Starting phenix.real_space_refine
on Fri May  9 20:21:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qsm_18636/05_2025/8qsm_18636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qsm_18636/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qsm_18636/05_2025/8qsm_18636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qsm_18636/05_2025/8qsm_18636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qsm_18636/05_2025/8qsm_18636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qsm_18636/05_2025/8qsm_18636.cif"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.72, per 1000 atoms: 0.76
  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: 1.03
  Conformation dependent library (CDL) restraints added in 455.6 milliseconds
  

  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: 0.29
  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: 0.95

  Time building geometry restraints manager: 1.14 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:             0.570
  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:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.970
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.610
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.004   0.001   TRP A 332 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.009   0.001   PHE A 198 
 TYR   0.006   0.001   TYR A  52 
 ARG   0.001   0.000   ARG A 192 

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

*********************** 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  : 0.411 
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: 0.1699
  time to fit residues: 36.6607
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  : 0.474 
-------------------------------------------------------------------------------
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 38 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0170
   chunk 19 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0770
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.3976

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.097800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.083656 restraints weight = 13324.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.085890 restraints weight = 7645.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.087503 restraints weight = 5114.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3458

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= 0.149
  Angle     :  0.727  10.213   4985  Z= 0.342
  Chirality :  0.040   0.168    574
  Planarity :  0.005   0.053    611
  Dihedral  :  5.718  54.646    502
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.50 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.40), residues: 456
  helix:  2.31 (0.27), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.84 (0.58), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  69 
 HIS   0.003   0.001   HIS A 521 
 PHE   0.034   0.002   PHE A 417 
 TYR   0.014   0.002   TYR A 444 
 ARG   0.006   0.001   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04393 (  281)
  hydrogen bonds       : angle       3.97149 (  837)
  covalent geometry    : bond        0.00314 ( 3672)
  covalent geometry    : angle       0.72716 ( 4985)

*********************** 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
  120 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6549 (ptp-170)
REVERT: A   91 PHE cc_start: 0.8880 (m-80) cc_final: 0.8641 (m-10)
REVERT: A  200 TRP cc_start: 0.9099 (t60) cc_final: 0.8435 (t60)
REVERT: A  235 LEU cc_start: 0.9525 (mt) cc_final: 0.8956 (tp)
REVERT: A  301 MET cc_start: 0.5912 (tpt) cc_final: 0.5673 (tmm)
REVERT: A  331 TYR cc_start: 0.8999 (t80) cc_final: 0.8538 (t80)
REVERT: A  369 LEU cc_start: 0.8989 (mt) cc_final: 0.8542 (mt)
REVERT: A  427 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8448 (mt)
REVERT: A  451 LEU cc_start: 0.9305 (tp) cc_final: 0.9068 (mp)
REVERT: A  535 TYR cc_start: 0.8868 (t80) cc_final: 0.8455 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 117
  average time/residue: 0.1078
  time to fit residues: 16.5319
Evaluate side-chains
  101 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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 16 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 35 optimal weight:    0.4980
   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 = 0.3861 r_free = 0.3861 target = 0.097265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.083505 restraints weight = 13395.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.085675 restraints weight = 7880.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.087159 restraints weight = 5366.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.4096

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= 0.137
  Angle     :  0.714  11.434   4985  Z= 0.332
  Chirality :  0.040   0.168    574
  Planarity :  0.005   0.054    611
  Dihedral  :  5.786  54.802    500
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 20.64 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.40), residues: 456
  helix:  2.01 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop : -1.87 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 521 
 PHE   0.042   0.002   PHE A 372 
 TYR   0.016   0.002   TYR A 335 
 ARG   0.004   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  281)
  hydrogen bonds       : angle       3.97177 (  837)
  covalent geometry    : bond        0.00290 ( 3672)
  covalent geometry    : angle       0.71386 ( 4985)

