains
  104 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  484 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    0.1980
   chunk 24 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.096063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.081394 restraints weight = 13354.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.083591 restraints weight = 7802.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.085146 restraints weight = 5353.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.086114 restraints weight = 4035.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.086933 restraints weight = 3332.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.5632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3672  Z= 0.146
  Angle     :  0.880  13.202   4985  Z= 0.394
  Chirality :  0.043   0.195    574
  Planarity :  0.004   0.044    611
  Dihedral  :  5.415  58.002    496
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 28.95 %
    Favored  : 68.10 %
  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:  1.78 (0.41), residues: 456
  helix:  1.91 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -2.21 (0.67), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  48 
 TYR   0.017   0.001   TYR A 477 
 PHE   0.059   0.001   PHE A 372 
 TRP   0.007   0.001   TRP A  94 
 HIS   0.001   0.000   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3672)
  covalent geometry    : angle       0.88021 ( 4985)
  hydrogen bonds       : bond        0.04220 (  281)
  hydrogen bonds       : angle       3.80599 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6418 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9159 (t60) cc_final: 0.8492 (t60)
REVERT: A  237 PHE cc_start: 0.9294 (t80) cc_final: 0.9065 (m-80)
REVERT: A  331 TYR cc_start: 0.9123 (t80) cc_final: 0.8770 (t80)
REVERT: A  371 MET cc_start: 0.8812 (ptp) cc_final: 0.8387 (mmm)
REVERT: A  535 TYR cc_start: 0.8953 (t80) cc_final: 0.8672 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 105
  average time/residue: 0.0364
  time to fit residues: 5.2592
Evaluate side-chains
  106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0070
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7400

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.096389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.081916 restraints weight = 13346.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.084068 restraints weight = 7953.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.085574 restraints weight = 5457.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.086677 restraints weight = 4123.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.087418 restraints weight = 3337.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.5742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3672  Z= 0.149
  Angle     :  0.898  14.439   4985  Z= 0.404
  Chirality :  0.045   0.267    574
  Planarity :  0.004   0.044    611
  Dihedral  :  5.036  54.315    496
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 28.95 %
    Favored  : 68.36 %
  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:  1.70 (0.40), residues: 456
  helix:  1.84 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.97 (0.67), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  48 
 TYR   0.018   0.001   TYR A 215 
 PHE   0.057   0.002   PHE A 372 
 TRP   0.009   0.001   TRP A 517 
 HIS   0.001   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3672)
  covalent geometry    : angle       0.89752 ( 4985)
  hydrogen bonds       : bond        0.04318 (  281)
  hydrogen bonds       : angle       3.83103 (  837)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6732 (mtt180)
REVERT: A  200 TRP cc_start: 0.9132 (t60) cc_final: 0.8479 (t60)
REVERT: A  331 TYR cc_start: 0.9061 (t80) cc_final: 0.8739 (t80)
REVERT: A  371 MET cc_start: 0.8736 (ptp) cc_final: 0.8315 (mmm)
REVERT: A  535 TYR cc_start: 0.8895 (t80) cc_final: 0.8644 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 103
  average time/residue: 0.0486
  time to fit residues: 6.7034
Evaluate side-chains
  101 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.094984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.081789 restraints weight = 13158.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.083942 restraints weight = 7732.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.085328 restraints weight = 5220.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.086386 restraints weight = 3926.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.087146 restraints weight = 3132.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.5987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3672  Z= 0.159
  Angle     :  0.908  12.849   4985  Z= 0.413
  Chirality :  0.045   0.203    574
  Planarity :  0.005   0.043    611
  Dihedral  :  4.893  54.312    495
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 28.95 %
    Favored  : 68.10 %
  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:  1.69 (0.41), residues: 456
  helix:  1.83 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.92 (0.67), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  48 
 TYR   0.016   0.001   TYR A 477 
 PHE   0.057   0.002   PHE A 372 
 TRP   0.010   0.001   TRP A 517 
 HIS   0.001   0.000   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3672)
  covalent geometry    : angle       0.90772 ( 4985)
  hydrogen bonds       : bond        0.04349 (  281)
  hydrogen bonds       : angle       3.92256 (  837)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 718.13 seconds
wall clock time: 13 minutes 3.91 seconds (783.91 seconds total)