Starting phenix.real_space_refine
on Fri May  9 21:31:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdj_37138/05_2025/8kdj_37138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdj_37138/05_2025/8kdj_37138.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdj_37138/05_2025/8kdj_37138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdj_37138/05_2025/8kdj_37138.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdj_37138/05_2025/8kdj_37138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdj_37138/05_2025/8kdj_37138.cif"
  }
  resolution = 3.73
  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=   0.002 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      22      5.16       5
     C    2720      2.51       5
     N     604      2.21       5
     O     665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4013
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 409
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 3451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3451
          Classifications: {'peptide': 447}
          Link IDs: {'PTRANS': 23, 'TRANS': 423}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 65
          Unusual residues: {'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'LBN:plan-3': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 88
          Unusual residues: {'CLR': 2, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'LBN:plan-3': 1}
          Unresolved non-hydrogen planarities: 2
  Time building chain proxies: 3.04, per 1000 atoms: 0.76
  Number of scatterers: 4013
  At special positions: 0
  Unit cell: (81.3285, 82.863, 81.3285, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     P       2     15.00
     O     665      8.00
     N     604      7.00
     C    2720      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.10

  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: 1.15
  Conformation dependent library (CDL) restraints added in 487.1 milliseconds
  

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  918

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 5.344A  pdb=" N   LYS A 171 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 207
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 4.054A  pdb=" N   GLY B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 71 through 80
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.609A  pdb=" N   ALA B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 124
      removed outlier: 3.858A  pdb=" N   TYR B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLU B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.603A  pdb=" N   PHE B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
      removed outlier: 3.522A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.803A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 222
      removed outlier: 4.269A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ALA B 201 " --> pdb=" O   GLN B 197 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   ALA B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ALA B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 254
      removed outlier: 3.531A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 261
      removed outlier: 3.689A  pdb=" N   LEU B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASN B 261 " --> pdb=" O   TRP B 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 256 through 261'
    Processing helix  chain 'B' and resid 262 through 267
    Processing helix  chain 'B' and resid 272 through 298
      removed outlier: 3.754A  pdb=" N   LEU B 276 " --> pdb=" O   ARG B 272 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 3.712A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 325
    Processing helix  chain 'B' and resid 326 through 345
    Processing helix  chain 'B' and resid 346 through 356
      removed outlier: 3.943A  pdb=" N   PHE B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 373 through 387
      removed outlier: 3.861A  pdb=" N   TYR B 387 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 390
      No H-bonds generated for 'chain 'B' and resid 388 through 390'
    Processing helix  chain 'B' and resid 392 through 422
    Processing helix  chain 'B' and resid 435 through 454
      removed outlier: 4.323A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   TRP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 467
      removed outlier: 3.765A  pdb=" N   CYS B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.279A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501

    285 hydrogen bonds defined for protein.
    828 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: 1.03

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 731
        1.33 -     1.47: 1482
        1.47 -     1.62: 1879
        1.62 -     1.76: 0
        1.76 -     1.90: 31
  Bond restraints: 4123
  Sorted by residual:
  bond pdb=" C   CYS B 381 "
       pdb=" N   VAL B 382 "
    ideal  model  delta    sigma   weight residual
    1.335  1.284  0.050 1.20e-02 6.94e+03 1.77e+01
  bond pdb=" CG  MET A 196 "
       pdb=" SD  MET A 196 "
    ideal  model  delta    sigma   weight residual
    1.803  1.899 -0.096 2.50e-02 1.60e+03 1.49e+01
  bond pdb=" CD  GLU B 303 "
       pdb=" OE1 GLU B 303 "
    ideal  model  delta    sigma   weight residual
    1.249  1.318 -0.069 1.90e-02 2.77e+03 1.32e+01
  bond pdb=" C   VAL B 166 "
       pdb=" N   PRO B 167 "
    ideal  model  delta    sigma   weight residual
