Starting phenix.real_space_refine
on Sun May 11 08:29:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gkh_40184/05_2025/8gkh_40184_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gkh_40184/05_2025/8gkh_40184.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gkh_40184/05_2025/8gkh_40184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gkh_40184/05_2025/8gkh_40184.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gkh_40184/05_2025/8gkh_40184_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gkh_40184/05_2025/8gkh_40184_neut.cif"
  }
  resolution = 2.7
  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=   0.026
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     125      5.49       5
     Mg      2      5.21       5
     S      32      5.16       5
     C    4337      2.51       5
     N    1358      2.21       5
     O    1715      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7570
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "N"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 308
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "P"
      Number of atoms: 4946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 600, 4946
          Classifications: {'peptide': 600}
          Link IDs: {'PTRANS': 25, 'TRANS': 574}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 695
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
          Chain breaks: 1
    Chain: "W"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1615
          Classifications: {'RNA': 76}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 11, 'rna3p': 64}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 2, ' ZN': 1}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
    Chain: "T"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "W"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4558  SG  CYS P 548      32.953  45.640  21.668  1.00 51.02           S
  ATOM   4582  SG  CYS P 551      30.062  44.068  19.775  1.00 57.06           S
  ATOM   4875  SG  CYS P 586      33.492  42.516  19.547  1.00 52.44           S
  ATOM   4911  SG  CYS P 591      32.800  45.814  17.814  1.00 44.29           S

  Time building chain proxies: 5.48, per 1000 atoms: 0.72
  Number of scatterers: 7570
  At special positions: 0
  Unit cell: (75.9, 107.25, 139.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      32     16.00
     P     125     15.00
     Mg      2     11.99
     O    1715      8.00
     N    1358      7.00
     C    4337      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 676.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN P 703 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 551 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 586 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 591 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 548 "
      Number of angles added : 6


  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1156

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      61.0% alpha, 7.7% beta
      52 base pairs and 76 stacking pairs defined.
    Time for finding SS restraints: 3.53
  Creating SS restraints...
    Processing helix  chain 'P' and resid 28 through 32
    Processing helix  chain 'P' and resid 35 through 68
    Processing helix  chain 'P' and resid 76 through 90
    Processing helix  chain 'P' and resid 91 through 93
      No H-bonds generated for 'chain 'P' and resid 91 through 93'
    Processing helix  chain 'P' and resid 97 through 119
      Proline residue:  P 109  - end of helix
      removed outlier: 4.072A  pdb=" N   GLN P 112 " --> pdb=" O   LEU P 108 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG P 113 " --> pdb=" O   PRO P 109 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 128 through 151
    Processing helix  chain 'P' and resid 151 through 164
    Processing helix  chain 'P' and resid 164 through 172
    Processing helix  chain 'P' and resid 176 through 194
      removed outlier: 3.630A  pdb=" N   PHE P 182 " --> pdb=" O   ALA P 178 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER P 191 " --> pdb=" O   ARG P 187 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL P 192 " --> pdb=" O   TYR P 188 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 200 through 207
    Processing helix  chain 'P' and resid 208 through 220
    Processing helix  chain 'P' and resid 230 through 238
    Processing helix  chain 'P' and resid 239 through 241
      No H-bonds generated for 'chain 'P' and resid 239 through 241'
    Processing helix  chain 'P' and resid 242 through 257
    Processing helix  chain 'P' and resid 279 through 286
    Processing helix  chain 'P' and resid 290 through 296
      removed outlier: 3.847A  pdb=" N   THR P 296 " --> pdb=" O   ARG P 292 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 298 through 305
      removed outlier: 3.601A  pdb=" N   ARG P 305 " --> pdb=" O   ASP P 301 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 311 through 315
    Processing helix  chain 'P' and resid 365 through 368
    Processing helix  chain 'P' and resid 369 through 376
    Processing helix  chain 'P' and resid 403 through 412
    Processing helix  chain 'P' and resid 412 through 428
    Processing helix  chain 'P' and resid 428 through 435
      removed outlier: 3.730A  pdb=" N   ARG P 435 " --> pdb=" O   LEU P 431 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 443 through 457
      removed outlier: 3.741A  pdb=" N   ASP P 457 " --> pdb=" O   VAL P 453 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 457 through 466
    Processing helix  chain 'P' and resid 468 through 497
    Processing helix  chain 'P' and resid 523 through 532
      removed outlier: 4.036A  pdb=" N   THR P 527 " --> pdb=" O   LYS P 523 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 568 through 575
    Processing helix  chain 'P' and resid 588 through 592
    Processing helix  chain 'P' and resid 605 through 622
    Processing sheet with id=AA1, first strand: chain 'P' and resid 21 through 27
      removed outlier: 4.929A  pdb=" N   SER P 325 " --> pdb=" O   TYR P 336 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 400 through 402
    Processing sheet with id=AA3, first strand: chain 'P' and resid 557 through 559
      removed outlier: 3.642A  pdb=" N   GLY P 585 " --> pdb=" O   GLU P 558 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 563 through 565

    271 hydrogen bonds defined for protein.
