Starting phenix.real_space_refine
on Wed Sep 17 08:26:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9izp_61038/09_2025/9izp_61038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9izp_61038/09_2025/9izp_61038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9izp_61038/09_2025/9izp_61038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9izp_61038/09_2025/9izp_61038.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9izp_61038/09_2025/9izp_61038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9izp_61038/09_2025/9izp_61038.map"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.014 sd=   0.231
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      92      5.49       5
     Mg      3      5.21       5
     S      25      5.16       5
     C    4263      2.51       5
     N    1199      2.21       5
     O    1604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7186
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 628, 5246
          Classifications: {'peptide': 628}
          Link IDs: {'PTRANS': 8, 'TRANS': 619}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1127
          Classifications: {'RNA': 53}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 9, 'rna3p': 43}
    Chain: "C"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 265
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "D"
      Number of atoms: 545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 545
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.07, per 1000 atoms: 0.29
  Number of scatterers: 7186
  At special positions: 0
  Unit cell: (89.64, 94.62, 110.805, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      25     16.00
     P      92     15.00
     Mg      3     11.99
     O    1604      8.00
     N    1199      7.00
     C    4263      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: 0.74
  Conformation dependent library (CDL) restraints added in 362.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      57.0% alpha, 10.0% beta
      37 base pairs and 61 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 37
      removed outlier: 3.591A  pdb=" N   ILE A  20 " --> pdb=" O   THR A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 55
    Processing helix  chain 'A' and resid 58 through 63
    Processing helix  chain 'A' and resid 73 through 79
    Processing helix  chain 'A' and resid 83 through 99
    Processing helix  chain 'A' and resid 111 through 116
    Processing helix  chain 'A' and resid 119 through 134
      removed outlier: 3.762A  pdb=" N   THR A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 132 " --> pdb=" O   TYR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 165
      removed outlier: 3.577A  pdb=" N   GLN A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 181
      removed outlier: 3.807A  pdb=" N   TRP A 172 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ASP A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE A 179 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLU A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 203
      removed outlier: 3.691A  pdb=" N   TYR A 193 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 196 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   CYS A 201 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU A 202 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASN A 203 " --> pdb=" O   CYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 218
    Processing helix  chain 'A' and resid 277 through 287
      removed outlier: 3.520A  pdb=" N   TYR A 287 " --> pdb=" O   PHE A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 353
    Processing helix  chain 'A' and resid 355 through 360
    Processing helix  chain 'A' and resid 363 through 375
      removed outlier: 3.556A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 391
      No H-bonds generated for 'chain 'A' and resid 389 through 391'
    Processing helix  chain 'A' and resid 397 through 418
    Processing helix  chain 'A' and resid 420 through 459
      removed outlier: 3.733A  pdb=" N   GLY A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 472
      removed outlier: 6.686A  pdb=" N   ASP A 472 " --> pdb=" O   GLU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 483 through 517
      removed outlier: 3.645A  pdb=" N   ASN A 487 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU A 488 " --> pdb=" O   PRO A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 548
    Processing helix  chain 'A' and resid 562 through 571
    Processing helix  chain 'A' and resid 590 through 610
      removed outlier: 3.795A  pdb=" N   MET A 606 " --> pdb=" O   PHE A 602 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   MET A 607 " --> pdb=" O   PHE A 603 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS A 608 " --> pdb=" O   ASN A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 624
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8
      removed outlier: 4.370A  pdb=" N   SER A 305 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ASN A 290 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245
    Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 379
      removed outlier: 4.942A  pdb=" N   VAL A 377 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE A 332 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER A 335 " --> pdb=" O   GLY A 322 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   GLY A 322 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 10.210A  pdb=" N   LYS A 337 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
      removed outlier: 13.177A  pdb=" N   THR A 320 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LYS A 319 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   ALA A 524 " --> pdb=" O   LYS A 319 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   VAL A 321 " --> pdb=" O   ALA A 524 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   GLU A 526 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU A 323 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 577
      removed outlier: 3.792A  pdb=" N   ASP A 586 " --> pdb=" O   ILE A 577 " (cutoff:3.500A)

    268 hydrogen bonds defined for protein.
