Starting phenix.real_space_refine
on Wed Jun  4 22:49:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wfi_37492/06_2025/8wfi_37492.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wfi_37492/06_2025/8wfi_37492.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wfi_37492/06_2025/8wfi_37492.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wfi_37492/06_2025/8wfi_37492.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wfi_37492/06_2025/8wfi_37492.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wfi_37492/06_2025/8wfi_37492.cif"
  }
  resolution = 2.58
  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=   0.067
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: 6
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     Cl      1      4.86       5
     Na      2      4.78       5
     C    2877      2.51       5
     N     676      2.21       5
     O     756      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4347
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 4302
          Classifications: {'peptide': 542}
          Link IDs: {'PTRANS': 25, 'TRANS': 516}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 40
          Unusual residues: {' CL': 1, ' NA': 2}
          Classifications: {'undetermined': 3, 'water': 37}
          Link IDs: {None: 39}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLY A 701 " occ=0.00
      ... (3 atoms not shown)
      pdb=" OXT GLY A 701 " occ=0.00
  Time building chain proxies: 3.68, per 1000 atoms: 0.85
  Number of scatterers: 4347
  At special positions: 0
  Unit cell: (75.65, 65.45, 93.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      35     16.00
     Na      2     11.00
     O     756      8.00
     N     676      7.00
     C    2877      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 175 " 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: 1.07
  Conformation dependent library (CDL) restraints added in 525.1 milliseconds
  

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  988

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      78.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 64
      removed outlier: 3.594A  pdb=" N   PHE A  55 " --> pdb=" O   ASN A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 4.054A  pdb=" N   VAL A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 79
      removed outlier: 4.124A  pdb=" N   TYR A  74 " --> pdb=" O   TRP A  70 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASN A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 83
    Processing helix  chain 'A' and resid 84 through 95
    Processing helix  chain 'A' and resid 95 through 111
      removed outlier: 3.942A  pdb=" N   ALA A 110 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 120
      removed outlier: 3.719A  pdb=" N   TRP A 118 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ARG A 119 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A 120 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 115 through 120'
    Processing helix  chain 'A' and resid 121 through 124
    Processing helix  chain 'A' and resid 125 through 156
      removed outlier: 3.649A  pdb=" N   TYR A 129 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TYR A 141 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ASN A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   VAL A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 218
    Processing helix  chain 'A' and resid 233 through 253
    Processing helix  chain 'A' and resid 254 through 257
    Processing helix  chain 'A' and resid 258 through 266
      removed outlier: 3.873A  pdb=" N   VAL A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   TYR A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 281
      removed outlier: 3.587A  pdb=" N   VAL A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 295
      removed outlier: 3.569A  pdb=" N   GLY A 289 " --> pdb=" O   GLY A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.897A  pdb=" N   TRP A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 330
      removed outlier: 3.721A  pdb=" N   THR A 327 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 372
      removed outlier: 3.929A  pdb=" N   ASP A 341 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER A 342 " --> pdb=" O   CYS A 338 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE A 363 " --> pdb=" O   VAL A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 395
      removed outlier: 4.555A  pdb=" N   TYR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      Proline residue:  A 391  - end of helix
    Processing helix  chain 'A' and resid 399 through 435
      removed outlier: 3.804A  pdb=" N   TRP A 403 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR A 418 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   CYS A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 441
      removed outlier: 3.692A  pdb=" N   LEU A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 459
    Processing helix  chain 'A' and resid 460 through 463
      removed outlier: 3.777A  pdb=" N   SER A 463 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 460 through 463'
    Processing helix  chain 'A' and resid 465 through 477
      removed outlier: 3.676A  pdb=" N   TRP A 469 " --> pdb=" O   ALA A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 496
    Processing helix  chain 'A' and resid 498 through 511
    Processing helix  chain 'A' and resid 515 through 540
      removed outlier: 5.656A  pdb=" N   SER A 526 " --> pdb=" O   TRP A 522 " (cutoff:3.500A)
      Proline residue:  A 527  - end of helix
    Processing helix  chain 'A' and resid 552 through 568
      removed outlier: 4.272A  pdb=" N   SER A 566 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   VAL A 567 " --> pdb=" O   ALA A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 579
    Processing helix  chain 'A' and resid 585 through 595
      removed outlier: 3.534A  pdb=" N   LYS A 595 " --> pdb=" O   LYS A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 608
    Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 546

    273 hydrogen bonds defined for protein.
