Starting phenix.real_space_refine
on Wed Mar 12 11:07:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gkh_40184/03_2025/8gkh_40184_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gkh_40184/03_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_40184/03_2025/8gkh_40184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gkh_40184/03_2025/8gkh_40184.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gkh_40184/03_2025/8gkh_40184_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gkh_40184/03_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-5624/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: 5.60, per 1000 atoms: 0.74
  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: 2.22
  Conformation dependent library (CDL) restraints added in 566.5 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: 3.54
  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: 3.04

  Time building geometry restraints manager: 2.58 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:             1.830
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     26.480
  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:             0.000
  Load rotamer database and sin/cos tables:12.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.020
-------------------------------------------------------------------------------
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   7991  Z= 0.130
  Angle     :  1.275  23.219  11370  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 

*********************** 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  : 0.569 
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: 1.4474
  time to fit residues: 194.5380
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  : 0.583 
-------------------------------------------------------------------------------
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 = 42)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.166551 restraints weight = 11110.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.4154 rms_B_bonded: 1.28
r_work: 0.4061 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3953 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3953
-------------------------------------------------------------------------------
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   7991  Z= 0.274
  Angle     :  0.665   9.946  11370  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 

*********************** 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  : 0.626 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5535 (t80) cc_final: 0.3941 (t80)
REVERT: P  238 ASP cc_start: 0.7361 (t0) cc_final: 0.7054 (t0)
REVERT: P  362 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7210 (mtmt)
REVERT: P  388 ASP cc_start: 0.7749 (m-30) cc_final: 0.7540 (m-30)
REVERT: P  445 MET cc_start: 0.4390 (OUTLIER) cc_final: 0.4006 (tmm)
REVERT: P  483 LYS cc_start: 0.8101 (tppt) cc_final: 0.7457 (tppt)
REVERT: P  487 ASP cc_start: 0.7372 (m-30) cc_final: 0.7139 (m-30)
REVERT: P  574 GLU cc_start: 0.7238 (tp30) cc_final: 0.6745 (tp30)
REVERT: P  602 TYR cc_start: 0.8087 (m-80) cc_final: 0.7769 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 125
  average time/residue: 1.2295
  time to fit residues: 162.3166
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  : 0.590 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4406 r_free = 0.4406 target = 0.189843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.166114 restraints weight = 11391.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 1.29
r_work: 0.4055 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3945 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7991  Z= 0.224
  Angle     :  0.611   8.217  11370  Z= 0.332
  Chirality :  0.039   0.223   1307
  Planarity :  0.004   0.037   1000
  Dihedral  : 24.964 167.368   2411
  Min Nonbonded Distance : 1.833

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:  1.64 (0.34), residues: 596
  helix:  1.72 (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   0.018   0.002   PHE P 630 
 TYR   0.017   0.002   TYR P 283 
 ARG   0.006   0.001   ARG P 374 

*********************** 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  : 0.574 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5644 (t80) cc_final: 0.3937 (t80)
REVERT: P  172 LEU cc_start: 0.6583 (mt) cc_final: 0.6380 (mt)
REVERT: P  238 ASP cc_start: 0.7471 (t0) cc_final: 0.7248 (t0)
REVERT: P  362 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7254 (mtmt)
REVERT: P  388 ASP cc_start: 0.7763 (m-30) cc_final: 0.7550 (m-30)
REVERT: P  442 MET cc_start: 0.4664 (OUTLIER) cc_final: 0.0385 (mpt)
REVERT: P  445 MET cc_start: 0.4464 (OUTLIER) cc_final: 0.4038 (tmm)
REVERT: P  483 LYS cc_start: 0.8182 (tppt) cc_final: 0.7574 (tppt)
REVERT: P  487 ASP cc_start: 0.7376 (m-30) cc_final: 0.7141 (m-30)
REVERT: P  574 GLU cc_start: 0.7214 (tp30) cc_final: 0.6841 (tp30)
REVERT: P  602 TYR cc_start: 0.8149 (m-80) cc_final: 0.7881 (m-80)
  outliers start: 19
  outliers final: 6
  residues processed: 125
  average time/residue: 1.3521
  time to fit residues: 177.8413
Evaluate side-chains
  131 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0470
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.189583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.165247 restraints weight = 11070.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.4139 rms_B_bonded: 1.26
r_work: 0.4043 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3929 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7991  Z= 0.217
  Angle     :  0.604   6.414  11370  Z= 0.328
  Chirality :  0.038   0.227   1307
  Planarity :  0.004   0.039   1000
  Dihedral  : 24.887 168.387   2411
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.71 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.34), residues: 596
  helix:  1.69 (0.28), residues: 337
  sheet:  0.18 (0.80), residues: 41
  loop :  0.31 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 
 PHE   0.019   0.002   PHE P 630 
 TYR   0.018   0.002   TYR P 283 
 ARG   0.008   0.001   ARG P 374 

