Starting phenix.real_space_refine
on Fri Feb 14 18:48:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9b_24931/02_2025/7s9b_24931.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9b_24931/02_2025/7s9b_24931.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s9b_24931/02_2025/7s9b_24931.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9b_24931/02_2025/7s9b_24931.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9b_24931/02_2025/7s9b_24931.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9b_24931/02_2025/7s9b_24931.cif"
  }
  resolution = 4.2
  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=   0.002
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      50      5.16       5
     C    6856      2.51       5
     N    1680      2.21       5
     O    1872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10458
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 678, 5229
          Classifications: {'peptide': 678}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 644}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 5229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 678, 5229
          Classifications: {'peptide': 678}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 644}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 5.95, per 1000 atoms: 0.57
  Number of scatterers: 10458
  At special positions: 0
  Unit cell: (115.867, 111.615, 117.993, 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      50     16.00
     O    1872      8.00
     N    1680      7.00
     C    6856      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2500

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      64.3% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 44 through 48
      removed outlier: 3.519A  pdb=" N   LYS A  47 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 65
      removed outlier: 3.617A  pdb=" N   ILE A  57 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 71
    Processing helix  chain 'A' and resid 78 through 105
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 126
      removed outlier: 3.960A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 138 through 152
    Processing helix  chain 'A' and resid 168 through 195
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'A' and resid 206 through 231
      removed outlier: 4.203A  pdb=" N   LYS A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TYR A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 258 through 282
      removed outlier: 3.539A  pdb=" N   PHE A 282 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 307
      removed outlier: 3.585A  pdb=" N   PHE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 363
      removed outlier: 3.724A  pdb=" N   ASP A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   ALA A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   ILE A 346 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 388
      removed outlier: 3.526A  pdb=" N   GLU A 374 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 406
      removed outlier: 4.015A  pdb=" N   SER A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.226A  pdb=" N   SER A 418 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 419 " --> pdb=" O   CYS A 415 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   VAL A 424 " --> pdb=" O   MET A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 448
    Processing helix  chain 'A' and resid 448 through 454
    Processing helix  chain 'A' and resid 456 through 465
      removed outlier: 3.748A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 482
    Processing helix  chain 'A' and resid 483 through 505
      removed outlier: 4.043A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 561
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 680 through 690
    Processing helix  chain 'A' and resid 697 through 702
      removed outlier: 4.010A  pdb=" N   LEU A 702 " --> pdb=" O   LEU A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 721
      removed outlier: 3.644A  pdb=" N   GLU A 721 " --> pdb=" O   GLU A 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 44 through 48
      removed outlier: 3.520A  pdb=" N   LYS B  47 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 65
      removed outlier: 3.616A  pdb=" N   ILE B  57 " --> pdb=" O   THR B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 78 through 105
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 3.959A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 138 through 152
    Processing helix  chain 'B' and resid 168 through 195
    Processing helix  chain 'B' and resid 200 through 205
    Processing helix  chain 'B' and resid 206 through 231
      removed outlier: 4.201A  pdb=" N   LYS B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   TYR B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 258 through 282
      removed outlier: 3.539A  pdb=" N   PHE B 282 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 307
      removed outlier: 3.584A  pdb=" N   PHE B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 363
      removed outlier: 3.723A  pdb=" N   ASP B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   ALA B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   ILE B 346 " --> pdb=" O   ASP B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
      removed outlier: 3.526A  pdb=" N   GLU B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 406
      removed outlier: 3.937A  pdb=" N   SER B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
      removed outlier: 4.226A  pdb=" N   SER B 418 " --> pdb=" O   GLY B 414 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B 419 " --> pdb=" O   CYS B 415 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   VAL B 424 " --> pdb=" O   MET B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 448
    Processing helix  chain 'B' and resid 448 through 454
    Processing helix  chain 'B' and resid 456 through 465
      removed outlier: 3.749A  pdb=" N   PHE B 460 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 482
    Processing helix  chain 'B' and resid 483 through 505
      removed outlier: 4.041A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 561
    Processing helix  chain 'B' and resid 563 through 579
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 680 through 690
    Processing helix  chain 'B' and resid 697 through 702
      removed outlier: 4.011A  pdb=" N   LEU B 702 " --> pdb=" O   LEU B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 721
      removed outlier: 3.643A  pdb=" N   GLU B 721 " --> pdb=" O   GLU B 717 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 511 through 513
    Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 539
      removed outlier: 6.622A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 511 through 513
    Processing sheet with id=AA4, first strand: chain 'B' and resid 535 through 539
      removed outlier: 6.623A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)

    612 hydrogen bonds defined for protein.