    801 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: 1.18

  Time building geometry restraints manager: 1.28 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: 1269
        1.34 -     1.46: 1078
        1.46 -     1.58: 2045
        1.58 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 4445
  Sorted by residual:
  bond pdb=" N   GLY A 701 "
       pdb=" CA  GLY A 701 "
    ideal  model  delta    sigma   weight residual
    1.451  1.477 -0.026 1.60e-02 3.91e+03 2.62e+00
  bond pdb=" N   GLY A 610 "
       pdb=" CA  GLY A 610 "
    ideal  model  delta    sigma   weight residual
    1.449  1.468 -0.018 1.45e-02 4.76e+03 1.61e+00
  bond pdb=" C   TYR A 141 "
       pdb=" O   TYR A 141 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.28e-02 6.10e+03 6.97e-01
  bond pdb=" CA  PHE A 268 "
       pdb=" C   PHE A 268 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.009 1.26e-02 6.30e+03 5.51e-01
  bond pdb=" CA  ILE A  97 "
       pdb=" C   ILE A  97 "
    ideal  model  delta    sigma   weight residual
    1.520  1.526 -0.007 8.80e-03 1.29e+04 5.46e-01
  ... (remaining 4440 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 5931
        1.55 -     3.11: 97
        3.11 -     4.66: 28
        4.66 -     6.21: 5
        6.21 -     7.77: 1
  Bond angle restraints: 6062
  Sorted by residual:
  angle pdb=" C   THR A 267 "
        pdb=" N   PHE A 268 "
        pdb=" CA  PHE A 268 "
      ideal   model   delta    sigma   weight residual
     120.09  123.98   -3.89 1.25e+00 6.40e-01 9.69e+00
  angle pdb=" O   GLY A 701 "
        pdb=" C   GLY A 701 "
        pdb=" OXT GLY A 701 "
      ideal   model   delta    sigma   weight residual
     118.00  125.77   -7.77 3.00e+00 1.11e-01 6.70e+00
  angle pdb=" C   PRO A  73 "
        pdb=" N   TYR A  74 "
        pdb=" CA  TYR A  74 "
      ideal   model   delta    sigma   weight residual
     121.14  117.03    4.11 1.75e+00 3.27e-01 5.53e+00
  angle pdb=" C   PRO A 398 "
        pdb=" N   ILE A 399 "
        pdb=" CA  ILE A 399 "
      ideal   model   delta    sigma   weight residual
     121.97  125.99   -4.02 1.80e+00 3.09e-01 4.99e+00
  angle pdb=" CA  TYR A  74 "
        pdb=" CB  TYR A  74 "
        pdb=" CG  TYR A  74 "
      ideal   model   delta    sigma   weight residual
     113.90  117.82   -3.92 1.80e+00 3.09e-01 4.74e+00
  ... (remaining 6057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 2274
       16.39 -    32.77: 191
       32.77 -    49.16: 30
       49.16 -    65.54: 6
       65.54 -    81.93: 3
  Dihedral angle restraints: 2504
    sinusoidal: 942
      harmonic: 1562
  Sorted by residual:
  dihedral pdb=" CA  PHE A 524 "
           pdb=" C   PHE A 524 "
           pdb=" N   VAL A 525 "
           pdb=" CA  VAL A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.65  -22.35     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  TRP A 118 "
           pdb=" C   TRP A 118 "
           pdb=" N   ARG A 119 "
           pdb=" CA  ARG A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.39   16.61     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CB  MET A 102 "
           pdb=" CG  MET A 102 "
           pdb=" SD  MET A 102 "
           pdb=" CE  MET A 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.29   51.29     3      1.50e+01 4.44e-03 9.00e+00
  ... (remaining 2501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 378
       0.026 -    0.051: 174
       0.051 -    0.077: 80
       0.077 -    0.102: 29
       0.102 -    0.128: 8
  Chirality restraints: 669
  Sorted by residual:
  chirality pdb=" CA  PRO A  73 "
            pdb=" N   PRO A  73 "
            pdb=" C   PRO A  73 "
            pdb=" CB  PRO A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  VAL A 160 "
            pdb=" N   VAL A 160 "
            pdb=" C   VAL A 160 "
            pdb=" CB  VAL A 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.33e-01
  chirality pdb=" CA  PRO A 122 "
            pdb=" N   PRO A 122 "
            pdb=" C   PRO A 122 "
            pdb=" CB  PRO A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.11 2.00e-01 2.50e+01 3.24e-01
  ... (remaining 666 not shown)

  Planarity restraints: 744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 106 "   -0.020 2.00e-02 2.50e+03   1.97e-02 6.77e+00
        pdb=" CG  PHE A 106 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 106 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 106 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 106 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 106 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 521 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.52e+00
        pdb=" C   CYS A 521 "    0.032 2.00e-02 2.50e+03
        pdb=" O   CYS A 521 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   TRP A 522 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 355 "    0.013 2.00e-02 2.50e+03   9.92e-03 1.97e+00
