Starting phenix.real_space_refine
on Tue Jul 29 03:54:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rdy_19078/07_2025/8rdy_19078_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rdy_19078/07_2025/8rdy_19078.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rdy_19078/07_2025/8rdy_19078.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rdy_19078/07_2025/8rdy_19078.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rdy_19078/07_2025/8rdy_19078_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rdy_19078/07_2025/8rdy_19078_trim.cif"
  }
  resolution = 3.33
  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=  -0.000 sd=   0.030
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
     P       2      5.49       5
     Mg      1      5.21       5
     S      24      5.16       5
     C    3483      2.51       5
     N     953      2.21       5
     O    1041      1.98       5
     H    5450      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10954
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 10712
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 665, 10664
          Classifications: {'peptide': 665}
          Link IDs: {'PTRANS': 35, 'TRANS': 629}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 665, 10664
          Classifications: {'peptide': 665}
          Link IDs: {'PTRANS': 35, 'TRANS': 629}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 10725
    Chain: "B"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 214
          Classifications: {'peptide': 15}
          Link IDs: {'TRANS': 14}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A 270 " occ=0.48
      ... (46 atoms not shown)
      pdb="HH22BARG A 270 " occ=0.52
    residue:
      pdb=" N  AARG A 430 " occ=0.73
      ... (46 atoms not shown)
      pdb="HH22BARG A 430 " occ=0.27
  Time building chain proxies: 9.22, per 1000 atoms: 0.84
  Number of scatterers: 10954
  At special positions: 0
  Unit cell: (63.84, 84, 105, 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)
     S      24     16.00
     P       2     15.00
     Mg      1     11.99
     O    1041      8.00
     N     953      7.00
     C    3483      6.00
     H    5450      1.00
    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: 2.67
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1292

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      48.7% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 68
      removed outlier: 3.509A  pdb=" N   ASP A  68 " --> pdb=" O   GLN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 93 through 108
      removed outlier: 4.075A  pdb=" N   ALA A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLN A  98 " --> pdb=" O   PRO A  94 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   ASP A 100 " --> pdb=" O   HIS A  96 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   GLU A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ASN A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 135
    Processing helix  chain 'A' and resid 136 through 139
    Processing helix  chain 'A' and resid 149 through 164
    Processing helix  chain 'A' and resid 193 through 203
    Processing helix  chain 'A' and resid 221 through 238
      removed outlier: 3.887A  pdb=" N   GLN A 233 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   LYS A 236 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ARG A 237 " --> pdb=" O   GLN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 259
    Processing helix  chain 'A' and resid 285 through 301
      removed outlier: 3.570A  pdb=" N   SER A 289 " --> pdb=" O   ASP A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 335
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 355 through 358
    Processing helix  chain 'A' and resid 417 through 427
    Processing helix  chain 'A' and resid 441 through 448
    Processing helix  chain 'A' and resid 455 through 460
      removed outlier: 4.173A  pdb=" N   SER A 460 " --> pdb=" O   ILE A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 472
      removed outlier: 3.675A  pdb=" N   THR A 465 " --> pdb=" O   ASN A 461 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 472 " --> pdb=" O   GLU A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 501
    Processing helix  chain 'A' and resid 511 through 520
      removed outlier: 3.850A  pdb=" N   PHE A 520 " --> pdb=" O   LEU A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 533
    Processing helix  chain 'A' and resid 534 through 537
      removed outlier: 3.526A  pdb=" N   GLN A 537 " --> pdb=" O   PHE A 534 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 534 through 537'
    Processing helix  chain 'A' and resid 538 through 550
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.855A  pdb=" N   PHE A 572 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 590
      removed outlier: 3.886A  pdb=" N   THR A 581 " --> pdb=" O   GLY A 577 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 582 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 598