    1800 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: 3.03

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2280
        1.33 -     1.45: 2325
        1.45 -     1.57: 6007
        1.57 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 10694
  Sorted by residual:
  bond pdb=" CB  PHE B 351 "
       pdb=" CG  PHE B 351 "
    ideal  model  delta    sigma   weight residual
    1.502  1.433  0.069 2.30e-02 1.89e+03 9.05e+00
  bond pdb=" CB  PHE A 351 "
       pdb=" CG  PHE A 351 "
    ideal  model  delta    sigma   weight residual
    1.502  1.434  0.068 2.30e-02 1.89e+03 8.87e+00
  bond pdb=" CA  SER B 400 "
       pdb=" CB  SER B 400 "
    ideal  model  delta    sigma   weight residual
    1.529  1.484  0.045 1.64e-02 3.72e+03 7.48e+00
  bond pdb=" CA  SER A 400 "
       pdb=" CB  SER A 400 "
    ideal  model  delta    sigma   weight residual
    1.528  1.486  0.043 1.66e-02 3.63e+03 6.56e+00
  bond pdb=" CD1 PHE A 351 "
       pdb=" CE1 PHE A 351 "
    ideal  model  delta    sigma   weight residual
    1.382  1.307  0.075 3.00e-02 1.11e+03 6.21e+00
  ... (remaining 10689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 14109
        2.12 -     4.24: 374
        4.24 -     6.35: 49
        6.35 -     8.47: 4
        8.47 -    10.59: 4
  Bond angle restraints: 14540
  Sorted by residual:
  angle pdb=" C   PHE B  23 "
        pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.27    9.27 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   PHE A  23 "
        pdb=" N   SER A  24 "
        pdb=" CA  SER A  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.32    9.22 1.91e+00 2.74e-01 2.33e+01
  angle pdb=" C   GLU A 404 "
        pdb=" N   GLY A 405 "
        pdb=" CA  GLY A 405 "
      ideal   model   delta    sigma   weight residual
     120.14  114.65    5.49 1.25e+00 6.40e-01 1.93e+01
  angle pdb=" N   LEU A 401 "
        pdb=" CA  LEU A 401 "
        pdb=" C   LEU A 401 "
      ideal   model   delta    sigma   weight residual
     111.71  106.99    4.72 1.15e+00 7.56e-01 1.68e+01
  angle pdb=" N   LEU B 401 "
        pdb=" CA  LEU B 401 "
        pdb=" C   LEU B 401 "
      ideal   model   delta    sigma   weight residual
     111.71  107.33    4.38 1.15e+00 7.56e-01 1.45e+01
  ... (remaining 14535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 5865
       17.04 -    34.08: 399
       34.08 -    51.12: 42
       51.12 -    68.16: 13
       68.16 -    85.20: 7
  Dihedral angle restraints: 6326
    sinusoidal: 2418
      harmonic: 3908
  Sorted by residual:
  dihedral pdb=" CA  LYS B  77 "
           pdb=" C   LYS B  77 "
           pdb=" N   GLU B  78 "
           pdb=" CA  GLU B  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.08   26.92     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  LYS A  77 "
           pdb=" C   LYS A  77 "
           pdb=" N   GLU A  78 "
           pdb=" CA  GLU A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.13   26.87     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  SER A  24 "
           pdb=" C   SER A  24 "
           pdb=" N   HIS A  25 "
           pdb=" CA  HIS A  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.67   25.33     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 6323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1224
       0.047 -    0.093: 407
       0.093 -    0.140: 85
       0.140 -    0.186: 8
       0.186 -    0.233: 4
  Chirality restraints: 1728
  Sorted by residual:
  chirality pdb=" CB  THR A 390 "
            pdb=" CA  THR A 390 "
            pdb=" OG1 THR A 390 "
            pdb=" CG2 THR A 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  THR B 390 "
            pdb=" CA  THR B 390 "
            pdb=" OG1 THR B 390 "
            pdb=" CG2 THR B 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  ILE A 344 "
            pdb=" CA  ILE A 344 "
            pdb=" CG1 ILE A 344 "
            pdb=" CG2 ILE A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.98e-01
  ... (remaining 1725 not shown)

  Planarity restraints: 1814
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 396 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.77e+00