        pdb=" CG  TYR A 355 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 355 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 355 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 355 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 355 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 355 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 355 "    0.002 2.00e-02 2.50e+03
  ... (remaining 741 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1148
        2.80 -     3.33: 3991
        3.33 -     3.85: 7270
        3.85 -     4.38: 8505
        4.38 -     4.90: 14699
  Nonbonded interactions: 35613
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 597 "
            pdb=" OD1 ASP A 599 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   PRO A 602 "
            pdb=" NH2 ARG A 608 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   SER A 479 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   TYR A 476 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OE1 GLN A  52 "
            pdb=" NH2 ARG A 340 "
     model   vdw
     2.372 3.120
  ... (remaining 35608 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=0.00 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:             2.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.240
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:11.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   30.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
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   0.029   4446  Z= 0.132
  Angle     :  0.568   7.766   6064  Z= 0.305
  Chirality :  0.038   0.128    669
  Planarity :  0.004   0.033    744
  Dihedral  : 12.583  81.926   1513
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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:  1.63 (0.36), residues: 538
  helix:  2.12 (0.27), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.16 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 499 
 PHE   0.045   0.002   PHE A 106 
 TYR   0.024   0.002   TYR A 355 
 ARG   0.006   0.001   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14329 (  273)
  hydrogen bonds       : angle       5.11487 (  801)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.95539 (    2)
  covalent geometry    : bond        0.00244 ( 4445)
  covalent geometry    : angle       0.56781 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7561 (tp30)
REVERT: A  260 LYS cc_start: 0.7546 (mttm) cc_final: 0.6799 (mmpt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 1.1811
  time to fit residues: 94.4115
Evaluate side-chains
  65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.0370
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0870
   chunk 42 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
A 607 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.150084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.130814 restraints weight = 4206.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.18
r_work: 0.3402 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.0818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4446  Z= 0.130
  Angle     :  0.528   5.918   6064  Z= 0.282
  Chirality :  0.039   0.123    669
  Planarity :  0.005   0.040    744
  Dihedral  :  3.926  22.419    594
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.59 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.80 (0.37), residues: 538
  helix:  2.21 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.24 (0.46), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 215 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.036   0.002   PHE A 106 
 TYR   0.024   0.002   TYR A  74 
 ARG   0.003   0.000   ARG A 608 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06065 (  273)
  hydrogen bonds       : angle       3.95713 (  801)
  SS BOND              : bond        0.00404 (    1)
  SS BOND              : angle       0.85875 (    2)
  covalent geometry    : bond        0.00248 ( 4445)
  covalent geometry    : angle       0.52788 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  507 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8118 (tt0)
REVERT: A  606 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7298 (pm20)
  outliers start: 5
  outliers final: 2
  residues processed: 62
  average time/residue: 1.2208
  time to fit residues: 78.6461
Evaluate side-chains
  61 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  606 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0050
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4794

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.155622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.137076 restraints weight = 4294.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.14
r_work: 0.3503 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.0976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4446  Z= 0.124
  Angle     :  0.512   6.075   6064  Z= 0.272