    1.333  1.370 -0.036 1.01e-02 9.80e+03 1.30e+01
  bond pdb=" CA  ALA B 253 "
       pdb=" CB  ALA B 253 "
    ideal  model  delta    sigma   weight residual
    1.528  1.477  0.051 1.59e-02 3.96e+03 1.03e+01
  ... (remaining 4118 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 4394
        1.96 -     3.92: 1064
        3.92 -     5.88: 156
        5.88 -     7.83: 17
        7.83 -     9.79: 7
  Bond angle restraints: 5638
  Sorted by residual:
  angle pdb=" CA  PHE B 403 "
        pdb=" CB  PHE B 403 "
        pdb=" CG  PHE B 403 "
      ideal   model   delta    sigma   weight residual
     113.80  107.62    6.18 1.00e+00 1.00e+00 3.82e+01
  angle pdb=" CA  ASP B 392 "
        pdb=" CB  ASP B 392 "
        pdb=" CG  ASP B 392 "
      ideal   model   delta    sigma   weight residual
     112.60  117.72   -5.12 1.00e+00 1.00e+00 2.62e+01
  angle pdb=" C   VAL B 322 "
        pdb=" N   MET B 323 "
        pdb=" CA  MET B 323 "
      ideal   model   delta    sigma   weight residual
     120.82  128.00   -7.18 1.50e+00 4.44e-01 2.29e+01
  angle pdb=" N   ILE B 393 "
        pdb=" CA  ILE B 393 "
        pdb=" C   ILE B 393 "
      ideal   model   delta    sigma   weight residual
     110.62  115.45   -4.83 1.02e+00 9.61e-01 2.24e+01
  angle pdb=" C   LEU B 359 "
        pdb=" N   PRO B 360 "
        pdb=" CA  PRO B 360 "
      ideal   model   delta    sigma   weight residual
     119.84  125.71   -5.87 1.25e+00 6.40e-01 2.21e+01
  ... (remaining 5633 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.58: 2461
       28.58 -    57.15: 65
       57.15 -    85.72: 7
       85.72 -   114.30: 3
      114.30 -   142.87: 3
  Dihedral angle restraints: 2539
    sinusoidal: 1109
      harmonic: 1430
  Sorted by residual:
  dihedral pdb=" CA  VAL B  70 "
           pdb=" C   VAL B  70 "
           pdb=" N   THR B  71 "
           pdb=" CA  THR B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.34  -29.66     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  HIS B 319 "
           pdb=" C   HIS B 319 "
           pdb=" N   LEU B 320 "
           pdb=" CA  LEU B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.23  -27.77     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  TYR B 259 "
           pdb=" C   TYR B 259 "
           pdb=" N   LEU B 260 "
           pdb=" CA  LEU B 260 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.83  -26.17     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 2536 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.057: 376
       0.057 -    0.113: 188
       0.113 -    0.169: 88
       0.169 -    0.226: 24
       0.226 -    0.282: 3
  Chirality restraints: 679
  Sorted by residual:
  chirality pdb=" CA  VAL B 374 "
            pdb=" N   VAL B 374 "
            pdb=" C   VAL B 374 "
            pdb=" CB  VAL B 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.16    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  VAL B 166 "
            pdb=" N   VAL B 166 "
            pdb=" C   VAL B 166 "
            pdb=" CB  VAL B 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  SER B 111 "
            pdb=" N   SER B 111 "
            pdb=" C   SER B 111 "
            pdb=" CB  SER B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 676 not shown)

  Planarity restraints: 652
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 141 "    0.374 9.50e-02 1.11e+02   1.68e-01 1.75e+01
        pdb=" NE  ARG B 141 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 141 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 141 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 141 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 427 "    0.338 9.50e-02 1.11e+02   1.51e-01 1.42e+01
        pdb=" NE  ARG B 427 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 427 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 427 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 427 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 193 "   -0.047 2.00e-02 2.50e+03   2.22e-02 1.24e+01
        pdb=" CG  TRP A 193 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 193 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 193 "    0.022 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 193 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 193 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 193 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 193 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 193 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 193 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 649 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 3
        2.57 -     3.15: 3193
        3.15 -     3.74: 6076
        3.74 -     4.32: 8473
        4.32 -     4.90: 14015
  Nonbonded interactions: 31760
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 475 "
            pdb=" O8  LBN B 603 "
     model   vdw
     1.990 3.040
  nonbonded pdb=" O   GLY B 475 "
            pdb=" C34 LBN B 603 "
     model   vdw
     2.490 3.270
  nonbonded pdb=" OG  SER B 395 "
            pdb=" OE2 GLU B 457 "
     model   vdw
     2.503 3.040
  nonbonded pdb=" OG  SER A 165 "
            pdb=" OE1 GLU A 167 "
     model   vdw
     2.600 3.040
  nonbonded pdb=" OG  SER B  81 "
            pdb=" OE1 GLU B 234 "
     model   vdw
     2.605 3.040
  ... (remaining 31755 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.060
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5855