        pdb=" C   SER A 396 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   SER A 396 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A 397 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 396 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.77e+00
        pdb=" C   SER B 396 "    0.045 2.00e-02 2.50e+03
        pdb=" O   SER B 396 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B 397 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 330 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.63e+00
        pdb=" N   PRO B 331 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 331 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 331 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1811 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1744
        2.75 -     3.29: 11763
        3.29 -     3.83: 17894
        3.83 -     4.36: 19870
        4.36 -     4.90: 32512
  Nonbonded interactions: 83783
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 154 "
            pdb=" NZ  LYS B 235 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OD2 ASP A 154 "
            pdb=" NZ  LYS A 235 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OE2 GLU A 627 "
            pdb=" N   GLN A 630 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OE2 GLU B 627 "
            pdb=" N   GLN B 630 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   HIS B 220 "
            pdb=" OG1 THR B 223 "
     model   vdw
     2.243 3.040
  ... (remaining 83778 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.170
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.050
  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:   29.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
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      :  0.006   0.075  10694  Z= 0.399
  Angle     :  0.824  10.589  14540  Z= 0.477
  Chirality :  0.047   0.233   1728
  Planarity :  0.005   0.041   1814
  Dihedral  : 11.725  85.201   3826
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.94 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  1.05 %
    Favored  : 98.17 %
  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: -0.99 (0.23), residues: 1348
  helix:  0.41 (0.18), residues: 828
  sheet: -0.21 (0.90), residues: 32
  loop : -2.60 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 472 
 HIS   0.010   0.002   HIS A  25 
 PHE   0.025   0.002   PHE A 117 
 TYR   0.027   0.002   TYR A 123 
 ARG   0.007   0.001   ARG A 236 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 182
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8633 (pp) cc_final: 0.8334 (pp)
REVERT: A  267 MET cc_start: 0.8414 (mmt) cc_final: 0.7986 (mmt)
REVERT: A  299 MET cc_start: 0.8540 (ppp) cc_final: 0.8189 (ppp)
REVERT: A  566 PHE cc_start: 0.7957 (m-80) cc_final: 0.7717 (m-80)
REVERT: B  266 LEU cc_start: 0.8631 (pp) cc_final: 0.8397 (pp)
REVERT: B  267 MET cc_start: 0.8412 (mmt) cc_final: 0.8062 (mmt)
REVERT: B  299 MET cc_start: 0.8561 (ppp) cc_final: 0.8179 (ppp)
REVERT: B  566 PHE cc_start: 0.7848 (m-80) cc_final: 0.7620 (m-80)
REVERT: B  693 PHE cc_start: 0.8257 (m-10) cc_final: 0.7946 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 189
  average time/residue: 0.1920
  time to fit residues: 55.1822
Evaluate side-chains
  150 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 143
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 34 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 689 GLN
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.087683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.068607 restraints weight = 39825.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.070485 restraints weight = 21443.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.071729 restraints weight = 14038.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10694  Z= 0.206
  Angle     :  0.639   8.141  14540  Z= 0.329
  Chirality :  0.044   0.154   1728
  Planarity :  0.005   0.037   1814
  Dihedral  :  4.630  26.428   1450
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.38 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.24), residues: 1348
  helix:  0.98 (0.19), residues: 820
