Starting phenix.real_space_refine
on Fri Aug 22 13:57:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qsn_18637/08_2025/8qsn_18637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qsn_18637/08_2025/8qsn_18637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qsn_18637/08_2025/8qsn_18637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qsn_18637/08_2025/8qsn_18637.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qsn_18637/08_2025/8qsn_18637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qsn_18637/08_2025/8qsn_18637.cif"
  }
  resolution = 3.54
  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: 0.93, per 1000 atoms: 0.26
  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: 0.19
  Conformation dependent library (CDL) restraints added in 99.5 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: 0.09
  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: 0.35

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.23 -     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:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.910
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
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  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6367 (mtm-85)
REVERT: A   44 GLU cc_start: 0.9074 (tp30) cc_final: 0.8872 (tp30)
REVERT: A   47 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: A   91 PHE cc_start: 0.8834 (m-80) cc_final: 0.8615 (m-10)
REVERT: A  198 PHE cc_start: 0.9062 (t80) cc_final: 0.8784 (t80)
REVERT: A  200 TRP cc_start: 0.9108 (t60) cc_final: 0.8457 (t60)
REVERT: A  313 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8758 (mm-30)
REVERT: A  342 TYR cc_start: 0.8828 (m-10) cc_final: 0.8493 (m-80)
REVERT: A  369 LEU cc_start: 0.8668 (mt) cc_final: 0.8262 (mt)
REVERT: A  427 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8093 (mt)
REVERT: A  451 LEU cc_start: 0.9283 (tp) cc_final: 0.9027 (mp)
REVERT: A  454 GLN cc_start: 0.8598 (tp40) cc_final: 0.8199 (tp40)
REVERT: A  457 GLN cc_start: 0.7851 (pt0) cc_final: 0.6235 (pt0)
REVERT: A  474 GLU cc_start: 0.8866 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: A  535 TYR cc_start: 0.8685 (t80) cc_final: 0.8193 (t80)
  outliers start: 14
  outliers final: 3
  residues processed: 181
  average time/residue: 0.0613
  time to fit residues: 13.3143
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  : 0.085 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0470
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4678

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.098449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.084364 restraints weight = 13672.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.086755 restraints weight = 7764.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.088241 restraints weight = 5136.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.089415 restraints weight = 3816.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.090157 restraints weight = 3008.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3407

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= 0.152
  Angle     :  0.720  10.108   4985  Z= 0.339
  Chirality :  0.040   0.164    574
  Planarity :  0.005   0.049    611
  Dihedral  :  5.719  54.764    502
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.50 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.40), residues: 456
  helix:  2.35 (0.27), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.81 (0.58), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 394 
 TYR   0.013   0.002   TYR A 342 
 PHE   0.034   0.002   PHE A 417 
 TRP   0.025   0.001   TRP A  69 
 HIS   0.003   0.001   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3672)
  covalent geometry    : angle       0.71977 ( 4985)
  hydrogen bonds       : bond        0.04397 (  281)
  hydrogen bonds       : angle       3.98003 (  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
  124 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6527 (ptp-170)
REVERT: A   44 GLU cc_start: 0.9321 (tp30) cc_final: 0.9044 (tp30)
REVERT: A   47 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8722 (tm-30)
REVERT: A   91 PHE cc_start: 0.8862 (m-80) cc_final: 0.8619 (m-10)
REVERT: A  200 TRP cc_start: 0.9090 (t60) cc_final: 0.8423 (t60)
REVERT: A  235 LEU cc_start: 0.9520 (mt) cc_final: 0.8954 (tp)
REVERT: A  309 GLU cc_start: 0.8836 (pm20) cc_final: 0.8246 (pm20)
REVERT: A  331 TYR cc_start: 0.9009 (t80) cc_final: 0.8493 (t80)
REVERT: A  369 LEU cc_start: 0.8942 (mt) cc_final: 0.8524 (mt)
REVERT: A  427 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8408 (mt)
REVERT: A  451 LEU cc_start: 0.9278 (tp) cc_final: 0.9009 (mp)
REVERT: A  465 GLU cc_start: 0.8436 (tp30) cc_final: 0.8180 (tp30)
REVERT: A  535 TYR cc_start: 0.8844 (t80) cc_final: 0.8415 (t80)
  outliers start: 14
  outliers final: 7
  residues processed: 120
  average time/residue: 0.0359
  time to fit residues: 5.7996
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
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  241 LEU
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:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.097210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.083615 restraints weight = 13559.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.085775 restraints weight = 7918.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.087242 restraints weight = 5350.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.088123 restraints weight = 4000.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.088867 restraints weight = 3301.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