    786 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      132 hydrogen bonds
      248 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      76 stacking parallelities
  Total time for adding SS restraints: 3.09

  Time building geometry restraints manager: 2.78 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: 1900
        1.34 -     1.45: 2153
        1.45 -     1.57: 3645
        1.57 -     1.69: 245
        1.69 -     1.81: 48
  Bond restraints: 7991
  Sorted by residual:
  bond pdb=" O3'  DG T -17 "
       pdb=" P    DA T -16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.625 -0.018 1.50e-02 4.44e+03 1.37e+00
  bond pdb=" C1'   A W  16 "
       pdb=" N9    A W  16 "
    ideal  model  delta    sigma   weight residual
    1.465  1.480 -0.015 1.50e-02 4.44e+03 1.07e+00
  bond pdb=" C1'   U W  15 "
       pdb=" N1    U W  15 "
    ideal  model  delta    sigma   weight residual
    1.470  1.484 -0.014 1.50e-02 4.44e+03 8.77e-01
  bond pdb=" C3'  DC T  -6 "
       pdb=" O3'  DC T  -6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.450 -0.028 3.00e-02 1.11e+03 8.52e-01
  bond pdb=" C3'  DA T  -8 "
       pdb=" O3'  DA T  -8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.449 -0.027 3.00e-02 1.11e+03 7.82e-01
  ... (remaining 7986 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.64: 11205
        4.64 -     9.29: 53
        9.29 -    13.93: 110
       13.93 -    18.58: 1
       18.58 -    23.22: 1
  Bond angle restraints: 11370
  Sorted by residual:
  angle pdb=" O3'  DG T -17 "
        pdb=" P    DA T -16 "
        pdb=" OP1  DA T -16 "
      ideal   model   delta    sigma   weight residual
     108.00  131.22  -23.22 3.00e+00 1.11e-01 5.99e+01
  angle pdb=" OP1  DA T -16 "
        pdb=" P    DA T -16 "
        pdb=" OP2  DA T -16 "
      ideal   model   delta    sigma   weight residual
     120.00  103.13   16.87 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" O3'   C W  19 "
        pdb=" C3'   C W  19 "
        pdb=" C2'   C W  19 "
      ideal   model   delta    sigma   weight residual
     109.50  116.88   -7.38 1.50e+00 4.44e-01 2.42e+01
  angle pdb=" C4'   U W  76 "
        pdb=" C3'   U W  76 "
        pdb=" O3'   U W  76 "
      ideal   model   delta    sigma   weight residual
     109.40  116.64   -7.24 1.50e+00 4.44e-01 2.33e+01
  angle pdb=" C4'   U W  15 "
        pdb=" C3'   U W  15 "
        pdb=" O3'   U W  15 "
      ideal   model   delta    sigma   weight residual
     109.40  115.86   -6.46 1.50e+00 4.44e-01 1.85e+01
  ... (remaining 11365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.94: 4417
       35.94 -    71.88: 334
       71.88 -   107.82: 31
      107.82 -   143.76: 8
      143.76 -   179.70: 11
  Dihedral angle restraints: 4801
    sinusoidal: 3023
      harmonic: 1778
  Sorted by residual:
  dihedral pdb=" C4'   U W  76 "
           pdb=" C3'   U W  76 "
           pdb=" C2'   U W  76 "
           pdb=" C1'   U W  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.12  -71.12     1      8.00e+00 1.56e-02 1.01e+02
  dihedral pdb=" C4'   A W  16 "
           pdb=" C3'   A W  16 "
           pdb=" C2'   A W  16 "
           pdb=" C1'   A W  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.70  -70.70     1      8.00e+00 1.56e-02 1.00e+02
  dihedral pdb=" C4'   C W  19 "
           pdb=" C3'   C W  19 "
           pdb=" C2'   C W  19 "
           pdb=" C1'   C W  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.27  -70.27     1      8.00e+00 1.56e-02 9.94e+01
  ... (remaining 4798 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.149: 1215
       0.149 -    0.299: 39
       0.299 -    0.448: 52
       0.448 -    0.598: 0
       0.598 -    0.747: 1
  Chirality restraints: 1307
  Sorted by residual:
  chirality pdb=" P    DA T -16 "
            pdb=" OP1  DA T -16 "
            pdb=" OP2  DA T -16 "
            pdb=" O5'  DA T -16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.09   -0.75 2.00e-01 2.50e+01 1.40e+01
  chirality pdb=" P    DC T   7 "
            pdb=" OP1  DC T   7 "
            pdb=" OP2  DC T   7 "
