Starting phenix.real_space_refine
on Fri May  9 19:39:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ygt_39263/05_2025/8ygt_39263.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ygt_39263/05_2025/8ygt_39263.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ygt_39263/05_2025/8ygt_39263.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ygt_39263/05_2025/8ygt_39263.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ygt_39263/05_2025/8ygt_39263.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ygt_39263/05_2025/8ygt_39263.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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: 4
    Type Number    sf(0)   Gaussians
     S      11      5.16       5
     C    2238      2.51       5
     N     590      2.21       5
     O     679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3518
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 94
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 94
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
    Chain: "B"
      Number of atoms: 1726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1726
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 8, 'TRANS': 207}
    Chain: "H"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 880
          Classifications: {'peptide': 114}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 818
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N   SER H  17 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER H  17 " occ=0.50
    residue:
      pdb=" N   SER H  61 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER H  61 " occ=0.50
    residue:
      pdb=" N   MET L  11 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET L  11 " occ=0.50
    residue:
      pdb=" N   ARG L  18 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG L  18 " occ=0.50
    residue:
      pdb=" N   GLN L  27 " occ=0.83
      ... (7 atoms not shown)
      pdb=" NE2 GLN L  27 " occ=0.83
    residue:
      pdb=" N   SER L  43 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER L  43 " occ=0.50
    residue:
      pdb=" N   SER L  50 " occ=0.90
      ... (4 atoms not shown)
      pdb=" OG  SER L  50 " occ=0.90
    residue:
      pdb=" N   SER L  67 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER L  67 " occ=0.50
    residue:
      pdb=" N   GLU L 105 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU L 105 " occ=0.50
  Time building chain proxies: 2.96, per 1000 atoms: 0.84
  Number of scatterers: 3518
  At special positions: 0
  Unit cell: (62.586, 88.938, 96.624, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      11     16.00
     O     679      8.00
     N     590      7.00
     C    2238      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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: 0.69
  Conformation dependent library (CDL) restraints added in 387.0 milliseconds
  

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  828

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 11 sheets defined
      3.3% alpha, 54.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'B' and resid 360 through 364
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 4.156A  pdb=" N   ALA H  90 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.583A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LEU L  83 " --> pdb=" O   ALA L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422
      removed outlier: 3.836A  pdb=" N   VAL B 409 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   LEU B 404 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   ALA B 431 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   SER B 406 " --> pdb=" O   ARG B 429 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   ARG B 429 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLY B 408 " --> pdb=" O   ARG B 427 " (cutoff:3.500A)
      removed outlier: 11.660A  pdb=" N   ASN B 422 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   ASP B 357 " --> pdb=" O   ASN B 422 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   LEU B 424 " --> pdb=" O   TYR B 355 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422
      removed outlier: 3.836A  pdb=" N   VAL B 409 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL B 378 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 263 through 275
      removed outlier: 3.714A  pdb=" N   SER B 472 " --> pdb=" O   MET B 265 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG B 269 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ARG B 467 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   ALA B 373 " --> pdb=" O   ARG B 467 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER B 469 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LEU B 371 " --> pdb=" O   SER B 469 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ILE B 471 " --> pdb=" O   ARG B 369 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283
      removed outlier: 8.710A  pdb=" N   TRP B 291 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   PHE B 342 " --> pdb=" O   TRP B 291 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   GLU B 293 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
      removed outlier: 11.047A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
      removed outlier: 9.864A  pdb=" N   SER B 295 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   SER B 340 " --> pdb=" O   PHE B 328 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   PHE B 328 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 279 through 283
      removed outlier: 8.710A  pdb=" N   TRP B 291 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   PHE B 342 " --> pdb=" O   TRP B 291 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   GLU B 293 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
      removed outlier: 11.047A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
      removed outlier: 9.864A  pdb=" N   SER B 295 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.807A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   MET H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL H  34 " --> pdb=" O   MET H  50 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   CYS H  95 " --> pdb=" O   TRP H 107 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   TRP H 107 " --> pdb=" O   CYS H  95 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ARG H  97 " --> pdb=" O   ASP H 105 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.807A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   MET H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL H  34 " --> pdb=" O   MET H  50 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.699A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.842A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    140 hydrogen bonds defined for protein.