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   0.032   3672  Z= 0.144
  Angle     :  0.715  11.370   4985  Z= 0.338
  Chirality :  0.040   0.153    574
  Planarity :  0.005   0.055    611
  Dihedral  :  5.714  54.751    500
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 20.91 %
    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:  2.13 (0.40), residues: 456
  helix:  2.13 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop : -1.83 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 192 
 TYR   0.017   0.002   TYR A 335 
 PHE   0.049   0.002   PHE A 372 
 TRP   0.009   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3672)
  covalent geometry    : angle       0.71541 ( 4985)
  hydrogen bonds       : bond        0.04253 (  281)
  hydrogen bonds       : angle       3.95519 (  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
  118 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6515 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9128 (t60) cc_final: 0.8457 (t60)
REVERT: A  301 MET cc_start: 0.6179 (tpt) cc_final: 0.5851 (tmm)
REVERT: A  307 PHE cc_start: 0.3825 (OUTLIER) cc_final: 0.3529 (m-80)
REVERT: A  331 TYR cc_start: 0.9062 (t80) cc_final: 0.8591 (t80)
REVERT: A  427 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8553 (mt)
REVERT: A  458 TYR cc_start: 0.8935 (m-80) cc_final: 0.8679 (m-80)
REVERT: A  474 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: A  489 MET cc_start: 0.9537 (tpp) cc_final: 0.9314 (tpp)
REVERT: A  535 TYR cc_start: 0.8868 (t80) cc_final: 0.8502 (t80)
  outliers start: 19
  outliers final: 11
  residues processed: 112
  average time/residue: 0.0339
  time to fit residues: 5.1591
Evaluate side-chains
  106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
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  427 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:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0050
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 203 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.097533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.083935 restraints weight = 13686.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.086156 restraints weight = 7912.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.087608 restraints weight = 5352.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.088634 restraints weight = 4036.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.089333 restraints weight = 3240.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3672  Z= 0.132
  Angle     :  0.672  11.019   4985  Z= 0.322
  Chirality :  0.040   0.174    574
  Planarity :  0.005   0.045    611
  Dihedral  :  5.873  54.283    500
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 23.32 %
    Favored  : 71.31 %
  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:  2.02 (0.40), residues: 456
  helix:  2.09 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.97 (0.62), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  48 
 TYR   0.013   0.001   TYR A 335 
 PHE   0.058   0.002   PHE A 372 
 TRP   0.007   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3672)
  covalent geometry    : angle       0.67224 ( 4985)
  hydrogen bonds       : bond        0.04068 (  281)
  hydrogen bonds       : angle       3.87706 (  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
  126 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6499 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9152 (t60) cc_final: 0.8456 (t60)
REVERT: A  213 ILE cc_start: 0.9442 (mm) cc_final: 0.9236 (tp)
REVERT: A  220 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7292 (m)
REVERT: A  301 MET cc_start: 0.6044 (tpt) cc_final: 0.5842 (tmm)
REVERT: A  307 PHE cc_start: 0.3813 (OUTLIER) cc_final: 0.3481 (m-80)
REVERT: A  310 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: A  331 TYR cc_start: 0.9088 (t80) cc_final: 0.8564 (t80)
REVERT: A  427 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8574 (mt)
REVERT: A  451 LEU cc_start: 0.9246 (tp) cc_final: 0.8997 (mp)
REVERT: A  458 TYR cc_start: 0.8994 (m-80) cc_final: 0.8762 (m-80)
REVERT: A  474 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8194 (mt-10)
REVERT: A  489 MET cc_start: 0.9538 (tpp) cc_final: 0.9337 (tpp)
REVERT: A  535 TYR cc_start: 0.8900 (t80) cc_final: 0.8522 (t80)
  outliers start: 20
  outliers final: 8
  residues processed: 120
  average time/residue: 0.0390
  time to fit residues: 6.2627
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  : 0.110 
-------------------------------------------------------------------------------
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  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  383 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  429 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 3 optimal weight:    0.4980