            pdb=" O5'  DC T   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.79   -0.44 2.00e-01 2.50e+01 4.91e+00
  chirality pdb=" P    DA T  -4 "
            pdb=" OP1  DA T  -4 "
            pdb=" OP2  DA T  -4 "
            pdb=" O5'  DA T  -4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.76   -0.42 2.00e-01 2.50e+01 4.32e+00
  ... (remaining 1304 not shown)

  Planarity restraints: 1000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W  20 "    0.014 2.00e-02 2.50e+03   7.39e-03 1.64e+00
        pdb=" N9    G W  20 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    G W  20 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    G W  20 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G W  20 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G W  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G W  20 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G W  20 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    G W  20 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G W  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    G W  20 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G W  20 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W  70 "   -0.016 2.00e-02 2.50e+03   7.29e-03 1.59e+00
        pdb=" N9    G W  70 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G W  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G W  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G W  70 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G W  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G W  70 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U W  27 "   -0.015 2.00e-02 2.50e+03   7.91e-03 1.41e+00
        pdb=" N1    U W  27 "    0.017 2.00e-02 2.50e+03
        pdb=" C2    U W  27 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U W  27 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U W  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U W  27 "   -0.002 2.00e-02 2.50e+03
        pdb=" O4    U W  27 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    U W  27 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U W  27 "    0.003 2.00e-02 2.50e+03
  ... (remaining 997 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 63
        2.48 -     3.09: 5215
        3.09 -     3.69: 12649
        3.69 -     4.30: 18239
        4.30 -     4.90: 28379
  Nonbonded interactions: 64545
  Sorted by model distance:
  nonbonded pdb="MG    MG P 702 "
            pdb=" O   HOH P 801 "
     model   vdw
     1.881 2.170
  nonbonded pdb=" OD1 ASN P 385 "
            pdb="MG    MG P 701 "
     model   vdw
     1.886 2.170
  nonbonded pdb=" OP1  DT T -19 "
            pdb="MG    MG P 701 "
     model   vdw
     1.900 2.170
  nonbonded pdb=" OP2  DT T -19 "
            pdb="MG    MG P 702 "
     model   vdw
     1.902 2.170
  nonbonded pdb=" O2'   G W  20 "
            pdb=" OP1   C W  21 "
     model   vdw
     1.902 3.040
  ... (remaining 64540 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     26.810
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
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   0.032   7995  Z= 0.115
  Angle     :  1.275  23.219  11376  Z= 0.504
  Chirality :  0.096   0.747   1307
  Planarity :  0.002   0.025   1000
  Dihedral  : 22.525 179.701   3645
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.05 (0.36), residues: 596
  helix:  2.95 (0.29), residues: 331
  sheet:  0.24 (0.83), residues: 41
  loop :  1.06 (0.44), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP P  93 
 HIS   0.002   0.001   HIS P  55 
 PHE   0.005   0.001   PHE P 151 
 TYR   0.016   0.001   TYR P 283 
 ARG   0.002   0.000   ARG P 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13323 (  403)
  hydrogen bonds       : angle       5.40211 ( 1034)
  metal coordination   : bond        0.00177 (    4)
  metal coordination   : angle       1.14425 (    6)
  covalent geometry    : bond        0.00228 ( 7991)
  covalent geometry    : angle       1.27470 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  238 ASP cc_start: 0.7088 (t0) cc_final: 0.6786 (t0)
REVERT: P  487 ASP cc_start: 0.7283 (m-30) cc_final: 0.7050 (m-30)