    342 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: 0.95

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1102
        1.34 -     1.46: 947
        1.46 -     1.58: 1540
        1.58 -     1.70: 0
        1.70 -     1.83: 16
  Bond restraints: 3605
  Sorted by residual:
  bond pdb=" CB  VAL B 365 "
       pdb=" CG2 VAL B 365 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.33e+00
  bond pdb=" CB  ILE B 345 "
       pdb=" CG2 ILE B 345 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.69e+00
  bond pdb=" C   GLY B 286 "
       pdb=" O   GLY B 286 "
    ideal  model  delta    sigma   weight residual
    1.233  1.224  0.009 6.90e-03 2.10e+04 1.59e+00
  bond pdb=" N   THR L  56 "
       pdb=" CA  THR L  56 "
    ideal  model  delta    sigma   weight residual
    1.459  1.473 -0.014 1.18e-02 7.18e+03 1.32e+00
  bond pdb=" CB  VAL B 323 "
       pdb=" CG1 VAL B 323 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.30e+00
  ... (remaining 3600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 4603
        1.91 -     3.81: 251
        3.81 -     5.72: 28
        5.72 -     7.63: 9
        7.63 -     9.53: 3
  Bond angle restraints: 4894
  Sorted by residual:
  angle pdb=" N   TYR L  55 "
        pdb=" CA  TYR L  55 "
        pdb=" C   TYR L  55 "
      ideal   model   delta    sigma   weight residual
     110.46  105.53    4.93 1.48e+00 4.57e-01 1.11e+01
  angle pdb=" CA  CYS L  88 "
        pdb=" CB  CYS L  88 "
        pdb=" SG  CYS L  88 "
      ideal   model   delta    sigma   weight residual
     114.40  121.10   -6.70 2.30e+00 1.89e-01 8.48e+00
  angle pdb=" C   THR L  56 "
        pdb=" CA  THR L  56 "
        pdb=" CB  THR L  56 "
      ideal   model   delta    sigma   weight residual
     110.95  115.30   -4.35 1.55e+00 4.16e-01 7.88e+00
  angle pdb=" CA  THR L  94 "
        pdb=" C   THR L  94 "
        pdb=" N   PRO L  95 "
      ideal   model   delta    sigma   weight residual
     118.44  122.88   -4.44 1.59e+00 3.96e-01 7.81e+00
  angle pdb=" CA  CYS L  23 "
        pdb=" CB  CYS L  23 "
        pdb=" SG  CYS L  23 "
      ideal   model   delta    sigma   weight residual
     114.40  120.75   -6.35 2.30e+00 1.89e-01 7.61e+00
  ... (remaining 4889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.20: 1997
       14.20 -    28.40: 83
       28.40 -    42.59: 20
       42.59 -    56.79: 1
       56.79 -    70.99: 3
  Dihedral angle restraints: 2104
    sinusoidal: 808
      harmonic: 1296
  Sorted by residual:
  dihedral pdb=" CA  SER B 445 "
           pdb=" C   SER B 445 "
           pdb=" N   ARG B 446 "
           pdb=" CA  ARG B 446 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.40   28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.42  -45.42     1      1.00e+01 1.00e-02 2.86e+01
  dihedral pdb=" CA  LEU B 444 "
           pdb=" C   LEU B 444 "
           pdb=" N   SER B 445 "
           pdb=" CA  SER B 445 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.42  -21.58     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 2101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 346
       0.049 -    0.098: 135
       0.098 -    0.147: 36
       0.147 -    0.196: 16
       0.196 -    0.245: 3
  Chirality restraints: 536
  Sorted by residual:
  chirality pdb=" CB  VAL B 320 "
            pdb=" CA  VAL B 320 "
            pdb=" CG1 VAL B 320 "
            pdb=" CG2 VAL B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  THR L  94 "
            pdb=" N   THR L  94 "
            pdb=" C   THR L  94 "
            pdb=" CB  THR L  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  VAL B 402 "
            pdb=" CA  VAL B 402 "
            pdb=" CG1 VAL B 402 "
            pdb=" CG2 VAL B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 533 not shown)

  Planarity restraints: 625
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  43 "    0.032 5.00e-02 4.00e+02   4.90e-02 3.84e+00
        pdb=" N   PRO L  44 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO L  44 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO L  44 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 333 "   -0.032 5.00e-02 4.00e+02   4.87e-02 3.80e+00