    777 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      89 hydrogen bonds
      174 hydrogen bond angles
      0 basepair planarities
      37 basepair parallelities
      61 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1212
        1.33 -     1.45: 2355
        1.45 -     1.57: 3722
        1.57 -     1.69: 182
        1.69 -     1.81: 39
  Bond restraints: 7510
  Sorted by residual:
  bond pdb=" CG1 ILE A   5 "
       pdb=" CD1 ILE A   5 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.23e+00
  bond pdb=" CG1 ILE A 514 "
       pdb=" CD1 ILE A 514 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 2.01e+00
  bond pdb=" CB  VAL A 273 "
       pdb=" CG1 VAL A 273 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.21e+00
  bond pdb=" CB  LYS A 246 "
       pdb=" CG  LYS A 246 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.10e+00
  bond pdb=" CG1 ILE A 238 "
       pdb=" CD1 ILE A 238 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.07e+00
  ... (remaining 7505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 9992
        1.14 -     2.29: 458
        2.29 -     3.43: 72
        3.43 -     4.57: 6
        4.57 -     5.71: 2
  Bond angle restraints: 10530
  Sorted by residual:
  angle pdb=" N   GLN A 272 "
        pdb=" CA  GLN A 272 "
        pdb=" C   GLN A 272 "
      ideal   model   delta    sigma   weight residual
     113.12  110.00    3.12 1.25e+00 6.40e-01 6.25e+00
  angle pdb=" C2'   G B   1 "
        pdb=" C1'   G B   1 "
        pdb=" N9    G B   1 "
      ideal   model   delta    sigma   weight residual
     112.00  115.73   -3.73 1.50e+00 4.44e-01 6.17e+00
  angle pdb=" CA  TYR A  60 "
        pdb=" CB  TYR A  60 "
        pdb=" CG  TYR A  60 "
      ideal   model   delta    sigma   weight residual
     113.90  118.07   -4.17 1.80e+00 3.09e-01 5.37e+00
  angle pdb=" CG1 VAL A 273 "
        pdb=" CB  VAL A 273 "
        pdb=" CG2 VAL A 273 "
      ideal   model   delta    sigma   weight residual
     110.80  106.13    4.67 2.20e+00 2.07e-01 4.51e+00
  angle pdb=" C2'   G B -33 "
        pdb=" C1'   G B -33 "
        pdb=" N9    G B -33 "
      ideal   model   delta    sigma   weight residual
     112.00  115.15   -3.15 1.50e+00 4.44e-01 4.41e+00
  ... (remaining 10525 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.07: 3810
       18.07 -    36.13: 432
       36.13 -    54.20: 171
       54.20 -    72.26: 95
       72.26 -    90.33: 7
  Dihedral angle restraints: 4515
    sinusoidal: 2636
      harmonic: 1879
  Sorted by residual:
  dihedral pdb=" CA  GLN A 272 "
           pdb=" C   GLN A 272 "
           pdb=" N   VAL A 273 "
           pdb=" CA  VAL A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.68   17.32     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  GLU A  68 "
           pdb=" C   GLU A  68 "
           pdb=" N   TRP A  69 "
           pdb=" CA  TRP A  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.33  -16.67     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ASN A 270 "
           pdb=" C   ASN A 270 "
           pdb=" N   ARG A 271 "
           pdb=" CA  ARG A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.42   16.58     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 4512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 743
       0.033 -    0.065: 315
       0.065 -    0.098: 97
       0.098 -    0.131: 40
       0.131 -    0.163: 3
  Chirality restraints: 1198
  Sorted by residual:
  chirality pdb=" C1'   G B   1 "
            pdb=" O4'   G B   1 "
            pdb=" C2'   G B   1 "
            pdb=" N9    G B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" C1'   G B -33 "
            pdb=" O4'   G B -33 "
            pdb=" C2'   G B -33 "
            pdb=" N9    G B -33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" C1'   A B -24 "
            pdb=" O4'   A B -24 "
            pdb=" C2'   A B -24 "
            pdb=" N9    A B -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1195 not shown)

  Planarity restraints: 1005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   1 "   -0.031 2.00e-02 2.50e+03   1.32e-02 5.25e+00
        pdb=" N9    G B   1 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    G B   1 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    G B   1 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B   1 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G B   1 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G B   1 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B   1 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G B   1 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G B   1 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B -33 "   -0.025 2.00e-02 2.50e+03   1.10e-02 3.66e+00