*********************** 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
  119 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6529 (ptp-170)
REVERT: A   91 PHE cc_start: 0.8900 (m-80) cc_final: 0.8665 (m-10)
REVERT: A  200 TRP cc_start: 0.9130 (t60) cc_final: 0.8435 (t60)
REVERT: A  301 MET cc_start: 0.6267 (tpt) cc_final: 0.6039 (tmm)
REVERT: A  307 PHE cc_start: 0.3857 (OUTLIER) cc_final: 0.3582 (m-80)
REVERT: A  310 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7463 (tm-30)
REVERT: A  331 TYR cc_start: 0.8935 (t80) cc_final: 0.8614 (t80)
REVERT: A  427 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8477 (mt)
REVERT: A  454 GLN cc_start: 0.8752 (tp40) cc_final: 0.8245 (tp40)
REVERT: A  474 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: A  535 TYR cc_start: 0.8790 (t80) cc_final: 0.8412 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 112
  average time/residue: 0.1101
  time to fit residues: 16.2047
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  : 0.392 
-------------------------------------------------------------------------------
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  207 ILE
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  532 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0470
   chunk 15 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.7682

-------------------------------------------------------------------------------
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**
A 559 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.097121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.083701 restraints weight = 13524.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.085876 restraints weight = 7914.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.087377 restraints weight = 5351.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4478

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= 0.130
  Angle     :  0.678  11.017   4985  Z= 0.327
  Chirality :  0.041   0.178    574
  Planarity :  0.004   0.045    611
  Dihedral  :  5.944  54.646    500
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 21.18 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.40), residues: 456
  helix:  1.99 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.81 (0.64), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 559 
 PHE   0.057   0.002   PHE A 372 
 TYR   0.017   0.002   TYR A 215 
 ARG   0.003   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  281)
  hydrogen bonds       : angle       3.87777 (  837)
  covalent geometry    : bond        0.00277 ( 3672)
  covalent geometry    : angle       0.67814 ( 4985)

*********************** 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
  120 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6488 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9178 (t60) cc_final: 0.8506 (t60)
REVERT: A  213 ILE cc_start: 0.9362 (mm) cc_final: 0.9157 (tp)
REVERT: A  307 PHE cc_start: 0.3904 (OUTLIER) cc_final: 0.3626 (m-80)
REVERT: A  331 TYR cc_start: 0.9002 (t80) cc_final: 0.8628 (t80)
REVERT: A  427 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8497 (mt)
REVERT: A  458 TYR cc_start: 0.8872 (m-80) cc_final: 0.8665 (m-80)
REVERT: A  535 TYR cc_start: 0.8773 (t80) cc_final: 0.8402 (t80)
  outliers start: 24
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1113
  time to fit residues: 16.7149
Evaluate side-chains
  104 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.1980
   chunk 19 optimal weight:    0.0870
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 559 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.096575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.082049 restraints weight = 13632.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.084272 restraints weight = 7955.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.085848 restraints weight = 5374.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4792

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= 0.130
  Angle     :  0.710  11.358   4985  Z= 0.334
  Chirality :  0.041   0.197    574
  Planarity :  0.004   0.044    611
  Dihedral  :  6.002  55.350    500
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 24.40 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.40), residues: 456
  helix:  2.05 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.94 (0.65), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 395 
 PHE   0.052   0.002   PHE A 372 
 TYR   0.013   0.001   TYR A 477 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  281)
  hydrogen bonds       : angle       3.74672 (  837)
  covalent geometry    : bond        0.00276 ( 3672)
  covalent geometry    : angle       0.70961 ( 4985)

*********************** 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
  111 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6500 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9192 (t60) cc_final: 0.8481 (t60)
REVERT: A  331 TYR cc_start: 0.9072 (t80) cc_final: 0.8677 (t80)
REVERT: A  427 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8553 (mt)
REVERT: A  535 TYR cc_start: 0.8833 (t80) cc_final: 0.8467 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1112
  time to fit residues: 15.5432
Evaluate side-chains
  104 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
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  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  324 VAL
Chi-restraints excluded: chain A residue  338 MET
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  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 43 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0050
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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**
A 559 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.095889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.082230 restraints weight = 13751.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.084467 restraints weight = 7980.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.085990 restraints weight = 5345.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4999