        pdb=" N   PRO B 334 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 334 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 334 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 291 "    0.013 2.00e-02 2.50e+03   1.22e-02 3.75e+00
        pdb=" CG  TRP B 291 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 291 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 291 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 291 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 291 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 291 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 291 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 291 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 291 "    0.005 2.00e-02 2.50e+03
  ... (remaining 622 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 1249
        2.88 -     3.38: 2636
        3.38 -     3.89: 5258
        3.89 -     4.39: 5692
        4.39 -     4.90: 10751
  Nonbonded interactions: 25586
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  63 "
            pdb=" OG1 THR L  74 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" O   LEU B 439 "
            pdb=" OG1 THR B 442 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" NE2 GLN B 266 "
            pdb=" OG  SER H  56 "
     model   vdw
     2.436 3.120
  nonbonded pdb=" NZ  LYS H   5 "
            pdb=" OE1 GLN H 109 "
     model   vdw
     2.477 3.120
  nonbonded pdb=" N   ASP B 325 "
            pdb=" OD1 ASP B 325 "
     model   vdw
     2.517 3.120
  ... (remaining 25581 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=0.50 max=1.00 mean=0.99
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:             1.350
  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:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.580
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
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      :  0.007   0.057   3607  Z= 0.311
  Angle     :  1.000   9.535   4898  Z= 0.562
  Chirality :  0.061   0.245    536
  Planarity :  0.007   0.049    625
  Dihedral  :  9.089  70.989   1270
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.35), residues: 441
  helix:  None (None), residues: 0
  sheet: -1.07 (0.34), residues: 220
  loop : -3.26 (0.30), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.004   TRP B 291 
 HIS   0.010   0.003   HIS L  91 
 PHE   0.034   0.003   PHE B 362 
 TYR   0.027   0.003   TYR B 267 
 ARG   0.006   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30290 (  120)
  hydrogen bonds       : angle       9.55385 (  342)
  SS BOND              : bond        0.00925 (    2)
  SS BOND              : angle       1.80344 (    4)
  covalent geometry    : bond        0.00706 ( 3605)
  covalent geometry    : angle       0.99919 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  421 LEU cc_start: 0.8569 (tt) cc_final: 0.8356 (tp)
REVERT: B  391 VAL cc_start: 0.8800 (t) cc_final: 0.8538 (p)
REVERT: B  396 VAL cc_start: 0.7832 (m) cc_final: 0.7584 (t)
REVERT: B  416 THR cc_start: 0.7969 (m) cc_final: 0.7664 (p)
REVERT: B  427 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7517 (ttp-170)
REVERT: H   15 SER cc_start: 0.8222 (m) cc_final: 0.7833 (p)
REVERT: H   20 ILE cc_start: 0.8313 (mt) cc_final: 0.8074 (mt)
REVERT: L   53 TYR cc_start: 0.7826 (t80) cc_final: 0.7418 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2399
  time to fit residues: 22.0222
Evaluate side-chains
  59 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0670
   chunk 21 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
B 266 GLN
B 364 ASN
H   3 GLN
H  73 ASN
L  90 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.099777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.088655 restraints weight = 5561.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.03
r_work: 0.2883 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3607  Z= 0.165
  Angle     :  0.684   7.310   4898  Z= 0.364
  Chirality :  0.046   0.146    536
  Planarity :  0.005   0.042    625
  Dihedral  :  5.585  29.039    488
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  :  5.13 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.35), residues: 441
  helix:  None (None), residues: 0
  sheet: -0.53 (0.33), residues: 224
  loop : -2.95 (0.32), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 107 