        pdb=" N9    G B -33 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    G B -33 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G B -33 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G B -33 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B -33 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B -33 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G B -33 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    G B -33 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2    G B -33 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G B -33 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G B -33 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   7 "   -0.024 2.00e-02 2.50e+03   1.07e-02 3.15e+00
        pdb=" N9    A B   7 "    0.024 2.00e-02 2.50e+03
        pdb=" C8    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A B   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A B   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A B   7 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A B   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A B   7 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A B   7 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1002 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 28
        2.57 -     3.15: 5448
        3.15 -     3.73: 11763
        3.73 -     4.32: 17565
        4.32 -     4.90: 25896
  Nonbonded interactions: 60700
  Sorted by model distance:
  nonbonded pdb=" OP1   G B -30 "
            pdb="MG    MG A 801 "
     model   vdw
     1.984 2.170
  nonbonded pdb=" OD1 ASP A 499 "
            pdb="MG    MG A 801 "
     model   vdw
     2.100 2.170
  nonbonded pdb=" O4    U B -23 "
            pdb="MG    MG B 102 "
     model   vdw
     2.149 2.170
  nonbonded pdb=" O2'   C B  -1 "
            pdb=" OP1   G B   1 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR A 437 "
            pdb=" O   PHE A 602 "
     model   vdw
     2.251 3.040
  ... (remaining 60695 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:             0.140
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.980
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7510  Z= 0.216
  Angle     :  0.554   5.713  10530  Z= 0.317
  Chirality :  0.041   0.163   1198
  Planarity :  0.003   0.042   1005
  Dihedral  : 18.573  90.329   3303
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.33), residues: 624
  helix:  0.51 (0.29), residues: 322
  sheet:  1.16 (0.84), residues: 41
  loop : -1.06 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 280 
 TYR   0.021   0.002   TYR A  92 
 PHE   0.012   0.002   PHE A 382 
 TRP   0.007   0.002   TRP A  33 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 7510)
  covalent geometry    : angle       0.55443 (10530)
  hydrogen bonds       : bond        0.15475 (  357)
  hydrogen bonds       : angle       6.06837 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7742 (mttt) cc_final: 0.7461 (mtpp)
REVERT: A   88 ASP cc_start: 0.8338 (m-30) cc_final: 0.8086 (m-30)
REVERT: A  242 LYS cc_start: 0.8832 (tptt) cc_final: 0.8592 (tppp)
REVERT: A  323 LEU cc_start: 0.8325 (mt) cc_final: 0.8020 (tp)
REVERT: A  324 ASP cc_start: 0.7779 (t0) cc_final: 0.7152 (m-30)
REVERT: A  413 LYS cc_start: 0.8255 (tttt) cc_final: 0.8021 (ttpp)
REVERT: A  447 TYR cc_start: 0.8842 (t80) cc_final: 0.8628 (t80)
REVERT: A  471 MET cc_start: 0.6247 (mtm) cc_final: 0.5723 (mtp)
REVERT: A  512 TYR cc_start: 0.8236 (t80) cc_final: 0.7990 (t80)
REVERT: A  545 LEU cc_start: 0.8002 (tp) cc_final: 0.7735 (tp)
REVERT: A  612 PHE cc_start: 0.8328 (m-80) cc_final: 0.8043 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.6025
  time to fit residues: 70.9408
Evaluate side-chains
  77 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 167 ASN
A 255 ASN
A 498 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.176989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139959 restraints weight = 8569.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.60
r_work: 0.3348 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7510  Z= 0.202
  Angle     :  0.564   5.802  10530  Z= 0.320
  Chirality :  0.040   0.158   1198
  Planarity :  0.003   0.040   1005
  Dihedral  : 21.160  91.595   1937
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.99 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.33), residues: 624
  helix:  1.01 (0.29), residues: 328
  sheet:  1.05 (0.71), residues: 54