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= 0.128
  Angle     :  0.690  10.197   4985  Z= 0.331
  Chirality :  0.040   0.172    574
  Planarity :  0.004   0.046    611
  Dihedral  :  6.012  55.513    500
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 23.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.41), residues: 456
  helix:  2.07 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -2.16 (0.67), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 395 
 PHE   0.056   0.001   PHE A 372 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.004   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  281)
  hydrogen bonds       : angle       3.65571 (  837)
  covalent geometry    : bond        0.00274 ( 3672)
  covalent geometry    : angle       0.68971 ( 4985)

*********************** 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
  119 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6497 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9189 (t60) cc_final: 0.8438 (t60)
REVERT: A  331 TYR cc_start: 0.9081 (t80) cc_final: 0.8670 (t80)
REVERT: A  427 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8560 (mt)
REVERT: A  535 TYR cc_start: 0.8864 (t80) cc_final: 0.8552 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 110
  average time/residue: 0.1037
  time to fit residues: 15.1321
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  : 0.382 
-------------------------------------------------------------------------------
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  299 CYS
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  459 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 12 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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**
A 528 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.090881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.077983 restraints weight = 13874.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.080014 restraints weight = 7969.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.081423 restraints weight = 5323.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.5418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3672  Z= 0.228
  Angle     :  0.835  13.350   4985  Z= 0.398
  Chirality :  0.044   0.151    574
  Planarity :  0.005   0.048    611
  Dihedral  :  5.841  58.682    498
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 26.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.41), residues: 456
  helix:  2.00 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -2.43 (0.66), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 517 
 HIS   0.002   0.001   HIS A 559 
 PHE   0.050   0.002   PHE A 372 
 TYR   0.014   0.001   TYR A 477 
 ARG   0.007   0.001   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04680 (  281)
  hydrogen bonds       : angle       4.02801 (  837)
  covalent geometry    : bond        0.00485 ( 3672)
  covalent geometry    : angle       0.83476 ( 4985)

*********************** 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
  110 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6568 (ptp-170)
REVERT: A   60 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9084 (tp)
REVERT: A  200 TRP cc_start: 0.9234 (t60) cc_final: 0.8749 (t60)
  outliers start: 18
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1117
  time to fit residues: 15.2098
Evaluate side-chains
  99 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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  157 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  423 GLU
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:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0000
   chunk 21 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0470
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0270
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.3340

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

Flipped N/Q/H residues before XYZ refinement:
A 559 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.094646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.081213 restraints weight = 13409.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.083400 restraints weight = 7615.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.084943 restraints weight = 5065.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.5611

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= 0.143
  Angle     :  0.843  13.329   4985  Z= 0.378
  Chirality :  0.043   0.297    574
  Planarity :  0.004   0.047    611
  Dihedral  :  5.488  58.799    496
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.41), residues: 456
  helix:  2.03 (0.28), residues: 371
  sheet:  None (None), residues: 0
  loop : -2.20 (0.68), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  94 
 HIS   0.001   0.000   HIS A 521 
 PHE   0.055   0.002   PHE A 372 
 TYR   0.019   0.002   TYR A 477 
 ARG   0.005   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04393 (  281)
  hydrogen bonds       : angle       3.77664 (  837)
  covalent geometry    : bond        0.00304 ( 3672)
  covalent geometry    : angle       0.84304 ( 4985)

*********************** 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
  113 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6394 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9144 (t60) cc_final: 0.8515 (t60)
REVERT: A  371 MET cc_start: 0.8865 (ptp) cc_final: 0.8520 (mpp)
REVERT: A  457 GLN cc_start: 0.8234 (pm20) cc_final: 0.7808 (pm20)
REVERT: A  504 SER cc_start: 0.9403 (t) cc_final: 0.9200 (p)
  outliers start: 17
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1113
  time to fit residues: 15.7777
Evaluate side-chains
  101 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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  157 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  258 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 39 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0570
   chunk 10 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8102