 HIS   0.008   0.003   HIS L  91 
 PHE   0.016   0.002   PHE B 342 
 TYR   0.014   0.002   TYR B 267 
 ARG   0.003   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05210 (  120)
  hydrogen bonds       : angle       5.86784 (  342)
  SS BOND              : bond        0.00987 (    2)
  SS BOND              : angle       1.28340 (    4)
  covalent geometry    : bond        0.00393 ( 3605)
  covalent geometry    : angle       0.68313 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.356 
Fit side-chains
REVERT: B  391 VAL cc_start: 0.8898 (t) cc_final: 0.8667 (p)
REVERT: B  416 THR cc_start: 0.7876 (m) cc_final: 0.7517 (p)
REVERT: B  432 VAL cc_start: 0.8903 (m) cc_final: 0.8590 (t)
REVERT: B  443 ARG cc_start: 0.5947 (tpt170) cc_final: 0.5431 (tpt170)
REVERT: B  446 ARG cc_start: 0.6723 (mtt180) cc_final: 0.6455 (mtt-85)
REVERT: H   15 SER cc_start: 0.8129 (m) cc_final: 0.7739 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 65
  average time/residue: 0.1956
  time to fit residues: 15.0982
Evaluate side-chains
  60 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 37 optimal weight:    0.1980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.098157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.087390 restraints weight = 5463.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.89
r_work: 0.2880 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3607  Z= 0.214
  Angle     :  0.716   8.497   4898  Z= 0.381
  Chirality :  0.048   0.148    536
  Planarity :  0.005   0.046    625
  Dihedral  :  5.668  28.534    488
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  :  5.90 %
    Favored  : 90.00 %
  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: -2.03 (0.36), residues: 441
  helix:  None (None), residues: 0
  sheet: -0.19 (0.33), residues: 224
  loop : -2.71 (0.34), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.008   0.003   HIS B 315 
 PHE   0.017   0.002   PHE B 342 
 TYR   0.014   0.002   TYR H  93 
 ARG   0.005   0.001   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05365 (  120)
  hydrogen bonds       : angle       5.46863 (  342)
  SS BOND              : bond        0.01042 (    2)
  SS BOND              : angle       1.38080 (    4)
  covalent geometry    : bond        0.00531 ( 3605)
  covalent geometry    : angle       0.71493 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.373 
Fit side-chains
REVERT: B  362 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7547 (t80)
REVERT: B  391 VAL cc_start: 0.8969 (t) cc_final: 0.8659 (p)
REVERT: B  432 VAL cc_start: 0.8672 (m) cc_final: 0.8443 (t)
REVERT: B  443 ARG cc_start: 0.5856 (tpt170) cc_final: 0.5322 (tpt90)
REVERT: B  446 ARG cc_start: 0.6499 (mtt180) cc_final: 0.6236 (mtt-85)
  outliers start: 16
  outliers final: 9
  residues processed: 64
  average time/residue: 0.2146
  time to fit residues: 16.1950
Evaluate side-chains
  62 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  362 PHE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    0.3980
   chunk 3 optimal weight:    0.0980
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.3780

-------------------------------------------------------------------------------
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 = 0.3226 r_free = 0.3226 target = 0.100438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.089289 restraints weight = 5501.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.99
r_work: 0.2905 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3607  Z= 0.131
  Angle     :  0.592   6.035   4898  Z= 0.316
  Chirality :  0.044   0.144    536
  Planarity :  0.005   0.042    625
  Dihedral  :  5.136  28.477    488
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  9.23 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.37), residues: 441
  helix:  None (None), residues: 0
  sheet:  0.08 (0.34), residues: 222
  loop : -2.55 (0.35), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 356 
 HIS   0.005   0.002   HIS L  91 
 PHE   0.017   0.002   PHE B 342 
 TYR   0.009   0.002   TYR B 305 
 ARG   0.004   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  120)
  hydrogen bonds       : angle       5.05157 (  342)
  SS BOND              : bond        0.00820 (    2)