REVERT: P  574 GLU cc_start: 0.7050 (tp30) cc_final: 0.6738 (tp30)
  outliers start: 0
  outliers final: 1
  residues processed: 128
  average time/residue: 1.3596
  time to fit residues: 182.4945
Evaluate side-chains
  121 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 129 GLN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN
P 581 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.189998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.166556 restraints weight = 11110.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.4154 rms_B_bonded: 1.28
r_work: 0.4062 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3952 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7995  Z= 0.209
  Angle     :  0.668   9.946  11376  Z= 0.356
  Chirality :  0.041   0.260   1307
  Planarity :  0.005   0.050   1000
  Dihedral  : 25.283 177.894   2411
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  9.21 %
    Favored  : 88.21 %
  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 (0.34), residues: 596
  helix:  2.07 (0.28), residues: 336
  sheet:  0.25 (0.80), residues: 41
  loop :  0.68 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP P 570 
 HIS   0.008   0.001   HIS P 566 
 PHE   0.019   0.002   PHE P  62 
 TYR   0.019   0.002   TYR P 283 
 ARG   0.008   0.001   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05213 (  403)
  hydrogen bonds       : angle       4.31117 ( 1034)
  metal coordination   : bond        0.00615 (    4)
  metal coordination   : angle       3.03058 (    6)
  covalent geometry    : bond        0.00449 ( 7991)
  covalent geometry    : angle       0.66473 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.580 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5543 (t80) cc_final: 0.3948 (t80)
REVERT: P  238 ASP cc_start: 0.7352 (t0) cc_final: 0.7050 (t0)
REVERT: P  362 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7188 (mtmt)
REVERT: P  388 ASP cc_start: 0.7746 (m-30) cc_final: 0.7535 (m-30)
REVERT: P  445 MET cc_start: 0.4394 (OUTLIER) cc_final: 0.4008 (tmm)
REVERT: P  483 LYS cc_start: 0.8113 (tppt) cc_final: 0.7469 (tppt)
REVERT: P  487 ASP cc_start: 0.7383 (m-30) cc_final: 0.7148 (m-30)
REVERT: P  574 GLU cc_start: 0.7248 (tp30) cc_final: 0.6750 (tp30)
REVERT: P  602 TYR cc_start: 0.8087 (m-80) cc_final: 0.7770 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 125
  average time/residue: 1.2126
  time to fit residues: 160.0494
Evaluate side-chains
  119 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  129 GLN
Chi-restraints excluded: chain P residue  270 LEU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  445 MET
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 129 GLN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.189375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.165595 restraints weight = 11377.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 1.29
r_work: 0.4049 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3939 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7995  Z= 0.179
  Angle     :  0.622   8.472  11376  Z= 0.335
  Chirality :  0.039   0.231   1307
  Planarity :  0.004   0.038   1000
  Dihedral  : 24.976 167.374   2411
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 11.42 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.34), residues: 596
  helix:  1.68 (0.28), residues: 337
  sheet:  0.20 (0.80), residues: 41
  loop :  0.42 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 
 PHE   0.017   0.002   PHE P 630 
 TYR   0.017   0.002   TYR P 283 
 ARG   0.006   0.001   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04808 (  403)
  hydrogen bonds       : angle       4.23457 ( 1034)
  metal coordination   : bond        0.00714 (    4)
  metal coordination   : angle       3.28290 (    6)
  covalent geometry    : bond        0.00384 ( 7991)
  covalent geometry    : angle       0.61728 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.645 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5664 (t80) cc_final: 0.3928 (t80)
REVERT: P  172 LEU cc_start: 0.6586 (mt) cc_final: 0.6386 (mt)
REVERT: P  238 ASP cc_start: 0.7479 (t0) cc_final: 0.7254 (t0)