  sheet:  0.21 (0.87), residues: 32
  loop : -2.24 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 472 
 HIS   0.008   0.001   HIS A  25 
 PHE   0.016   0.001   PHE A 117 
 TYR   0.030   0.002   TYR B 340 
 ARG   0.004   0.001   ARG A 236 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8243 (tp40)
REVERT: A  266 LEU cc_start: 0.8661 (pp) cc_final: 0.8403 (pp)
REVERT: A  267 MET cc_start: 0.8276 (mmt) cc_final: 0.7938 (mmt)
REVERT: A  299 MET cc_start: 0.8710 (ppp) cc_final: 0.8340 (ppp)
REVERT: A  453 MET cc_start: 0.9136 (mmt) cc_final: 0.8905 (mmt)
REVERT: B   94 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8181 (mm-40)
REVERT: B  266 LEU cc_start: 0.8660 (pp) cc_final: 0.8409 (pp)
REVERT: B  267 MET cc_start: 0.8415 (mmt) cc_final: 0.8009 (mmt)
REVERT: B  299 MET cc_start: 0.8699 (ppp) cc_final: 0.8272 (ppp)
REVERT: B  566 PHE cc_start: 0.8165 (m-80) cc_final: 0.7648 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1834
  time to fit residues: 52.9105
Evaluate side-chains
  154 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 118 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0980
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
A  25 HIS
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 HIS
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.088241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.068893 restraints weight = 39998.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.070856 restraints weight = 21393.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.072159 restraints weight = 13915.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10694  Z= 0.202
  Angle     :  0.614   8.108  14540  Z= 0.313
  Chirality :  0.043   0.193   1728
  Planarity :  0.004   0.031   1814
  Dihedral  :  4.422  26.720   1450
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.68 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  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:  0.02 (0.24), residues: 1348
  helix:  1.20 (0.19), residues: 826
  sheet:  0.39 (0.90), residues: 32
  loop : -2.17 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 472 
 HIS   0.006   0.001   HIS A  25 
 PHE   0.011   0.001   PHE B 566 
 TYR   0.021   0.001   TYR A 123 
 ARG   0.004   0.000   ARG B 399 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 PHE cc_start: 0.8204 (m-10) cc_final: 0.7921 (m-10)
REVERT: A  207 GLU cc_start: 0.8273 (tt0) cc_final: 0.7816 (tm-30)
REVERT: A  236 ARG cc_start: 0.8228 (tmm160) cc_final: 0.7897 (tmm160)
REVERT: A  267 MET cc_start: 0.8313 (mmt) cc_final: 0.7947 (mmt)
REVERT: A  299 MET cc_start: 0.8809 (ppp) cc_final: 0.8515 (ppp)
REVERT: A  469 LEU cc_start: 0.9093 (tp) cc_final: 0.8829 (tp)
REVERT: B   94 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8151 (tp40)
REVERT: B  198 PHE cc_start: 0.8465 (m-10) cc_final: 0.8050 (m-10)
REVERT: B  207 GLU cc_start: 0.8170 (tt0) cc_final: 0.7482 (tm-30)
REVERT: B  267 MET cc_start: 0.8424 (mmt) cc_final: 0.8070 (mmt)
REVERT: B  299 MET cc_start: 0.8790 (ppp) cc_final: 0.8512 (ppp)
REVERT: B  469 LEU cc_start: 0.9057 (tp) cc_final: 0.8801 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1910
  time to fit residues: 53.0430
Evaluate side-chains
  144 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 108 optimal weight:    0.1980
   chunk 31 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 363 ASN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.088530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.069219 restraints weight = 39926.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.071161 restraints weight = 21800.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.072430 restraints weight = 14393.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10694  Z= 0.202
  Angle     :  0.601   8.432  14540  Z= 0.306
  Chirality :  0.043   0.165   1728
  Planarity :  0.004   0.031   1814
  Dihedral  :  4.337  27.401   1450
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.94 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.24), residues: 1348
  helix:  1.24 (0.19), residues: 830
  sheet:  0.55 (0.92), residues: 32
