Starting phenix.real_space_refine
on Wed Apr 30 08:46:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvb_4646/04_2025/6qvb_4646.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvb_4646/04_2025/6qvb_4646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qvb_4646/04_2025/6qvb_4646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvb_4646/04_2025/6qvb_4646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvb_4646/04_2025/6qvb_4646.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvb_4646/04_2025/6qvb_4646.cif"
  }
  resolution = 4.34
  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=   0.003
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      70      5.16       5
     C    6109      2.51       5
     N    1482      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9237
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4617
          Classifications: {'peptide': 596}
          Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 566}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 4620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4620
          Classifications: {'peptide': 597}
          Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 567}
          Chain breaks: 3
  Time building chain proxies: 5.84, per 1000 atoms: 0.63
  Number of scatterers: 9237
  At special positions: 0
  Unit cell: (110.21, 118.77, 108.07, 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      70     16.00
     O    1576      8.00
     N    1482      7.00
     C    6109      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: 2.18
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 6 sheets defined
      66.6% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'B' and resid 115 through 153
    Processing helix  chain 'B' and resid 158 through 181
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 4.499A  pdb=" N   MET B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 4.283A  pdb=" N   VAL B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B 214 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
    Processing helix  chain 'B' and resid 263 through 280
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 298 through 323
      removed outlier: 3.778A  pdb=" N   TYR B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL B 321 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 375
      removed outlier: 3.717A  pdb=" N   ALA B 352 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   CYS B 357 " --> pdb=" O   ALA B 353 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY B 359 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 388
    Processing helix  chain 'B' and resid 389 through 393
      removed outlier: 3.546A  pdb=" N   LEU B 392 " --> pdb=" O   HIS B 389 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR B 393 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 389 through 393'
    Processing helix  chain 'B' and resid 394 through 404
      removed outlier: 3.520A  pdb=" N   THR B 398 " --> pdb=" O   PRO B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 415
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 444 through 450
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 4.867A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 506
    Processing helix  chain 'B' and resid 521 through 538
      removed outlier: 4.613A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 551
      removed outlier: 3.881A  pdb=" N   VAL B 544 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 574
    Processing helix  chain 'B' and resid 576 through 585
      removed outlier: 3.723A  pdb=" N   SER B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 632
      removed outlier: 4.074A  pdb=" N   THR B 632 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 666
    Processing helix  chain 'B' and resid 833 through 845
    Processing helix  chain 'B' and resid 863 through 872
      removed outlier: 3.947A  pdb=" N   GLY B 872 " --> pdb=" O   LYS B 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 153
    Processing helix  chain 'A' and resid 158 through 181
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 199
      removed outlier: 4.492A  pdb=" N   MET A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 209 through 224
      removed outlier: 4.269A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
    Processing helix  chain 'A' and resid 263 through 280
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 298 through 323
      removed outlier: 3.872A  pdb=" N   TYR A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL A 321 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 375
      removed outlier: 3.692A  pdb=" N   ALA A 352 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   CYS A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.549A  pdb=" N   LEU A 392 " --> pdb=" O   HIS A 389 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TYR A 393 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 389 through 393'
    Processing helix  chain 'A' and resid 394 through 404
      removed outlier: 3.670A  pdb=" N   THR A 398 " --> pdb=" O   PRO A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 444 through 450
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 4.763A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 506
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 4.738A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 551
      removed outlier: 4.060A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 574
    Processing helix  chain 'A' and resid 576 through 585
      removed outlier: 3.696A  pdb=" N   SER A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 632
      removed outlier: 4.082A  pdb=" N   THR A 632 " --> pdb=" O   LEU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 666
    Processing helix  chain 'A' and resid 833 through 845
    Processing helix  chain 'A' and resid 862 through 872
      removed outlier: 3.830A  pdb=" N   LEU A 866 " --> pdb=" O   ALA A 862 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLY A 872 " --> pdb=" O   LYS A 868 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640
      removed outlier: 6.078A  pdb=" N   LEU B 637 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER B 651 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU B 639 " --> pdb=" O   LEU B 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853
      removed outlier: 5.978A  pdb=" N   ALA B 849 " --> pdb=" O   VAL B 860 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL B 860 " --> pdb=" O   ALA B 849 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 851 " --> pdb=" O   ARG B 858 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512
    Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640
      removed outlier: 6.020A  pdb=" N   LEU A 637 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER A 651 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU A 639 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853
      removed outlier: 5.979A  pdb=" N   ALA A 849 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL A 860 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL A 851 " --> pdb=" O   ARG A 858 " (cutoff:3.500A)

    561 hydrogen bonds defined for protein.
