Starting phenix.real_space_refine
on Thu Feb 13 20:38:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvb_4646/02_2025/6qvb_4646.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvb_4646/02_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_4646/02_2025/6qvb_4646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvb_4646/02_2025/6qvb_4646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvb_4646/02_2025/6qvb_4646.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvb_4646/02_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-5592/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: 5.80, 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: 2.41
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.87
  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: 2.55

  Time building geometry restraints manager: 2.79 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:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.560
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.710
-------------------------------------------------------------------------------
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= 0.621
  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 

*********************** 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  : 1.030 
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: 0.1989
  time to fit residues: 74.2256
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  : 1.026 
-------------------------------------------------------------------------------
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 = 0.060438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.047505 restraints weight = 56579.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.048875 restraints weight = 37525.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.049846 restraints weight = 27576.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2893

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= 0.256
  Angle     :  0.927   9.958  12861  Z= 0.484
  Chirality :  0.051   0.236   1519
  Planarity :  0.006   0.051   1573
  Dihedral  :  8.017  55.704   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 : -3.91 (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 

*********************** 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
  212 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 208
  time to evaluate  : 1.080 
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: 0.9417 (t80) cc_final: 0.9200 (t80)
REVERT: B  399 PHE cc_start: 0.8790 (m-80) cc_final: 0.8485 (m-10)
REVERT: B  410 MET cc_start: 0.9519 (tpt) cc_final: 0.9188 (tpp)
REVERT: B  414 MET cc_start: 0.9304 (tmm) cc_final: 0.9022 (tmm)
REVERT: B  417 GLU cc_start: 0.8973 (tt0) cc_final: 0.8589 (tm-30)
REVERT: B  429 ASP cc_start: 0.8997 (t70) cc_final: 0.8429 (p0)
REVERT: B  470 MET cc_start: 0.8747 (ppp) cc_final: 0.8513 (ppp)
REVERT: B  548 GLU cc_start: 0.8714 (pp20) cc_final: 0.8278 (pp20)
REVERT: B  559 MET cc_start: 0.9384 (ptp) cc_final: 0.9129 (ptm)
REVERT: B  565 LEU cc_start: 0.9610 (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: 0.8721 (t80) cc_final: 0.7848 (t80)
REVERT: A  250 MET cc_start: 0.9145 (tmm) cc_final: 0.8774 (tmm)
REVERT: A  399 PHE cc_start: 0.8920 (m-80) cc_final: 0.8288 (m-80)
REVERT: A  404 PHE cc_start: 0.8735 (p90) cc_final: 0.8451 (p90)
REVERT: A  410 MET cc_start: 0.9492 (tpt) cc_final: 0.9064 (tpp)
REVERT: A  449 TRP cc_start: 0.9172 (m100) cc_final: 0.8966 (m100)
REVERT: A  466 MET cc_start: 0.9051 (tpt) cc_final: 0.8828 (tpt)
REVERT: A  488 PHE cc_start: 0.9220 (m-10) cc_final: 0.8503 (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: 0.9035 (mmp) cc_final: 0.8299 (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: 211
  average time/residue: 0.1889
  time to fit residues: 58.2966
Evaluate side-chains
  159 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0010
   chunk 89 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
B 369 HIS
B 567 ASN
A 369 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.061421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.048260 restraints weight = 57724.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.049748 restraints weight = 37825.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.050779 restraints weight = 27421.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3395

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= 0.222
  Angle     :  0.879  10.236  12861  Z= 0.453
  Chirality :  0.048   0.222   1519
  Planarity :  0.005   0.043   1573
  Dihedral  :  7.553  57.181   1260
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.80 %
    Favored  : 94.99 %
  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: -1.99 (0.23), residues: 1177
  helix: -0.05 (0.18), residues: 763
  sheet: -2.70 (0.68), residues: 44
  loop : -3.88 (0.27), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 469 
 HIS   0.006   0.001   HIS B 379 
 PHE   0.049   0.002   PHE B 488 
 TYR   0.016   0.002   TYR B 622 
 ARG   0.004   0.000   ARG A 334 