  loop : -2.07 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B  25 
 PHE   0.015   0.001   PHE A 191 
 TYR   0.020   0.001   TYR B 340 
 ARG   0.004   0.001   ARG A 399 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 ILE cc_start: 0.7971 (mm) cc_final: 0.7758 (mm)
REVERT: A  207 GLU cc_start: 0.8226 (tt0) cc_final: 0.7774 (tm-30)
REVERT: A  267 MET cc_start: 0.8394 (mmt) cc_final: 0.8024 (mmt)
REVERT: A  299 MET cc_start: 0.8824 (ppp) cc_final: 0.8501 (ppp)
REVERT: A  469 LEU cc_start: 0.9137 (tp) cc_final: 0.8885 (tp)
REVERT: B   94 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8085 (tp40)
REVERT: B  198 PHE cc_start: 0.8326 (m-10) cc_final: 0.8092 (m-10)
REVERT: B  207 GLU cc_start: 0.8152 (tt0) cc_final: 0.7555 (tm-30)
REVERT: B  236 ARG cc_start: 0.8207 (tmm160) cc_final: 0.7947 (tmm160)
REVERT: B  267 MET cc_start: 0.8377 (mmt) cc_final: 0.8002 (mmt)
REVERT: B  299 MET cc_start: 0.8829 (ppp) cc_final: 0.8530 (ppp)
REVERT: B  469 LEU cc_start: 0.9102 (tp) cc_final: 0.8845 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2004
  time to fit residues: 56.5235
Evaluate side-chains
  148 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 118 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 108 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0970
   chunk 112 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.089191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.069617 restraints weight = 39685.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.071643 restraints weight = 21265.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.072960 restraints weight = 13832.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10694  Z= 0.188
  Angle     :  0.599   8.060  14540  Z= 0.305
  Chirality :  0.043   0.190   1728
  Planarity :  0.004   0.033   1814
  Dihedral  :  4.313  27.660   1450
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.05 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  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:  0.22 (0.24), residues: 1348
  helix:  1.30 (0.19), residues: 832
  sheet:  0.84 (0.90), residues: 32
  loop : -2.03 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 704 
 PHE   0.014   0.001   PHE A 538 
 TYR   0.042   0.001   TYR A 123 
 ARG   0.007   0.000   ARG A 236 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 PHE cc_start: 0.8114 (m-10) cc_final: 0.7901 (m-10)
REVERT: A  207 GLU cc_start: 0.8145 (tt0) cc_final: 0.7732 (tm-30)
REVERT: A  266 LEU cc_start: 0.8636 (pp) cc_final: 0.8434 (pp)
REVERT: A  267 MET cc_start: 0.8414 (mmt) cc_final: 0.8028 (mmt)
REVERT: A  299 MET cc_start: 0.8846 (ppp) cc_final: 0.8530 (ppp)
REVERT: A  469 LEU cc_start: 0.9113 (tp) cc_final: 0.8870 (tp)
REVERT: B   94 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8127 (tp40)
REVERT: B  198 PHE cc_start: 0.8327 (m-10) cc_final: 0.8058 (m-10)
REVERT: B  207 GLU cc_start: 0.8183 (tt0) cc_final: 0.7606 (tm-30)
REVERT: B  267 MET cc_start: 0.8422 (mmt) cc_final: 0.8033 (mmt)
REVERT: B  299 MET cc_start: 0.8840 (ppp) cc_final: 0.8543 (ppp)
REVERT: B  469 LEU cc_start: 0.9094 (tp) cc_final: 0.8849 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2111
  time to fit residues: 58.6452
Evaluate side-chains
  147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 104 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 67 optimal weight:    7.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 504 GLN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.089046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.069766 restraints weight = 40161.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.071778 restraints weight = 21321.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.073080 restraints weight = 13770.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10694  Z= 0.197
  Angle     :  0.599   8.558  14540  Z= 0.303
  Chirality :  0.043   0.160   1728
  Planarity :  0.004   0.033   1814
  Dihedral  :  4.306  27.196   1450
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.72 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1348
  helix:  1.38 (0.19), residues: 830
  sheet:  0.89 (0.87), residues: 32
