Starting phenix.real_space_refine
on Sun Apr 27 00:01:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wjg_37579/04_2025/8wjg_37579.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wjg_37579/04_2025/8wjg_37579.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wjg_37579/04_2025/8wjg_37579.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wjg_37579/04_2025/8wjg_37579.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wjg_37579/04_2025/8wjg_37579.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wjg_37579/04_2025/8wjg_37579.cif"
  }
  resolution = 3.0
  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=   0.004 sd=   0.167
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      31      5.16       5
     C    2569      2.51       5
     N     672      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3952
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 3952
          Classifications: {'peptide': 533}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 29, 'TRANS': 503}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 41
  Time building chain proxies: 5.28, per 1000 atoms: 1.34
  Number of scatterers: 3952
  At special positions: 0
  Unit cell: (104.86, 85.6, 64.2, 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      31     16.00
     O     680      8.00
     N     672      7.00
     C    2569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 139 " distance=2.03

  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: 1.40
  Conformation dependent library (CDL) restraints added in 653.6 milliseconds
  

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  978

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 2 sheets defined
      83.3% alpha, 1.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.732A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 42
      removed outlier: 4.754A  pdb=" N   GLU A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   ASN A  39 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 56 through 62
    Processing helix  chain 'A' and resid 68 through 77
    Processing helix  chain 'A' and resid 80 through 84
      removed outlier: 3.776A  pdb=" N   ARG A  84 " --> pdb=" O   PRO A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 100
    Processing helix  chain 'A' and resid 109 through 111
      No H-bonds generated for 'chain 'A' and resid 109 through 111'
    Processing helix  chain 'A' and resid 130 through 136
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 143 through 171
      Proline residue:  A 165  - end of helix
    Processing helix  chain 'A' and resid 171 through 192
      removed outlier: 3.550A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 225
    Processing helix  chain 'A' and resid 229 through 255
      removed outlier: 3.829A  pdb=" N   PHE A 241 " --> pdb=" O   ASN A 237 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER A 242 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 267
    Processing helix  chain 'A' and resid 267 through 277
      removed outlier: 3.922A  pdb=" N   LEU A 271 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 289
    Processing helix  chain 'A' and resid 291 through 306
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.785A  pdb=" N   ASP A 313 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 329
    Processing helix  chain 'A' and resid 336 through 343
      removed outlier: 3.742A  pdb=" N   LEU A 340 " --> pdb=" O   SER A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 368
      removed outlier: 3.950A  pdb=" N   PHE A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ARG A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 365 " --> pdb=" O   GLY A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 375
      removed outlier: 3.754A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 403
      Proline residue:  A 391  - end of helix
    Processing helix  chain 'A' and resid 404 through 426
      removed outlier: 3.751A  pdb=" N   THR A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 460
      removed outlier: 3.889A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 490
      removed outlier: 4.476A  pdb=" N   MET A 466 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   THR A 467 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
      Proline residue:  A 484  - end of helix
    Processing helix  chain 'A' and resid 495 through 513
      Proline residue:  A 505  - end of helix
    Processing helix  chain 'A' and resid 526 through 538
      removed outlier: 3.535A  pdb=" N   VAL A 530 " --> pdb=" O   THR A 526 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91

    305 hydrogen bonds defined for protein.