   chunk 14 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.097629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.084237 restraints weight = 13768.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.086428 restraints weight = 7876.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.087683 restraints weight = 5306.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.088797 restraints weight = 4097.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.089530 restraints weight = 3254.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3672  Z= 0.131
  Angle     :  0.716  12.672   4985  Z= 0.333
  Chirality :  0.040   0.188    574
  Planarity :  0.005   0.044    611
  Dihedral  :  5.951  56.085    500
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 24.66 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.40), residues: 456
  helix:  1.99 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -2.22 (0.63), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  48 
 TYR   0.016   0.001   TYR A 444 
 PHE   0.057   0.002   PHE A 372 
 TRP   0.005   0.001   TRP A  69 
 HIS   0.000   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3672)
  covalent geometry    : angle       0.71589 ( 4985)
  hydrogen bonds       : bond        0.04076 (  281)
  hydrogen bonds       : angle       3.81959 (  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
  125 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6517 (ptp-170)
REVERT: A   44 GLU cc_start: 0.9167 (tp30) cc_final: 0.8721 (tp30)
REVERT: A  200 TRP cc_start: 0.9185 (t60) cc_final: 0.8494 (t60)
REVERT: A  213 ILE cc_start: 0.9411 (mm) cc_final: 0.9198 (tp)
REVERT: A  301 MET cc_start: 0.6116 (tpt) cc_final: 0.5837 (tmm)
REVERT: A  307 PHE cc_start: 0.3846 (OUTLIER) cc_final: 0.3523 (m-80)
REVERT: A  331 TYR cc_start: 0.9066 (t80) cc_final: 0.8611 (t80)
REVERT: A  371 MET cc_start: 0.8740 (mtt) cc_final: 0.8528 (ptp)
REVERT: A  427 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8580 (mt)
REVERT: A  454 GLN cc_start: 0.8836 (tp40) cc_final: 0.8177 (tp40)
REVERT: A  474 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8184 (mt-10)
REVERT: A  535 TYR cc_start: 0.8914 (t80) cc_final: 0.8568 (t80)
  outliers start: 23
  outliers final: 12
  residues processed: 118
  average time/residue: 0.0398
  time to fit residues: 6.2419
Evaluate side-chains
  108 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
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  191 THR
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  307 PHE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  559 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0030
   chunk 1 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.6790

-------------------------------------------------------------------------------
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 = 0.3921 r_free = 0.3921 target = 0.097847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.083941 restraints weight = 13941.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.086145 restraints weight = 8054.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.087644 restraints weight = 5418.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.088714 restraints weight = 4050.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.089384 restraints weight = 3263.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.4991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3672  Z= 0.137
  Angle     :  0.749  13.814   4985  Z= 0.352
  Chirality :  0.040   0.175    574
  Planarity :  0.004   0.046    611
  Dihedral  :  6.017  57.157    500
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 25.47 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.41), residues: 456
  helix:  2.04 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.98 (0.64), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  48 
 TYR   0.013   0.001   TYR A 458 
 PHE   0.053   0.001   PHE A 372 
 TRP   0.007   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3672)
  covalent geometry    : angle       0.74904 ( 4985)
  hydrogen bonds       : bond        0.04050 (  281)
  hydrogen bonds       : angle       3.79368 (  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
  112 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6535 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9173 (t60) cc_final: 0.8459 (t60)
REVERT: A  213 ILE cc_start: 0.9415 (mm) cc_final: 0.9201 (tp)
REVERT: A  301 MET cc_start: 0.6397 (tpt) cc_final: 0.6113 (tmm)
REVERT: A  307 PHE cc_start: 0.3797 (OUTLIER) cc_final: 0.3462 (m-80)
REVERT: A  331 TYR cc_start: 0.9114 (t80) cc_final: 0.8694 (t80)
REVERT: A  427 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8574 (mt)
REVERT: A  474 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8311 (mt-10)
REVERT: A  535 TYR cc_start: 0.8899 (t80) cc_final: 0.8563 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0411
  time to fit residues: 5.8295
Evaluate side-chains
  106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
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  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  324 VAL
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  484 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.095837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.082245 restraints weight = 14357.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.084482 restraints weight = 8117.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.085942 restraints weight = 5376.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.086954 restraints weight = 4009.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.087622 restraints weight = 3233.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.5153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3672  Z= 0.146