  loop : -1.94 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.003   0.001   HIS B 704 
 PHE   0.009   0.001   PHE A 101 
 TYR   0.037   0.001   TYR A 123 
 ARG   0.006   0.000   ARG B 236 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9041 (mmm) cc_final: 0.8633 (tpp)
REVERT: A  198 PHE cc_start: 0.8117 (m-10) cc_final: 0.7880 (m-10)
REVERT: A  207 GLU cc_start: 0.8216 (tt0) cc_final: 0.7730 (tm-30)
REVERT: A  266 LEU cc_start: 0.8637 (pp) cc_final: 0.8425 (pp)
REVERT: A  267 MET cc_start: 0.8450 (mmt) cc_final: 0.8023 (mmt)
REVERT: A  299 MET cc_start: 0.8876 (ppp) cc_final: 0.8558 (ppp)
REVERT: A  378 LEU cc_start: 0.9341 (tp) cc_final: 0.9132 (tp)
REVERT: A  382 ASN cc_start: 0.8936 (t0) cc_final: 0.8609 (t0)
REVERT: A  469 LEU cc_start: 0.9136 (tp) cc_final: 0.8892 (tp)
REVERT: B   94 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8101 (tp40)
REVERT: B  198 PHE cc_start: 0.8255 (m-10) cc_final: 0.8027 (m-10)
REVERT: B  207 GLU cc_start: 0.8221 (tt0) cc_final: 0.7585 (tm-30)
REVERT: B  266 LEU cc_start: 0.8608 (pp) cc_final: 0.8394 (pp)
REVERT: B  267 MET cc_start: 0.8437 (mmt) cc_final: 0.8036 (mmt)
REVERT: B  299 MET cc_start: 0.8882 (ppp) cc_final: 0.8577 (ppp)
REVERT: B  382 ASN cc_start: 0.8966 (t0) cc_final: 0.8636 (t0)
REVERT: B  420 MET cc_start: 0.8797 (tmm) cc_final: 0.8512 (ptp)
REVERT: B  469 LEU cc_start: 0.9118 (tp) cc_final: 0.8876 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1979
  time to fit residues: 54.7296
Evaluate side-chains
  155 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 132 optimal weight:    0.0370
   chunk 112 optimal weight:    5.9990
   chunk 101 optimal weight:    0.5980
   chunk 9 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:    7.9990
   chunk 98 optimal weight:    0.0010
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.4666

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

Flipped N/Q/H residues before XYZ refinement:
A 365 HIS
B  59 ASN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.090923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.071584 restraints weight = 39996.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.073654 restraints weight = 20980.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.075004 restraints weight = 13475.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10694  Z= 0.154
  Angle     :  0.604   8.883  14540  Z= 0.301
  Chirality :  0.043   0.198   1728
  Planarity :  0.004   0.033   1814
  Dihedral  :  4.302  27.989   1450
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.24), residues: 1348
  helix:  1.40 (0.19), residues: 830
  sheet:  1.24 (0.86), residues: 32
  loop : -1.91 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 337 
 PHE   0.010   0.001   PHE B  64 
 TYR   0.030   0.001   TYR A 123 
 ARG   0.004   0.000   ARG B 236 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9059 (mmm) cc_final: 0.8651 (tpp)
REVERT: A  186 THR cc_start: 0.9359 (m) cc_final: 0.8921 (p)
REVERT: A  198 PHE cc_start: 0.8112 (m-10) cc_final: 0.7807 (m-10)
REVERT: A  207 GLU cc_start: 0.8037 (tt0) cc_final: 0.7606 (tm-30)
REVERT: A  266 LEU cc_start: 0.8636 (pp) cc_final: 0.8431 (pp)
REVERT: A  267 MET cc_start: 0.8359 (mmt) cc_final: 0.7971 (mmt)
REVERT: A  299 MET cc_start: 0.8866 (ppp) cc_final: 0.8565 (ppp)
REVERT: A  382 ASN cc_start: 0.8956 (t0) cc_final: 0.8603 (t0)
REVERT: B  186 THR cc_start: 0.9364 (m) cc_final: 0.8923 (p)
REVERT: B  198 PHE cc_start: 0.8206 (m-10) cc_final: 0.7951 (m-10)
REVERT: B  207 GLU cc_start: 0.8066 (tt0) cc_final: 0.7459 (tm-30)
REVERT: B  267 MET cc_start: 0.8404 (mmt) cc_final: 0.7973 (mmt)
REVERT: B  299 MET cc_start: 0.8909 (ppp) cc_final: 0.8599 (ppp)
REVERT: B  382 ASN cc_start: 0.8985 (t0) cc_final: 0.8631 (t0)
REVERT: B  420 MET cc_start: 0.8836 (tmm) cc_final: 0.8506 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1934
  time to fit residues: 53.9559
Evaluate side-chains
  157 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 89 optimal weight:    8.9990
   chunk 105 optimal weight:    6.9990
   chunk 124 optimal weight:    0.5980
   chunk 118 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 HIS
