Starting phenix.real_space_refine
on Fri May  9 20:21:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qsn_18637/05_2025/8qsn_18637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qsn_18637/05_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_18637/05_2025/8qsn_18637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qsn_18637/05_2025/8qsn_18637.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qsn_18637/05_2025/8qsn_18637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qsn_18637/05_2025/8qsn_18637.cif"
  }
  resolution = 3.54
  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: 2.94, per 1000 atoms: 0.82
  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: 0.87
  Conformation dependent library (CDL) restraints added in 406.3 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: 0.33
  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: 0.87

  Time building geometry restraints manager: 1.03 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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.880
  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:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.540
-------------------------------------------------------------------------------
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 (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  : 0.364 
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: 0.1648
  time to fit residues: 35.6159
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  : 0.434 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 34 optimal weight:    0.0170
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 26 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.098020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.084244 restraints weight = 13317.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.086517 restraints weight = 7613.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.088073 restraints weight = 5076.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3445

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= 0.152
  Angle     :  0.721  10.088   4985  Z= 0.340
  Chirality :  0.040   0.157    574
  Planarity :  0.005   0.051    611
  Dihedral  :  5.720  54.712    502
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.77 %
    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 (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:  2.36 (0.40), residues: 456
  helix:  2.37 (0.27), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.82 (0.58), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  69 
 HIS   0.003   0.001   HIS A 521 
 PHE   0.036   0.002   PHE A 417 
 TYR   0.013   0.002   TYR A 477 
 ARG   0.005   0.001   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04408 (  281)
  hydrogen bonds       : angle       3.98937 (  837)
  covalent geometry    : bond        0.00332 ( 3672)
  covalent geometry    : angle       0.72114 ( 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
  122 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6553 (ptp-170)
REVERT: A   44 GLU cc_start: 0.9326 (tp30) cc_final: 0.9070 (tp30)
REVERT: A   47 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8747 (tm-30)
REVERT: A   91 PHE cc_start: 0.8885 (m-80) cc_final: 0.8644 (m-10)
REVERT: A  200 TRP cc_start: 0.9091 (t60) cc_final: 0.8394 (t60)
REVERT: A  235 LEU cc_start: 0.9524 (mt) cc_final: 0.8956 (tp)
REVERT: A  301 MET cc_start: 0.5935 (tpt) cc_final: 0.5696 (tmm)
REVERT: A  309 GLU cc_start: 0.8847 (pm20) cc_final: 0.8263 (pm20)
REVERT: A  331 TYR cc_start: 0.9033 (t80) cc_final: 0.8525 (t80)
REVERT: A  427 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8441 (mt)
REVERT: A  451 LEU cc_start: 0.9285 (tp) cc_final: 0.9017 (mp)
REVERT: A  465 GLU cc_start: 0.8444 (tp30) cc_final: 0.8232 (tp30)
REVERT: A  535 TYR cc_start: 0.8831 (t80) cc_final: 0.8378 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 119
  average time/residue: 0.1088
  time to fit residues: 16.9442
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 521 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.096802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.083162 restraints weight = 13676.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.085339 restraints weight = 7922.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.086613 restraints weight = 5367.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3672  Z= 0.144
  Angle     :  0.700  10.918   4985  Z= 0.330
  Chirality :  0.040   0.161    574
  Planarity :  0.005   0.055    611
  Dihedral  :  5.766  54.740    500
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 20.11 %
    Favored  : 74.80 %
  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:  2.14 (0.40), residues: 456
  helix:  2.15 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.85 (0.62), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 521 
 PHE   0.044   0.002   PHE A 372 
 TYR   0.014   0.002   TYR A 335 
 ARG   0.003   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04254 (  281)
  hydrogen bonds       : angle       3.98318 (  837)
  covalent geometry    : bond        0.00312 ( 3672)
  covalent geometry    : angle       0.70018 ( 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
  122 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6545 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9132 (t60) cc_final: 0.8460 (t60)
REVERT: A  213 ILE cc_start: 0.9468 (mm) cc_final: 0.9249 (tp)
REVERT: A  301 MET cc_start: 0.6196 (tpt) cc_final: 0.5930 (tmm)
REVERT: A  307 PHE cc_start: 0.3835 (OUTLIER) cc_final: 0.3529 (m-80)
REVERT: A  331 TYR cc_start: 0.9095 (t80) cc_final: 0.8617 (t80)
REVERT: A  413 MET cc_start: 0.8866 (tmm) cc_final: 0.8600 (tmm)
REVERT: A  427 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8580 (mt)
REVERT: A  458 TYR cc_start: 0.8940 (m-80) cc_final: 0.8706 (m-80)
REVERT: A  474 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8292 (mt-10)
REVERT: A  489 MET cc_start: 0.9531 (tpp) cc_final: 0.9324 (tpp)
REVERT: A  535 TYR cc_start: 0.8905 (t80) cc_final: 0.8530 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 116
  average time/residue: 0.1063
  time to fit residues: 16.3309
Evaluate side-chains
  108 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 203 ASN
** A 339 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 = 0.3909 r_free = 0.3909 target = 0.096450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.083180 restraints weight = 13740.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.085381 restraints weight = 7866.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.086816 restraints weight = 5250.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.4548