REVERT: P  362 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7257 (mtmt)
REVERT: P  388 ASP cc_start: 0.7769 (m-30) cc_final: 0.7554 (m-30)
REVERT: P  442 MET cc_start: 0.4674 (OUTLIER) cc_final: 0.0399 (mpt)
REVERT: P  445 MET cc_start: 0.4477 (OUTLIER) cc_final: 0.4051 (tmm)
REVERT: P  483 LYS cc_start: 0.8176 (tppt) cc_final: 0.7565 (tppt)
REVERT: P  487 ASP cc_start: 0.7372 (m-30) cc_final: 0.7132 (m-30)
REVERT: P  574 GLU cc_start: 0.7220 (tp30) cc_final: 0.6850 (tp30)
REVERT: P  602 TYR cc_start: 0.8146 (m-80) cc_final: 0.7887 (m-80)
  outliers start: 19
  outliers final: 6
  residues processed: 125
  average time/residue: 1.3220
  time to fit residues: 173.8812
Evaluate side-chains
  128 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  270 LEU
Chi-restraints excluded: chain P residue  323 GLU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  445 MET
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P  58 HIS
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.187793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.163418 restraints weight = 11029.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 1.24
r_work: 0.4022 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3909 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7995  Z= 0.199
  Angle     :  0.639   6.964  11376  Z= 0.344
  Chirality :  0.040   0.268   1307
  Planarity :  0.005   0.044   1000
  Dihedral  : 24.913 166.469   2411
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.60 %
    Favored  : 85.45 %
  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:  1.32 (0.34), residues: 596
  helix:  1.43 (0.28), residues: 338
  sheet:  0.26 (0.80), residues: 41
  loop :  0.27 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 
 PHE   0.020   0.002   PHE P 630 
 TYR   0.018   0.002   TYR P 283 
 ARG   0.007   0.001   ARG P 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05015 (  403)
  hydrogen bonds       : angle       4.27842 ( 1034)
  metal coordination   : bond        0.00802 (    4)
  metal coordination   : angle       3.40452 (    6)
  covalent geometry    : bond        0.00428 ( 7991)
  covalent geometry    : angle       0.63485 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.645 
Fit side-chains
REVERT: P   91 GLU cc_start: 0.7166 (mp0) cc_final: 0.6662 (mp0)
REVERT: P  172 LEU cc_start: 0.6673 (mt) cc_final: 0.6434 (mt)
REVERT: P  238 ASP cc_start: 0.7557 (t0) cc_final: 0.7287 (t0)
REVERT: P  388 ASP cc_start: 0.7780 (m-30) cc_final: 0.7573 (m-30)
REVERT: P  421 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6669 (mt-10)
REVERT: P  442 MET cc_start: 0.4707 (OUTLIER) cc_final: 0.0433 (mpt)
REVERT: P  483 LYS cc_start: 0.8206 (tppt) cc_final: 0.7520 (tppt)
REVERT: P  487 ASP cc_start: 0.7367 (m-30) cc_final: 0.7121 (m-30)
REVERT: P  574 GLU cc_start: 0.7310 (tp30) cc_final: 0.7088 (tp30)
REVERT: P  602 TYR cc_start: 0.8182 (m-80) cc_final: 0.7919 (m-80)
  outliers start: 16
  outliers final: 7
  residues processed: 117
  average time/residue: 1.3936
  time to fit residues: 171.4042
Evaluate side-chains
  120 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  270 LEU
Chi-restraints excluded: chain P residue  323 GLU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  421 GLU
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 396 ASN
P 590 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.183654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.159637 restraints weight = 10967.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 1.26
r_work: 0.3980 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3869 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7995  Z= 0.275
  Angle     :  0.718   9.103  11376  Z= 0.381
  Chirality :  0.044   0.344   1307
  Planarity :  0.006   0.054   1000
  Dihedral  : 24.847 162.875   2411
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 12.71 %
    Favored  : 83.79 %
  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:  0.62 (0.33), residues: 596
  helix:  0.84 (0.27), residues: 340
  sheet: -0.31 (0.76), residues: 46
  loop :  0.09 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP P 570 