    1629 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: 2.56

  Time building geometry restraints manager: 2.62 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: 2735
        1.34 -     1.46: 2230
        1.46 -     1.58: 4384
        1.58 -     1.70: 2
        1.70 -     1.82: 116
  Bond restraints: 9467
  Sorted by residual:
  bond pdb=" CB  MET B 414 "
       pdb=" CG  MET B 414 "
    ideal  model  delta    sigma   weight residual
    1.520  1.389  0.131 3.00e-02 1.11e+03 1.91e+01
  bond pdb=" CB  TYR A 302 "
       pdb=" CG  TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.512  1.429  0.083 2.20e-02 2.07e+03 1.42e+01
  bond pdb=" CG  TYR A 302 "
       pdb=" CD1 TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.389  1.320  0.069 2.10e-02 2.27e+03 1.07e+01
  bond pdb=" CE1 TYR A 302 "
       pdb=" CZ  TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.378  1.304  0.074 2.40e-02 1.74e+03 9.49e+00
  bond pdb=" CD1 TYR A 302 "
       pdb=" CE1 TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.382  1.291  0.091 3.00e-02 1.11e+03 9.26e+00
  ... (remaining 9462 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.26: 12470
        4.26 -     8.53: 320
        8.53 -    12.79: 53
       12.79 -    17.05: 15
       17.05 -    21.31: 3
  Bond angle restraints: 12861
  Sorted by residual:
  angle pdb=" C   TYR B 589 "
        pdb=" N   LEU B 593 "
        pdb=" CA  LEU B 593 "
      ideal   model   delta    sigma   weight residual
     121.70  135.34  -13.64 1.80e+00 3.09e-01 5.74e+01
  angle pdb=" C   TYR A 589 "
        pdb=" N   LEU A 593 "
        pdb=" CA  LEU A 593 "
      ideal   model   delta    sigma   weight residual
     121.70  135.33  -13.63 1.80e+00 3.09e-01 5.73e+01
  angle pdb=" CA  TRP A 469 "
        pdb=" CB  TRP A 469 "
        pdb=" CG  TRP A 469 "
      ideal   model   delta    sigma   weight residual
     113.60  127.33  -13.73 1.90e+00 2.77e-01 5.22e+01
  angle pdb=" CA  TYR B 589 "
        pdb=" C   TYR B 589 "
        pdb=" N   LEU B 593 "
      ideal   model   delta    sigma   weight residual
     116.84  128.50  -11.66 1.71e+00 3.42e-01 4.65e+01
  angle pdb=" CA  TYR A 589 "
        pdb=" C   TYR A 589 "
        pdb=" N   LEU A 593 "
      ideal   model   delta    sigma   weight residual
     116.84  128.38  -11.54 1.71e+00 3.42e-01 4.55e+01
  ... (remaining 12856 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.51: 4914
       14.51 -    29.02: 466
       29.02 -    43.53: 120
       43.53 -    58.04: 23
       58.04 -    72.55: 4
  Dihedral angle restraints: 5527
    sinusoidal: 2104
      harmonic: 3423
  Sorted by residual:
  dihedral pdb=" CA  LYS A 324 "
           pdb=" C   LYS A 324 "
           pdb=" N   ASP A 325 "
           pdb=" CA  ASP A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.16  -42.84     0      5.00e+00 4.00e-02 7.34e+01
  dihedral pdb=" CA  LYS B 324 "
           pdb=" C   LYS B 324 "
           pdb=" N   ASP B 325 "
           pdb=" CA  ASP B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.26  -42.74     0      5.00e+00 4.00e-02 7.31e+01
  dihedral pdb=" CA  ARG B 670 "
           pdb=" C   ARG B 670 "
           pdb=" N   LEU B 671 "
           pdb=" CA  LEU B 671 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.73  -42.27     0      5.00e+00 4.00e-02 7.15e+01
  ... (remaining 5524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1183
       0.094 -    0.188: 270
       0.188 -    0.282: 47
       0.282 -    0.377: 9
       0.377 -    0.471: 10
  Chirality restraints: 1519
  Sorted by residual:
  chirality pdb=" CG  LEU B 671 "
            pdb=" CB  LEU B 671 "
            pdb=" CD1 LEU B 671 "
            pdb=" CD2 LEU B 671 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.12   -0.47 2.00e-01 2.50e+01 5.54e+00
  chirality pdb=" CA  PHE B 488 "
            pdb=" N   PHE B 488 "
            pdb=" C   PHE B 488 "
            pdb=" CB  PHE B 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.25e+00
  chirality pdb=" CG  LEU A 671 "
            pdb=" CB  LEU A 671 "
            pdb=" CD1 LEU A 671 "
            pdb=" CD2 LEU A 671 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.15   -0.44 2.00e-01 2.50e+01 4.83e+00
  ... (remaining 1516 not shown)

  Planarity restraints: 1573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 517 "    0.068 2.00e-02 2.50e+03   5.24e-02 5.49e+01
        pdb=" CG  TYR B 517 "   -0.127 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 517 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 517 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 517 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 517 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 517 "    0.026 2.00e-02 2.50e+03
        pdb=" OH  TYR B 517 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 517 "    0.068 2.00e-02 2.50e+03   5.22e-02 5.46e+01
        pdb=" CG  TYR A 517 "   -0.126 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 517 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 517 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 517 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 517 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 517 "    0.027 2.00e-02 2.50e+03
        pdb=" OH  TYR A 517 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 469 "   -0.056 2.00e-02 2.50e+03   4.11e-02 4.22e+01
        pdb=" CG  TRP A 469 "    0.110 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 469 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 469 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 469 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 469 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 469 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 469 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 469 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 469 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1570 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 535