  Chirality :  0.038   0.123    669
  Planarity :  0.004   0.041    744
  Dihedral  :  3.848  22.668    594
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  7.47 %
    Favored  : 90.77 %
  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:  1.93 (0.37), residues: 538
  helix:  2.35 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.26 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 499 
 PHE   0.026   0.001   PHE A 106 
 TYR   0.021   0.002   TYR A  74 
 ARG   0.002   0.000   ARG A 608 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05782 (  273)
  hydrogen bonds       : angle       3.84895 (  801)
  SS BOND              : bond        0.00382 (    1)
  SS BOND              : angle       0.81047 (    2)
  covalent geometry    : bond        0.00237 ( 4445)
  covalent geometry    : angle       0.51222 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A  507 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8076 (tt0)
REVERT: A  550 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6922 (mm-40)
REVERT: A  606 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7302 (pm20)
  outliers start: 8
  outliers final: 3
  residues processed: 62
  average time/residue: 1.1437
  time to fit residues: 73.9050
Evaluate side-chains
  65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  606 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.157775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.142245 restraints weight = 4281.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 0.89
r_work: 0.3479 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4446  Z= 0.131
  Angle     :  0.523   5.921   6064  Z= 0.278
  Chirality :  0.039   0.127    669
  Planarity :  0.005   0.042    744
  Dihedral  :  3.873  22.833    594
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.23 %
    Favored  : 88.79 %
  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 (0.37), residues: 538
  helix:  2.35 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.24 (0.46), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 499 
 PHE   0.024   0.002   PHE A 106 
 TYR   0.022   0.002   TYR A  74 
 ARG   0.002   0.000   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06093 (  273)
  hydrogen bonds       : angle       3.85851 (  801)
  SS BOND              : bond        0.00464 (    1)
  SS BOND              : angle       0.89942 (    2)
  covalent geometry    : bond        0.00257 ( 4445)
  covalent geometry    : angle       0.52321 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A  507 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8135 (tt0)
REVERT: A  550 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7110 (mm-40)
  outliers start: 9
  outliers final: 4
  residues processed: 66
  average time/residue: 1.2836
  time to fit residues: 87.8690
Evaluate side-chains
  63 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  550 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0970
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.157168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.139110 restraints weight = 4334.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.12
r_work: 0.3485 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4446  Z= 0.125
  Angle     :  0.509   5.994   6064  Z= 0.270
  Chirality :  0.038   0.123    669
  Planarity :  0.004   0.041    744
  Dihedral  :  3.829  22.878    594
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.11 %
    Favored  : 88.13 %
  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:  2.05 (0.37), residues: 538
  helix:  2.42 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.19 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 499 
 PHE   0.019   0.001   PHE A 106 
 TYR   0.020   0.002   TYR A  74 
 ARG   0.002   0.000   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05787 (  273)
  hydrogen bonds       : angle       3.81910 (  801)
  SS BOND              : bond        0.00402 (    1)
  SS BOND              : angle       0.83095 (    2)
  covalent geometry    : bond        0.00242 ( 4445)
  covalent geometry    : angle       0.50891 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  507 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8089 (tt0)
REVERT: A  550 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7023 (mm-40)
REVERT: A  606 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7078 (pm20)
  outliers start: 8
  outliers final: 5
  residues processed: 64
  average time/residue: 1.2001
  time to fit residues: 79.8402
Evaluate side-chains
  65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  606 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.152600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.136830 restraints weight = 4208.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 0.89
r_work: 0.3396 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4446  Z= 0.163