    882 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: 1.21

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1252
        1.34 -     1.47: 984
        1.47 -     1.59: 1761
        1.59 -     1.71: 0
        1.71 -     1.84: 50
  Bond restraints: 4047
  Sorted by residual:
  bond pdb=" C   MET A  36 "
       pdb=" O   MET A  36 "
    ideal  model  delta    sigma   weight residual
    1.235  1.263 -0.028 1.38e-02 5.25e+03 4.04e+00
  bond pdb=" CG  PRO A 194 "
       pdb=" CD  PRO A 194 "
    ideal  model  delta    sigma   weight residual
    1.503  1.438  0.065 3.40e-02 8.65e+02 3.64e+00
  bond pdb=" N   PRO A 194 "
       pdb=" CA  PRO A 194 "
    ideal  model  delta    sigma   weight residual
    1.469  1.445  0.024 1.28e-02 6.10e+03 3.47e+00
  bond pdb=" N   PRO A 194 "
       pdb=" CD  PRO A 194 "
    ideal  model  delta    sigma   weight residual
    1.473  1.498 -0.025 1.40e-02 5.10e+03 3.25e+00
  bond pdb=" CB  MET A 222 "
       pdb=" CG  MET A 222 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.75e+00
  ... (remaining 4042 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 5385
        3.17 -     6.34: 113
        6.34 -     9.51: 17
        9.51 -    12.68: 6
       12.68 -    15.85: 5
  Bond angle restraints: 5526
  Sorted by residual:
  angle pdb=" CA  PRO A 194 "
        pdb=" N   PRO A 194 "
        pdb=" CD  PRO A 194 "
      ideal   model   delta    sigma   weight residual
     112.00   97.41   14.59 1.40e+00 5.10e-01 1.09e+02
  angle pdb=" C   ALA A 323 "
        pdb=" N   MET A 324 "
        pdb=" CA  MET A 324 "
      ideal   model   delta    sigma   weight residual
     121.66  109.91   11.75 1.76e+00 3.23e-01 4.45e+01
  angle pdb=" CB  MET A 222 "
        pdb=" CG  MET A 222 "
        pdb=" SD  MET A 222 "
      ideal   model   delta    sigma   weight residual
     112.70   97.37   15.33 3.00e+00 1.11e-01 2.61e+01
  angle pdb=" C   THR A 518 "
        pdb=" N   GLN A 519 "
        pdb=" CA  GLN A 519 "
      ideal   model   delta    sigma   weight residual
     125.66  134.53   -8.87 1.85e+00 2.92e-01 2.30e+01
  angle pdb=" CB  MET A 324 "
        pdb=" CG  MET A 324 "
        pdb=" SD  MET A 324 "
      ideal   model   delta    sigma   weight residual
     112.70  125.54  -12.84 3.00e+00 1.11e-01 1.83e+01
  ... (remaining 5521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 2132
       17.27 -    34.55: 160
       34.55 -    51.82: 51
       51.82 -    69.09: 19
       69.09 -    86.36: 4
  Dihedral angle restraints: 2366
    sinusoidal: 849
      harmonic: 1517
  Sorted by residual:
  dihedral pdb=" CA  GLY A 375 "
           pdb=" C   GLY A 375 "
           pdb=" N   SER A 376 "
           pdb=" CA  SER A 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.34  -25.66     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CB  CYS A  88 "
           pdb=" SG  CYS A  88 "
           pdb=" SG  CYS A 139 "
           pdb=" CB  CYS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  135.06  -42.06     1      1.00e+01 1.00e-02 2.47e+01
  dihedral pdb=" CD  ARG A 487 "
           pdb=" NE  ARG A 487 "
           pdb=" CZ  ARG A 487 "
           pdb=" NH1 ARG A 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -28.91   28.91     1      1.00e+01 1.00e-02 1.20e+01
  ... (remaining 2363 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 459
       0.051 -    0.101: 135
       0.101 -    0.152: 45
       0.152 -    0.202: 12
       0.202 -    0.252: 4
  Chirality restraints: 655
  Sorted by residual:
  chirality pdb=" CA  MET A 466 "
            pdb=" N   MET A 466 "
            pdb=" C   MET A 466 "
            pdb=" CB  MET A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CG  LEU A  13 "
            pdb=" CB  LEU A  13 "
            pdb=" CD1 LEU A  13 "
            pdb=" CD2 LEU A  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ARG A  89 "
            pdb=" N   ARG A  89 "
            pdb=" C   ARG A  89 "
            pdb=" CB  ARG A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 652 not shown)

  Planarity restraints: 691
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 193 "   -0.143 5.00e-02 4.00e+02   2.05e-01 6.75e+01
        pdb=" N   PRO A 194 "    0.354 5.00e-02 4.00e+02
        pdb=" CA  PRO A 194 "   -0.119 5.00e-02 4.00e+02
        pdb=" CD  PRO A 194 "   -0.093 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 487 "   -0.387 9.50e-02 1.11e+02   1.75e-01 2.36e+01
        pdb=" NE  ARG A 487 "    0.037 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 487 "   -0.034 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 487 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 487 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 291 "    0.311 9.50e-02 1.11e+02   1.40e-01 1.49e+01
        pdb=" NE  ARG A 291 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 291 "    0.026 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 291 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 291 "    0.001 2.00e-02 2.50e+03
  ... (remaining 688 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 386
        2.75 -     3.29: 4110