  loop : -1.01 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 280 
 TYR   0.020   0.002   TYR A 437 
 PHE   0.018   0.002   PHE A 382 
 TRP   0.006   0.001   TRP A 268 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 7510)
  covalent geometry    : angle       0.56422 (10530)
  hydrogen bonds       : bond        0.04873 (  357)
  hydrogen bonds       : angle       4.54545 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7889 (mttt) cc_final: 0.7623 (mtpp)
REVERT: A   88 ASP cc_start: 0.8183 (m-30) cc_final: 0.7977 (m-30)
REVERT: A  242 LYS cc_start: 0.8656 (tptt) cc_final: 0.8314 (tptp)
REVERT: A  323 LEU cc_start: 0.8254 (mt) cc_final: 0.8024 (tp)
REVERT: A  324 ASP cc_start: 0.7641 (t0) cc_final: 0.7087 (m-30)
REVERT: A  385 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7835 (mp10)
REVERT: A  413 LYS cc_start: 0.8385 (tttt) cc_final: 0.7923 (ttpp)
REVERT: A  437 TYR cc_start: 0.8012 (t80) cc_final: 0.7703 (t80)
REVERT: A  471 MET cc_start: 0.6199 (mtm) cc_final: 0.5709 (mtp)
REVERT: A  512 TYR cc_start: 0.8384 (t80) cc_final: 0.8168 (t80)
REVERT: A  526 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6604 (tp30)
REVERT: A  537 GLN cc_start: 0.7502 (pm20) cc_final: 0.7267 (pm20)
  outliers start: 6
  outliers final: 1
  residues processed: 83
  average time/residue: 0.6430
  time to fit residues: 56.1674
Evaluate side-chains
  79 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0470
   chunk 59 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.0086

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.176433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.139381 restraints weight = 8387.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 1.59
r_work: 0.3336 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7510  Z= 0.210
  Angle     :  0.552   5.293  10530  Z= 0.314
  Chirality :  0.040   0.160   1198
  Planarity :  0.003   0.038   1005
  Dihedral  : 21.144  92.578   1937
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  9.01 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.33), residues: 624
  helix:  1.09 (0.29), residues: 328
  sheet:  0.65 (0.69), residues: 54
  loop : -0.85 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.022   0.002   TYR A 437 
 PHE   0.017   0.002   PHE A 382 
 TRP   0.006   0.001   TRP A 268 
 HIS   0.003   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 7510)
  covalent geometry    : angle       0.55184 (10530)
  hydrogen bonds       : bond        0.04739 (  357)
  hydrogen bonds       : angle       4.35327 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 LYS cc_start: 0.8628 (tptt) cc_final: 0.8289 (tptp)
REVERT: A  323 LEU cc_start: 0.8322 (mt) cc_final: 0.8114 (tp)
REVERT: A  324 ASP cc_start: 0.7559 (t0) cc_final: 0.7146 (m-30)
REVERT: A  385 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7957 (mp10)
REVERT: A  413 LYS cc_start: 0.8396 (tttt) cc_final: 0.7983 (ttpp)
REVERT: A  471 MET cc_start: 0.6153 (mtm) cc_final: 0.5606 (mtp)
REVERT: A  526 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6726 (tp30)
REVERT: A  571 ASN cc_start: 0.6799 (m110) cc_final: 0.6460 (m110)
REVERT: A  588 LYS cc_start: 0.8980 (mtmp) cc_final: 0.8708 (mtmm)
  outliers start: 11
  outliers final: 1
  residues processed: 88
  average time/residue: 0.5852
  time to fit residues: 54.2768
Evaluate side-chains
  78 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 18 optimal weight:   40.0000
   chunk 61 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0970
   overall best weight:    3.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.175802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.138602 restraints weight = 8521.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.60
r_work: 0.3327 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7510  Z= 0.227
  Angle     :  0.569   5.479  10530  Z= 0.322
  Chirality :  0.041   0.164   1198
  Planarity :  0.003   0.038   1005
  Dihedral  : 21.181  93.320   1937
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.73 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.33), residues: 624
  helix:  1.08 (0.28), residues: 329
  sheet:  0.51 (0.68), residues: 54
  loop : -0.82 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.023   0.002   TYR A 437 
 PHE   0.016   0.002   PHE A 382 
 TRP   0.006   0.001   TRP A 268 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 7510)
  covalent geometry    : angle       0.56947 (10530)
  hydrogen bonds       : bond        0.04760 (  357)
  hydrogen bonds       : angle       4.31865 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 LEU cc_start: 0.8342 (mt) cc_final: 0.8141 (tp)