    Processing helix  chain 'A' and resid 598 through 606
    Processing helix  chain 'A' and resid 609 through 631
    Processing helix  chain 'A' and resid 643 through 654
    Processing helix  chain 'A' and resid 714 through 718
    Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181
      removed outlier: 6.726A  pdb=" N   GLY A 173 " --> pdb=" O   TYR A 190 " (cutoff:3.500A)
      removed outlier: 8.595A  pdb=" N   THR A 192 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   SER A 175 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   VAL A 143 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   MET A 191 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   CYS A 145 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLN A 142 " --> pdb=" O   CYS A 211 " (cutoff:3.500A)
      removed outlier: 8.507A  pdb=" N   ILE A 213 " --> pdb=" O   GLN A 142 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ALA A 144 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   SER A 210 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   ILE A 244 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE A 212 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   MET A 246 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU A 214 " --> pdb=" O   MET A 246 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET A 112 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 9.053A  pdb=" N   LEU A 265 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL A 113 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   VAL A 267 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   VAL A 115 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 343
      removed outlier: 6.538A  pdb=" N   SER A 340 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   ILE A 374 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   TYR A 342 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASP A 305 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   VAL A 392 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU A 307 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   VAL A 389 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   PHE A 437 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   VAL A 391 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLU A 275 " --> pdb=" O   CYS A 436 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   ARG A 438 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   TYR A 277 " --> pdb=" O   ARG A 438 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL A 274 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   VAL B 131 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LEU A 276 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 396 through 403
      removed outlier: 3.639A  pdb=" N   VAL A 408 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 660 through 663
      removed outlier: 7.658A  pdb=" N   ILE A 707 " --> pdb=" O   ASP A 678 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A 680 " --> pdb=" O   ILE A 707 " (cutoff:3.500A)
      removed outlier: 8.802A  pdb=" N   THR A 709 " --> pdb=" O   LEU A 680 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ILE A 707 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 707 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   THR A 709 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN A 697 " --> pdb=" O   THR A 709 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    663 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.59

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5443
        1.03 -     1.23: 8
        1.23 -     1.42: 2332
        1.42 -     1.62: 3246
        1.62 -     1.81: 41
  Bond restraints: 11070
  Sorted by residual:
  bond pdb=" C4  ADP A1201 "
       pdb=" C5  ADP A1201 "
    ideal  model  delta    sigma   weight residual
    1.490  1.467  0.023 2.00e-02 2.50e+03 1.27e+00
  bond pdb=" C   VAL A 389 "
       pdb=" O   VAL A 389 "
    ideal  model  delta    sigma   weight residual
    1.245  1.235  0.010 1.41e-02 5.03e+03 4.83e-01
  bond pdb=" C5  ADP A1201 "
       pdb=" C6  ADP A1201 "
    ideal  model  delta    sigma   weight residual
    1.490  1.476  0.014 2.00e-02 2.50e+03 4.64e-01
  bond pdb=" N   VAL A 710 "
       pdb=" CA  VAL A 710 "
    ideal  model  delta    sigma   weight residual
    1.458  1.450  0.008 1.24e-02 6.50e+03 4.41e-01
  bond pdb=" CB  ARG A 284 "
       pdb=" CG  ARG A 284 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 3.00e-02 1.11e+03 4.10e-01
  ... (remaining 11065 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 19067
        1.14 -     2.28: 890
        2.28 -     3.41: 39
        3.41 -     4.55: 20
        4.55 -     5.69: 7
  Bond angle restraints: 20023
  Sorted by residual:
  angle pdb=" N   VAL A 389 "
        pdb=" CA  VAL A 389 "
        pdb=" C   VAL A 389 "