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= 0.137
  Angle     :  0.659  10.709   4985  Z= 0.318
  Chirality :  0.040   0.159    574
  Planarity :  0.005   0.046    611
  Dihedral  :  5.930  55.205    500
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 23.32 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.04 (0.40), residues: 456
  helix:  2.07 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.75 (0.65), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 559 
 PHE   0.051   0.002   PHE A 372 
 TYR   0.018   0.001   TYR A 215 
 ARG   0.004   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  281)
  hydrogen bonds       : angle       3.86185 (  837)
  covalent geometry    : bond        0.00292 ( 3672)
  covalent geometry    : angle       0.65879 ( 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
  125 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6558 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9178 (t60) cc_final: 0.8480 (t60)
REVERT: A  213 ILE cc_start: 0.9457 (mm) cc_final: 0.9249 (tp)
REVERT: A  301 MET cc_start: 0.6329 (tpt) cc_final: 0.6068 (tmm)
REVERT: A  307 PHE cc_start: 0.3915 (OUTLIER) cc_final: 0.3638 (m-80)
REVERT: A  310 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: A  331 TYR cc_start: 0.9128 (t80) cc_final: 0.8709 (t80)
REVERT: A  427 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8592 (mt)
REVERT: A  432 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7698 (mm-30)
REVERT: A  474 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8126 (mt-10)
REVERT: A  535 TYR cc_start: 0.8898 (t80) cc_final: 0.8528 (t80)
  outliers start: 24
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1136
  time to fit residues: 17.4079
Evaluate side-chains
  107 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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  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  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:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.096847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.083482 restraints weight = 14120.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.085695 restraints weight = 8031.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.086981 restraints weight = 5347.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.4886

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= 0.136
  Angle     :  0.717  12.195   4985  Z= 0.333
  Chirality :  0.041   0.178    574
  Planarity :  0.004   0.044    611
  Dihedral  :  5.990  55.789    500
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 24.13 %
    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 (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:  2.00 (0.40), residues: 456
  helix:  2.06 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.88 (0.65), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 559 
 PHE   0.055   0.002   PHE A 372 
 TYR   0.017   0.001   TYR A 444 
 ARG   0.004   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  281)
  hydrogen bonds       : angle       3.76881 (  837)
  covalent geometry    : bond        0.00294 ( 3672)
  covalent geometry    : angle       0.71702 ( 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
  124 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6515 (ptp-170)
REVERT: A   44 GLU cc_start: 0.9198 (tp30) cc_final: 0.8767 (tp30)
REVERT: A  200 TRP cc_start: 0.9184 (t60) cc_final: 0.8440 (t60)
REVERT: A  213 ILE cc_start: 0.9461 (mm) cc_final: 0.9247 (tp)
REVERT: A  301 MET cc_start: 0.6371 (tpt) cc_final: 0.6134 (tmm)
REVERT: A  307 PHE cc_start: 0.3853 (OUTLIER) cc_final: 0.3539 (m-80)
REVERT: A  331 TYR cc_start: 0.9159 (t80) cc_final: 0.8732 (t80)
REVERT: A  427 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8601 (mt)
REVERT: A  432 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7771 (mm-30)
REVERT: A  451 LEU cc_start: 0.9257 (tp) cc_final: 0.9030 (mp)
REVERT: A  457 GLN cc_start: 0.7941 (mp10) cc_final: 0.7653 (mp10)
REVERT: A  458 TYR cc_start: 0.8955 (m-80) cc_final: 0.8753 (m-80)
REVERT: A  465 GLU cc_start: 0.8683 (tp30) cc_final: 0.8459 (tp30)
REVERT: A  474 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8299 (mt-10)
REVERT: A  535 TYR cc_start: 0.8950 (t80) cc_final: 0.8634 (t80)
  outliers start: 25
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1139
  time to fit residues: 17.1097
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  : 0.416 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0040
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.9596