*********************** 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
  208 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 206
  time to evaluate  : 0.969 
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  127 LEU cc_start: 0.9614 (pp) cc_final: 0.9097 (pp)
REVERT: B  128 MET cc_start: 0.9575 (mmt) cc_final: 0.9224 (mmm)
REVERT: B  143 LEU cc_start: 0.9227 (tp) cc_final: 0.8948 (pp)
REVERT: B  223 LEU cc_start: 0.9506 (tp) cc_final: 0.9299 (tp)
REVERT: B  235 PHE cc_start: 0.8955 (t80) cc_final: 0.8075 (t80)
REVERT: B  250 MET cc_start: 0.9206 (tmm) cc_final: 0.8923 (tmm)
REVERT: B  267 LEU cc_start: 0.9725 (mp) cc_final: 0.9458 (tp)
REVERT: B  307 PHE cc_start: 0.9411 (t80) cc_final: 0.9134 (t80)
REVERT: B  410 MET cc_start: 0.9452 (tpt) cc_final: 0.9128 (tpp)
REVERT: B  417 GLU cc_start: 0.9001 (tt0) cc_final: 0.8667 (tm-30)
REVERT: B  560 MET cc_start: 0.9232 (mpp) cc_final: 0.8943 (mpp)
REVERT: B  565 LEU cc_start: 0.9570 (mt) cc_final: 0.9311 (tt)
REVERT: B  609 MET cc_start: 0.9169 (mmp) cc_final: 0.8574 (mmp)
REVERT: B  646 MET cc_start: 0.9546 (mmp) cc_final: 0.9256 (mmm)
REVERT: B  854 MET cc_start: 0.8479 (tmm) cc_final: 0.8262 (tmm)
REVERT: A  128 MET cc_start: 0.9279 (mtm) cc_final: 0.8887 (mtp)
REVERT: A  143 LEU cc_start: 0.9247 (tp) cc_final: 0.8905 (pp)
REVERT: A  164 TRP cc_start: 0.9548 (t-100) cc_final: 0.9190 (t-100)
REVERT: A  235 PHE cc_start: 0.8845 (t80) cc_final: 0.7892 (t80)
REVERT: A  339 MET cc_start: 0.8797 (pmm) cc_final: 0.8405 (pmm)
REVERT: A  399 PHE cc_start: 0.8912 (m-80) cc_final: 0.8307 (m-80)
REVERT: A  410 MET cc_start: 0.9407 (tpt) cc_final: 0.9027 (tpp)
REVERT: A  485 MET cc_start: 0.9427 (mmp) cc_final: 0.9037 (mmm)
REVERT: A  488 PHE cc_start: 0.9196 (m-10) cc_final: 0.8920 (m-10)
REVERT: A  548 GLU cc_start: 0.8594 (pp20) cc_final: 0.8165 (pp20)
REVERT: A  565 LEU cc_start: 0.9571 (mt) cc_final: 0.9220 (tt)
REVERT: A  609 MET cc_start: 0.9372 (mmp) cc_final: 0.8725 (mmp)
REVERT: A  646 MET cc_start: 0.9498 (mmp) cc_final: 0.9157 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 208
  average time/residue: 0.1655
  time to fit residues: 50.9567
Evaluate side-chains
  151 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 94 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN
** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 152 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 = 0.3336 r_free = 0.3336 target = 0.060532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.047752 restraints weight = 58144.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.049176 restraints weight = 37884.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.050235 restraints weight = 27652.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9467  Z= 0.240
  Angle     :  0.866  11.548  12861  Z= 0.446
  Chirality :  0.048   0.200   1519
  Planarity :  0.005   0.040   1573
  Dihedral  :  7.232  53.071   1260
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  5.01 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.09 %
  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: -1.46 (0.24), residues: 1177
  helix:  0.40 (0.18), residues: 761
  sheet: -2.36 (0.75), residues: 44
  loop : -3.77 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 469 
 HIS   0.006   0.001   HIS A 538 
 PHE   0.045   0.002   PHE B 488 
 TYR   0.043   0.003   TYR B 589 
 ARG   0.003   0.000   ARG A 626 