*********************** 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
  125 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: P   91 GLU cc_start: 0.7095 (mp0) cc_final: 0.6616 (mp0)
REVERT: P  129 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7891 (mm-40)
REVERT: P  172 LEU cc_start: 0.6596 (mt) cc_final: 0.6395 (mt)
REVERT: P  238 ASP cc_start: 0.7537 (t0) cc_final: 0.7267 (t0)
REVERT: P  388 ASP cc_start: 0.7797 (m-30) cc_final: 0.7593 (m-30)
REVERT: P  421 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6635 (mt-10)
REVERT: P  442 MET cc_start: 0.4623 (OUTLIER) cc_final: 0.0429 (mpt)
REVERT: P  483 LYS cc_start: 0.8205 (tppt) cc_final: 0.7676 (tppt)
REVERT: P  574 GLU cc_start: 0.7252 (tp30) cc_final: 0.6835 (tp30)
REVERT: P  602 TYR cc_start: 0.8179 (m-80) cc_final: 0.7941 (m-80)
  outliers start: 13
  outliers final: 4
  residues processed: 114
  average time/residue: 1.5049
  time to fit residues: 180.4446
Evaluate side-chains
  114 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  129 GLN
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  442 MET
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:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8920

-------------------------------------------------------------------------------
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 396 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.186101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.162071 restraints weight = 10961.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.4099 rms_B_bonded: 1.24
r_work: 0.4003 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3888 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7991  Z= 0.291
  Angle     :  0.655   7.785  11370  Z= 0.353
  Chirality :  0.041   0.296   1307
  Planarity :  0.005   0.047   1000
  Dihedral  : 24.771 165.019   2411
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 12.52 %
    Favored  : 84.16 %
  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:  1.14 (0.34), residues: 596
  helix:  1.31 (0.28), residues: 337
  sheet:  0.33 (0.80), residues: 41
  loop :  0.10 (0.41), residues: 218

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   0.020   0.002   TYR P 450 
 ARG   0.008   0.001   ARG P 374 

*********************** 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
  128 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.664 
Fit side-chains
REVERT: P  172 LEU cc_start: 0.6718 (mt) cc_final: 0.6464 (mt)
REVERT: P  238 ASP cc_start: 0.7555 (t0) cc_final: 0.7313 (t0)
REVERT: P  388 ASP cc_start: 0.7765 (m-30) cc_final: 0.7557 (m-30)
REVERT: P  421 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6558 (mt-10)
REVERT: P  442 MET cc_start: 0.4714 (mpt) cc_final: 0.0201 (mpt)
REVERT: P  483 LYS cc_start: 0.8175 (tppt) cc_final: 0.7826 (tppt)
REVERT: P  574 GLU cc_start: 0.7319 (tp30) cc_final: 0.7104 (tp30)
  outliers start: 18
  outliers final: 8
  residues processed: 117
  average time/residue: 1.4712
  time to fit residues: 181.0700
Evaluate side-chains
  118 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.4347 r_free = 0.4347 target = 0.184292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.160340 restraints weight = 11079.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 1.28
r_work: 0.3986 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3875 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7991  Z= 0.335
  Angle     :  0.671   8.438  11370  Z= 0.365
  Chirality :  0.042   0.310   1307
  Planarity :  0.005   0.054   1000
  Dihedral  : 24.650 164.023   2411
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.81 %
    Favored  : 83.98 %
  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:  0.67 (0.33), residues: 596
  helix:  0.89 (0.27), residues: 340
  sheet: -0.31 (0.76), residues: 46
  loop :  0.10 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP P 570 
 HIS   0.007   0.001   HIS P 566 
 PHE   0.023   0.002   PHE P 630 
 TYR   0.025   0.003   TYR P 450 
 ARG   0.009   0.001   ARG P 374 