      ideal   model   delta    sigma   weight residual
     113.71  110.41    3.30 9.50e-01 1.11e+00 1.20e+01
  angle pdb=" CA  VAL A 389 "
        pdb=" C   VAL A 389 "
        pdb=" N   TYR A 390 "
      ideal   model   delta    sigma   weight residual
     119.87  117.12    2.75 1.34e+00 5.57e-01 4.21e+00
  angle pdb=" O1B ADP A1201 "
        pdb=" PB  ADP A1201 "
        pdb=" O3B ADP A1201 "
      ideal   model   delta    sigma   weight residual
     119.90  114.21    5.69 3.00e+00 1.11e-01 3.60e+00
  angle pdb=" C2' ADP A1201 "
        pdb=" C3' ADP A1201 "
        pdb=" C4' ADP A1201 "
      ideal   model   delta    sigma   weight residual
     111.00  105.65    5.35 3.00e+00 1.11e-01 3.17e+00
  angle pdb=" O2B ADP A1201 "
        pdb=" PB  ADP A1201 "
        pdb=" O3B ADP A1201 "
      ideal   model   delta    sigma   weight residual
     119.90  114.69    5.21 3.00e+00 1.11e-01 3.02e+00
  ... (remaining 20018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.10: 4990
       34.10 -    68.21: 190
       68.21 -   102.31: 18
      102.31 -   136.42: 1
      136.42 -   170.52: 1
  Dihedral angle restraints: 5200
    sinusoidal: 2872
      harmonic: 2328
  Sorted by residual:
  dihedral pdb=" O2A ADP A1201 "
           pdb=" O3A ADP A1201 "
           pdb=" PA  ADP A1201 "
           pdb=" PB  ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  110.52 -170.52     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" C5' ADP A1201 "
           pdb=" O5' ADP A1201 "
           pdb=" PA  ADP A1201 "
           pdb=" O2A ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   67.64 -127.63     1      2.00e+01 2.50e-03 3.87e+01
  dihedral pdb=" CB  GLU A  92 "
           pdb=" CG  GLU A  92 "
           pdb=" CD  GLU A  92 "
           pdb=" OE1 GLU A  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.63   89.63     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 517
       0.027 -    0.054: 218
       0.054 -    0.080: 45
       0.080 -    0.107: 42
       0.107 -    0.134: 22
  Chirality restraints: 844
  Sorted by residual:
  chirality pdb=" CA  ILE A 695 "
            pdb=" N   ILE A 695 "
            pdb=" C   ILE A 695 "
            pdb=" CB  ILE A 695 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  VAL A 143 "
            pdb=" N   VAL A 143 "
            pdb=" C   VAL A 143 "
            pdb=" CB  VAL A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  PRO A 524 "
            pdb=" N   PRO A 524 "
            pdb=" C   PRO A 524 "
            pdb=" CB  PRO A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.37e-01
  ... (remaining 841 not shown)

  Planarity restraints: 1635
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  80 "    0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO A  81 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  81 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  81 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 714 "    0.018 5.00e-02 4.00e+02   2.78e-02 1.24e+00
        pdb=" N   PRO A 715 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 715 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 715 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 523 "    0.018 5.00e-02 4.00e+02   2.65e-02 1.13e+00
        pdb=" N   PRO A 524 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 524 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 524 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1632 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 938
        2.22 -     2.81: 23189
        2.81 -     3.41: 28356
        3.41 -     4.00: 37960
        4.00 -     4.60: 58752
  Nonbonded interactions: 149195
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 609 "
            pdb=" H   SER A 612 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" OE1 GLU A 362 "
            pdb=" H   GLU A 362 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" HZ3 LYS A 122 "
            pdb=" O2B ADP A1201 "
     model   vdw
     1.646 2.450
  nonbonded pdb=" O   GLU A 117 "
            pdb=" HG  SER A 120 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" O   HIS A 574 "
            pdb=" H   ASP A 576 "
     model   vdw
     1.679 2.450
  ... (remaining 149190 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=0.27 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:             1.550
  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:             0.200
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     29.960
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
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      :  0.003   0.030   5620  Z= 0.125
  Angle     :  0.502   5.689   7615  Z= 0.249
  Chirality :  0.039   0.134    844
  Planarity :  0.003   0.029    989
  Dihedral  : 17.785 170.520   2137
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 20.17 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.19 (0.33), residues: 680
  helix:  1.87 (0.31), residues: 294