 HIS   0.007   0.001   HIS P 566 
 PHE   0.022   0.003   PHE P 630 
 TYR   0.027   0.003   TYR P 450 
 ARG   0.012   0.001   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05788 (  403)
  hydrogen bonds       : angle       4.51877 ( 1034)
  metal coordination   : bond        0.01097 (    4)
  metal coordination   : angle       4.39342 (    6)
  covalent geometry    : bond        0.00596 ( 7991)
  covalent geometry    : angle       0.71075 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.606 
Fit side-chains
REVERT: P  129 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8055 (tp-100)
REVERT: P  172 LEU cc_start: 0.6869 (mt) cc_final: 0.6656 (mt)
REVERT: P  388 ASP cc_start: 0.7734 (m-30) cc_final: 0.7491 (m-30)
REVERT: P  483 LYS cc_start: 0.8233 (tppt) cc_final: 0.7530 (tppt)
REVERT: P  487 ASP cc_start: 0.7426 (m-30) cc_final: 0.7165 (m-30)
REVERT: P  574 GLU cc_start: 0.7346 (tp30) cc_final: 0.7121 (tp30)
  outliers start: 19
  outliers final: 10
  residues processed: 122
  average time/residue: 1.3206
  time to fit residues: 169.4074
Evaluate side-chains
  114 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  129 GLN
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  270 LEU
Chi-restraints excluded: chain P residue  304 MET
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.184103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.160552 restraints weight = 11085.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 1.25
r_work: 0.3986 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3875 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.3659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7995  Z= 0.249
  Angle     :  0.673   8.156  11376  Z= 0.363
  Chirality :  0.042   0.301   1307
  Planarity :  0.005   0.056   1000
  Dihedral  : 24.661 163.397   2411
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.00 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.33), residues: 596
  helix:  0.75 (0.27), residues: 340
  sheet: -0.35 (0.76), residues: 46
  loop :  0.04 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 
 PHE   0.023   0.002   PHE P 630 
 TYR   0.026   0.003   TYR P 450 
 ARG   0.011   0.001   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05475 (  403)
  hydrogen bonds       : angle       4.45369 ( 1034)
  metal coordination   : bond        0.00894 (    4)
  metal coordination   : angle       3.26379 (    6)
  covalent geometry    : bond        0.00540 ( 7991)
  covalent geometry    : angle       0.66898 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.581 
Fit side-chains
REVERT: P  172 LEU cc_start: 0.6864 (mt) cc_final: 0.6659 (mt)
REVERT: P  442 MET cc_start: 0.4899 (mpt) cc_final: 0.0269 (mpt)
REVERT: P  483 LYS cc_start: 0.8240 (tppt) cc_final: 0.7579 (tppt)
REVERT: P  487 ASP cc_start: 0.7383 (m-30) cc_final: 0.7131 (m-30)
REVERT: P  574 GLU cc_start: 0.7316 (tp30) cc_final: 0.7101 (tp30)
REVERT: P  605 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7631 (ttm170)
  outliers start: 15
  outliers final: 10
  residues processed: 117
  average time/residue: 1.3143
  time to fit residues: 161.7066
Evaluate side-chains
  117 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  270 LEU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  605 ARG
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P  55 HIS
P 129 GLN
P 321 HIS
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.186156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.162566 restraints weight = 10948.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 1.25
r_work: 0.4018 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3908 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7995  Z= 0.184
  Angle     :  0.627   6.962  11376  Z= 0.337
  Chirality :  0.039   0.259   1307
  Planarity :  0.005   0.054   1000
  Dihedral  : 24.578 164.852   2411
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.55 %
    Favored  : 83.43 %
  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:  0.79 (0.33), residues: 596
  helix:  1.01 (0.27), residues: 338
  sheet:  0.23 (0.83), residues: 41