*********************** 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
  204 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 199
  time to evaluate  : 1.051 
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: 0.9581 (mmt) cc_final: 0.9376 (mmm)
REVERT: B  143 LEU cc_start: 0.9256 (tp) cc_final: 0.8957 (pp)
REVERT: B  235 PHE cc_start: 0.8792 (t80) cc_final: 0.8003 (t80)
REVERT: B  250 MET cc_start: 0.9170 (tmm) cc_final: 0.8958 (tmm)
REVERT: B  267 LEU cc_start: 0.9730 (mp) cc_final: 0.9506 (tt)
REVERT: B  307 PHE cc_start: 0.9418 (t80) cc_final: 0.9132 (t80)
REVERT: B  373 MET cc_start: 0.9003 (mmp) cc_final: 0.8661 (mtp)
REVERT: B  410 MET cc_start: 0.9433 (tpt) cc_final: 0.9001 (tpp)
REVERT: B  548 GLU cc_start: 0.8620 (pp20) cc_final: 0.8152 (pp20)
REVERT: B  560 MET cc_start: 0.9253 (mpp) cc_final: 0.9021 (mpp)
REVERT: B  565 LEU cc_start: 0.9540 (mt) cc_final: 0.9230 (tt)
REVERT: B  609 MET cc_start: 0.9231 (mmp) cc_final: 0.8745 (mmp)
REVERT: B  646 MET cc_start: 0.9573 (mmp) cc_final: 0.9275 (mmm)
REVERT: A  128 MET cc_start: 0.9304 (mtm) cc_final: 0.8934 (mtp)
REVERT: A  164 TRP cc_start: 0.9580 (t-100) cc_final: 0.9331 (t-100)
REVERT: A  174 PHE cc_start: 0.9331 (m-80) cc_final: 0.9056 (m-80)
REVERT: A  235 PHE cc_start: 0.8812 (t80) cc_final: 0.7885 (t80)
REVERT: A  339 MET cc_start: 0.8813 (pmm) cc_final: 0.8446 (pmm)
REVERT: A  399 PHE cc_start: 0.8899 (m-80) cc_final: 0.8283 (m-80)
REVERT: A  400 VAL cc_start: 0.9741 (p) cc_final: 0.9492 (p)
REVERT: A  410 MET cc_start: 0.9413 (tpt) cc_final: 0.9058 (tpp)
REVERT: A  417 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8620 (tm-30)
REVERT: A  466 MET cc_start: 0.9349 (tpt) cc_final: 0.9144 (tpt)
REVERT: A  485 MET cc_start: 0.9455 (mmp) cc_final: 0.9150 (mmm)
REVERT: A  488 PHE cc_start: 0.9209 (m-10) cc_final: 0.8963 (m-10)
REVERT: A  548 GLU cc_start: 0.8630 (pp20) cc_final: 0.8200 (pp20)
REVERT: A  609 MET cc_start: 0.9372 (mmp) cc_final: 0.8722 (mmp)
REVERT: A  646 MET cc_start: 0.9515 (mmp) cc_final: 0.9188 (mtp)
  outliers start: 5
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1742
  time to fit residues: 52.5801
Evaluate side-chains
  148 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 35 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0670
   chunk 11 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 116 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9860

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN
B 827 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.061874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.049311 restraints weight = 57792.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.050705 restraints weight = 38473.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.051747 restraints weight = 28167.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9467  Z= 0.212
  Angle     :  0.854  10.268  12861  Z= 0.432
  Chirality :  0.047   0.168   1519
  Planarity :  0.004   0.042   1573
  Dihedral  :  6.853  45.629   1260
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.20 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

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: -1.09 (0.24), residues: 1177
  helix:  0.71 (0.18), residues: 767
  sheet: -2.28 (0.75), residues: 44
  loop : -3.75 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 164 
 HIS   0.004   0.001   HIS A 538 
 PHE   0.047   0.002   PHE B 488 
 TYR   0.029   0.002   TYR A 589 
 ARG   0.003   0.000   ARG A 338 