REVERT: A  324 ASP cc_start: 0.7602 (t0) cc_final: 0.7217 (m-30)
REVERT: A  385 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7881 (mp10)
REVERT: A  413 LYS cc_start: 0.8391 (tttt) cc_final: 0.7995 (ttpp)
REVERT: A  471 MET cc_start: 0.6218 (mtm) cc_final: 0.5727 (mtp)
REVERT: A  526 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6776 (tp30)
REVERT: A  566 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8026 (mmtt)
  outliers start: 10
  outliers final: 3
  residues processed: 78
  average time/residue: 0.6065
  time to fit residues: 49.8212
Evaluate side-chains
  78 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    4.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.173752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.136540 restraints weight = 8544.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.57
r_work: 0.3308 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   7510  Z= 0.312
  Angle     :  0.648   6.310  10530  Z= 0.361
  Chirality :  0.045   0.189   1198
  Planarity :  0.004   0.040   1005
  Dihedral  : 21.340  94.230   1937
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.12 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.33), residues: 624
  helix:  0.88 (0.28), residues: 329
  sheet:  0.44 (0.69), residues: 54
  loop : -0.87 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 192 
 TYR   0.027   0.003   TYR A 437 
 PHE   0.016   0.002   PHE A 382 
 TRP   0.006   0.002   TRP A 268 
 HIS   0.004   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00700 ( 7510)
  covalent geometry    : angle       0.64797 (10530)
  hydrogen bonds       : bond        0.05451 (  357)
  hydrogen bonds       : angle       4.40795 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.7899 (pptt) cc_final: 0.7593 (pmtt)
REVERT: A  323 LEU cc_start: 0.8399 (mt) cc_final: 0.8184 (tp)
REVERT: A  324 ASP cc_start: 0.7646 (t0) cc_final: 0.7279 (m-30)
REVERT: A  385 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7878 (mp10)
REVERT: A  413 LYS cc_start: 0.8350 (tttt) cc_final: 0.7926 (ttpp)
REVERT: A  471 MET cc_start: 0.6327 (mtm) cc_final: 0.6074 (mtm)
REVERT: A  526 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6844 (tp30)
REVERT: A  588 LYS cc_start: 0.8941 (mtmp) cc_final: 0.8615 (mtmm)
  outliers start: 10
  outliers final: 3
  residues processed: 81
  average time/residue: 0.5892
  time to fit residues: 50.1909
Evaluate side-chains
  75 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
A 209 ASN
A 218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.180757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144612 restraints weight = 8552.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.58
r_work: 0.3414 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7510  Z= 0.126
  Angle     :  0.498   6.174  10530  Z= 0.287
  Chirality :  0.037   0.139   1198
  Planarity :  0.003   0.041   1005
  Dihedral  : 21.101  93.649   1937
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.12 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.34), residues: 624
  helix:  1.35 (0.28), residues: 332
  sheet:  0.51 (0.69), residues: 54
  loop : -0.92 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.017   0.001   TYR A 437 
 PHE   0.012   0.001   PHE A 382 
 TRP   0.006   0.001   TRP A  33 
 HIS   0.002   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7510)
  covalent geometry    : angle       0.49831 (10530)
  hydrogen bonds       : bond        0.03821 (  357)
  hydrogen bonds       : angle       4.05894 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 GLU cc_start: 0.7085 (mp0) cc_final: 0.6612 (mp0)
REVERT: A  324 ASP cc_start: 0.7521 (t0) cc_final: 0.7107 (m-30)
REVERT: A  372 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7596 (pt0)
REVERT: A  385 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7834 (mp10)
REVERT: A  413 LYS cc_start: 0.8358 (tttt) cc_final: 0.7955 (ttpp)
REVERT: A  437 TYR cc_start: 0.7949 (t80) cc_final: 0.7687 (t80)
REVERT: A  455 ASP cc_start: 0.7876 (m-30) cc_final: 0.7506 (m-30)
REVERT: A  471 MET cc_start: 0.6169 (mtm) cc_final: 0.5660 (mtp)
REVERT: A  526 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6703 (tp30)
REVERT: A  586 ASP cc_start: 0.8160 (t0) cc_final: 0.7429 (m-30)
REVERT: A  588 LYS cc_start: 0.8984 (mtmp) cc_final: 0.8688 (mtmm)
  outliers start: 9
  outliers final: 3
  residues processed: 87
  average time/residue: 0.5591
  time to fit residues: 51.3220
Evaluate side-chains