  Angle     :  0.781  14.164   4985  Z= 0.357
  Chirality :  0.041   0.167    574
  Planarity :  0.004   0.047    611
  Dihedral  :  6.079  57.851    500
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 26.81 %
    Favored  : 68.63 %
  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:  1.84 (0.41), residues: 456
  helix:  1.98 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -2.29 (0.66), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  48 
 TYR   0.014   0.001   TYR A 477 
 PHE   0.056   0.002   PHE A 372 
 TRP   0.004   0.001   TRP A 453 
 HIS   0.001   0.000   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3672)
  covalent geometry    : angle       0.78092 ( 4985)
  hydrogen bonds       : bond        0.04116 (  281)
  hydrogen bonds       : angle       3.81010 (  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
  113 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6458 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9175 (t60) cc_final: 0.8438 (t60)
REVERT: A  213 ILE cc_start: 0.9411 (mm) cc_final: 0.9206 (tp)
REVERT: A  301 MET cc_start: 0.6440 (tpt) cc_final: 0.6178 (tmm)
REVERT: A  310 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: A  371 MET cc_start: 0.8591 (mtt) cc_final: 0.8110 (mmm)
REVERT: A  427 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8647 (mt)
REVERT: A  474 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8320 (mt-10)
REVERT: A  535 TYR cc_start: 0.8936 (t80) cc_final: 0.8616 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0490
  time to fit residues: 7.1500
Evaluate side-chains
  101 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
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  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  324 VAL
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  429 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:    0.0570
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.097196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.084342 restraints weight = 14119.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.086542 restraints weight = 8005.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.087828 restraints weight = 5273.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.088947 restraints weight = 3994.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.089699 restraints weight = 3176.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3672  Z= 0.140
  Angle     :  0.790  12.717   4985  Z= 0.361
  Chirality :  0.043   0.365    574
  Planarity :  0.004   0.047    611
  Dihedral  :  6.130  59.070    500
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.61 %
    Favored  : 67.83 %
  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:  1.92 (0.41), residues: 456
  helix:  2.00 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.86 (0.67), residues: 90

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   0.053   0.001   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        0.00311 ( 3672)
  covalent geometry    : angle       0.78960 ( 4985)
  hydrogen bonds       : bond        0.04114 (  281)
  hydrogen bonds       : angle       3.82677 (  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
  110 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6439 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9116 (t60) cc_final: 0.8464 (t60)
REVERT: A  301 MET cc_start: 0.6417 (tpt) cc_final: 0.6186 (tmm)
REVERT: A  371 MET cc_start: 0.8585 (mtt) cc_final: 0.8148 (mmm)
REVERT: A  427 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8606 (mt)
REVERT: A  474 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8303 (mt-10)
REVERT: A  535 TYR cc_start: 0.8954 (t80) cc_final: 0.8713 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0529
  time to fit residues: 7.3405
Evaluate side-chains
  103 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
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  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  324 VAL
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  429 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:    0.0030
   chunk 30 optimal weight:    0.0370
   chunk 9 optimal weight:    0.0270
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.1524

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.098197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.083976 restraints weight = 13728.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.086202 restraints weight = 7917.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.087789 restraints weight = 5339.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.088897 restraints weight = 3985.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.089657 restraints weight = 3210.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.5509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3672  Z= 0.146
  Angle     :  0.838  12.868   4985  Z= 0.376
  Chirality :  0.044   0.332    574
  Planarity :  0.004   0.043    611
  Dihedral  :  6.164  59.587    500
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.72
  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:  1.81 (0.40), residues: 456