  sheet:  0.02 (0.51), residues: 110
  loop :  0.04 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 136 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.007   0.001   PHE A 480 
 TYR   0.011   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14583 (  230)
  hydrogen bonds       : angle       5.77651 (  663)
  covalent geometry    : bond        0.00290 ( 5620)
  covalent geometry    : angle       0.50227 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  65 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.3510
  time to fit residues: 30.9556
Evaluate side-chains
  65 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.145916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.114998 restraints weight = 37453.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 3.45
r_work: 0.3056 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.0542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5620  Z= 0.121
  Angle     :  0.512   5.966   7615  Z= 0.254
  Chirality :  0.041   0.150    844
  Planarity :  0.004   0.035    989
  Dihedral  :  7.614 161.801    766
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 19.50 %
    Favored  : 79.67 %
  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:  1.15 (0.33), residues: 680
  helix:  1.92 (0.31), residues: 298
  sheet: -0.16 (0.51), residues: 104
  loop : -0.07 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 602 
 HIS   0.004   0.001   HIS A 137 
 PHE   0.007   0.001   PHE A  79 
 TYR   0.013   0.001   TYR A 644 
 ARG   0.004   0.000   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04434 (  230)
  hydrogen bonds       : angle       4.72058 (  663)
  covalent geometry    : bond        0.00278 ( 5620)
  covalent geometry    : angle       0.51183 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7671 (mt0)
REVERT: B  130 GLU cc_start: 0.6860 (tp30) cc_final: 0.5974 (pm20)
  outliers start: 3
  outliers final: 2
  residues processed: 67
  average time/residue: 0.3516
  time to fit residues: 32.0848
Evaluate side-chains
  64 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  477 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.146390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.116513 restraints weight = 31777.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.19
r_work: 0.3155 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.0736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5620  Z= 0.114
  Angle     :  0.493   6.026   7615  Z= 0.243
  Chirality :  0.040   0.147    844
  Planarity :  0.004   0.039    989
  Dihedral  :  7.087 161.706    766
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 19.50 %
    Favored  : 79.83 %
  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:  1.13 (0.33), residues: 680
  helix:  1.89 (0.31), residues: 300
  sheet: -0.10 (0.51), residues: 104
  loop : -0.10 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 602 
 HIS   0.004   0.001   HIS A 137 
 PHE   0.009   0.001   PHE A 534 
 TYR   0.012   0.001   TYR A 644 
 ARG   0.003   0.000   ARG A 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 (  230)
  hydrogen bonds       : angle       4.53140 (  663)
  covalent geometry    : bond        0.00266 ( 5620)
  covalent geometry    : angle       0.49288 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.6984 (tp30) cc_final: 0.6127 (pm20)
  outliers start: 2
  outliers final: 1
  residues processed: 68
  average time/residue: 0.3383
  time to fit residues: 31.4415
Evaluate side-chains
  63 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  477 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 13 optimal weight:    0.0370
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.145388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.116875 restraints weight = 29168.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.99
r_work: 0.2923 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.0946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5620  Z= 0.090
  Angle     :  0.475   5.588   7615  Z= 0.231
  Chirality :  0.040   0.142    844
  Planarity :  0.004   0.038    989
  Dihedral  :  6.791 157.641    766
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 19.67 %
    Favored  : 79.67 %
  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:  1.40 (0.34), residues: 680
  helix:  2.09 (0.31), residues: 300
  sheet:  0.13 (0.48), residues: 122
  loop :  0.03 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 602 
 HIS   0.002   0.000   HIS A 137 
 PHE   0.005   0.001   PHE A  79 
 TYR   0.010   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03300 (  230)
  hydrogen bonds       : angle       4.22801 (  663)
  covalent geometry    : bond        0.00205 ( 5620)
  covalent geometry    : angle       0.47497 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.6845 (tp30) cc_final: 0.5909 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 70
  average time/residue: 0.4720
  time to fit residues: 43.5147