        2.70 -     3.25: 9654
        3.25 -     3.80: 15800
        3.80 -     4.35: 18494
        4.35 -     4.90: 29057
  Nonbonded interactions: 73540
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 302 "
            pdb=" O   GLU A 291 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   ILE B 401 "
            pdb=" OG1 THR B 405 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" O   CYS A 179 "
            pdb=" OG  SER A 183 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   CYS B 179 "
            pdb=" OG  SER B 183 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   CYS A 546 "
            pdb=" OG1 THR A 550 "
     model   vdw
     2.227 3.040
  ... (remaining 73535 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 115 through 671 or resid 819 through 872))
  selection = (chain 'B' and (resid 115 through 671 or resid 819 through 872))
}

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:             2.750
  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:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.950
  Find NCS groups from input model:        0.370
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
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      :  0.010   0.131   9467  Z= 0.438
  Angle     :  1.720  21.313  12861  Z= 0.891
  Chirality :  0.090   0.471   1519
  Planarity :  0.012   0.073   1573
  Dihedral  : 12.748  72.553   3325
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 10.28 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  :  8.91 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.73 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 1.59 %

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: -4.45 (0.19), residues: 1177
  helix: -2.20 (0.15), residues: 740
  sheet: -3.20 (0.60), residues: 44
  loop : -4.22 (0.23), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.110   0.008   TRP A 469 
 HIS   0.017   0.003   HIS A 555 
 PHE   0.073   0.006   PHE B 341 
 TYR   0.127   0.007   TYR B 517 
 ARG   0.017   0.001   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16569 (  561)
  hydrogen bonds       : angle       7.28631 ( 1629)
  covalent geometry    : bond        0.00957 ( 9467)
  covalent geometry    : angle       1.71980 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 243
  time to evaluate  : 0.951 
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: symmetry clash
REVERT: B  169 LEU cc_start: 0.9691 (mt) cc_final: 0.9371 (mt)
REVERT: B  267 LEU cc_start: 0.9701 (mp) cc_final: 0.9500 (tt)
REVERT: B  307 PHE cc_start: 0.9541 (t80) cc_final: 0.9098 (t80)
REVERT: B  417 GLU cc_start: 0.9011 (tt0) cc_final: 0.8712 (tm-30)
REVERT: B  464 PHE cc_start: 0.9589 (t80) cc_final: 0.9352 (t80)
REVERT: B  559 MET cc_start: 0.9560 (ptp) cc_final: 0.9270 (ptm)
REVERT: B  565 LEU cc_start: 0.9672 (mt) cc_final: 0.9365 (tt)
REVERT: B  660 LEU cc_start: 0.9761 (tt) cc_final: 0.9554 (mt)
REVERT: B  854 MET cc_start: 0.8638 (tmm) cc_final: 0.8354 (tmm)
REVERT: A  128 MET cc_start: 0.9708 (tpp) cc_final: 0.9052 (tpp)
REVERT: A  143 LEU cc_start: 0.9459 (tp) cc_final: 0.9067 (tp)
REVERT: A  399 PHE cc_start: 0.8710 (m-80) cc_final: 0.8463 (m-80)
REVERT: A  417 GLU cc_start: 0.9197 (tt0) cc_final: 0.8670 (tm-30)
REVERT: A  419 MET cc_start: 0.9507 (mmp) cc_final: 0.9178 (mmt)
REVERT: A  466 MET cc_start: 0.9174 (tpt) cc_final: 0.8961 (tpt)
REVERT: A  473 VAL cc_start: 0.9609 (p) cc_final: 0.9392 (m)
REVERT: A  488 PHE cc_start: 0.9396 (m-10) cc_final: 0.9189 (m-10)
REVERT: A  559 MET cc_start: 0.9558 (ptp) cc_final: 0.9253 (ptm)
REVERT: A  564 ILE cc_start: 0.9757 (mm) cc_final: 0.9505 (mm)
REVERT: A  565 LEU cc_start: 0.9633 (mt) cc_final: 0.9215 (tt)
REVERT: A  854 MET cc_start: 0.8894 (tmm) cc_final: 0.8600 (tmm)
  outliers start: 31
  outliers final: 9
  residues processed: 265
  average time/residue: 0.1886
  time to fit residues: 70.6561
Evaluate side-chains
  165 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 156
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 47 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
B 823 GLN
A 379 HIS
A 823 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.060431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.047502 restraints weight = 56580.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.048871 restraints weight = 37490.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.049839 restraints weight = 27562.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9467  Z= 0.190
  Angle     :  0.927   9.955  12861  Z= 0.484
  Chirality :  0.051   0.228   1519
  Planarity :  0.006   0.051   1573
  Dihedral  :  8.020  55.729   1260
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.11 %
    Favored  : 93.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.80 %

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: -2.61 (0.22), residues: 1177
  helix: -0.60 (0.17), residues: 758
  sheet: -2.93 (0.61), residues: 44
  loop : -3.92 (0.27), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 469 
 HIS   0.005   0.001   HIS B 369 
 PHE   0.059   0.003   PHE B 488 
 TYR   0.023   0.002   TYR A 517 
 ARG   0.007   0.001   ARG A 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05836 (  561)
  hydrogen bonds       : angle       5.51215 ( 1629)
  covalent geometry    : bond        0.00396 ( 9467)
  covalent geometry    : angle       0.92706 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 207
  time to evaluate  : 0.939 