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.093953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.080496 restraints weight = 13391.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.082597 restraints weight = 7690.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.084079 restraints weight = 5159.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.5787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3672  Z= 0.151
  Angle     :  0.843  12.145   4985  Z= 0.384
  Chirality :  0.044   0.278    574
  Planarity :  0.004   0.042    611
  Dihedral  :  4.936  54.329    496
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 30.56 %
    Favored  : 66.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.41), residues: 456
  helix:  1.89 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -2.24 (0.68), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 517 
 HIS   0.001   0.000   HIS A 521 
 PHE   0.052   0.002   PHE A 372 
 TYR   0.018   0.001   TYR A 477 
 ARG   0.004   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04384 (  281)
  hydrogen bonds       : angle       3.84669 (  837)
  covalent geometry    : bond        0.00342 ( 3672)
  covalent geometry    : angle       0.84257 ( 4985)

*********************** 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
  106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6789 (mtt180)
REVERT: A  200 TRP cc_start: 0.9138 (t60) cc_final: 0.8517 (t60)
REVERT: A  371 MET cc_start: 0.8858 (ptp) cc_final: 0.8532 (mpp)
REVERT: A  504 SER cc_start: 0.9417 (t) cc_final: 0.9201 (p)
  outliers start: 12
  outliers final: 10
  residues processed: 102
  average time/residue: 0.1100
  time to fit residues: 14.7613
Evaluate side-chains
  102 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
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  247 PHE
Chi-restraints excluded: chain A residue  258 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0770
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.095069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.081936 restraints weight = 13147.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.083966 restraints weight = 7721.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.085230 restraints weight = 5253.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3672  Z= 0.150
  Angle     :  0.883  12.361   4985  Z= 0.403
  Chirality :  0.045   0.285    574
  Planarity :  0.005   0.044    611
  Dihedral  :  4.811  54.331    495
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 31.10 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.41), residues: 456
  helix:  1.85 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -2.04 (0.67), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 517 
 HIS   0.001   0.000   HIS A 521 
 PHE   0.051   0.002   PHE A 372 
 TYR   0.019   0.001   TYR A 215 
 ARG   0.004   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  281)
  hydrogen bonds       : angle       3.86826 (  837)
  covalent geometry    : bond        0.00333 ( 3672)
  covalent geometry    : angle       0.88256 ( 4985)

********************** 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
  104 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6773 (mtt180)
REVERT: A  200 TRP cc_start: 0.9118 (t60) cc_final: 0.8489 (t60)
REVERT: A  235 LEU cc_start: 0.9367 (mm) cc_final: 0.9083 (mt)
REVERT: A  331 TYR cc_start: 0.9075 (t80) cc_final: 0.8701 (t80)
REVERT: A  371 MET cc_start: 0.8791 (ptp) cc_final: 0.8503 (mpp)
REVERT: A  489 MET cc_start: 0.9250 (tpp) cc_final: 0.9049 (tpp)
REVERT: A  504 SER cc_start: 0.9391 (t) cc_final: 0.9188 (p)
  outliers start: 9
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1146
  time to fit residues: 14.8680
Evaluate side-chains
  102 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
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  247 PHE
Chi-restraints excluded: chain A residue  258 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0970
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.095832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.082023 restraints weight = 13454.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.084252 restraints weight = 7833.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.085713 restraints weight = 5261.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.6118

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= 0.150
  Angle     :  0.893  12.293   4985  Z= 0.408
  Chirality :  0.045   0.260    574
  Planarity :  0.004   0.042    611
  Dihedral  :  4.815  54.309    495
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 31.64 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.41), residues: 456
  helix:  1.83 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -2.02 (0.67), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 332 
 HIS   0.002   0.000   HIS A 521 
 PHE   0.055   0.002   PHE A 372 
 TYR   0.017   0.001   TYR A 477 
 ARG   0.006   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  281)
  hydrogen bonds       : angle       3.86587 (  837)
  covalent geometry    : bond        0.00333 ( 3672)
  covalent geometry    : angle       0.89263 ( 4985)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1453.73 seconds
wall clock time: 26 minutes 8.34 seconds (1568.34 seconds total)