  Angle     :  0.579   6.120   6064  Z= 0.310
  Chirality :  0.041   0.137    669
  Planarity :  0.005   0.045    744
  Dihedral  :  4.085  23.171    594
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.11 %
    Favored  : 87.91 %
  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 (0.37), residues: 538
  helix:  2.21 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -1.33 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 215 
 HIS   0.006   0.001   HIS A 499 
 PHE   0.023   0.002   PHE A 106 
 TYR   0.024   0.002   TYR A  74 
 ARG   0.004   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07280 (  273)
  hydrogen bonds       : angle       3.98797 (  801)
  SS BOND              : bond        0.00708 (    1)
  SS BOND              : angle       1.16086 (    2)
  covalent geometry    : bond        0.00344 ( 4445)
  covalent geometry    : angle       0.57920 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  507 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8159 (tt0)
REVERT: A  550 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7199 (mm-40)
REVERT: A  606 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7176 (pm20)
  outliers start: 9
  outliers final: 5
  residues processed: 64
  average time/residue: 1.3680
  time to fit residues: 91.2650
Evaluate side-chains
  67 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  606 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0070
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6600

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.154294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138644 restraints weight = 4219.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 0.88
r_work: 0.3435 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4446  Z= 0.139
  Angle     :  0.538   6.127   6064  Z= 0.287
  Chirality :  0.039   0.129    669
  Planarity :  0.005   0.044    744
  Dihedral  :  3.982  23.325    594
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  9.89 %
    Favored  : 87.91 %
  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:  1.83 (0.37), residues: 538
  helix:  2.23 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.23 (0.47), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 499 
 PHE   0.017   0.002   PHE A 106 
 TYR   0.021   0.002   TYR A  74 
 ARG   0.002   0.000   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06465 (  273)
  hydrogen bonds       : angle       3.91589 (  801)
  SS BOND              : bond        0.00489 (    1)
  SS BOND              : angle       0.95393 (    2)
  covalent geometry    : bond        0.00278 ( 4445)
  covalent geometry    : angle       0.53802 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7218 (tp)
REVERT: A  507 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8144 (tt0)
REVERT: A  550 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7176 (mm-40)
REVERT: A  606 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7152 (pm20)
  outliers start: 10
  outliers final: 5
  residues processed: 62
  average time/residue: 1.2384
  time to fit residues: 79.9267
Evaluate side-chains
  66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  606 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.151442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.135852 restraints weight = 4191.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 0.87
r_work: 0.3401 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4446  Z= 0.177
  Angle     :  0.605   6.228   6064  Z= 0.325
  Chirality :  0.042   0.139    669
  Planarity :  0.005   0.047    744
  Dihedral  :  4.201  23.432    594
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.11 %
    Favored  : 87.91 %
  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:  1.57 (0.36), residues: 538
  helix:  2.06 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.38 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 215 
 HIS   0.006   0.001   HIS A 499 
 PHE   0.022   0.002   PHE A 106 
 TYR   0.024   0.002   TYR A  74 
 ARG   0.004   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07721 (  273)
  hydrogen bonds       : angle       4.03676 (  801)
  SS BOND              : bond        0.00778 (    1)
  SS BOND              : angle       1.24541 (    2)
  covalent geometry    : bond        0.00381 ( 4445)
  covalent geometry    : angle       0.60494 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   71 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7924 (ttt-90)
REVERT: A  507 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8173 (tt0)
REVERT: A  550 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7189 (mm-40)
REVERT: A  606 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7129 (pm20)
  outliers start: 9
  outliers final: 5
  residues processed: 65
  average time/residue: 1.1536
  time to fit residues: 78.1916
Evaluate side-chains