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: B  246 LEU cc_start: 0.9520 (tp) cc_final: 0.9201 (mt)
REVERT: B  250 MET cc_start: 0.9230 (tmm) cc_final: 0.8930 (tmm)
REVERT: B  267 LEU cc_start: 0.9734 (mp) cc_final: 0.9479 (tp)
REVERT: B  307 PHE cc_start: 0.9418 (t80) cc_final: 0.9201 (t80)
REVERT: B  410 MET cc_start: 0.9519 (tpt) cc_final: 0.9189 (tpp)
REVERT: B  414 MET cc_start: 0.9305 (tmm) cc_final: 0.9022 (tmm)
REVERT: B  417 GLU cc_start: 0.8972 (tt0) cc_final: 0.8588 (tm-30)
REVERT: B  429 ASP cc_start: 0.8997 (t70) cc_final: 0.8429 (p0)
REVERT: B  470 MET cc_start: 0.8744 (ppp) cc_final: 0.8513 (ppp)
REVERT: B  548 GLU cc_start: 0.8714 (pp20) cc_final: 0.8277 (pp20)
REVERT: B  559 MET cc_start: 0.9384 (ptp) cc_final: 0.9129 (ptm)
REVERT: B  565 LEU cc_start: 0.9611 (mt) cc_final: 0.9250 (tt)
REVERT: B  609 MET cc_start: 0.9051 (mmp) cc_final: 0.8410 (mmp)
REVERT: B  646 MET cc_start: 0.9521 (mmp) cc_final: 0.9233 (mmm)
REVERT: A  235 PHE cc_start: 0.8722 (t80) cc_final: 0.7849 (t80)
REVERT: A  250 MET cc_start: 0.9146 (tmm) cc_final: 0.8774 (tmm)
REVERT: A  399 PHE cc_start: 0.8917 (m-80) cc_final: 0.8284 (m-80)
REVERT: A  410 MET cc_start: 0.9493 (tpt) cc_final: 0.9069 (tpp)
REVERT: A  449 TRP cc_start: 0.9173 (m100) cc_final: 0.8965 (m100)
REVERT: A  488 PHE cc_start: 0.9221 (m-10) cc_final: 0.8502 (m-10)
REVERT: A  559 MET cc_start: 0.9440 (ptp) cc_final: 0.9240 (ptm)
REVERT: A  565 LEU cc_start: 0.9612 (mt) cc_final: 0.9243 (tt)
REVERT: A  609 MET cc_start: 0.9034 (mmp) cc_final: 0.8300 (mmp)
REVERT: A  646 MET cc_start: 0.9493 (mmp) cc_final: 0.9175 (mtt)
REVERT: A  854 MET cc_start: 0.8725 (tmm) cc_final: 0.8453 (tmm)
  outliers start: 4
  outliers final: 1
  residues processed: 210
  average time/residue: 0.1714
  time to fit residues: 52.8048
Evaluate side-chains
  158 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 85 optimal weight:    0.3980
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN
B 369 HIS
B 567 ASN
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 369 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.060215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.047273 restraints weight = 58675.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.048653 restraints weight = 39173.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.049610 restraints weight = 28875.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9467  Z= 0.192
  Angle     :  0.887  10.740  12861  Z= 0.462
  Chirality :  0.049   0.288   1519
  Planarity :  0.005   0.042   1573
  Dihedral  :  7.577  56.457   1260
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  6.21 %
    Favored  : 93.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

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: -1.71 (0.23), residues: 1177
  helix:  0.13 (0.18), residues: 756
  sheet: -2.78 (0.79), residues: 34
  loop : -3.60 (0.28), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 469 
 HIS   0.006   0.002   HIS B 379 
 PHE   0.049   0.003   PHE B 488 
 TYR   0.019   0.002   TYR A 517 
 ARG   0.005   0.001   ARG A 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05283 (  561)
  hydrogen bonds       : angle       5.25237 ( 1629)
  covalent geometry    : bond        0.00402 ( 9467)
  covalent geometry    : angle       0.88665 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 197
  time to evaluate  : 1.361 
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: B  127 LEU cc_start: 0.9616 (pp) cc_final: 0.9117 (pp)
REVERT: B  128 MET cc_start: 0.9594 (mmt) cc_final: 0.9305 (mmm)
REVERT: B  250 MET cc_start: 0.9196 (tmm) cc_final: 0.8959 (tmm)
REVERT: B  267 LEU cc_start: 0.9734 (mp) cc_final: 0.9485 (tt)
REVERT: B  307 PHE cc_start: 0.9429 (t80) cc_final: 0.9150 (t80)
REVERT: B  410 MET cc_start: 0.9471 (tpt) cc_final: 0.9095 (tpp)
REVERT: B  559 MET cc_start: 0.9395 (ptp) cc_final: 0.9174 (ptm)
REVERT: B  565 LEU cc_start: 0.9581 (mt) cc_final: 0.9202 (tt)
REVERT: B  609 MET cc_start: 0.9115 (mmp) cc_final: 0.8564 (mmp)
REVERT: B  646 MET cc_start: 0.9532 (mmp) cc_final: 0.9247 (mmm)
REVERT: B  854 MET cc_start: 0.8533 (tmm) cc_final: 0.8309 (tmm)
REVERT: A  128 MET cc_start: 0.9360 (mtm) cc_final: 0.9053 (mtp)
REVERT: A  143 LEU cc_start: 0.9275 (tp) cc_final: 0.8920 (pp)
REVERT: A  235 PHE cc_start: 0.8896 (t80) cc_final: 0.7975 (t80)
REVERT: A  339 MET cc_start: 0.8747 (pmm) cc_final: 0.8385 (pmm)
REVERT: A  399 PHE cc_start: 0.8926 (m-80) cc_final: 0.8303 (m-80)
REVERT: A  400 VAL cc_start: 0.9729 (p) cc_final: 0.9468 (p)
REVERT: A  410 MET cc_start: 0.9442 (tpt) cc_final: 0.9084 (tpp)
REVERT: A  548 GLU cc_start: 0.8621 (pp20) cc_final: 0.8176 (pp20)
REVERT: A  559 MET cc_start: 0.9486 (ptp) cc_final: 0.9285 (ptm)
REVERT: A  609 MET cc_start: 0.9378 (mmp) cc_final: 0.8694 (mmp)
REVERT: A  646 MET cc_start: 0.9505 (mmp) cc_final: 0.9179 (mtp)
  outliers start: 3
  outliers final: 2
  residues processed: 200
  average time/residue: 0.1695
  time to fit residues: 50.7645
Evaluate side-chains
  153 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 64 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 114 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 94 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.059990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.047293 restraints weight = 59288.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.048677 restraints weight = 39072.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.049546 restraints weight = 28465.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9467  Z= 0.178
  Angle     :  0.869  10.761  12861  Z= 0.445
  Chirality :  0.049   0.424   1519
  Planarity :  0.005   0.041   1573
  Dihedral  :  7.203  53.766   1260