*********************** 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
  203 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 1.008 
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  127 LEU cc_start: 0.9674 (pp) cc_final: 0.9344 (pp)
REVERT: B  128 MET cc_start: 0.9564 (mmt) cc_final: 0.9326 (mmm)
REVERT: B  143 LEU cc_start: 0.9235 (tp) cc_final: 0.8959 (pp)
REVERT: B  174 PHE cc_start: 0.9494 (m-10) cc_final: 0.9199 (m-80)
REVERT: B  235 PHE cc_start: 0.8753 (t80) cc_final: 0.7968 (t80)
REVERT: B  250 MET cc_start: 0.9199 (tmm) cc_final: 0.8971 (tmm)
REVERT: B  267 LEU cc_start: 0.9732 (mp) cc_final: 0.9528 (tt)
REVERT: B  307 PHE cc_start: 0.9435 (t80) cc_final: 0.9139 (t80)
REVERT: B  373 MET cc_start: 0.8935 (mmp) cc_final: 0.8709 (mtp)
REVERT: B  399 PHE cc_start: 0.8869 (m-80) cc_final: 0.8258 (m-80)
REVERT: B  410 MET cc_start: 0.9412 (tpt) cc_final: 0.9118 (tpp)
REVERT: B  470 MET cc_start: 0.8838 (ppp) cc_final: 0.8536 (tmm)
REVERT: B  565 LEU cc_start: 0.9503 (mt) cc_final: 0.9231 (tt)
REVERT: B  567 ASN cc_start: 0.9364 (OUTLIER) cc_final: 0.9049 (m-40)
REVERT: B  609 MET cc_start: 0.9234 (mmp) cc_final: 0.8741 (mmp)
REVERT: B  646 MET cc_start: 0.9555 (mmp) cc_final: 0.9251 (mmm)
REVERT: A  128 MET cc_start: 0.9281 (mtm) cc_final: 0.8919 (mtp)
REVERT: A  174 PHE cc_start: 0.9305 (m-80) cc_final: 0.9079 (m-80)
REVERT: A  235 PHE cc_start: 0.8694 (t80) cc_final: 0.7723 (t80)
REVERT: A  339 MET cc_start: 0.8909 (pmm) cc_final: 0.8546 (pmm)
REVERT: A  399 PHE cc_start: 0.8910 (m-80) cc_final: 0.8334 (m-80)
REVERT: A  400 VAL cc_start: 0.9750 (p) cc_final: 0.9491 (p)
REVERT: A  410 MET cc_start: 0.9361 (tpt) cc_final: 0.8978 (tpp)
REVERT: A  466 MET cc_start: 0.9251 (tpt) cc_final: 0.9049 (tpt)
REVERT: A  470 MET cc_start: 0.8889 (ppp) cc_final: 0.8629 (ppp)
REVERT: A  485 MET cc_start: 0.9452 (mmp) cc_final: 0.9233 (mmm)
REVERT: A  488 PHE cc_start: 0.9223 (m-10) cc_final: 0.8965 (m-10)
REVERT: A  609 MET cc_start: 0.9303 (mmp) cc_final: 0.8722 (mmp)
REVERT: A  646 MET cc_start: 0.9522 (mmp) cc_final: 0.9205 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 202
  average time/residue: 0.1693
  time to fit residues: 50.6413
Evaluate side-chains
  147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 145
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 36 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0980
   chunk 3 optimal weight:    5.9990
   chunk 113 optimal weight:    0.0970
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
B 451 HIS
A 379 HIS
A 451 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.062879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.050080 restraints weight = 56264.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.051564 restraints weight = 36718.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052477 restraints weight = 26759.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4661

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= 0.209
  Angle     :  0.859   9.864  12861  Z= 0.432
  Chirality :  0.048   0.173   1519
  Planarity :  0.005   0.074   1573
  Dihedral  :  6.552  40.736   1260
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  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: -0.96 (0.25), residues: 1177
  helix:  0.80 (0.19), residues: 770
  sheet: -2.08 (0.76), residues: 44
  loop : -3.75 (0.28), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 164 
 HIS   0.002   0.001   HIS B 664 
 PHE   0.053   0.002   PHE B 488 
 TYR   0.018   0.002   TYR A 589 
 ARG   0.004   0.000   ARG A 300 