  81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 54 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    4.4988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.175083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137318 restraints weight = 8523.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.66
r_work: 0.3310 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   7510  Z= 0.286
  Angle     :  0.632   6.166  10530  Z= 0.353
  Chirality :  0.044   0.181   1198
  Planarity :  0.004   0.038   1005
  Dihedral  : 21.242  94.633   1937
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.12 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.33), residues: 624
  helix:  1.15 (0.28), residues: 329
  sheet:  0.42 (0.69), residues: 54
  loop : -0.95 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 271 
 TYR   0.026   0.003   TYR A 437 
 PHE   0.021   0.002   PHE A 478 
 TRP   0.005   0.002   TRP A 268 
 HIS   0.004   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 7510)
  covalent geometry    : angle       0.63152 (10530)
  hydrogen bonds       : bond        0.05126 (  357)
  hydrogen bonds       : angle       4.27684 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8395 (m-40)
REVERT: A  324 ASP cc_start: 0.7662 (t0) cc_final: 0.7193 (m-30)
REVERT: A  385 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7901 (mp10)
REVERT: A  413 LYS cc_start: 0.8406 (tttt) cc_final: 0.7999 (ttpp)
REVERT: A  455 ASP cc_start: 0.7925 (m-30) cc_final: 0.7610 (m-30)
REVERT: A  471 MET cc_start: 0.6299 (mtm) cc_final: 0.5739 (mtp)
REVERT: A  588 LYS cc_start: 0.8974 (mtmp) cc_final: 0.8642 (mtmm)
  outliers start: 14
  outliers final: 6
  residues processed: 81
  average time/residue: 0.5653
  time to fit residues: 48.4072
Evaluate side-chains
  78 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 18 optimal weight:   40.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.178553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.141284 restraints weight = 8588.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 1.63
r_work: 0.3363 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7510  Z= 0.163
  Angle     :  0.542   6.359  10530  Z= 0.309
  Chirality :  0.038   0.153   1198
  Planarity :  0.003   0.039   1005
  Dihedral  : 21.137  94.971   1937
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.14 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.33), residues: 624
  helix:  1.27 (0.28), residues: 332
  sheet:  0.48 (0.69), residues: 54
  loop : -1.01 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.020   0.002   TYR A 437 
 PHE   0.015   0.001   PHE A 478 
 TRP   0.005   0.001   TRP A 268 
 HIS   0.002   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7510)
  covalent geometry    : angle       0.54155 (10530)
  hydrogen bonds       : bond        0.04144 (  357)
  hydrogen bonds       : angle       4.10406 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.8023 (m-30) cc_final: 0.7752 (m-30)
REVERT: A  155 MET cc_start: 0.7249 (pp-130) cc_final: 0.6858 (ppp)
REVERT: A  220 LYS cc_start: 0.7392 (mppt) cc_final: 0.6797 (tppt)
REVERT: A  296 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8385 (m-40)
REVERT: A  324 ASP cc_start: 0.7525 (t0) cc_final: 0.7129 (m-30)
REVERT: A  385 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7926 (mp10)
REVERT: A  413 LYS cc_start: 0.8380 (tttt) cc_final: 0.7963 (ttpp)
REVERT: A  455 ASP cc_start: 0.7768 (m-30) cc_final: 0.7490 (m-30)
REVERT: A  471 MET cc_start: 0.6137 (mtm) cc_final: 0.5617 (mtp)
REVERT: A  526 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6733 (tp30)
REVERT: A  586 ASP cc_start: 0.8164 (t0) cc_final: 0.7546 (m-30)
REVERT: A  588 LYS cc_start: 0.8978 (mtmp) cc_final: 0.8666 (mtmm)
  outliers start: 10
  outliers final: 5
  residues processed: 80
  average time/residue: 0.5903
  time to fit residues: 49.8249
Evaluate side-chains
  80 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 48 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:   20.0000
   chunk 17 optimal weight:   50.0000
   chunk 19 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    3.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.176595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.139206 restraints weight = 8442.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.60
r_work: 0.3324 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097   7510  Z= 0.242
  Angle     :  0.609   6.683  10530  Z= 0.343
  Chirality :  0.042   0.173   1198
  Planarity :  0.004   0.039   1005
  Dihedral  : 21.192  95.768   1937
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.31 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.33), residues: 624