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  4.70 %
    Favored  : 94.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.24), residues: 1177
  helix:  0.48 (0.18), residues: 763
  sheet: -2.47 (0.74), residues: 44
  loop : -3.64 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 469 
 HIS   0.006   0.001   HIS A 538 
 PHE   0.044   0.002   PHE B 488 
 TYR   0.056   0.003   TYR A 589 
 ARG   0.004   0.000   ARG B 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 (  561)
  hydrogen bonds       : angle       5.04471 ( 1629)
  covalent geometry    : bond        0.00376 ( 9467)
  covalent geometry    : angle       0.86908 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 194
  time to evaluate  : 1.035 
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: B  128 MET cc_start: 0.9575 (mmt) cc_final: 0.9350 (mmm)
REVERT: B  143 LEU cc_start: 0.9259 (tp) cc_final: 0.8960 (pp)
REVERT: B  174 PHE cc_start: 0.9507 (m-10) cc_final: 0.9252 (m-80)
REVERT: B  250 MET cc_start: 0.9232 (tmm) cc_final: 0.9008 (tmm)
REVERT: B  267 LEU cc_start: 0.9754 (mp) cc_final: 0.9500 (tp)
REVERT: B  307 PHE cc_start: 0.9444 (t80) cc_final: 0.9158 (t80)
REVERT: B  339 MET cc_start: 0.8864 (ptp) cc_final: 0.8483 (ptp)
REVERT: B  373 MET cc_start: 0.9009 (mmp) cc_final: 0.8635 (mtp)
REVERT: B  374 LEU cc_start: 0.9053 (tp) cc_final: 0.8846 (mt)
REVERT: B  410 MET cc_start: 0.9448 (tpt) cc_final: 0.8987 (tpp)
REVERT: B  559 MET cc_start: 0.9396 (ptp) cc_final: 0.9196 (ptm)
REVERT: B  609 MET cc_start: 0.9212 (mmp) cc_final: 0.8810 (mmp)
REVERT: B  646 MET cc_start: 0.9597 (mmp) cc_final: 0.9318 (mmm)
REVERT: A  128 MET cc_start: 0.9259 (mtm) cc_final: 0.8900 (mtp)
REVERT: A  164 TRP cc_start: 0.9587 (t-100) cc_final: 0.9360 (t-100)
REVERT: A  174 PHE cc_start: 0.9352 (m-80) cc_final: 0.9085 (m-80)
REVERT: A  235 PHE cc_start: 0.8839 (t80) cc_final: 0.7912 (t80)
REVERT: A  339 MET cc_start: 0.8885 (pmm) cc_final: 0.8475 (pmm)
REVERT: A  399 PHE cc_start: 0.8908 (m-80) cc_final: 0.8270 (m-80)
REVERT: A  400 VAL cc_start: 0.9745 (p) cc_final: 0.9480 (p)
REVERT: A  410 MET cc_start: 0.9429 (tpt) cc_final: 0.9082 (tpp)
REVERT: A  609 MET cc_start: 0.9384 (mmp) cc_final: 0.8779 (mmp)
REVERT: A  646 MET cc_start: 0.9567 (mmp) cc_final: 0.9250 (mtp)
  outliers start: 4
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1697
  time to fit residues: 50.0257
Evaluate side-chains
  147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0170
   chunk 11 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 116 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
B 567 ASN
B 827 GLN
A 379 HIS
** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.062180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.049178 restraints weight = 56871.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.050643 restraints weight = 37584.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.051652 restraints weight = 27380.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9467  Z= 0.155
  Angle     :  0.856  10.191  12861  Z= 0.431
  Chirality :  0.048   0.173   1519
  Planarity :  0.005   0.067   1573
  Dihedral  :  6.813  45.922   1260
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.30 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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: -0.97 (0.24), residues: 1177
  helix:  0.79 (0.18), residues: 765
  sheet: -2.34 (0.75), residues: 44
  loop : -3.66 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 164 
 HIS   0.003   0.001   HIS A 538 
 PHE   0.046   0.002   PHE B 488 
 TYR   0.029   0.002   TYR A 589 
 ARG   0.002   0.000   ARG B 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04553 (  561)
  hydrogen bonds       : angle       4.87264 ( 1629)
  covalent geometry    : bond        0.00319 ( 9467)
  covalent geometry    : angle       0.85642 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9531 (mmt) cc_final: 0.9224 (mtp)
REVERT: B  143 LEU cc_start: 0.9216 (tp) cc_final: 0.8956 (pp)
REVERT: B  174 PHE cc_start: 0.9536 (m-10) cc_final: 0.9289 (m-80)
REVERT: B  250 MET cc_start: 0.9211 (tmm) cc_final: 0.8990 (tmm)
REVERT: B  267 LEU cc_start: 0.9746 (mp) cc_final: 0.9527 (tp)
REVERT: B  273 VAL cc_start: 0.9530 (p) cc_final: 0.9180 (m)
REVERT: B  307 PHE cc_start: 0.9442 (t80) cc_final: 0.9145 (t80)
REVERT: B  339 MET cc_start: 0.8782 (ptp) cc_final: 0.8444 (ptp)
REVERT: B  373 MET cc_start: 0.8932 (mmp) cc_final: 0.8664 (mtp)
REVERT: B  374 LEU cc_start: 0.9046 (tp) cc_final: 0.8816 (mt)
REVERT: B  399 PHE cc_start: 0.8996 (m-80) cc_final: 0.8480 (m-80)
REVERT: B  410 MET cc_start: 0.9387 (tpt) cc_final: 0.9080 (tpp)
REVERT: B  470 MET cc_start: 0.8770 (ppp) cc_final: 0.8549 (ppp)
REVERT: B  560 MET cc_start: 0.9205 (mpp) cc_final: 0.8933 (mpp)
REVERT: B  567 ASN cc_start: 0.9346 (OUTLIER) cc_final: 0.9023 (m-40)
REVERT: B  609 MET cc_start: 0.9172 (mmp) cc_final: 0.8745 (mmp)
REVERT: B  646 MET cc_start: 0.9583 (mmp) cc_final: 0.9285 (mmm)
REVERT: B  854 MET cc_start: 0.8567 (tmm) cc_final: 0.8359 (tmm)
REVERT: A  128 MET cc_start: 0.9272 (mtm) cc_final: 0.8846 (mtp)
REVERT: A  164 TRP cc_start: 0.9535 (t-100) cc_final: 0.9318 (t-100)
REVERT: A  174 PHE cc_start: 0.9331 (m-80) cc_final: 0.9115 (m-80)
REVERT: A  235 PHE cc_start: 0.8682 (t80) cc_final: 0.7695 (t80)
REVERT: A  339 MET cc_start: 0.8855 (pmm) cc_final: 0.8477 (pmm)
REVERT: A  399 PHE cc_start: 0.8866 (m-80) cc_final: 0.8276 (m-80)
REVERT: A  400 VAL cc_start: 0.9766 (p) cc_final: 0.9519 (p)
REVERT: A  410 MET cc_start: 0.9329 (tpt) cc_final: 0.8955 (tpp)
REVERT: A  609 MET cc_start: 0.9279 (mmp) cc_final: 0.8792 (mmp)
REVERT: A  646 MET cc_start: 0.9561 (mmp) cc_final: 0.9239 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1683