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.090647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.071485 restraints weight = 39054.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.073530 restraints weight = 20784.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.074861 restraints weight = 13412.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10694  Z= 0.158
  Angle     :  0.597   8.198  14540  Z= 0.296
  Chirality :  0.043   0.259   1728
  Planarity :  0.004   0.032   1814
  Dihedral  :  4.201  27.826   1450
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.05 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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:  0.46 (0.24), residues: 1348
  helix:  1.45 (0.19), residues: 832
  sheet:  1.28 (0.83), residues: 32
  loop : -1.87 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 310 
 PHE   0.007   0.001   PHE A 101 
 TYR   0.028   0.001   TYR A 123 
 ARG   0.009   0.000   ARG B 399 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9077 (mmm) cc_final: 0.8703 (tpp)
REVERT: A  186 THR cc_start: 0.9358 (m) cc_final: 0.9021 (p)
REVERT: A  198 PHE cc_start: 0.8013 (m-10) cc_final: 0.7686 (m-10)
REVERT: A  207 GLU cc_start: 0.8035 (tt0) cc_final: 0.7586 (tm-30)
REVERT: A  266 LEU cc_start: 0.8598 (pp) cc_final: 0.8395 (pp)
REVERT: A  267 MET cc_start: 0.8325 (mmt) cc_final: 0.7922 (mmt)
REVERT: A  299 MET cc_start: 0.8882 (ppp) cc_final: 0.8571 (ppp)
REVERT: A  357 MET cc_start: 0.8647 (tpt) cc_final: 0.8435 (tpt)
REVERT: A  382 ASN cc_start: 0.8920 (t0) cc_final: 0.8598 (t0)
REVERT: B  186 THR cc_start: 0.9363 (m) cc_final: 0.9035 (p)
REVERT: B  198 PHE cc_start: 0.8193 (m-10) cc_final: 0.7894 (m-10)
REVERT: B  207 GLU cc_start: 0.8077 (tt0) cc_final: 0.7436 (tm-30)
REVERT: B  266 LEU cc_start: 0.8616 (pp) cc_final: 0.8408 (pp)
REVERT: B  267 MET cc_start: 0.8365 (mmt) cc_final: 0.7972 (mmt)
REVERT: B  299 MET cc_start: 0.8912 (ppp) cc_final: 0.8596 (ppp)
REVERT: B  382 ASN cc_start: 0.8987 (t0) cc_final: 0.8629 (t0)
REVERT: B  420 MET cc_start: 0.8873 (tmm) cc_final: 0.8523 (ptp)
REVERT: B  508 TYR cc_start: 0.8552 (m-80) cc_final: 0.8124 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1882
  time to fit residues: 52.3382
Evaluate side-chains
  157 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 89 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 130 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 689 GLN
B 363 ASN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 689 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.088968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.069635 restraints weight = 40374.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.071633 restraints weight = 21468.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072861 restraints weight = 13875.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10694  Z= 0.226
  Angle     :  0.609   8.280  14540  Z= 0.309
  Chirality :  0.044   0.246   1728
  Planarity :  0.004   0.041   1814
  Dihedral  :  4.206  26.040   1450
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.82 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  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:  0.41 (0.24), residues: 1348
  helix:  1.39 (0.19), residues: 830
  sheet:  1.19 (0.83), residues: 32
  loop : -1.84 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.003   0.001   HIS B 704 
 PHE   0.010   0.001   PHE A 191 
 TYR   0.027   0.001   TYR A 123 
 ARG   0.003   0.000   ARG A 236 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9081 (mmm) cc_final: 0.8770 (tpp)
REVERT: A  186 THR cc_start: 0.9360 (m) cc_final: 0.9026 (p)
REVERT: A  198 PHE cc_start: 0.8048 (m-10) cc_final: 0.7723 (m-10)
REVERT: A  207 GLU cc_start: 0.8131 (tt0) cc_final: 0.7701 (tm-30)
REVERT: A  266 LEU cc_start: 0.8614 (pp) cc_final: 0.8408 (pp)
REVERT: A  267 MET cc_start: 0.8332 (mmt) cc_final: 0.7898 (mmt)
REVERT: A  299 MET cc_start: 0.8910 (ppp) cc_final: 0.8602 (ppp)
REVERT: A  382 ASN cc_start: 0.8833 (t0) cc_final: 0.8469 (t0)
REVERT: A  469 LEU cc_start: 0.9117 (tp) cc_final: 0.8886 (tp)
REVERT: A  489 ILE cc_start: 0.8695 (tp) cc_final: 0.8474 (tp)