        3.29 -     3.82: 6933
        3.82 -     4.36: 7768
        4.36 -     4.90: 13339
  Nonbonded interactions: 32536
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 455 "
            pdb=" O   PRO A 516 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER A 412 "
            pdb=" O   GLY A 444 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG  SER A 167 "
            pdb=" OD1 ASN A 216 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OD1 ASP A 257 "
            pdb=" OG1 THR A 259 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ALA A 359 "
            pdb=" OG1 THR A 363 "
     model   vdw
     2.297 3.040
  ... (remaining 32531 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.330
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:18.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
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      :  0.005   0.070   4049  Z= 0.261
  Angle     :  1.213  15.847   5530  Z= 0.660
  Chirality :  0.059   0.252    655
  Planarity :  0.014   0.205    691
  Dihedral  : 15.276  86.364   1382
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.83 %
    Favored  : 76.14 %
  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:  0.84 (0.34), residues: 529
  helix:  1.01 (0.25), residues: 391
  sheet:  None (None), residues: 0
  loop : -0.54 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP A 294 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.032   0.003   PHE A 208 
 TYR   0.030   0.008   TYR A 275 
 ARG   0.039   0.003   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12105 (  305)
  hydrogen bonds       : angle       6.01772 (  882)
  SS BOND              : bond        0.00328 (    2)
  SS BOND              : angle       3.34807 (    4)
  covalent geometry    : bond        0.00517 ( 4047)
  covalent geometry    : angle       1.21033 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 64
  average time/residue: 1.1061
  time to fit residues: 73.4962
Evaluate side-chains
  59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.174906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.132931 restraints weight = 3941.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.05
r_work: 0.3598 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4049  Z= 0.159
  Angle     :  0.675  11.273   5530  Z= 0.328
  Chirality :  0.041   0.134    655
  Planarity :  0.006   0.095    691
  Dihedral  :  5.100  50.618    571
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.81 %
    Favored  : 75.38 %
  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 (0.38), residues: 529
  helix:  1.64 (0.26), residues: 399
  sheet: -1.07 (1.35), residues: 10
  loop : -0.29 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 294 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.019   0.002   PHE A 208 
 TYR   0.017   0.003   TYR A 275 
 ARG   0.006   0.001   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05734 (  305)
  hydrogen bonds       : angle       4.97003 (  882)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       2.04402 (    4)
  covalent geometry    : bond        0.00329 ( 4047)
  covalent geometry    : angle       0.67280 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.6988 (mp0) cc_final: 0.6645 (mp0)
REVERT: A   38 GLU cc_start: 0.8127 (tt0) cc_final: 0.7927 (tp30)
REVERT: A   39 ASN cc_start: 0.8051 (t0) cc_final: 0.7813 (t0)
REVERT: A  170 PHE cc_start: 0.8462 (m-80) cc_final: 0.8213 (m-80)
REVERT: A  529 ASP cc_start: 0.6921 (t0) cc_final: 0.6679 (t0)
  outliers start: 15
  outliers final: 4
  residues processed: 80
  average time/residue: 0.9332
  time to fit residues: 77.9561
Evaluate side-chains
  65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 31 optimal weight:    0.0070
   chunk 34 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.169872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.129375 restraints weight = 4130.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.05
r_work: 0.3511 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4049  Z= 0.138
  Angle     :  0.636   9.707   5530  Z= 0.306
  Chirality :  0.038   0.120    655
  Planarity :  0.005   0.062    691
  Dihedral  :  4.874  57.018    569
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.83 %
    Favored  : 75.38 %
  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:  2.09 (0.37), residues: 529
  helix:  1.93 (0.26), residues: 387
  sheet: -1.25 (1.34), residues: 10
  loop :  0.06 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 294 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.020   0.002   PHE A 208 
 TYR   0.019   0.003   TYR A 275 
 ARG   0.006   0.001   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05377 (  305)
  hydrogen bonds       : angle       4.70465 (  882)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       1.63344 (    4)
  covalent geometry    : bond        0.00273 ( 4047)
  covalent geometry    : angle       0.63485 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.7130 (mp0) cc_final: 0.6792 (mp0)
REVERT: A   38 GLU cc_start: 0.7953 (tt0) cc_final: 0.7639 (tp30)