  time to fit residues: 48.8864
Evaluate side-chains
  146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 89 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0770
   chunk 3 optimal weight:    6.9990
   chunk 113 optimal weight:    0.0870
   overall best weight:    0.3294

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

Flipped N/Q/H residues before XYZ refinement:
B 451 HIS
A 369 HIS
A 451 HIS
** A 867 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.062998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.050214 restraints weight = 55366.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.051645 restraints weight = 37194.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.052550 restraints weight = 27481.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9467  Z= 0.152
  Angle     :  0.853   9.914  12861  Z= 0.425
  Chirality :  0.047   0.179   1519
  Planarity :  0.005   0.061   1573
  Dihedral  :  6.484  39.553   1260
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.07 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.90 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -0.72 (0.25), residues: 1177
  helix:  0.97 (0.19), residues: 767
  sheet: -2.26 (0.87), residues: 34
  loop : -3.53 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 469 
 HIS   0.003   0.001   HIS A 451 
 PHE   0.052   0.002   PHE B 488 
 TYR   0.020   0.002   TYR A 589 
 ARG   0.003   0.000   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04417 (  561)
  hydrogen bonds       : angle       4.80275 ( 1629)
  covalent geometry    : bond        0.00315 ( 9467)
  covalent geometry    : angle       0.85332 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9555 (mmt) cc_final: 0.9340 (mtt)
REVERT: B  143 LEU cc_start: 0.9286 (tp) cc_final: 0.8956 (pp)
REVERT: B  174 PHE cc_start: 0.9548 (m-10) cc_final: 0.9311 (m-80)
REVERT: B  191 ILE cc_start: 0.9721 (pt) cc_final: 0.9356 (pt)
REVERT: B  267 LEU cc_start: 0.9708 (mp) cc_final: 0.9504 (tt)
REVERT: B  307 PHE cc_start: 0.9459 (t80) cc_final: 0.8657 (t80)
REVERT: B  399 PHE cc_start: 0.8990 (m-80) cc_final: 0.8467 (m-80)
REVERT: B  410 MET cc_start: 0.9364 (tpt) cc_final: 0.9029 (tpp)
REVERT: B  470 MET cc_start: 0.8807 (ppp) cc_final: 0.8487 (ppp)
REVERT: B  609 MET cc_start: 0.9194 (mmp) cc_final: 0.8815 (mmp)
REVERT: B  646 MET cc_start: 0.9553 (mmp) cc_final: 0.9246 (mmm)
REVERT: B  868 LYS cc_start: 0.9664 (tmtt) cc_final: 0.9448 (tptp)
REVERT: A  128 MET cc_start: 0.9240 (mtm) cc_final: 0.8802 (mtp)
REVERT: A  174 PHE cc_start: 0.9332 (m-80) cc_final: 0.9117 (m-80)
REVERT: A  181 LEU cc_start: 0.8356 (mm) cc_final: 0.8003 (mt)
REVERT: A  235 PHE cc_start: 0.8546 (t80) cc_final: 0.7500 (t80)
REVERT: A  399 PHE cc_start: 0.8872 (m-80) cc_final: 0.8338 (m-80)
REVERT: A  410 MET cc_start: 0.9285 (tpt) cc_final: 0.8926 (tpp)
REVERT: A  560 MET cc_start: 0.9561 (mtm) cc_final: 0.9352 (mtp)
REVERT: A  609 MET cc_start: 0.9256 (mmp) cc_final: 0.8749 (mmp)
REVERT: A  646 MET cc_start: 0.9536 (mmp) cc_final: 0.9203 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 195
  average time/residue: 0.1592
  time to fit residues: 46.6509
Evaluate side-chains
  142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 110 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 98 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
A 369 HIS
A 838 HIS
** A 867 GLN ** 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 = 0.3349 r_free = 0.3349 target = 0.061730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.048983 restraints weight = 58873.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.050354 restraints weight = 39439.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.051368 restraints weight = 29061.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9467  Z= 0.179
  Angle     :  0.867  12.620  12861  Z= 0.441
  Chirality :  0.047   0.177   1519
  Planarity :  0.005   0.049   1573
  Dihedral  :  6.526  43.789   1260
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.61 (0.25), residues: 1177
  helix:  1.05 (0.19), residues: 766
  sheet: -2.24 (0.85), residues: 34
  loop : -3.45 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 164 
 HIS   0.004   0.001   HIS A 369 
 PHE   0.048   0.002   PHE B 488 
 TYR   0.073   0.003   TYR B 589 
 ARG   0.002   0.000   ARG A 626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  561)
  hydrogen bonds       : angle       4.84783 ( 1629)
  covalent geometry    : bond        0.00386 ( 9467)
  covalent geometry    : angle       0.86671 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.948 
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: B  143 LEU cc_start: 0.9284 (tp) cc_final: 0.9002 (pp)
REVERT: B  174 PHE cc_start: 0.9540 (m-10) cc_final: 0.9297 (m-80)
REVERT: B  246 LEU cc_start: 0.9347 (tp) cc_final: 0.9128 (tp)
REVERT: B  267 LEU cc_start: 0.9737 (mp) cc_final: 0.9526 (tt)
REVERT: B  399 PHE cc_start: 0.9028 (m-80) cc_final: 0.8479 (m-80)
REVERT: B  410 MET cc_start: 0.9344 (tpt) cc_final: 0.9091 (tpp)
REVERT: B  559 MET cc_start: 0.9658 (ttp) cc_final: 0.9347 (ptm)
REVERT: B  560 MET cc_start: 0.9293 (mpp) cc_final: 0.8931 (mpp)
REVERT: B  609 MET cc_start: 0.9166 (mmp) cc_final: 0.8849 (mmp)
REVERT: B  646 MET cc_start: 0.9563 (mmp) cc_final: 0.9289 (mmm)
REVERT: A  128 MET cc_start: 0.9279 (mtm) cc_final: 0.8874 (mtp)
REVERT: A  181 LEU cc_start: 0.8418 (mm) cc_final: 0.8056 (mt)
REVERT: A  399 PHE cc_start: 0.8886 (m-80) cc_final: 0.8330 (m-80)
REVERT: A  410 MET cc_start: 0.9354 (tpt) cc_final: 0.9025 (tpp)
REVERT: A  560 MET cc_start: 0.9580 (mtm) cc_final: 0.9376 (mtm)
REVERT: A  609 MET cc_start: 0.9293 (mmp) cc_final: 0.8770 (mmp)