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      :  0.012   0.096   4124  Z= 0.712
  Angle     :  1.721   9.793   5640  Z= 1.134
  Chirality :  0.081   0.282    679
  Planarity :  0.012   0.168    652
  Dihedral  : 14.822 142.873   1618
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  4.30 %
    Favored  : 95.23 %
  Cbeta Deviations :  0.22 %
  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: -2.57 (0.31), residues: 493
  helix: -1.41 (0.22), residues: 363
  sheet:  None (None), residues: 0
  loop : -2.03 (0.48), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.005   TRP A 193 
 HIS   0.003   0.002   HIS B 358 
 PHE   0.020   0.004   PHE B 403 
 TYR   0.029   0.005   TYR B 146 
 ARG   0.008   0.001   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18207 (  285)
  hydrogen bonds       : angle       7.08016 (  828)
  SS BOND              : bond        0.06403 (    1)
  SS BOND              : angle       3.75465 (    2)
  covalent geometry    : bond        0.01146 ( 4123)
  covalent geometry    : angle       1.71977 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  211 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.5952 (ttp-170)
REVERT: B  119 TYR cc_start: 0.5988 (m-10) cc_final: 0.5673 (m-10)
REVERT: B  186 ASN cc_start: 0.6876 (m-40) cc_final: 0.6668 (m-40)
REVERT: B  205 LEU cc_start: 0.6048 (mt) cc_final: 0.5738 (mp)
REVERT: B  248 TYR cc_start: 0.7877 (m-10) cc_final: 0.7594 (m-80)
REVERT: B  365 MET cc_start: 0.8806 (mtt) cc_final: 0.8084 (mmm)
REVERT: B  367 HIS cc_start: 0.7176 (t70) cc_final: 0.6825 (t-90)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1655
  time to fit residues: 23.4034
Evaluate side-chains
  75 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 37 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.168001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.126890 restraints weight = 4153.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.130491 restraints weight = 2895.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.133023 restraints weight = 2308.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4124  Z= 0.153
  Angle     :  0.739   7.791   5640  Z= 0.377
  Chirality :  0.045   0.173    679
  Planarity :  0.006   0.041    652
  Dihedral  : 13.645 142.738    777
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.41 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.37), residues: 493
  helix:  1.20 (0.26), residues: 368
  sheet:  None (None), residues: 0
  loop : -1.11 (0.54), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 417 
 HIS   0.002   0.001   HIS B 367 
 PHE   0.022   0.002   PHE B 474 
 TYR   0.012   0.002   TYR B 296 
 ARG   0.002   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05126 (  285)
  hydrogen bonds       : angle       4.10509 (  828)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       2.51992 (    2)
  covalent geometry    : bond        0.00327 ( 4123)
  covalent geometry    : angle       0.73778 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.416 
Fit side-chains
REVERT: B  266 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5851 (mm-30)
REVERT: B  294 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7472 (mm)
REVERT: B  365 MET cc_start: 0.8417 (mtt) cc_final: 0.7130 (mtt)
REVERT: B  383 MET cc_start: 0.7950 (tpp) cc_final: 0.7704 (tpp)
REVERT: B  387 TYR cc_start: 0.9077 (m-80) cc_final: 0.8477 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1698
  time to fit residues: 18.9841
Evaluate side-chains
  70 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  489 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 GLN
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.165217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.128477 restraints weight = 4242.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.128997 restraints weight = 3170.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.129223 restraints weight = 2537.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4124  Z= 0.146
  Angle     :  0.683   7.693   5640  Z= 0.346
  Chirality :  0.043   0.162    679
  Planarity :  0.005   0.047    652
  Dihedral  : 12.780 135.505    777
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 15.99 %
    Favored  : 79.71 %
  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:  1.41 (0.38), residues: 493
  helix:  1.59 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.09 (0.54), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 417 
 HIS   0.002   0.001   HIS B 367 
 PHE   0.022   0.002   PHE B 403 
 TYR   0.018   0.002   TYR B 155 
 ARG   0.003   0.000   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  285)
  hydrogen bonds       : angle       3.79603 (  828)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       2.93050 (    2)
  covalent geometry    : bond        0.00324 ( 4123)
  covalent geometry    : angle       0.68114 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.423 
Fit side-chains
REVERT: B  266 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5710 (mm-30)
REVERT: B  387 TYR cc_start: 0.9138 (m-80) cc_final: 0.8632 (m-80)
REVERT: B  432 ASN cc_start: 0.7529 (t0) cc_final: 0.6788 (m110)
REVERT: B  500 MET cc_start: 0.8010 (mtm) cc_final: 0.7560 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 81
  average time/residue: 0.1420
  time to fit residues: 14.8585
Evaluate side-chains