REVERT: A  114 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6478 (pp20)
REVERT: A  297 GLN cc_start: 0.7415 (tm-30) cc_final: 0.6722 (tp40)
REVERT: A  430 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6481 (mmm)
REVERT: A  529 ASP cc_start: 0.6970 (t0) cc_final: 0.6762 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 72
  average time/residue: 1.0125
  time to fit residues: 75.8828
Evaluate side-chains
  63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.165904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124676 restraints weight = 4198.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.12
r_work: 0.3480 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4049  Z= 0.150
  Angle     :  0.625   7.346   5530  Z= 0.304
  Chirality :  0.038   0.124    655
  Planarity :  0.005   0.048    691
  Dihedral  :  4.879  59.563    569
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.56 %
    Favored  : 76.65 %
  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 (0.37), residues: 529
  helix:  1.82 (0.26), residues: 395
  sheet: -1.02 (1.37), residues: 10
  loop : -0.11 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 294 
 HIS   0.005   0.001   HIS A 245 
 PHE   0.020   0.002   PHE A 208 
 TYR   0.019   0.002   TYR A 275 
 ARG   0.010   0.001   ARG A 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05451 (  305)
  hydrogen bonds       : angle       4.63853 (  882)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       1.54912 (    4)
  covalent geometry    : bond        0.00316 ( 4047)
  covalent geometry    : angle       0.62428 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.7012 (mp0) cc_final: 0.6791 (mp0)
REVERT: A   38 GLU cc_start: 0.7932 (tt0) cc_final: 0.7669 (tp30)
REVERT: A  228 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8222 (ttp80)
REVERT: A  297 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6802 (tp40)
REVERT: A  430 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6522 (mmm)
REVERT: A  466 MET cc_start: 0.8102 (mmm) cc_final: 0.7841 (mmm)
REVERT: A  529 ASP cc_start: 0.7007 (t0) cc_final: 0.6799 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 66
  average time/residue: 1.0857
  time to fit residues: 74.3889
Evaluate side-chains
  56 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 6 optimal weight:   30.0000
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.165126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.123804 restraints weight = 4333.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.09
r_work: 0.3438 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4049  Z= 0.146
  Angle     :  0.613   7.404   5530  Z= 0.299
  Chirality :  0.038   0.122    655
  Planarity :  0.004   0.037    691
  Dihedral  :  4.842  57.851    569
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.56 %
    Favored  : 75.63 %
  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:  2.00 (0.37), residues: 529
  helix:  1.87 (0.26), residues: 393
  sheet: -1.35 (1.35), residues: 10
  loop : -0.06 (0.61), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 294 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.019   0.002   PHE A 208 
 TYR   0.019   0.002   TYR A 275 
 ARG   0.007   0.001   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05362 (  305)
  hydrogen bonds       : angle       4.56700 (  882)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       1.47528 (    4)
  covalent geometry    : bond        0.00307 ( 4047)
  covalent geometry    : angle       0.61243 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.7920 (tt0) cc_final: 0.7667 (tp30)
REVERT: A  228 ARG cc_start: 0.8738 (ttp-110) cc_final: 0.8297 (ttp80)
REVERT: A  297 GLN cc_start: 0.7446 (tm-30) cc_final: 0.6822 (tp40)
REVERT: A  300 TRP cc_start: 0.7039 (m-10) cc_final: 0.6803 (m100)
REVERT: A  320 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6270 (tp)
REVERT: A  369 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7522 (mt)
REVERT: A  430 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6516 (mmm)
REVERT: A  466 MET cc_start: 0.8098 (mmm) cc_final: 0.7834 (mmm)
  outliers start: 15
  outliers final: 6
  residues processed: 75
  average time/residue: 1.1896
  time to fit residues: 93.2886
Evaluate side-chains
  65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0050
   chunk 31 optimal weight:    0.9980
   chunk 48 optimal weight:    0.1980
   chunk 45 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
A 262 GLN
A 306 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.166353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124756 restraints weight = 4180.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.10
r_work: 0.3442 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4049  Z= 0.130
  Angle     :  0.595   9.049   5530  Z= 0.289
  Chirality :  0.037   0.121    655
  Planarity :  0.004   0.035    691
  Dihedral  :  4.710  54.475    569
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.84 %
    Favored  : 73.60 %
  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 (0.37), residues: 529
  helix:  1.98 (0.26), residues: 393