  69 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  606 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    0.0040
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.4992

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.153538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.135021 restraints weight = 4364.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.15
r_work: 0.3482 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4446  Z= 0.128
  Angle     :  0.520   6.108   6064  Z= 0.275
  Chirality :  0.039   0.122    669
  Planarity :  0.005   0.042    744
  Dihedral  :  3.920  23.308    594
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.77 %
    Favored  : 87.25 %
  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:  1.88 (0.37), residues: 538
  helix:  2.28 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.26 (0.46), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 499 
 PHE   0.014   0.001   PHE A 106 
 TYR   0.019   0.001   TYR A  74 
 ARG   0.001   0.000   ARG A 611 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05998 (  273)
  hydrogen bonds       : angle       3.88550 (  801)
  SS BOND              : bond        0.00374 (    1)
  SS BOND              : angle       0.88885 (    2)
  covalent geometry    : bond        0.00246 ( 4445)
  covalent geometry    : angle       0.51959 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
REVERT: A  507 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8088 (tt0)
REVERT: A  550 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7004 (mm-40)
REVERT: A  606 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6975 (pm20)
  outliers start: 9
  outliers final: 4
  residues processed: 64
  average time/residue: 1.5252
  time to fit residues: 101.6283
Evaluate side-chains
  66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  606 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0030
   chunk 48 optimal weight:    0.0870
   chunk 25 optimal weight:    0.4980
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0570
   overall best weight:    0.3086

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.160309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.142363 restraints weight = 4212.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.12
r_work: 0.3528 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4446  Z= 0.112
  Angle     :  0.490   5.847   6064  Z= 0.256
  Chirality :  0.038   0.117    669
  Planarity :  0.004   0.041    744
  Dihedral  :  3.724  22.605    594
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.99 %
    Favored  : 87.91 %
  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:  2.15 (0.37), residues: 538
  helix:  2.51 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.18 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 215 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.010   0.001   PHE A 106 
 TYR   0.017   0.001   TYR A  74 
 ARG   0.001   0.000   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05078 (  273)
  hydrogen bonds       : angle       3.76008 (  801)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       0.66887 (    2)
  covalent geometry    : bond        0.00211 ( 4445)
  covalent geometry    : angle       0.48978 ( 6062)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: A  550 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6897 (mm-40)
  outliers start: 5
  outliers final: 2
  residues processed: 62
  average time/residue: 1.1729
  time to fit residues: 75.7737
Evaluate side-chains
  61 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  550 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0060
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.153040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.134469 restraints weight = 4338.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.14
r_work: 0.3470 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4446  Z= 0.138
  Angle     :  0.536   5.869   6064  Z= 0.285
  Chirality :  0.039   0.118    669
  Planarity :  0.005   0.042    744
  Dihedral  :  3.900  22.877    594
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 11.43 %
    Favored  : 87.91 %
  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 (0.37), residues: 538
  helix:  2.33 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.23 (0.46), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 215 
 HIS   0.005   0.001   HIS A 499 
 PHE   0.014   0.002   PHE A 106 
 TYR   0.013   0.002   TYR A  74 
 ARG   0.002   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06276 (  273)
  hydrogen bonds       : angle       3.85613 (  801)
  SS BOND              : bond        0.00490 (    1)
  SS BOND              : angle       0.92751 (    2)
  covalent geometry    : bond        0.00280 ( 4445)
  covalent geometry    : angle       0.53543 ( 6062)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3732.86 seconds
wall clock time: 66 minutes 30.71 seconds (3990.71 seconds total)