  loop : -0.03 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 
 PHE   0.023   0.002   PHE P 630 
 TYR   0.020   0.002   TYR P 450 
 ARG   0.011   0.001   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04874 (  403)
  hydrogen bonds       : angle       4.27979 ( 1034)
  metal coordination   : bond        0.00623 (    4)
  metal coordination   : angle       3.77175 (    6)
  covalent geometry    : bond        0.00395 ( 7991)
  covalent geometry    : angle       0.62156 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: P  172 LEU cc_start: 0.6772 (mt) cc_final: 0.6569 (mt)
REVERT: P  442 MET cc_start: 0.4852 (mpt) cc_final: 0.0226 (mpt)
REVERT: P  483 LYS cc_start: 0.8245 (tppt) cc_final: 0.7702 (tppt)
REVERT: P  487 ASP cc_start: 0.7356 (m-30) cc_final: 0.7137 (m-30)
REVERT: P  602 TYR cc_start: 0.8149 (m-80) cc_final: 0.7913 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 115
  average time/residue: 1.2879
  time to fit residues: 155.8765
Evaluate side-chains
  112 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  270 LEU
Chi-restraints excluded: chain P residue  323 GLU
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 129 GLN
P 321 HIS
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.185676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.162143 restraints weight = 11013.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 1.25
r_work: 0.4011 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3901 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7995  Z= 0.200
  Angle     :  0.635   8.810  11376  Z= 0.340
  Chirality :  0.040   0.275   1307
  Planarity :  0.005   0.054   1000
  Dihedral  : 24.544 165.773   2411
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.92 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.34), residues: 596
  helix:  0.99 (0.27), residues: 339
  sheet:  0.23 (0.84), residues: 41
  loop : -0.12 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 
 PHE   0.023   0.002   PHE P 630 
 TYR   0.022   0.002   TYR P 450 
 ARG   0.010   0.001   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05071 (  403)
  hydrogen bonds       : angle       4.30046 ( 1034)
  metal coordination   : bond        0.00689 (    4)
  metal coordination   : angle       4.11130 (    6)
  covalent geometry    : bond        0.00432 ( 7991)
  covalent geometry    : angle       0.62851 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.657 
Fit side-chains
REVERT: P   44 ASP cc_start: 0.7839 (m-30) cc_final: 0.7633 (m-30)
REVERT: P  172 LEU cc_start: 0.6786 (mt) cc_final: 0.6579 (mt)
REVERT: P  388 ASP cc_start: 0.7816 (m-30) cc_final: 0.7581 (m-30)
REVERT: P  442 MET cc_start: 0.4828 (mpt) cc_final: 0.0196 (mpt)
REVERT: P  483 LYS cc_start: 0.8262 (tppt) cc_final: 0.7708 (tppt)
REVERT: P  487 ASP cc_start: 0.7372 (m-30) cc_final: 0.7143 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 108
  average time/residue: 1.2067
  time to fit residues: 137.6448
Evaluate side-chains
  115 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  270 LEU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    9.9990
   chunk 22 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0070
   chunk 12 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 321 HIS
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.187474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.163828 restraints weight = 11273.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 1.28
r_work: 0.4030 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3920 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7995  Z= 0.162
  Angle     :  0.612   8.158  11376  Z= 0.328
  Chirality :  0.038   0.236   1307
  Planarity :  0.005   0.051   1000
  Dihedral  : 24.464 166.628   2411
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.02 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.34), residues: 596
  helix:  1.26 (0.27), residues: 338
  sheet:  0.13 (0.85), residues: 41
  loop : -0.12 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 
 PHE   0.022   0.002   PHE P 630 
 TYR   0.017   0.002   TYR P 450 