  sheet: -1.69 (1.38), residues: 10
  loop : -0.03 (0.61), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 294 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.022   0.002   PHE A  40 
 TYR   0.018   0.002   TYR A 275 
 ARG   0.007   0.000   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05036 (  305)
  hydrogen bonds       : angle       4.44769 (  882)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       1.33542 (    4)
  covalent geometry    : bond        0.00259 ( 4047)
  covalent geometry    : angle       0.59388 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.7618 (mp0) cc_final: 0.7163 (mp0)
REVERT: A   38 GLU cc_start: 0.7674 (tt0) cc_final: 0.7421 (tp30)
REVERT: A  228 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8200 (ttp80)
REVERT: A  297 GLN cc_start: 0.7426 (tm-30) cc_final: 0.6752 (tp40)
REVERT: A  300 TRP cc_start: 0.7062 (m-10) cc_final: 0.6808 (m100)
REVERT: A  364 PHE cc_start: 0.7423 (t80) cc_final: 0.7200 (t80)
REVERT: A  369 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7395 (mt)
  outliers start: 14
  outliers final: 6
  residues processed: 70
  average time/residue: 1.0402
  time to fit residues: 75.7660
Evaluate side-chains
  66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.165019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123560 restraints weight = 4191.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.09
r_work: 0.3419 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4049  Z= 0.138
  Angle     :  0.615   9.905   5530  Z= 0.296
  Chirality :  0.038   0.132    655
  Planarity :  0.004   0.035    691
  Dihedral  :  4.650  51.918    569
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 24.37 %
    Favored  : 72.59 %
  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:  2.07 (0.37), residues: 529
  helix:  1.95 (0.26), residues: 395
  sheet: -1.72 (1.44), residues: 10
  loop : -0.17 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 294 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.020   0.002   PHE A  40 
 TYR   0.019   0.002   TYR A 275 
 ARG   0.009   0.001   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05049 (  305)
  hydrogen bonds       : angle       4.39803 (  882)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       1.35790 (    4)
  covalent geometry    : bond        0.00290 ( 4047)
  covalent geometry    : angle       0.61427 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.7662 (mp0) cc_final: 0.7202 (mp0)
REVERT: A  228 ARG cc_start: 0.8740 (ttp-110) cc_final: 0.8400 (ttp80)
REVERT: A  297 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6743 (tp40)
REVERT: A  300 TRP cc_start: 0.7147 (m-10) cc_final: 0.6872 (m100)
REVERT: A  369 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7340 (mt)
REVERT: A  529 ASP cc_start: 0.7018 (t0) cc_final: 0.6765 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 70
  average time/residue: 1.1499
  time to fit residues: 83.6562
Evaluate side-chains
  65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.165141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.123637 restraints weight = 4186.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 2.13
r_work: 0.3444 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4049  Z= 0.144
  Angle     :  0.630  10.559   5530  Z= 0.303
  Chirality :  0.038   0.123    655
  Planarity :  0.004   0.035    691
  Dihedral  :  4.603  48.662    569
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 24.62 %
    Favored  : 71.83 %
  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:  2.04 (0.38), residues: 529
  helix:  1.91 (0.26), residues: 396
  sheet: -1.73 (1.44), residues: 10
  loop : -0.13 (0.62), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 495 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.019   0.002   PHE A  40 
 TYR   0.020   0.002   TYR A 275 
 ARG   0.007   0.000   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05192 (  305)
  hydrogen bonds       : angle       4.40422 (  882)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       1.37908 (    4)
  covalent geometry    : bond        0.00310 ( 4047)
  covalent geometry    : angle       0.62877 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.7773 (mp0) cc_final: 0.7291 (mp0)
REVERT: A  228 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.8430 (ttp80)
REVERT: A  297 GLN cc_start: 0.7437 (tm-30) cc_final: 0.6750 (tp40)
REVERT: A  300 TRP cc_start: 0.7216 (m-10) cc_final: 0.6979 (m-10)
REVERT: A  369 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7380 (mt)
REVERT: A  452 ILE cc_start: 0.8422 (tp) cc_final: 0.8186 (OUTLIER)
  outliers start: 14
  outliers final: 9
  residues processed: 71
  average time/residue: 1.0919
  time to fit residues: 80.4401
Evaluate side-chains
  70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.163284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.121756 restraints weight = 4231.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.13
r_work: 0.3432 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4049  Z= 0.148
  Angle     :  0.644  11.260   5530  Z= 0.307
  Chirality :  0.039   0.146    655