  helix:  1.16 (0.28), residues: 331
  sheet:  0.39 (0.69), residues: 54
  loop : -0.99 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 271 
 TYR   0.024   0.002   TYR A 437 
 PHE   0.014   0.002   PHE A 382 
 TRP   0.005   0.001   TRP A 268 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 7510)
  covalent geometry    : angle       0.60903 (10530)
  hydrogen bonds       : bond        0.04767 (  357)
  hydrogen bonds       : angle       4.28333 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8393 (m-40)
REVERT: A  324 ASP cc_start: 0.7550 (t0) cc_final: 0.7130 (m-30)
REVERT: A  385 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7887 (mp10)
REVERT: A  413 LYS cc_start: 0.8424 (tttt) cc_final: 0.8002 (ttpp)
REVERT: A  455 ASP cc_start: 0.7861 (m-30) cc_final: 0.7523 (m-30)
REVERT: A  471 MET cc_start: 0.6313 (mtm) cc_final: 0.5724 (mtp)
REVERT: A  588 LYS cc_start: 0.8997 (mtmp) cc_final: 0.8671 (mtmm)
  outliers start: 10
  outliers final: 6
  residues processed: 82
  average time/residue: 0.5901
  time to fit residues: 51.0585
Evaluate side-chains
  83 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 11 optimal weight:    0.0270
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 16 optimal weight:   50.0000
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.184348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.148930 restraints weight = 8529.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.59
r_work: 0.3460 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7510  Z= 0.122
  Angle     :  0.514   6.845  10530  Z= 0.296
  Chirality :  0.036   0.136   1198
  Planarity :  0.003   0.040   1005
  Dihedral  : 20.952  95.128   1937
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.82 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.34), residues: 624
  helix:  1.53 (0.29), residues: 331
  sheet:  0.68 (0.70), residues: 54
  loop : -0.77 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.017   0.001   TYR A 437 
 PHE   0.021   0.001   PHE A 478 
 TRP   0.006   0.001   TRP A  33 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7510)
  covalent geometry    : angle       0.51399 (10530)
  hydrogen bonds       : bond        0.03690 (  357)
  hydrogen bonds       : angle       3.99728 (  951)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7187 (tpt) cc_final: 0.6671 (tmm)
REVERT: A  155 MET cc_start: 0.7210 (pp-130) cc_final: 0.6846 (ppp)
REVERT: A  220 LYS cc_start: 0.7235 (mppt) cc_final: 0.6742 (tppt)
REVERT: A  324 ASP cc_start: 0.7441 (t0) cc_final: 0.7058 (m-30)
REVERT: A  385 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7825 (mp10)
REVERT: A  413 LYS cc_start: 0.8363 (tttt) cc_final: 0.7955 (ttpp)
REVERT: A  447 TYR cc_start: 0.8813 (t80) cc_final: 0.8584 (t80)
REVERT: A  455 ASP cc_start: 0.7589 (m-30) cc_final: 0.7232 (m-30)
REVERT: A  471 MET cc_start: 0.6171 (mtm) cc_final: 0.5567 (mtp)
REVERT: A  526 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6672 (tp30)
REVERT: A  566 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8145 (mmtt)
REVERT: A  586 ASP cc_start: 0.8168 (t0) cc_final: 0.7458 (m-30)
REVERT: A  588 LYS cc_start: 0.9011 (mtmp) cc_final: 0.8666 (mtmm)
  outliers start: 8
  outliers final: 4
  residues processed: 83
  average time/residue: 0.5350
  time to fit residues: 47.0018
Evaluate side-chains
  81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.177944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140510 restraints weight = 8564.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.61
r_work: 0.3349 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   7510  Z= 0.211
  Angle     :  0.595   7.524  10530  Z= 0.332
  Chirality :  0.040   0.164   1198
  Planarity :  0.003   0.038   1005
  Dihedral  : 21.042  95.953   1937
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 16.67 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.34), residues: 624
  helix:  1.40 (0.29), residues: 331
  sheet:  0.68 (0.71), residues: 54
  loop : -0.80 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.023   0.002   TYR A 437 
 PHE   0.013   0.002   PHE A 382 
 TRP   0.005   0.001   TRP A  33 
 HIS   0.003   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 7510)
  covalent geometry    : angle       0.59478 (10530)
  hydrogen bonds       : bond        0.04434 (  357)
  hydrogen bonds       : angle       4.19095 (  951)

===============================================================================
Job complete
usr+sys time: 2613.77 seconds
wall clock time: 45 minutes 23.82 seconds (2723.82 seconds total)