*********************** 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
  204 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9564 (mmt) cc_final: 0.9285 (mtt)
REVERT: B  143 LEU cc_start: 0.9202 (tp) cc_final: 0.8924 (pp)
REVERT: B  174 PHE cc_start: 0.9536 (m-10) cc_final: 0.9299 (m-80)
REVERT: B  191 ILE cc_start: 0.9714 (pt) cc_final: 0.9351 (pt)
REVERT: B  250 MET cc_start: 0.9187 (tmm) cc_final: 0.8972 (tmm)
REVERT: B  267 LEU cc_start: 0.9694 (mp) cc_final: 0.9482 (tt)
REVERT: B  307 PHE cc_start: 0.9439 (t80) cc_final: 0.8590 (t80)
REVERT: B  339 MET cc_start: 0.8868 (ptp) cc_final: 0.8501 (ptp)
REVERT: B  399 PHE cc_start: 0.9060 (m-80) cc_final: 0.8499 (m-80)
REVERT: B  410 MET cc_start: 0.9363 (tpt) cc_final: 0.9009 (tpp)
REVERT: B  470 MET cc_start: 0.8793 (ppp) cc_final: 0.8381 (tmm)
REVERT: B  560 MET cc_start: 0.9286 (mpp) cc_final: 0.8983 (mpp)
REVERT: B  565 LEU cc_start: 0.9505 (mt) cc_final: 0.9245 (tt)
REVERT: B  609 MET cc_start: 0.9207 (mmp) cc_final: 0.8694 (mmp)
REVERT: B  646 MET cc_start: 0.9535 (mmp) cc_final: 0.9221 (mmm)
REVERT: B  868 LYS cc_start: 0.9659 (tmtt) cc_final: 0.9442 (tptp)
REVERT: A  128 MET cc_start: 0.9267 (mtm) cc_final: 0.8825 (mtp)
REVERT: A  144 GLN cc_start: 0.9453 (pt0) cc_final: 0.9194 (pp30)
REVERT: A  174 PHE cc_start: 0.9368 (m-10) cc_final: 0.9158 (m-80)
REVERT: A  235 PHE cc_start: 0.8639 (t80) cc_final: 0.7640 (t80)
REVERT: A  339 MET cc_start: 0.8802 (pmm) cc_final: 0.8469 (pmm)
REVERT: A  399 PHE cc_start: 0.8907 (m-80) cc_final: 0.8333 (m-80)
REVERT: A  400 VAL cc_start: 0.9765 (p) cc_final: 0.9543 (p)
REVERT: A  410 MET cc_start: 0.9248 (tpt) cc_final: 0.8914 (tpp)
REVERT: A  485 MET cc_start: 0.9452 (mmp) cc_final: 0.9245 (mmm)
REVERT: A  488 PHE cc_start: 0.9227 (m-10) cc_final: 0.8972 (m-10)
REVERT: A  559 MET cc_start: 0.9625 (ptm) cc_final: 0.9004 (ppp)
REVERT: A  560 MET cc_start: 0.9546 (mtm) cc_final: 0.8915 (ptp)
REVERT: A  609 MET cc_start: 0.9240 (mmp) cc_final: 0.8659 (mmp)
REVERT: A  646 MET cc_start: 0.9501 (mmp) cc_final: 0.9179 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1690
  time to fit residues: 51.4480
Evaluate side-chains
  145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 54 optimal weight:    0.0000
   chunk 14 optimal weight:    5.9990
   chunk 116 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 110 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 38 optimal weight:    0.1980
   overall best weight:    1.0188

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

Flipped N/Q/H residues before XYZ refinement:
** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.062983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.050250 restraints weight = 58680.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.051779 restraints weight = 37985.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052730 restraints weight = 27328.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9467  Z= 0.211
  Angle     :  0.862  12.586  12861  Z= 0.432
  Chirality :  0.047   0.178   1519
  Planarity :  0.005   0.056   1573
  Dihedral  :  6.421  43.500   1260
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  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: -0.87 (0.25), residues: 1177
  helix:  0.86 (0.19), residues: 769
  sheet: -1.92 (0.77), residues: 44
  loop : -3.69 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 469 
 HIS   0.010   0.001   HIS A 555 
 PHE   0.048   0.002   PHE B 488 
 TYR   0.072   0.003   TYR B 589 
 ARG   0.003   0.000   ARG A 338 