  Planarity :  0.004   0.035    691
  Dihedral  :  4.544  44.559    569
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 25.63 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.96 (0.38), residues: 529
  helix:  1.86 (0.26), residues: 396
  sheet: -1.65 (1.45), residues: 10
  loop : -0.18 (0.62), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 495 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.019   0.002   PHE A  40 
 TYR   0.020   0.002   TYR A 275 
 ARG   0.007   0.000   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05267 (  305)
  hydrogen bonds       : angle       4.42012 (  882)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       1.34287 (    4)
  covalent geometry    : bond        0.00320 ( 4047)
  covalent geometry    : angle       0.64300 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7861 (mp0) cc_final: 0.7300 (mp0)
REVERT: A  114 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6406 (pp20)
REVERT: A  228 ARG cc_start: 0.8803 (ttp-110) cc_final: 0.8414 (ttp80)
REVERT: A  297 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6725 (tp40)
REVERT: A  300 TRP cc_start: 0.7290 (m-10) cc_final: 0.7068 (m-10)
REVERT: A  369 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7081 (mt)
REVERT: A  452 ILE cc_start: 0.8433 (tp) cc_final: 0.8192 (OUTLIER)
REVERT: A  529 ASP cc_start: 0.7064 (t0) cc_final: 0.6813 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 78
  average time/residue: 1.0267
  time to fit residues: 83.2020
Evaluate side-chains
  74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0670
   chunk 4 optimal weight:    0.0770
   chunk 20 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.3276

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.166518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125021 restraints weight = 4157.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.10
r_work: 0.3513 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4049  Z= 0.128
  Angle     :  0.637  11.946   5530  Z= 0.301
  Chirality :  0.038   0.118    655
  Planarity :  0.004   0.034    691
  Dihedral  :  4.394  38.192    569
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 25.89 %
    Favored  : 71.32 %
  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 (0.38), residues: 529
  helix:  1.92 (0.26), residues: 397
  sheet: -1.81 (1.49), residues: 10
  loop : -0.17 (0.62), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 495 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.018   0.002   PHE A  40 
 TYR   0.019   0.002   TYR A 275 
 ARG   0.008   0.001   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04899 (  305)
  hydrogen bonds       : angle       4.35217 (  882)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       1.18012 (    4)
  covalent geometry    : bond        0.00258 ( 4047)
  covalent geometry    : angle       0.63608 ( 5526)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7889 (mp0) cc_final: 0.7309 (mp0)
REVERT: A   88 CYS cc_start: 0.6699 (m) cc_final: 0.6349 (m)
REVERT: A  114 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6280 (pp20)
REVERT: A  228 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8400 (ttp80)
REVERT: A  297 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6717 (tp40)
REVERT: A  300 TRP cc_start: 0.7282 (m-10) cc_final: 0.7039 (m100)
REVERT: A  364 PHE cc_start: 0.7372 (t80) cc_final: 0.7052 (t80)
REVERT: A  452 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8111 (OUTLIER)
REVERT: A  495 TRP cc_start: 0.6604 (p-90) cc_final: 0.6139 (p90)
  outliers start: 11
  outliers final: 8
  residues processed: 73
  average time/residue: 0.9661
  time to fit residues: 73.4098
Evaluate side-chains
  71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0170
   chunk 12 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.165000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.123584 restraints weight = 4182.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.11
r_work: 0.3482 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4049  Z= 0.137
  Angle     :  0.651  11.470   5530  Z= 0.307
  Chirality :  0.038   0.120    655
  Planarity :  0.004   0.035    691
  Dihedral  :  4.321  34.153    569
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 26.14 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.96 (0.38), residues: 529
  helix:  1.88 (0.26), residues: 397
  sheet: -1.63 (1.49), residues: 10
  loop : -0.28 (0.61), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 495 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.018   0.002   PHE A 208 
 TYR   0.020   0.002   TYR A 275 
 ARG   0.006   0.001   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05067 (  305)
  hydrogen bonds       : angle       4.37112 (  882)
  SS BOND              : bond        0.00133 (    2)
  SS BOND              : angle       1.53353 (    4)
  covalent geometry    : bond        0.00289 ( 4047)
  covalent geometry    : angle       0.64999 ( 5526)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5659.78 seconds
wall clock time: 99 minutes 20.95 seconds (5960.95 seconds total)