*********************** 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
  131 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 1.440 
Fit side-chains
REVERT: P  172 LEU cc_start: 0.6756 (mt) cc_final: 0.6543 (mt)
REVERT: P  238 ASP cc_start: 0.7535 (t0) cc_final: 0.7329 (t0)
REVERT: P  388 ASP cc_start: 0.7788 (m-30) cc_final: 0.7564 (m-30)
REVERT: P  421 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6526 (mt-10)
REVERT: P  442 MET cc_start: 0.4968 (mpt) cc_final: 0.0466 (mpt)
REVERT: P  483 LYS cc_start: 0.8174 (tppt) cc_final: 0.7883 (tppt)
REVERT: P  574 GLU cc_start: 0.7312 (tp30) cc_final: 0.7102 (tp30)
  outliers start: 12
  outliers final: 6
  residues processed: 125
  average time/residue: 2.4334
  time to fit residues: 317.1887
Evaluate side-chains
  120 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  421 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4366 r_free = 0.4366 target = 0.185990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.162560 restraints weight = 10955.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 1.25
r_work: 0.4016 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3905 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7991  Z= 0.249
  Angle     :  0.624   8.230  11370  Z= 0.340
  Chirality :  0.039   0.261   1307
  Planarity :  0.005   0.053   1000
  Dihedral  : 24.557 164.900   2411
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.18 %
    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:  0.86 (0.33), residues: 596
  helix:  1.08 (0.27), residues: 338
  sheet:  0.26 (0.80), residues: 41
  loop : -0.01 (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   0.024   0.002   PHE P 630 
 TYR   0.020   0.002   TYR P 450 
 ARG   0.010   0.001   ARG P 374 

*********************** 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
  129 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
REVERT: P   91 GLU cc_start: 0.7203 (mp0) cc_final: 0.6518 (mp0)
REVERT: P  172 LEU cc_start: 0.6701 (mt) cc_final: 0.6485 (mt)
REVERT: P  238 ASP cc_start: 0.7535 (t0) cc_final: 0.7317 (t0)
REVERT: P  388 ASP cc_start: 0.7795 (m-30) cc_final: 0.7571 (m-30)
REVERT: P  421 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6443 (mt-10)
REVERT: P  442 MET cc_start: 0.4891 (mpt) cc_final: 0.0349 (mpt)
REVERT: P  483 LYS cc_start: 0.8178 (tppt) cc_final: 0.7912 (tppt)
  outliers start: 13
  outliers final: 8
  residues processed: 123
  average time/residue: 1.4232
  time to fit residues: 183.2570
Evaluate side-chains
  119 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  323 GLU
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  421 GLU
Chi-restraints excluded: chain P residue  450 TYR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.7320

-------------------------------------------------------------------------------
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 = 0.4374 r_free = 0.4374 target = 0.186339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.162133 restraints weight = 10963.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 1.26
r_work: 0.4007 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3892 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7991  Z= 0.259
  Angle     :  0.633   7.897  11370  Z= 0.343
  Chirality :  0.040   0.269   1307
  Planarity :  0.005   0.053   1000
  Dihedral  : 24.544 165.892   2411
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.10 %
    Favored  : 82.69 %
  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: 339
  sheet:  0.26 (0.80), residues: 41
  loop : -0.04 (0.42), residues: 216

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   0.020   0.002   TYR P  45 
 ARG   0.011   0.001   ARG P 374 

*********************** 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
  123 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: P  172 LEU cc_start: 0.6715 (mt) cc_final: 0.6501 (mt)
REVERT: P  238 ASP cc_start: 0.7546 (t0) cc_final: 0.7323 (t0)
REVERT: P  388 ASP cc_start: 0.7821 (m-30) cc_final: 0.7586 (m-30)
REVERT: P  421 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6463 (mt-10)
REVERT: P  442 MET cc_start: 0.4768 (mpt) cc_final: 0.0094 (mpt)
REVERT: P  483 LYS cc_start: 0.8170 (tppt) cc_final: 0.7945 (tppt)
REVERT: P  605 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7663 (ttm170)
  outliers start: 12
  outliers final: 5
  residues processed: 114
  average time/residue: 1.2653
  time to fit residues: 152.3169
Evaluate side-chains
  115 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  421 GLU
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  605 ARG
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:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0060
   chunk 12 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.4380 r_free = 0.4380 target = 0.187328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.163776 restraints weight = 11285.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.4121 rms_B_bonded: 1.28
r_work: 0.4030 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3920 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7991  Z= 0.229
  Angle     :  0.610   7.189  11370  Z= 0.331
  Chirality :  0.038   0.245   1307
  Planarity :  0.005   0.051   1000
  Dihedral  : 24.501 166.361   2409
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.84 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.33), residues: 596
  helix:  1.13 (0.27), residues: 338
  sheet:  0.23 (0.81), residues: 41
  loop : -0.07 (0.42), 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   0.022   0.002   PHE P 630 
 TYR   0.018   0.002   TYR P  45 
 ARG   0.011   0.001   ARG P 374 