Evaluate side-chains
  67 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  697 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  57 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.113181 restraints weight = 31462.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 3.19
r_work: 0.2892 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5620  Z= 0.113
  Angle     :  0.482   5.808   7615  Z= 0.236
  Chirality :  0.040   0.143    844
  Planarity :  0.004   0.039    989
  Dihedral  :  7.150 168.931    766
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 20.50 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.34), residues: 680
  helix:  2.08 (0.31), residues: 300
  sheet:  0.06 (0.47), residues: 122
  loop : -0.07 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 602 
 HIS   0.003   0.001   HIS A 137 
 PHE   0.006   0.001   PHE A 480 
 TYR   0.013   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  230)
  hydrogen bonds       : angle       4.23961 (  663)
  covalent geometry    : bond        0.00266 ( 5620)
  covalent geometry    : angle       0.48198 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.6851 (tp30) cc_final: 0.5820 (pm20)
  outliers start: 3
  outliers final: 3
  residues processed: 69
  average time/residue: 0.4093
  time to fit residues: 37.4128
Evaluate side-chains
  68 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  697 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.147409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.117095 restraints weight = 34044.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 3.31
r_work: 0.2876 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5620  Z= 0.109
  Angle     :  0.479   5.842   7615  Z= 0.234
  Chirality :  0.040   0.143    844
  Planarity :  0.004   0.039    989
  Dihedral  :  7.313 173.992    766
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 20.00 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.34), residues: 680
  helix:  2.08 (0.31), residues: 300
  sheet:  0.06 (0.48), residues: 122
  loop : -0.07 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 602 
 HIS   0.003   0.001   HIS A 137 
 PHE   0.006   0.001   PHE A 480 
 TYR   0.012   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03482 (  230)
  hydrogen bonds       : angle       4.18241 (  663)
  covalent geometry    : bond        0.00256 ( 5620)
  covalent geometry    : angle       0.47897 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.6852 (tp30) cc_final: 0.5791 (pm20)
  outliers start: 6
  outliers final: 6
  residues processed: 70
  average time/residue: 0.3933
  time to fit residues: 36.4613
Evaluate side-chains
  70 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  697 ASN
Chi-restraints excluded: chain A residue  718 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0030
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.147682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.117838 restraints weight = 32151.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 3.21
r_work: 0.2920 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5620  Z= 0.101
  Angle     :  0.475   5.744   7615  Z= 0.232
  Chirality :  0.040   0.143    844
  Planarity :  0.004   0.039    989
  Dihedral  :  7.360 175.937    766
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 20.00 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.31 (0.34), residues: 680
  helix:  2.12 (0.31), residues: 300
  sheet: -0.10 (0.52), residues: 104
  loop : -0.07 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 602 
 HIS   0.004   0.001   HIS A 137 
 PHE   0.005   0.001   PHE A 480 
 TYR   0.012   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03372 (  230)
  hydrogen bonds       : angle       4.09405 (  663)
  covalent geometry    : bond        0.00237 ( 5620)
  covalent geometry    : angle       0.47533 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.6912 (tp30) cc_final: 0.5915 (pm20)
  outliers start: 4
  outliers final: 4
  residues processed: 69
  average time/residue: 0.3627
  time to fit residues: 33.7996
Evaluate side-chains
  68 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  697 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.147208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.116632 restraints weight = 36097.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 3.39
r_work: 0.3101 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5620  Z= 0.112
  Angle     :  0.479   5.809   7615  Z= 0.235
  Chirality :  0.040   0.143    844
  Planarity :  0.004   0.039    989
  Dihedral  :  7.491 179.639    766
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 19.67 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.34 (0.34), residues: 680
  helix:  2.10 (0.31), residues: 300
  sheet:  0.09 (0.48), residues: 122
  loop : -0.08 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 602 
 HIS   0.004   0.001   HIS A 137 