REVERT: A  646 MET cc_start: 0.9555 (mmp) cc_final: 0.9233 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1579
  time to fit residues: 43.1271
Evaluate side-chains
  135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 109 optimal weight:    0.0170
   chunk 88 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 46 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
A 369 HIS
** A 867 GLN ** 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 = 0.3378 r_free = 0.3378 target = 0.063067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.050074 restraints weight = 57740.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.051524 restraints weight = 38556.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.052486 restraints weight = 28457.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.5155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9467  Z= 0.151
  Angle     :  0.888  11.998  12861  Z= 0.437
  Chirality :  0.047   0.181   1519
  Planarity :  0.005   0.049   1573
  Dihedral  :  6.284  34.935   1260
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.49 (0.25), residues: 1177
  helix:  1.09 (0.19), residues: 771
  sheet: -2.36 (1.01), residues: 24
  loop : -3.29 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 469 
 HIS   0.003   0.001   HIS A 369 
 PHE   0.050   0.002   PHE B 488 
 TYR   0.054   0.002   TYR B 589 
 ARG   0.004   0.000   ARG A 611 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04353 (  561)
  hydrogen bonds       : angle       4.81251 ( 1629)
  covalent geometry    : bond        0.00320 ( 9467)
  covalent geometry    : angle       0.88795 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.958 
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: B  128 MET cc_start: 0.9208 (mtm) cc_final: 0.8948 (mtt)
REVERT: B  143 LEU cc_start: 0.9275 (tp) cc_final: 0.8957 (pp)
REVERT: B  174 PHE cc_start: 0.9542 (m-10) cc_final: 0.9298 (m-80)
REVERT: B  194 MET cc_start: 0.9256 (ptp) cc_final: 0.9034 (ptp)
REVERT: B  246 LEU cc_start: 0.9330 (tp) cc_final: 0.9093 (tp)
REVERT: B  250 MET cc_start: 0.8554 (mmp) cc_final: 0.8345 (mmm)
REVERT: B  267 LEU cc_start: 0.9753 (mp) cc_final: 0.9544 (tt)
REVERT: B  307 PHE cc_start: 0.9308 (t80) cc_final: 0.9076 (t80)
REVERT: B  399 PHE cc_start: 0.8985 (m-80) cc_final: 0.8447 (m-80)
REVERT: B  410 MET cc_start: 0.9337 (tpt) cc_final: 0.9017 (tpp)
REVERT: B  414 MET cc_start: 0.9283 (tmm) cc_final: 0.8916 (tmm)
REVERT: B  449 TRP cc_start: 0.8882 (m100) cc_final: 0.8646 (m-10)
REVERT: B  609 MET cc_start: 0.9207 (mmp) cc_final: 0.8540 (mmp)
REVERT: B  646 MET cc_start: 0.9556 (mmp) cc_final: 0.9269 (mmm)
REVERT: A  128 MET cc_start: 0.9224 (mtm) cc_final: 0.8819 (mtp)
REVERT: A  174 PHE cc_start: 0.9333 (m-10) cc_final: 0.9111 (m-80)
REVERT: A  181 LEU cc_start: 0.8323 (mm) cc_final: 0.8081 (mm)
REVERT: A  319 LEU cc_start: 0.9694 (tp) cc_final: 0.9451 (tp)
REVERT: A  399 PHE cc_start: 0.8858 (m-80) cc_final: 0.8316 (m-80)
REVERT: A  410 MET cc_start: 0.9271 (tpt) cc_final: 0.8912 (tpp)
REVERT: A  466 MET cc_start: 0.9331 (tpt) cc_final: 0.9123 (tpt)
REVERT: A  609 MET cc_start: 0.8648 (mmp) cc_final: 0.8314 (mmp)
REVERT: A  646 MET cc_start: 0.9552 (mmp) cc_final: 0.9218 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1651
  time to fit residues: 47.6225
Evaluate side-chains
  141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0970
   chunk 49 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
B 237 HIS
** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 827 GLN
** A 867 GLN ** 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 = 0.3384 r_free = 0.3384 target = 0.063541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.050504 restraints weight = 56855.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.051969 restraints weight = 37677.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052990 restraints weight = 27549.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.5385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9467  Z= 0.149
  Angle     :  0.872  11.321  12861  Z= 0.429
  Chirality :  0.047   0.185   1519
  Planarity :  0.005   0.079   1573
  Dihedral  :  6.163  33.755   1260
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 18.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 (0.25), residues: 1177
  helix:  1.07 (0.19), residues: 772
  sheet: -2.33 (1.02), residues: 24
  loop : -3.33 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 469 
 HIS   0.009   0.001   HIS B 555 
 PHE   0.051   0.002   PHE B 488 
 TYR   0.047   0.002   TYR B 589 
 ARG   0.002   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04289 (  561)
  hydrogen bonds       : angle       4.83228 ( 1629)
  covalent geometry    : bond        0.00324 ( 9467)
  covalent geometry    : angle       0.87202 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9232 (mtm) cc_final: 0.8955 (mtt)
REVERT: B  143 LEU cc_start: 0.9203 (tp) cc_final: 0.8949 (pp)
REVERT: B  174 PHE cc_start: 0.9506 (m-10) cc_final: 0.9273 (m-80)
REVERT: B  246 LEU cc_start: 0.9320 (tp) cc_final: 0.9082 (tp)
REVERT: B  307 PHE cc_start: 0.9172 (t80) cc_final: 0.8781 (t80)
REVERT: B  399 PHE cc_start: 0.8983 (m-80) cc_final: 0.8489 (m-80)
REVERT: B  410 MET cc_start: 0.9249 (tpt) cc_final: 0.9008 (tpp)
REVERT: B  449 TRP cc_start: 0.8964 (m100) cc_final: 0.8720 (m-10)
REVERT: B  470 MET cc_start: 0.8783 (ppp) cc_final: 0.8554 (tmm)
REVERT: B  485 MET cc_start: 0.9246 (mtm) cc_final: 0.8898 (mtp)
REVERT: B  609 MET cc_start: 0.9197 (mmp) cc_final: 0.8779 (mmp)
REVERT: B  646 MET cc_start: 0.9530 (mmp) cc_final: 0.9247 (mmm)
REVERT: A  128 MET cc_start: 0.9232 (mtm) cc_final: 0.8829 (mtp)
REVERT: A  174 PHE cc_start: 0.9299 (m-10) cc_final: 0.9071 (m-80)