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.096577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.082528 restraints weight = 14312.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.084817 restraints weight = 8156.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.086328 restraints weight = 5459.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3672  Z= 0.138
  Angle     :  0.744  14.887   4985  Z= 0.344
  Chirality :  0.041   0.172    574
  Planarity :  0.004   0.046    611
  Dihedral  :  6.036  56.329    500
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 25.74 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.41), residues: 456
  helix:  2.02 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.97 (0.66), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 303 
 PHE   0.055   0.002   PHE A 372 
 TYR   0.014   0.001   TYR A 215 
 ARG   0.004   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  281)
  hydrogen bonds       : angle       3.77708 (  837)
  covalent geometry    : bond        0.00303 ( 3672)
  covalent geometry    : angle       0.74436 ( 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
  113 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6501 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9181 (t60) cc_final: 0.8431 (t60)
REVERT: A  213 ILE cc_start: 0.9463 (mm) cc_final: 0.9260 (tp)
REVERT: A  301 MET cc_start: 0.6421 (tpt) cc_final: 0.6201 (tmm)
REVERT: A  307 PHE cc_start: 0.3845 (OUTLIER) cc_final: 0.3528 (m-80)
REVERT: A  371 MET cc_start: 0.8636 (mtt) cc_final: 0.8432 (ptp)
REVERT: A  427 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8662 (mt)
REVERT: A  432 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7851 (mm-30)
REVERT: A  451 LEU cc_start: 0.9257 (tp) cc_final: 0.9034 (mp)
REVERT: A  474 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8308 (mt-10)
REVERT: A  535 TYR cc_start: 0.8975 (t80) cc_final: 0.8707 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1075
  time to fit residues: 15.4151
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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  176 THR
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.095453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.081826 restraints weight = 14100.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.083954 restraints weight = 8088.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.085445 restraints weight = 5423.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.5322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3672  Z= 0.165
  Angle     :  0.771  13.952   4985  Z= 0.354
  Chirality :  0.041   0.162    574
  Planarity :  0.004   0.045    611
  Dihedral  :  5.689  59.891    498
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 26.81 %
    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 (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:  1.86 (0.41), residues: 456
  helix:  1.97 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -2.22 (0.67), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 559 
 PHE   0.047   0.002   PHE A 372 
 TYR   0.015   0.001   TYR A 477 
 ARG   0.005   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04196 (  281)
  hydrogen bonds       : angle       3.85506 (  837)
  covalent geometry    : bond        0.00371 ( 3672)
  covalent geometry    : angle       0.77056 ( 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
  118 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6547 (ptp-170)
REVERT: A  110 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9411 (tt)
REVERT: A  200 TRP cc_start: 0.9191 (t60) cc_final: 0.8469 (t60)
REVERT: A  301 MET cc_start: 0.6501 (tpt) cc_final: 0.6278 (tmm)
REVERT: A  310 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7315 (tm-30)
REVERT: A  427 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8721 (mt)
REVERT: A  474 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8275 (mt-10)
REVERT: A  535 TYR cc_start: 0.9038 (t80) cc_final: 0.8780 (t80)
  outliers start: 20
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1178
  time to fit residues: 17.2993
Evaluate side-chains
  105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    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   60 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  110 LEU
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  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  328 LEU
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
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:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 24 optimal weight:    0.4980
   chunk 21 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 34 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.096670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.083004 restraints weight = 13843.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.085153 restraints weight = 8006.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.086630 restraints weight = 5418.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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= 0.143
  Angle     :  0.831  12.630   4985  Z= 0.375
  Chirality :  0.044   0.377    574
  Planarity :  0.004   0.045    611
  Dihedral  :  5.721  59.849    498
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 29.76 %
    Favored  : 65.95 %
  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:  1.60 (0.41), residues: 456
  helix:  1.79 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop : -2.52 (0.68), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 453 
 HIS   0.001   0.000   HIS A 303 
 PHE   0.046   0.002   PHE A 372 
 TYR   0.018   0.001   TYR A 215 
 ARG   0.005   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  281)
  hydrogen bonds       : angle       3.84774 (  837)
  covalent geometry    : bond        0.00307 ( 3672)
  covalent geometry    : angle       0.83099 ( 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
  114 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6799 (mtt180)
REVERT: A  200 TRP cc_start: 0.9107 (t60) cc_final: 0.8424 (t60)
REVERT: A  213 ILE cc_start: 0.9331 (mt) cc_final: 0.9044 (tp)
REVERT: A  451 LEU cc_start: 0.9277 (tp) cc_final: 0.9050 (mp)
REVERT: A  474 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8270 (mt-10)
REVERT: A  535 TYR cc_start: 0.9020 (t80) cc_final: 0.8788 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.1086
  time to fit residues: 15.3814
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  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  260 MET
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  412 VAL
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 39 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0060
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0070
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.4414