 PHE   0.006   0.001   PHE A 480 
 TYR   0.012   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  230)
  hydrogen bonds       : angle       4.11274 (  663)
  covalent geometry    : bond        0.00265 ( 5620)
  covalent geometry    : angle       0.47948 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.6974 (tp30) cc_final: 0.5829 (pt0)
  outliers start: 6
  outliers final: 5
  residues processed: 71
  average time/residue: 0.3644
  time to fit residues: 35.1145
Evaluate side-chains
  70 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  697 ASN
Chi-restraints excluded: chain A residue  718 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.145010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.114490 restraints weight = 34867.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 3.37
r_work: 0.2873 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5620  Z= 0.109
  Angle     :  0.480   5.793   7615  Z= 0.235
  Chirality :  0.040   0.143    844
  Planarity :  0.004   0.039    989
  Dihedral  :  7.426 177.456    766
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 19.50 %
    Favored  : 79.17 %
  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:  1.29 (0.34), residues: 680
  helix:  2.12 (0.31), residues: 300
  sheet: -0.13 (0.52), residues: 104
  loop : -0.09 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 602 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.006   0.001   PHE A 132 
 TYR   0.012   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  230)
  hydrogen bonds       : angle       4.07393 (  663)
  covalent geometry    : bond        0.00257 ( 5620)
  covalent geometry    : angle       0.47970 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.6886 (tp30) cc_final: 0.5628 (pt0)
  outliers start: 6
  outliers final: 5
  residues processed: 70
  average time/residue: 0.4396
  time to fit residues: 42.9476
Evaluate side-chains
  71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  718 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0040
   chunk 41 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.147688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.117189 restraints weight = 35602.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 3.38
r_work: 0.2880 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5620  Z= 0.097
  Angle     :  0.476   5.720   7615  Z= 0.232
  Chirality :  0.040   0.142    844
  Planarity :  0.004   0.039    989
  Dihedral  :  7.404 177.237    766
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 20.17 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.40 (0.34), residues: 680
  helix:  2.13 (0.31), residues: 300
  sheet:  0.12 (0.48), residues: 122
  loop : -0.03 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 602 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.005   0.001   PHE A 255 
 TYR   0.011   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03281 (  230)
  hydrogen bonds       : angle       4.02679 (  663)
  covalent geometry    : bond        0.00228 ( 5620)
  covalent geometry    : angle       0.47613 ( 7615)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  123 is missing expected H atoms. Skipping.
Evaluate side-chains
  71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 LYS cc_start: 0.8447 (tptt) cc_final: 0.7990 (ttmm)
REVERT: A  693 TRP cc_start: 0.8779 (m100) cc_final: 0.8544 (m100)
REVERT: B  130 GLU cc_start: 0.6848 (tp30) cc_final: 0.5564 (pt0)
  outliers start: 3
  outliers final: 3
  residues processed: 70
  average time/residue: 0.3605
  time to fit residues: 33.5352
Evaluate side-chains
  70 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  654 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 29 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.147998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.119197 restraints weight = 28124.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 3.00
r_work: 0.2914 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5620  Z= 0.096
  Angle     :  0.473   5.705   7615  Z= 0.230
  Chirality :  0.039   0.141    844
  Planarity :  0.004   0.038    989
  Dihedral  :  7.350 176.017    766
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 19.83 %
    Favored  : 79.17 %
  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:  1.39 (0.34), residues: 680
  helix:  2.20 (0.31), residues: 300
  sheet: -0.09 (0.52), residues: 104
  loop : -0.02 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 602 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.005   0.001   PHE A 132 
 TYR   0.011   0.001   TYR A 644 
 ARG   0.001   0.000   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (  230)
  hydrogen bonds       : angle       3.96823 (  663)
  covalent geometry    : bond        0.00223 ( 5620)
  covalent geometry    : angle       0.47336 ( 7615)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6618.90 seconds
wall clock time: 115 minutes 36.85 seconds (6936.85 seconds total)