REVERT: B  186 THR cc_start: 0.9364 (m) cc_final: 0.9035 (p)
REVERT: B  198 PHE cc_start: 0.8206 (m-10) cc_final: 0.7935 (m-10)
REVERT: B  207 GLU cc_start: 0.8170 (tt0) cc_final: 0.7534 (tm-30)
REVERT: B  266 LEU cc_start: 0.8605 (pp) cc_final: 0.8391 (pp)
REVERT: B  267 MET cc_start: 0.8364 (mmt) cc_final: 0.7963 (mmt)
REVERT: B  299 MET cc_start: 0.8945 (ppp) cc_final: 0.8637 (ppp)
REVERT: B  382 ASN cc_start: 0.8910 (t0) cc_final: 0.8549 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2080
  time to fit residues: 56.7308
Evaluate side-chains
  160 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 70 optimal weight:    0.2980
   chunk 109 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0060
   chunk 131 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 122 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 130 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.4602

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

Flipped N/Q/H residues before XYZ refinement:
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.090086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.070769 restraints weight = 39602.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.072801 restraints weight = 20991.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.074114 restraints weight = 13532.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10694  Z= 0.175
  Angle     :  0.611   8.588  14540  Z= 0.306
  Chirality :  0.043   0.240   1728
  Planarity :  0.004   0.036   1814
  Dihedral  :  4.194  27.060   1450
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.90 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.24), residues: 1348
  helix:  1.40 (0.19), residues: 832
  sheet:  1.40 (0.83), residues: 32
  loop : -1.82 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 707 
 PHE   0.011   0.001   PHE B 191 
 TYR   0.026   0.001   TYR A 123 
 ARG   0.003   0.000   ARG A 236 

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9053 (mmm) cc_final: 0.8741 (tpp)
REVERT: A  186 THR cc_start: 0.9351 (m) cc_final: 0.9012 (p)
REVERT: A  198 PHE cc_start: 0.8124 (m-10) cc_final: 0.7821 (m-10)
REVERT: A  207 GLU cc_start: 0.8047 (tt0) cc_final: 0.7626 (tm-30)
REVERT: A  266 LEU cc_start: 0.8631 (pp) cc_final: 0.8424 (pp)
REVERT: A  267 MET cc_start: 0.8315 (mmt) cc_final: 0.7877 (mmt)
REVERT: A  299 MET cc_start: 0.8888 (ppp) cc_final: 0.8583 (ppp)
REVERT: A  382 ASN cc_start: 0.8937 (t0) cc_final: 0.8584 (t0)
REVERT: B  186 THR cc_start: 0.9352 (m) cc_final: 0.9016 (p)
REVERT: B  207 GLU cc_start: 0.8093 (tt0) cc_final: 0.7450 (tm-30)
REVERT: B  267 MET cc_start: 0.8366 (mmt) cc_final: 0.7964 (mmt)
REVERT: B  299 MET cc_start: 0.8923 (ppp) cc_final: 0.8609 (ppp)
REVERT: B  382 ASN cc_start: 0.8931 (t0) cc_final: 0.8595 (t0)
REVERT: B  420 MET cc_start: 0.8870 (tmm) cc_final: 0.8523 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1829
  time to fit residues: 49.8780
Evaluate side-chains
  157 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 121 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   chunk 69 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3505 r_free = 0.3505 target = 0.089725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.070443 restraints weight = 39369.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.072441 restraints weight = 20945.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.073738 restraints weight = 13521.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10694  Z= 0.183
  Angle     :  0.602   8.696  14540  Z= 0.301
  Chirality :  0.043   0.234   1728
  Planarity :  0.004   0.032   1814
  Dihedral  :  4.179  26.582   1450
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.68 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.24), residues: 1348
  helix:  1.48 (0.19), residues: 830
  sheet:  1.42 (0.82), residues: 32
  loop : -1.80 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 704 
 PHE   0.014   0.001   PHE A  23 
 TYR   0.026   0.001   TYR B 340 
 ARG   0.003   0.000   ARG A 236 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2756.23 seconds
wall clock time: 50 minutes 40.65 seconds (3040.65 seconds total)