 ARG   0.012   0.000   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04692 (  403)
  hydrogen bonds       : angle       4.16345 ( 1034)
  metal coordination   : bond        0.00552 (    4)
  metal coordination   : angle       3.18736 (    6)
  covalent geometry    : bond        0.00347 ( 7991)
  covalent geometry    : angle       0.60787 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.609 
Fit side-chains
REVERT: P  172 LEU cc_start: 0.6713 (mt) cc_final: 0.6502 (mt)
REVERT: P  442 MET cc_start: 0.4736 (mpt) cc_final: 0.0082 (mpt)
REVERT: P  483 LYS cc_start: 0.8286 (tppt) cc_final: 0.7710 (tppt)
REVERT: P  487 ASP cc_start: 0.7390 (m-30) cc_final: 0.7175 (m-30)
REVERT: P  602 TYR cc_start: 0.8170 (m-80) cc_final: 0.7929 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 111
  average time/residue: 1.1926
  time to fit residues: 139.7892
Evaluate side-chains
  112 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 54 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0970
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.188020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.164285 restraints weight = 11025.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 1.23
r_work: 0.4028 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3916 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7995  Z= 0.157
  Angle     :  0.595   8.067  11376  Z= 0.320
  Chirality :  0.037   0.227   1307
  Planarity :  0.005   0.050   1000
  Dihedral  : 24.428 167.250   2411
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.21 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.34), residues: 596
  helix:  1.38 (0.27), residues: 338
  sheet:  0.10 (0.83), residues: 41
  loop : -0.16 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 
 PHE   0.017   0.002   PHE P 630 
 TYR   0.017   0.002   TYR P 283 
 ARG   0.011   0.001   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04645 (  403)
  hydrogen bonds       : angle       4.11882 ( 1034)
  metal coordination   : bond        0.00634 (    4)
  metal coordination   : angle       3.02023 (    6)
  covalent geometry    : bond        0.00335 ( 7991)
  covalent geometry    : angle       0.59079 (11370)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.666 
Fit side-chains
REVERT: P  172 LEU cc_start: 0.6697 (mt) cc_final: 0.6489 (mt)
REVERT: P  483 LYS cc_start: 0.8254 (tppt) cc_final: 0.7693 (tppt)
REVERT: P  487 ASP cc_start: 0.7396 (m-30) cc_final: 0.7173 (m-30)
REVERT: P  602 TYR cc_start: 0.8190 (m-80) cc_final: 0.7893 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 111
  average time/residue: 1.2214
  time to fit residues: 143.2262
Evaluate side-chains
  112 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 3 optimal weight:    0.1980
   chunk 53 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0010
   chunk 38 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.188776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.165138 restraints weight = 11140.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 1.26
r_work: 0.4049 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3939 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7995  Z= 0.151
  Angle     :  0.595   9.002  11376  Z= 0.319
  Chirality :  0.037   0.220   1307
  Planarity :  0.005   0.049   1000
  Dihedral  : 24.408 167.759   2411
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.57 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.33), residues: 596
  helix:  1.42 (0.27), residues: 337
  sheet:  0.01 (0.82), residues: 41
  loop : -0.22 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 
 PHE   0.019   0.001   PHE P 630 
 TYR   0.017   0.002   TYR P 283 
 ARG   0.011   0.000   ARG P 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04570 (  403)
  hydrogen bonds       : angle       4.11532 ( 1034)
  metal coordination   : bond        0.00570 (    4)
  metal coordination   : angle       2.96406 (    6)
  covalent geometry    : bond        0.00323 ( 7991)
  covalent geometry    : angle       0.59167 (11370)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6560.06 seconds
wall clock time: 113 minutes 29.45 seconds (6809.45 seconds total)