*********************** 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
  191 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  143 LEU cc_start: 0.9248 (tp) cc_final: 0.8948 (pp)
REVERT: B  174 PHE cc_start: 0.9545 (m-10) cc_final: 0.9329 (m-80)
REVERT: B  267 LEU cc_start: 0.9731 (mp) cc_final: 0.9520 (tp)
REVERT: B  339 MET cc_start: 0.8865 (ptp) cc_final: 0.8465 (ptp)
REVERT: B  399 PHE cc_start: 0.9048 (m-80) cc_final: 0.8463 (m-80)
REVERT: B  410 MET cc_start: 0.9357 (tpt) cc_final: 0.9041 (tpp)
REVERT: B  470 MET cc_start: 0.8843 (ppp) cc_final: 0.8520 (tmm)
REVERT: B  565 LEU cc_start: 0.9513 (mt) cc_final: 0.9240 (tt)
REVERT: B  609 MET cc_start: 0.9170 (mmp) cc_final: 0.8420 (mmp)
REVERT: B  646 MET cc_start: 0.9548 (mmp) cc_final: 0.9247 (mmm)
REVERT: A  128 MET cc_start: 0.9298 (mtm) cc_final: 0.8855 (mtp)
REVERT: A  144 GLN cc_start: 0.9462 (pt0) cc_final: 0.9184 (pp30)
REVERT: A  174 PHE cc_start: 0.9337 (m-10) cc_final: 0.9113 (m-80)
REVERT: A  235 PHE cc_start: 0.8674 (t80) cc_final: 0.7680 (t80)
REVERT: A  311 PHE cc_start: 0.8998 (m-80) cc_final: 0.8237 (m-80)
REVERT: A  339 MET cc_start: 0.8792 (pmm) cc_final: 0.8430 (pmm)
REVERT: A  399 PHE cc_start: 0.8897 (m-80) cc_final: 0.8344 (m-80)
REVERT: A  410 MET cc_start: 0.9227 (tpt) cc_final: 0.8894 (tpp)
REVERT: A  466 MET cc_start: 0.9322 (tpt) cc_final: 0.9050 (tpt)
REVERT: A  488 PHE cc_start: 0.9237 (m-10) cc_final: 0.9005 (m-10)
REVERT: A  609 MET cc_start: 0.9244 (mmp) cc_final: 0.8694 (mmp)
REVERT: A  646 MET cc_start: 0.9550 (mmp) cc_final: 0.9228 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1698
  time to fit residues: 48.5109
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  : 1.128 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 88 optimal weight:    0.0570
   chunk 93 optimal weight:    0.6980
   chunk 99 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0270
   chunk 23 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.4156

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

Flipped N/Q/H residues before XYZ refinement:
** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.063449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.050505 restraints weight = 58258.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052032 restraints weight = 38115.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.053043 restraints weight = 27794.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
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   0.043   9467  Z= 0.207
  Angle     :  0.880  11.900  12861  Z= 0.433
  Chirality :  0.047   0.178   1519
  Planarity :  0.005   0.053   1573
  Dihedral  :  6.192  34.819   1260
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  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: -0.78 (0.25), residues: 1177
  helix:  0.90 (0.19), residues: 767
  sheet: -1.87 (0.88), residues: 34
  loop : -3.52 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 469 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.050   0.002   PHE B 488 
 TYR   0.053   0.002   TYR B 589 
 ARG   0.003   0.000   ARG A 338 