  helix:  1.91 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -2.08 (0.68), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  48 
 TYR   0.018   0.001   TYR A 215 
 PHE   0.050   0.002   PHE A 372 
 TRP   0.008   0.001   TRP A 517 
 HIS   0.003   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3672)
  covalent geometry    : angle       0.83796 ( 4985)
  hydrogen bonds       : bond        0.04044 (  281)
  hydrogen bonds       : angle       3.82064 (  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
  112 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6434 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9087 (t60) cc_final: 0.8499 (t60)
REVERT: A  237 PHE cc_start: 0.9330 (t80) cc_final: 0.9106 (m-80)
REVERT: A  331 TYR cc_start: 0.9003 (t80) cc_final: 0.8608 (t80)
REVERT: A  371 MET cc_start: 0.8574 (mtt) cc_final: 0.8137 (mmm)
REVERT: A  427 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8479 (mt)
REVERT: A  474 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8192 (mt-10)
REVERT: A  535 TYR cc_start: 0.8879 (t80) cc_final: 0.8574 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0461
  time to fit residues: 6.6726
Evaluate side-chains
  103 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    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   45 LEU
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  427 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  484 MET
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:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0470
   chunk 15 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0980
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.097189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.082814 restraints weight = 13767.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.085029 restraints weight = 8063.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.086609 restraints weight = 5445.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.087704 restraints weight = 4067.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.088435 restraints weight = 3270.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.5741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3672  Z= 0.150
  Angle     :  0.870  13.199   4985  Z= 0.396
  Chirality :  0.044   0.313    574
  Planarity :  0.004   0.043    611
  Dihedral  :  5.803  54.813    500
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 29.22 %
    Favored  : 67.29 %
  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:  1.83 (0.40), residues: 456
  helix:  1.94 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.95 (0.66), residues: 90

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   0.054   0.001   PHE A 372 
 TRP   0.005   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3672)
  covalent geometry    : angle       0.87034 ( 4985)
  hydrogen bonds       : bond        0.04004 (  281)
  hydrogen bonds       : angle       3.86647 (  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
  112 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6470 (ptp-170)
REVERT: A  172 LYS cc_start: 0.9295 (mmmt) cc_final: 0.9064 (mmmt)
REVERT: A  200 TRP cc_start: 0.9093 (t60) cc_final: 0.8482 (t60)
REVERT: A  331 TYR cc_start: 0.9003 (t80) cc_final: 0.8614 (t80)
REVERT: A  371 MET cc_start: 0.8602 (mtt) cc_final: 0.8149 (mmm)
REVERT: A  427 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8507 (mt)
REVERT: A  474 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: A  535 TYR cc_start: 0.8885 (t80) cc_final: 0.8544 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0443
  time to fit residues: 6.4439
Evaluate side-chains
  106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  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  115 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  429 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:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   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 = 0.3882 r_free = 0.3882 target = 0.097143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.082491 restraints weight = 13256.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.084742 restraints weight = 7815.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.086370 restraints weight = 5279.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.087398 restraints weight = 3940.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.088243 restraints weight = 3199.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3672  Z= 0.156
  Angle     :  0.895  13.005   4985  Z= 0.409
  Chirality :  0.045   0.297    574
  Planarity :  0.004   0.043    611
  Dihedral  :  5.642  54.695    499
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 29.22 %
    Favored  : 66.76 %
  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:  1.75 (0.40), residues: 456
  helix:  1.91 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -2.30 (0.66), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  48 
 TYR   0.022   0.001   TYR A 477 
 PHE   0.061   0.002   PHE A 372 
 TRP   0.009   0.001   TRP A 517 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3672)
  covalent geometry    : angle       0.89488 ( 4985)
  hydrogen bonds       : bond        0.04076 (  281)
  hydrogen bonds       : angle       3.95931 (  837)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 753.78 seconds
wall clock time: 13 minutes 46.60 seconds (826.60 seconds total)