  73 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  489 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 47 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    0.3980
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.168540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.127617 restraints weight = 4269.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.131178 restraints weight = 2979.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.133627 restraints weight = 2359.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4124  Z= 0.127
  Angle     :  0.642   8.459   5640  Z= 0.320
  Chirality :  0.041   0.152    679
  Planarity :  0.005   0.045    652
  Dihedral  : 11.607 122.314    777
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 15.51 %
    Favored  : 80.43 %
  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:  1.78 (0.39), residues: 493
  helix:  1.74 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.66 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 417 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.019   0.002   PHE B 403 
 TYR   0.013   0.001   TYR B 155 
 ARG   0.004   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03991 (  285)
  hydrogen bonds       : angle       3.63902 (  828)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       2.84081 (    2)
  covalent geometry    : bond        0.00275 ( 4123)
  covalent geometry    : angle       0.63945 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 ILE cc_start: 0.7462 (mm) cc_final: 0.6796 (mt)
REVERT: B  141 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7239 (mmm-85)
REVERT: B  266 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5661 (mm-30)
REVERT: B  305 MET cc_start: 0.8516 (ttm) cc_final: 0.8252 (ttm)
REVERT: B  365 MET cc_start: 0.8307 (mtt) cc_final: 0.7815 (mtt)
REVERT: B  432 ASN cc_start: 0.7446 (t0) cc_final: 0.6712 (m110)
REVERT: B  500 MET cc_start: 0.7979 (mtm) cc_final: 0.7749 (mtm)
  outliers start: 17
  outliers final: 13
  residues processed: 85
  average time/residue: 0.1755
  time to fit residues: 18.1816
Evaluate side-chains
  76 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  141 ARG
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  464 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 26 optimal weight:    0.2980
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 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 = 0.3830 r_free = 0.3830 target = 0.168942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.129116 restraints weight = 4350.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.132840 restraints weight = 2980.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.135029 restraints weight = 2348.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4124  Z= 0.119
  Angle     :  0.614   7.402   5640  Z= 0.307
  Chirality :  0.041   0.164    679
  Planarity :  0.005   0.044    652
  Dihedral  : 10.726 112.771    777
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 16.23 %
    Favored  : 79.71 %
  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 (0.39), residues: 493
  helix:  1.89 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.69 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.001   0.000   HIS B 420 
 PHE   0.020   0.002   PHE B 474 
 TYR   0.012   0.001   TYR B 155 
 ARG   0.003   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  285)
  hydrogen bonds       : angle       3.52634 (  828)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       1.59164 (    2)
  covalent geometry    : bond        0.00255 ( 4123)
  covalent geometry    : angle       0.61381 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.5441 (ptt90) cc_final: 0.5129 (ptt90)
REVERT: B  141 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7162 (mmm-85)
REVERT: B  266 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5631 (mm-30)
REVERT: B  305 MET cc_start: 0.8695 (ttm) cc_final: 0.8352 (ttm)
REVERT: B  365 MET cc_start: 0.8325 (mtt) cc_final: 0.7772 (mtt)
REVERT: B  432 ASN cc_start: 0.7310 (t0) cc_final: 0.6572 (m110)
REVERT: B  500 MET cc_start: 0.8050 (mtm) cc_final: 0.7670 (mtm)
  outliers start: 17
  outliers final: 14
  residues processed: 83
  average time/residue: 0.1590
  time to fit residues: 16.3878
Evaluate side-chains
  84 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  141 ARG
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  489 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 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 = 0.3814 r_free = 0.3814 target = 0.167385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.126833 restraints weight = 4357.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.130096 restraints weight = 3073.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.132573 restraints weight = 2466.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4124  Z= 0.128
  Angle     :  0.616   7.647   5640  Z= 0.307
  Chirality :  0.041   0.152    679
  Planarity :  0.005   0.042    652
  Dihedral  : 10.422 110.488    777
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 16.23 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.39), residues: 493
  helix:  1.87 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.64 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 417 
 HIS   0.001   0.001   HIS B 367 
 PHE   0.019   0.002   PHE B 474 
 TYR   0.017   0.002   TYR B 155 
 ARG   0.004   0.000   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  285)