  SS BOND              : angle       0.96921 (    4)
  covalent geometry    : bond        0.00306 ( 3605)
  covalent geometry    : angle       0.59151 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.356 
Fit side-chains
REVERT: B  362 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7649 (t80)
REVERT: B  391 VAL cc_start: 0.8950 (t) cc_final: 0.8633 (p)
REVERT: B  443 ARG cc_start: 0.5867 (tpt170) cc_final: 0.5278 (tpt90)
REVERT: B  446 ARG cc_start: 0.6588 (mtt180) cc_final: 0.6358 (mtt-85)
  outliers start: 12
  outliers final: 9
  residues processed: 65
  average time/residue: 0.2039
  time to fit residues: 15.6994
Evaluate side-chains
  64 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  362 PHE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain H residue   15 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   79 PHE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   17 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0970
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.097207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.085693 restraints weight = 5538.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.07
r_work: 0.2910 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2775
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3607  Z= 0.169
  Angle     :  0.654   6.871   4898  Z= 0.344
  Chirality :  0.046   0.146    536
  Planarity :  0.005   0.045    625
  Dihedral  :  5.257  27.303    488
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 11.03 %
    Favored  : 85.38 %
  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: -1.60 (0.38), residues: 441
  helix:  None (None), residues: 0
  sheet:  0.11 (0.34), residues: 222
  loop : -2.42 (0.36), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.007   0.003   HIS L  91 
 PHE   0.017   0.002   PHE B 342 
 TYR   0.011   0.002   TYR H  93 
 ARG   0.004   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 (  120)
  hydrogen bonds       : angle       5.05244 (  342)
  SS BOND              : bond        0.00961 (    2)
  SS BOND              : angle       1.17035 (    4)
  covalent geometry    : bond        0.00410 ( 3605)
  covalent geometry    : angle       0.65321 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.394 
Fit side-chains
REVERT: B  362 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7655 (t80)
REVERT: B  391 VAL cc_start: 0.8961 (t) cc_final: 0.8636 (p)
REVERT: B  443 ARG cc_start: 0.5891 (tpt170) cc_final: 0.5288 (tpt90)
  outliers start: 14
  outliers final: 12
  residues processed: 62
  average time/residue: 0.2183
  time to fit residues: 15.9418
Evaluate side-chains
  65 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  362 PHE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain H residue   15 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   79 PHE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.099356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.088142 restraints weight = 5603.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.01
r_work: 0.2918 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3607  Z= 0.166
  Angle     :  0.640   6.227   4898  Z= 0.339
  Chirality :  0.046   0.146    536
  Planarity :  0.005   0.045    625
  Dihedral  :  5.218  28.802    488
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 10.51 %
    Favored  : 84.87 %
  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: -1.49 (0.38), residues: 441
  helix:  None (None), residues: 0
  sheet:  0.11 (0.34), residues: 226
  loop : -2.29 (0.36), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 356 
 HIS   0.006   0.002   HIS L  91 
 PHE   0.016   0.002   PHE B 342 
 TYR   0.011   0.002   TYR H  93 
 ARG   0.004   0.001   ARG B 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04554 (  120)
  hydrogen bonds       : angle       5.01390 (  342)
  SS BOND              : bond        0.00917 (    2)
  SS BOND              : angle       1.11395 (    4)
  covalent geometry    : bond        0.00404 ( 3605)
  covalent geometry    : angle       0.63985 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.404 
Fit side-chains
REVERT: B  362 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7694 (t80)