*********************** 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
  194 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.022 
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: 0.9203 (mtm) cc_final: 0.8922 (mtt)
REVERT: B  136 ASP cc_start: 0.8861 (p0) cc_final: 0.8631 (p0)
REVERT: B  143 LEU cc_start: 0.9228 (tp) cc_final: 0.8910 (pp)
REVERT: B  174 PHE cc_start: 0.9533 (m-10) cc_final: 0.9295 (m-80)
REVERT: B  194 MET cc_start: 0.9253 (ptp) cc_final: 0.9012 (ptp)
REVERT: B  246 LEU cc_start: 0.9311 (tp) cc_final: 0.9065 (tp)
REVERT: B  307 PHE cc_start: 0.9398 (t80) cc_final: 0.8561 (t80)
REVERT: B  319 LEU cc_start: 0.9670 (tp) cc_final: 0.9461 (tp)
REVERT: B  339 MET cc_start: 0.8835 (ptp) cc_final: 0.8493 (ptp)
REVERT: B  399 PHE cc_start: 0.9050 (m-80) cc_final: 0.8496 (m-80)
REVERT: B  410 MET cc_start: 0.9299 (tpt) cc_final: 0.9035 (tpp)
REVERT: B  414 MET cc_start: 0.9246 (tmm) cc_final: 0.8893 (tmm)
REVERT: B  432 THR cc_start: 0.9484 (p) cc_final: 0.9155 (p)
REVERT: B  470 MET cc_start: 0.8808 (ppp) cc_final: 0.8458 (tmm)
REVERT: B  559 MET cc_start: 0.9748 (ttt) cc_final: 0.9121 (ppp)
REVERT: B  560 MET cc_start: 0.9339 (mpp) cc_final: 0.8202 (mpp)
REVERT: B  565 LEU cc_start: 0.9487 (mt) cc_final: 0.9222 (tt)
REVERT: B  609 MET cc_start: 0.9165 (mmp) cc_final: 0.8629 (mmp)
REVERT: B  646 MET cc_start: 0.9543 (mmp) cc_final: 0.9242 (mmm)
REVERT: B  657 LEU cc_start: 0.9662 (mt) cc_final: 0.9352 (tt)
REVERT: A  128 MET cc_start: 0.9286 (mtm) cc_final: 0.8888 (mtp)
REVERT: A  174 PHE cc_start: 0.9358 (m-10) cc_final: 0.9136 (m-80)
REVERT: A  311 PHE cc_start: 0.8993 (m-80) cc_final: 0.8207 (m-80)
REVERT: A  319 LEU cc_start: 0.9675 (tp) cc_final: 0.9396 (tt)
REVERT: A  339 MET cc_start: 0.8805 (pmm) cc_final: 0.8442 (pmm)
REVERT: A  399 PHE cc_start: 0.8867 (m-80) cc_final: 0.8332 (m-80)
REVERT: A  410 MET cc_start: 0.9138 (tpt) cc_final: 0.8837 (tpp)
REVERT: A  466 MET cc_start: 0.9328 (tpt) cc_final: 0.8986 (tpt)
REVERT: A  485 MET cc_start: 0.9474 (mmp) cc_final: 0.9161 (mmm)
REVERT: A  488 PHE cc_start: 0.9238 (m-10) cc_final: 0.9032 (m-10)
REVERT: A  560 MET cc_start: 0.9502 (mtm) cc_final: 0.9176 (mpp)
REVERT: A  609 MET cc_start: 0.9225 (mmp) cc_final: 0.8661 (mmp)
REVERT: A  646 MET cc_start: 0.9546 (mmp) cc_final: 0.9222 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1685
  time to fit residues: 49.0193
Evaluate side-chains
  140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   chunk 43 optimal weight:    0.2980
   chunk 2 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.061503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.049033 restraints weight = 58670.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.050465 restraints weight = 38276.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.051350 restraints weight = 27574.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.5290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9467  Z= 0.261
  Angle     :  0.893  11.303  12861  Z= 0.451
  Chirality :  0.048   0.177   1519
  Planarity :  0.005   0.074   1573
  Dihedral  :  6.227  34.737   1260
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 19.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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: -0.62 (0.25), residues: 1177
  helix:  0.97 (0.19), residues: 771
  sheet: -2.28 (1.00), residues: 24
  loop : -3.32 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 469 
 HIS   0.008   0.001   HIS B 555 
 PHE   0.049   0.002   PHE B 488 
 TYR   0.050   0.002   TYR B 589 
 ARG   0.002   0.000   ARG A 670 

*********************** 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
  179 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.108 
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: 0.9304 (mtm) cc_final: 0.9016 (mtt)
REVERT: B  136 ASP cc_start: 0.8845 (p0) cc_final: 0.8544 (p0)
REVERT: B  143 LEU cc_start: 0.9246 (tp) cc_final: 0.8999 (pp)
REVERT: B  174 PHE cc_start: 0.9534 (m-10) cc_final: 0.9292 (m-80)
REVERT: B  246 LEU cc_start: 0.9346 (tp) cc_final: 0.9127 (tp)
REVERT: B  250 MET cc_start: 0.8529 (mmp) cc_final: 0.8314 (mmm)
REVERT: B  311 PHE cc_start: 0.8637 (m-80) cc_final: 0.8156 (m-80)
REVERT: B  339 MET cc_start: 0.8843 (ptp) cc_final: 0.8527 (ptp)
REVERT: B  399 PHE cc_start: 0.9065 (m-80) cc_final: 0.8531 (m-80)
REVERT: B  410 MET cc_start: 0.9331 (tpt) cc_final: 0.9104 (tpp)
REVERT: B  470 MET cc_start: 0.8814 (ppp) cc_final: 0.8554 (tmm)
REVERT: B  559 MET cc_start: 0.9769 (ttt) cc_final: 0.9221 (ppp)
REVERT: B  560 MET cc_start: 0.9370 (mpp) cc_final: 0.8199 (mpp)
REVERT: B  565 LEU cc_start: 0.9541 (mt) cc_final: 0.9279 (tt)
REVERT: B  609 MET cc_start: 0.9159 (mmp) cc_final: 0.8702 (mmp)
REVERT: B  646 MET cc_start: 0.9552 (mmp) cc_final: 0.9255 (mmm)
REVERT: A  128 MET cc_start: 0.9312 (mtm) cc_final: 0.8880 (mtp)
REVERT: A  339 MET cc_start: 0.8884 (pmm) cc_final: 0.8508 (pmm)
REVERT: A  399 PHE cc_start: 0.8888 (m-80) cc_final: 0.8325 (m-80)
REVERT: A  410 MET cc_start: 0.9240 (tpt) cc_final: 0.8913 (tpp)
REVERT: A  466 MET cc_start: 0.9318 (tpt) cc_final: 0.8974 (tpt)
REVERT: A  609 MET cc_start: 0.9200 (mmp) cc_final: 0.8676 (mmp)
REVERT: A  646 MET cc_start: 0.9566 (mmp) cc_final: 0.9250 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1701
  time to fit residues: 45.8206
Evaluate side-chains
  134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 106 optimal weight:   20.0000
   chunk 113 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.062749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.049912 restraints weight = 57877.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.051413 restraints weight = 38113.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.052337 restraints weight = 27527.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.5484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9467  Z= 0.213
  Angle     :  0.898  11.109  12861  Z= 0.443
  Chirality :  0.048   0.204   1519
  Planarity :  0.005   0.062   1573
  Dihedral  :  6.121  32.634   1260
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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: -0.51 (0.25), residues: 1177
  helix:  1.04 (0.19), residues: 772
  sheet: -2.09 (1.03), residues: 24
  loop : -3.25 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 469 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.054   0.002   PHE B 488 
 TYR   0.046   0.002   TYR B 589 
 ARG   0.002   0.000   ARG A 338 