  hydrogen bonds       : angle       3.55818 (  828)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       1.30757 (    2)
  covalent geometry    : bond        0.00292 ( 4123)
  covalent geometry    : angle       0.61592 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: B  141 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7189 (mmm-85)
REVERT: B  266 GLU cc_start: 0.6334 (mm-30) cc_final: 0.5836 (mm-30)
REVERT: B  305 MET cc_start: 0.8739 (ttm) cc_final: 0.8368 (ttm)
REVERT: B  365 MET cc_start: 0.8275 (mtt) cc_final: 0.7788 (mtt)
REVERT: B  500 MET cc_start: 0.8051 (mtm) cc_final: 0.7607 (mtm)
  outliers start: 21
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1688
  time to fit residues: 17.6439
Evaluate side-chains
  78 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  141 ARG
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  464 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 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 = 0.3907 r_free = 0.3907 target = 0.176232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.135805 restraints weight = 4244.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.139379 restraints weight = 2887.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.142246 restraints weight = 2288.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4124  Z= 0.118
  Angle     :  0.637  12.051   5640  Z= 0.305
  Chirality :  0.040   0.145    679
  Planarity :  0.005   0.040    652
  Dihedral  : 10.239 108.033    777
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 16.95 %
    Favored  : 78.52 %
  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:  2.10 (0.39), residues: 493
  helix:  1.92 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.44 (0.61), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.001   0.000   HIS B 367 
 PHE   0.019   0.002   PHE B 445 
 TYR   0.014   0.002   TYR B 155 
 ARG   0.005   0.001   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  285)
  hydrogen bonds       : angle       3.47725 (  828)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.83915 (    2)
  covalent geometry    : bond        0.00260 ( 4123)
  covalent geometry    : angle       0.63671 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.5583 (ptt90) cc_final: 0.5206 (ptt90)
REVERT: B  120 MET cc_start: 0.6501 (mmt) cc_final: 0.6258 (mmt)
REVERT: B  141 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7139 (mmm-85)
REVERT: B  197 GLN cc_start: 0.7142 (tp40) cc_final: 0.6670 (tp40)
REVERT: B  266 GLU cc_start: 0.6423 (mm-30) cc_final: 0.5933 (mm-30)
REVERT: B  305 MET cc_start: 0.8714 (ttm) cc_final: 0.8368 (ttm)
REVERT: B  365 MET cc_start: 0.8155 (mtt) cc_final: 0.7834 (mtt)
REVERT: B  500 MET cc_start: 0.8007 (mtm) cc_final: 0.7562 (mtm)
  outliers start: 19
  outliers final: 17
  residues processed: 77
  average time/residue: 0.1527
  time to fit residues: 14.9997
Evaluate side-chains
  84 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  141 ARG
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  464 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0070
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.6002

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 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 = 0.3926 r_free = 0.3926 target = 0.177837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137488 restraints weight = 4153.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.141348 restraints weight = 2851.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.143980 restraints weight = 2251.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4124  Z= 0.115
  Angle     :  0.611   8.170   5640  Z= 0.299
  Chirality :  0.040   0.146    679
  Planarity :  0.005   0.040    652
  Dihedral  :  9.896 109.423    777
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 17.90 %
    Favored  : 78.04 %
  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:  2.18 (0.39), residues: 493
  helix:  1.99 (0.27), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.50 (0.61), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.001   0.000   HIS B 367 
 PHE   0.016   0.002   PHE B 474 
 TYR   0.013   0.002   TYR B 155 
 ARG   0.005   0.001   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  285)
  hydrogen bonds       : angle       3.47155 (  828)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.82537 (    2)
  covalent geometry    : bond        0.00246 ( 4123)
  covalent geometry    : angle       0.61075 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.438 
Fit side-chains
REVERT: B  182 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8271 (mm)
REVERT: B  197 GLN cc_start: 0.7128 (tp40) cc_final: 0.6676 (tp40)
REVERT: B  266 GLU cc_start: 0.6440 (mm-30) cc_final: 0.5958 (mm-30)
REVERT: B  305 MET cc_start: 0.8765 (ttm) cc_final: 0.8435 (ttm)
REVERT: B  365 MET cc_start: 0.8023 (mtt) cc_final: 0.7604 (mtt)
REVERT: B  439 PHE cc_start: 0.6775 (t80) cc_final: 0.6264 (t80)
REVERT: B  458 CYS cc_start: 0.7701 (m) cc_final: 0.6604 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 80
  average time/residue: 0.1545
  time to fit residues: 15.9468
Evaluate side-chains
  77 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  464 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 27 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.179075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.138677 restraints weight = 4241.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.142608 restraints weight = 2872.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.145541 restraints weight = 2247.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.4787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4124  Z= 0.117