REVERT: A  181 LEU cc_start: 0.8254 (mm) cc_final: 0.8008 (mm)
REVERT: A  311 PHE cc_start: 0.9033 (m-80) cc_final: 0.8231 (m-80)
REVERT: A  399 PHE cc_start: 0.8825 (m-80) cc_final: 0.8262 (m-80)
REVERT: A  410 MET cc_start: 0.9191 (tpt) cc_final: 0.8873 (tpp)
REVERT: A  466 MET cc_start: 0.9344 (tpt) cc_final: 0.9001 (tpt)
REVERT: A  560 MET cc_start: 0.9370 (mtm) cc_final: 0.9160 (mpp)
REVERT: A  609 MET cc_start: 0.8658 (mmp) cc_final: 0.8298 (mmp)
REVERT: A  646 MET cc_start: 0.9564 (mmp) cc_final: 0.9224 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1685
  time to fit residues: 48.2851
Evaluate side-chains
  141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 113 optimal weight:    0.0980
   chunk 68 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
** A 867 GLN ** 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 = 0.3392 r_free = 0.3392 target = 0.064038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.051066 restraints weight = 57449.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.052535 restraints weight = 38148.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.053412 restraints weight = 27905.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.5627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9467  Z= 0.149
  Angle     :  0.885  11.228  12861  Z= 0.434
  Chirality :  0.047   0.183   1519
  Planarity :  0.005   0.065   1573
  Dihedral  :  6.001  30.747   1260
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.49 (0.25), residues: 1177
  helix:  1.06 (0.19), residues: 768
  sheet: -2.24 (1.03), residues: 24
  loop : -3.21 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 469 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.047   0.002   PHE B 488 
 TYR   0.046   0.002   TYR B 589 
 ARG   0.005   0.000   ARG B 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04253 (  561)
  hydrogen bonds       : angle       4.86752 ( 1629)
  covalent geometry    : bond        0.00325 ( 9467)
  covalent geometry    : angle       0.88524 (12861)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9315 (mtm) cc_final: 0.9059 (mpp)
REVERT: B  143 LEU cc_start: 0.9136 (tp) cc_final: 0.8928 (pp)
REVERT: B  174 PHE cc_start: 0.9485 (m-10) cc_final: 0.9255 (m-80)
REVERT: B  181 LEU cc_start: 0.8577 (mm) cc_final: 0.8207 (mt)
REVERT: B  246 LEU cc_start: 0.9333 (tp) cc_final: 0.9107 (tp)
REVERT: B  250 MET cc_start: 0.8478 (mmp) cc_final: 0.8270 (mmm)
REVERT: B  307 PHE cc_start: 0.9091 (t80) cc_final: 0.8212 (t80)
REVERT: B  311 PHE cc_start: 0.8693 (m-80) cc_final: 0.8371 (m-80)
REVERT: B  399 PHE cc_start: 0.8967 (m-80) cc_final: 0.8497 (m-80)
REVERT: B  410 MET cc_start: 0.9261 (tpt) cc_final: 0.9005 (tpp)
REVERT: B  414 MET cc_start: 0.9224 (tmm) cc_final: 0.8829 (tmm)
REVERT: B  432 THR cc_start: 0.9477 (p) cc_final: 0.9169 (p)
REVERT: B  470 MET cc_start: 0.8774 (ppp) cc_final: 0.8533 (tmm)
REVERT: B  609 MET cc_start: 0.9152 (mmp) cc_final: 0.8729 (mmp)
REVERT: B  646 MET cc_start: 0.9532 (mmp) cc_final: 0.9247 (mmm)
REVERT: A  128 MET cc_start: 0.9276 (mtm) cc_final: 0.8959 (mtp)
REVERT: A  136 ASP cc_start: 0.8811 (p0) cc_final: 0.8487 (p0)
REVERT: A  174 PHE cc_start: 0.9317 (m-10) cc_final: 0.9087 (m-80)
REVERT: A  181 LEU cc_start: 0.8178 (mm) cc_final: 0.7921 (mm)
REVERT: A  311 PHE cc_start: 0.9014 (m-80) cc_final: 0.8262 (m-80)
REVERT: A  319 LEU cc_start: 0.9660 (tp) cc_final: 0.9372 (tt)
REVERT: A  399 PHE cc_start: 0.8804 (m-80) cc_final: 0.8277 (m-80)
REVERT: A  410 MET cc_start: 0.9172 (tpt) cc_final: 0.8818 (tpp)
REVERT: A  414 MET cc_start: 0.8907 (tmm) cc_final: 0.8655 (tmm)
REVERT: A  432 THR cc_start: 0.9413 (p) cc_final: 0.9080 (p)
REVERT: A  466 MET cc_start: 0.9333 (tpt) cc_final: 0.8968 (tpt)
REVERT: A  470 MET cc_start: 0.8844 (ppp) cc_final: 0.8635 (ppp)
REVERT: A  560 MET cc_start: 0.9398 (mtm) cc_final: 0.9061 (mpp)
REVERT: A  609 MET cc_start: 0.8648 (mmp) cc_final: 0.8270 (mmp)
REVERT: A  646 MET cc_start: 0.9564 (mmp) cc_final: 0.9225 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1635
  time to fit residues: 46.9211
Evaluate side-chains
  144 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 24 optimal weight:    0.4980
   chunk 90 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    0.1980
   chunk 114 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
** A 867 GLN ** 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 = 0.3402 r_free = 0.3402 target = 0.064422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.051207 restraints weight = 57257.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.052724 restraints weight = 38052.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.053824 restraints weight = 27905.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.5786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9467  Z= 0.147
  Angle     :  0.878  11.054  12861  Z= 0.429
  Chirality :  0.047   0.176   1519
  Planarity :  0.005   0.057   1573
  Dihedral  :  5.941  29.458   1260
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    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: -0.47 (0.25), residues: 1177
  helix:  1.03 (0.19), residues: 773
  sheet: -2.08 (1.12), residues: 22
  loop : -3.16 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 469 
 HIS   0.005   0.001   HIS B 555 
 PHE   0.056   0.002   PHE B 488 
 TYR   0.043   0.002   TYR B 589 
 ARG   0.003   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 (  561)
  hydrogen bonds       : angle       4.78939 ( 1629)
  covalent geometry    : bond        0.00320 ( 9467)
  covalent geometry    : angle       0.87808 (12861)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3134.69 seconds
wall clock time: 55 minutes 21.91 seconds (3321.91 seconds total)