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.097006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.082710 restraints weight = 13647.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.084995 restraints weight = 7929.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.086557 restraints weight = 5345.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.5699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3672  Z= 0.143
  Angle     :  0.853  12.139   4985  Z= 0.386
  Chirality :  0.044   0.343    574
  Planarity :  0.004   0.045    611
  Dihedral  :  4.808  54.518    495
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 30.83 %
    Favored  : 67.02 %
  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:  1.68 (0.40), residues: 456
  helix:  1.84 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -2.08 (0.65), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 517 
 HIS   0.005   0.001   HIS A 395 
 PHE   0.042   0.002   PHE A 372 
 TYR   0.015   0.001   TYR A 477 
 ARG   0.006   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  281)
  hydrogen bonds       : angle       3.85535 (  837)
  covalent geometry    : bond        0.00316 ( 3672)
  covalent geometry    : angle       0.85310 ( 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
  107 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6415 (ptp-170)
REVERT: A  200 TRP cc_start: 0.9094 (t60) cc_final: 0.8446 (t60)
REVERT: A  213 ILE cc_start: 0.9308 (mt) cc_final: 0.9029 (tp)
REVERT: A  310 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7053 (tm-30)
REVERT: A  331 TYR cc_start: 0.9089 (t80) cc_final: 0.8664 (t80)
REVERT: A  474 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8212 (mt-10)
REVERT: A  504 SER cc_start: 0.9436 (t) cc_final: 0.9219 (p)
REVERT: A  535 TYR cc_start: 0.8946 (t80) cc_final: 0.8714 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 104
  average time/residue: 0.0964
  time to fit residues: 13.5099
Evaluate side-chains
  98 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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  299 CYS
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  429 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   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 = 0.3881 r_free = 0.3881 target = 0.096444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.083064 restraints weight = 13713.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.085292 restraints weight = 7872.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.086797 restraints weight = 5248.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.5853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3672  Z= 0.152
  Angle     :  0.879  12.186   4985  Z= 0.405
  Chirality :  0.046   0.338    574
  Planarity :  0.004   0.044    611
  Dihedral  :  4.843  54.337    495
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 32.17 %
    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:  1.74 (0.40), residues: 456
  helix:  1.89 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -2.00 (0.66), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 521 
 PHE   0.053   0.002   PHE A 372 
 TYR   0.019   0.001   TYR A 215 
 ARG   0.006   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  281)
  hydrogen bonds       : angle       3.93288 (  837)
  covalent geometry    : bond        0.00343 ( 3672)
  covalent geometry    : angle       0.87902 ( 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: 8
    poor density    : 96
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6411 (ptp-170)
REVERT: A  172 LYS cc_start: 0.9211 (mmmt) cc_final: 0.9005 (mmpt)
REVERT: A  200 TRP cc_start: 0.9098 (t60) cc_final: 0.8462 (t60)
REVERT: A  213 ILE cc_start: 0.9292 (mt) cc_final: 0.9002 (tp)
REVERT: A  331 TYR cc_start: 0.9095 (t80) cc_final: 0.8655 (t80)
REVERT: A  474 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8239 (mt-10)
REVERT: A  489 MET cc_start: 0.9335 (tpp) cc_final: 0.9074 (tpp)
REVERT: A  493 PHE cc_start: 0.9473 (m-80) cc_final: 0.9262 (m-80)
REVERT: A  504 SER cc_start: 0.9461 (t) cc_final: 0.9238 (p)
  outliers start: 8
  outliers final: 7
  residues processed: 101
  average time/residue: 0.1127
  time to fit residues: 14.7295
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  : 0.370 
-------------------------------------------------------------------------------
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  299 CYS
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  429 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0670
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7318

-------------------------------------------------------------------------------
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 = 0.3886 r_free = 0.3886 target = 0.096705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.083331 restraints weight = 13805.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.085530 restraints weight = 7974.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.087033 restraints weight = 5293.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.6065

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= 0.153
  Angle     :  0.887  11.844   4985  Z= 0.410
  Chirality :  0.045   0.317    574
  Planarity :  0.005   0.043    611
  Dihedral  :  4.911  54.356    495
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 31.37 %
    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:  1.65 (0.40), residues: 456
  helix:  1.83 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -2.07 (0.65), residues: 90

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   0.055   0.002   PHE A 372 
 TYR   0.015   0.001   TYR A 477 
 ARG   0.006   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  281)
  hydrogen bonds       : angle       3.97075 (  837)
  covalent geometry    : bond        0.00339 ( 3672)
  covalent geometry    : angle       0.88726 ( 4985)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1462.45 seconds
wall clock time: 26 minutes 12.92 seconds (1572.92 seconds total)