  Angle     :  0.609   8.368   5640  Z= 0.298
  Chirality :  0.040   0.154    679
  Planarity :  0.005   0.039    652
  Dihedral  :  9.700 109.486    777
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 19.09 %
    Favored  : 77.33 %
  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:  2.32 (0.39), residues: 493
  helix:  2.15 (0.28), residues: 377
  sheet:  None (None), residues: 0
  loop : -0.55 (0.58), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 134 
 HIS   0.002   0.000   HIS B 367 
 PHE   0.024   0.002   PHE B 474 
 TYR   0.022   0.002   TYR B 289 
 ARG   0.004   0.001   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03393 (  285)
  hydrogen bonds       : angle       3.43525 (  828)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.68016 (    2)
  covalent geometry    : bond        0.00263 ( 4123)
  covalent geometry    : angle       0.60884 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  211 ARG cc_start: 0.5586 (ptt90) cc_final: 0.5231 (ptt90)
REVERT: B  120 MET cc_start: 0.6620 (mmt) cc_final: 0.6389 (mmm)
REVERT: B  182 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8284 (mm)
REVERT: B  197 GLN cc_start: 0.7125 (tp40) cc_final: 0.6695 (tp40)
REVERT: B  266 GLU cc_start: 0.6430 (mm-30) cc_final: 0.5933 (mm-30)
REVERT: B  305 MET cc_start: 0.8823 (ttm) cc_final: 0.8487 (ttm)
REVERT: B  365 MET cc_start: 0.8044 (mtt) cc_final: 0.7607 (mtt)
REVERT: B  439 PHE cc_start: 0.6739 (t80) cc_final: 0.6274 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 73
  average time/residue: 0.1418
  time to fit residues: 13.4284
Evaluate side-chains
  76 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  464 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0170
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 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 = 0.3922 r_free = 0.3922 target = 0.177143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.136594 restraints weight = 4248.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.140459 restraints weight = 2944.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.142701 restraints weight = 2298.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4124  Z= 0.132
  Angle     :  0.633   8.209   5640  Z= 0.312
  Chirality :  0.040   0.153    679
  Planarity :  0.005   0.039    652
  Dihedral  :  9.555 110.144    777
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 18.85 %
    Favored  : 77.33 %
  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:  2.26 (0.39), residues: 493
  helix:  2.17 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.76 (0.57), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 417 
 HIS   0.002   0.001   HIS B 358 
 PHE   0.024   0.002   PHE B 474 
 TYR   0.016   0.002   TYR B 155 
 ARG   0.004   0.001   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  285)
  hydrogen bonds       : angle       3.47409 (  828)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       0.86156 (    2)
  covalent geometry    : bond        0.00310 ( 4123)
  covalent geometry    : angle       0.63300 ( 5638)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.6574 (mmt) cc_final: 0.6369 (mmm)
REVERT: B  197 GLN cc_start: 0.7163 (tp40) cc_final: 0.6693 (tp40)
REVERT: B  266 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6058 (mm-30)
REVERT: B  305 MET cc_start: 0.8892 (ttm) cc_final: 0.8543 (ttm)
REVERT: B  365 MET cc_start: 0.7883 (mtt) cc_final: 0.7534 (mtt)
REVERT: B  439 PHE cc_start: 0.6780 (t80) cc_final: 0.6091 (t80)
  outliers start: 16
  outliers final: 16
  residues processed: 70
  average time/residue: 0.1396
  time to fit residues: 12.6988
Evaluate side-chains
  77 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  464 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.178528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.138360 restraints weight = 4244.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.142233 restraints weight = 2904.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.144609 restraints weight = 2283.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.4868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4124  Z= 0.119
  Angle     :  0.618   8.141   5640  Z= 0.302
  Chirality :  0.040   0.145    679
  Planarity :  0.005   0.039    652
  Dihedral  :  9.384 111.506    777
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.57 %
    Favored  : 77.09 %
  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:  2.34 (0.39), residues: 493
  helix:  2.19 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop : -0.63 (0.58), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 134 
 HIS   0.001   0.001   HIS B 358 
 PHE   0.024   0.002   PHE B 474 
 TYR   0.014   0.002   TYR B 155 
 ARG   0.008   0.001   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  285)
  hydrogen bonds       : angle       3.43399 (  828)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.51244 (    2)
  covalent geometry    : bond        0.00264 ( 4123)
  covalent geometry    : angle       0.61806 ( 5638)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1491.59 seconds
wall clock time: 26 minutes 57.29 seconds (1617.29 seconds total)