*********************** 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
  126 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.592 
Fit side-chains
REVERT: P  172 LEU cc_start: 0.6665 (mt) cc_final: 0.6451 (mt)
REVERT: P  238 ASP cc_start: 0.7497 (t0) cc_final: 0.7267 (t0)
REVERT: P  388 ASP cc_start: 0.7779 (m-30) cc_final: 0.7541 (m-30)
REVERT: P  421 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6464 (mt-10)
REVERT: P  442 MET cc_start: 0.4682 (mpt) cc_final: 0.0011 (mpt)
REVERT: P  483 LYS cc_start: 0.8172 (tppt) cc_final: 0.7963 (tppt)
REVERT: P  574 GLU cc_start: 0.7233 (tp30) cc_final: 0.7027 (tm-30)
REVERT: P  602 TYR cc_start: 0.8147 (m-80) cc_final: 0.7907 (m-80)
REVERT: P  605 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7663 (ttm170)
  outliers start: 13
  outliers final: 7
  residues processed: 117
  average time/residue: 1.3639
  time to fit residues: 168.0491
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  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  152 MET
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  421 GLU
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  605 ARG
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:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.1980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4387 r_free = 0.4387 target = 0.188044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.164495 restraints weight = 11160.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 1.26
r_work: 0.4040 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3930 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7991  Z= 0.218
  Angle     :  0.608   9.022  11370  Z= 0.330
  Chirality :  0.038   0.235   1307
  Planarity :  0.005   0.050   1000
  Dihedral  : 24.492 167.281   2409
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.76 %
    Favored  : 81.03 %
  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:  0.94 (0.33), residues: 596
  helix:  1.19 (0.27), residues: 338
  sheet:  0.28 (0.80), residues: 41
  loop : -0.08 (0.41), 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   0.019   0.002   TYR P  45 
 ARG   0.011   0.000   ARG P 374 

********************** 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
  121 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.629 
Fit side-chains
REVERT: P  172 LEU cc_start: 0.6631 (mt) cc_final: 0.6425 (mt)
REVERT: P  238 ASP cc_start: 0.7482 (t0) cc_final: 0.7238 (t0)
REVERT: P  388 ASP cc_start: 0.7774 (m-30) cc_final: 0.7538 (m-30)
REVERT: P  421 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6476 (mt-10)
REVERT: P  442 MET cc_start: 0.4595 (mpt) cc_final: 0.0009 (mpt)
REVERT: P  602 TYR cc_start: 0.8146 (m-80) cc_final: 0.7899 (m-80)
REVERT: P  605 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7697 (ttm170)
  outliers start: 12
  outliers final: 9
  residues processed: 111
  average time/residue: 1.2491
  time to fit residues: 146.4085
Evaluate side-chains
  122 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
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  419 ARG
Chi-restraints excluded: chain P residue  421 GLU
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  541 GLU
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  605 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0060
   chunk 3 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.4377 r_free = 0.4377 target = 0.186999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.163343 restraints weight = 11087.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.4118 rms_B_bonded: 1.26
r_work: 0.4027 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3916 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7991  Z= 0.247
  Angle     :  0.617   8.701  11370  Z= 0.335
  Chirality :  0.039   0.256   1307
  Planarity :  0.005   0.052   1000
  Dihedral  : 24.513 167.021   2409
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.13 %
    Favored  : 80.66 %
  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:  0.80 (0.33), residues: 596
  helix:  1.08 (0.27), residues: 339
  sheet:  0.26 (0.82), residues: 41
  loop : -0.16 (0.42), residues: 216

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   0.019   0.002   TYR P  45 
 ARG   0.012   0.001   ARG P 374 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6957.02 seconds
wall clock time: 123 minutes 7.60 seconds (7387.60 seconds total)