REVERT: B  391 VAL cc_start: 0.8936 (t) cc_final: 0.8613 (p)
REVERT: B  432 VAL cc_start: 0.8660 (m) cc_final: 0.8443 (t)
REVERT: B  443 ARG cc_start: 0.5862 (tpt170) cc_final: 0.5186 (tpt90)
  outliers start: 18
  outliers final: 15
  residues processed: 61
  average time/residue: 0.1987
  time to fit residues: 14.4178
Evaluate side-chains
  65 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  362 PHE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   79 PHE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.099508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.088266 restraints weight = 5411.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.00
r_work: 0.2919 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2785
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2785
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3607  Z= 0.158
  Angle     :  0.631   6.981   4898  Z= 0.333
  Chirality :  0.045   0.145    536
  Planarity :  0.005   0.044    625
  Dihedral  :  5.126  25.747    488
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 11.54 %
    Favored  : 84.62 %
  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 (0.38), residues: 441
  helix:  None (None), residues: 0
  sheet:  0.19 (0.34), residues: 226
  loop : -2.17 (0.37), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 356 
 HIS   0.006   0.002   HIS L  91 
 PHE   0.016   0.002   PHE B 342 
 TYR   0.011   0.002   TYR B 462 
 ARG   0.003   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  120)
  hydrogen bonds       : angle       4.97129 (  342)
  SS BOND              : bond        0.00899 (    2)
  SS BOND              : angle       1.06560 (    4)
  covalent geometry    : bond        0.00380 ( 3605)
  covalent geometry    : angle       0.63076 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.408 
Fit side-chains
REVERT: B  362 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7521 (t80)
REVERT: B  391 VAL cc_start: 0.8941 (t) cc_final: 0.8613 (p)
REVERT: B  443 ARG cc_start: 0.5872 (tpt170) cc_final: 0.5519 (tpt170)
  outliers start: 15
  outliers final: 13
  residues processed: 63
  average time/residue: 0.2014
  time to fit residues: 15.0383
Evaluate side-chains
  66 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  362 PHE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain H residue   15 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   79 PHE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   17 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 3 optimal weight:    0.0000
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0980
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4184

-------------------------------------------------------------------------------
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 = 0.3190 r_free = 0.3190 target = 0.098283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.086921 restraints weight = 5496.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.07
r_work: 0.2930 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3607  Z= 0.138
  Angle     :  0.601   6.660   4898  Z= 0.317
  Chirality :  0.044   0.144    536
  Planarity :  0.004   0.043    625
  Dihedral  :  4.968  24.127    488
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 11.28 %
    Favored  : 85.13 %
  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: -1.23 (0.39), residues: 441
  helix:  None (None), residues: 0
  sheet:  0.26 (0.34), residues: 226
  loop : -2.09 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 356 
 HIS   0.006   0.002   HIS L  91 
 PHE   0.016   0.002   PHE B 342 
 TYR   0.011   0.002   TYR B 462 
 ARG   0.003   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  120)
  hydrogen bonds       : angle       4.87896 (  342)
  SS BOND              : bond        0.00849 (    2)
  SS BOND              : angle       0.98561 (    4)
  covalent geometry    : bond        0.00327 ( 3605)
  covalent geometry    : angle       0.60095 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.360 
Fit side-chains
REVERT: B  362 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7472 (t80)
REVERT: B  391 VAL cc_start: 0.8914 (t) cc_final: 0.8579 (p)
  outliers start: 14
  outliers final: 12
  residues processed: 56
  average time/residue: 0.1580
  time to fit residues: 11.0200
Evaluate side-chains
  59 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  362 PHE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   79 PHE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   17 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 9 optimal weight:    0.1980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3215 r_free = 0.3215 target = 0.099808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.088815 restraints weight = 5459.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.98
r_work: 0.2900 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3607  Z= 0.138
  Angle     :  0.602   6.589   4898  Z= 0.317
  Chirality :  0.044   0.145    536
  Planarity :  0.004   0.043    625
  Dihedral  :  4.937  21.097    488
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 11.28 %
    Favored  : 85.38 %
  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 (0.39), residues: 441
  helix:  None (None), residues: 0
  sheet:  0.28 (0.35), residues: 226
  loop : -2.06 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 356 
 HIS   0.006   0.002   HIS L  91 
 PHE   0.016   0.002   PHE B 342 
 TYR   0.011   0.002   TYR B 462 
 ARG   0.002   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04224 (  120)
  hydrogen bonds       : angle       4.86873 (  342)
  SS BOND              : bond        0.00855 (    2)
  SS BOND              : angle       0.97287 (    4)
  covalent geometry    : bond        0.00328 ( 3605)
  covalent geometry    : angle       0.60124 ( 4894)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.420 
Fit side-chains
REVERT: B  362 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7525 (t80)
REVERT: B  391 VAL cc_start: 0.8914 (t) cc_final: 0.8573 (p)
REVERT: B  443 ARG cc_start: 0.6084 (tpt170) cc_final: 0.5692 (tpt170)
  outliers start: 13
  outliers final: 12
  residues processed: 60
  average time/residue: 0.2124
  time to fit residues: 15.1276
Evaluate side-chains
  64 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  362 PHE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   79 PHE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   17 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2876 > 50:
  distance: 34 - 137:  34.180
  distance: 37 - 134:  30.131
  distance: 72 - 76:  34.522
  distance: 76 - 77:  41.370
  distance: 77 - 78:  40.862
  distance: 78 - 81:  18.003
  distance: 81 - 82:  25.711
  distance: 82 - 83:  13.188
  distance: 82 - 85:  31.740
  distance: 83 - 84:  19.231
  distance: 83 - 88:  15.404
  distance: 85 - 86:  23.434
  distance: 88 - 89:  39.299
  distance: 89 - 90:  20.486
  distance: 89 - 92:  25.194
  distance: 90 - 91:  55.899
  distance: 93 - 94:  49.754
  distance: 94 - 95:  40.294
  distance: 94 - 96:  56.302
  distance: 99 - 100:  50.056
  distance: 102 - 103:  55.948
  distance: 103 - 104:  40.984
  distance: 106 - 107:  56.404
  distance: 106 - 112:  36.145
  distance: 108 - 113:  40.058
  distance: 110 - 111:  56.809
  distance: 111 - 112:  41.419
  distance: 113 - 114:  13.080
  distance: 114 - 115:  39.588
  distance: 114 - 117:  48.504
  distance: 115 - 123:   3.359
  distance: 117 - 118:  11.697
  distance: 118 - 119:  21.129
  distance: 120 - 122:  14.338
  distance: 121 - 122:   8.087
  distance: 123 - 124:  39.737
  distance: 124 - 125:  39.958
  distance: 124 - 127:   9.892
  distance: 125 - 126:  40.425
  distance: 125 - 134:  49.231
  distance: 127 - 128:  11.720
  distance: 128 - 129:  41.177
  distance: 129 - 131:  32.083
  distance: 130 - 132:  15.166
  distance: 131 - 133:  49.967
  distance: 132 - 133:  20.349
  distance: 134 - 135:   6.711
  distance: 135 - 136:   3.630
  distance: 136 - 137:   4.285
  distance: 136 - 143:   6.520
  distance: 138 - 139:  39.949
  distance: 139 - 140:  35.848
  distance: 140 - 141:  17.188
  distance: 141 - 142:  41.896
  distance: 143 - 144:  21.405
  distance: 144 - 145:  17.700
  distance: 144 - 147:   6.494
  distance: 145 - 151:  56.579
  distance: 147 - 148:  10.661
  distance: 148 - 149:  39.659
  distance: 151 - 152:  54.627
  distance: 152 - 153:  34.624
  distance: 152 - 155:  32.311
  distance: 153 - 154:  18.165
  distance: 153 - 158:  28.496
  distance: 155 - 157:  40.941