********************** 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
  186 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.028 
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: 0.9316 (mtm) cc_final: 0.9019 (mpp)
REVERT: B  136 ASP cc_start: 0.8831 (p0) cc_final: 0.8529 (p0)
REVERT: B  143 LEU cc_start: 0.9260 (tp) cc_final: 0.8975 (pp)
REVERT: B  174 PHE cc_start: 0.9530 (m-10) cc_final: 0.9281 (m-80)
REVERT: B  181 LEU cc_start: 0.8587 (mm) cc_final: 0.8377 (mm)
REVERT: B  246 LEU cc_start: 0.9330 (tp) cc_final: 0.9110 (tp)
REVERT: B  250 MET cc_start: 0.8541 (mmp) cc_final: 0.8335 (mmm)
REVERT: B  319 LEU cc_start: 0.9657 (tp) cc_final: 0.9457 (tp)
REVERT: B  339 MET cc_start: 0.8843 (ptp) cc_final: 0.8468 (ptp)
REVERT: B  399 PHE cc_start: 0.9032 (m-80) cc_final: 0.8497 (m-80)
REVERT: B  410 MET cc_start: 0.9343 (tpt) cc_final: 0.9055 (tpp)
REVERT: B  414 MET cc_start: 0.9271 (tmm) cc_final: 0.8868 (tmm)
REVERT: B  449 TRP cc_start: 0.8922 (m100) cc_final: 0.8708 (m-10)
REVERT: B  470 MET cc_start: 0.8902 (ppp) cc_final: 0.8495 (tmm)
REVERT: B  565 LEU cc_start: 0.9516 (mt) cc_final: 0.9266 (tt)
REVERT: B  609 MET cc_start: 0.9158 (mmp) cc_final: 0.8695 (mmp)
REVERT: B  646 MET cc_start: 0.9537 (mmp) cc_final: 0.9233 (mmm)
REVERT: A  128 MET cc_start: 0.9299 (mtm) cc_final: 0.8875 (mtp)
REVERT: A  136 ASP cc_start: 0.8807 (p0) cc_final: 0.8474 (p0)
REVERT: A  167 PHE cc_start: 0.9479 (t80) cc_final: 0.9184 (t80)
REVERT: A  174 PHE cc_start: 0.9329 (m-10) cc_final: 0.9097 (m-80)
REVERT: A  311 PHE cc_start: 0.9009 (m-80) cc_final: 0.8254 (m-80)
REVERT: A  319 LEU cc_start: 0.9680 (tp) cc_final: 0.9436 (tp)
REVERT: A  339 MET cc_start: 0.8864 (pmm) cc_final: 0.8440 (pmm)
REVERT: A  399 PHE cc_start: 0.8838 (m-80) cc_final: 0.8255 (m-80)
REVERT: A  410 MET cc_start: 0.9264 (tpt) cc_final: 0.8870 (tpp)
REVERT: A  414 MET cc_start: 0.8942 (tmm) cc_final: 0.8629 (tmm)
REVERT: A  432 THR cc_start: 0.9454 (p) cc_final: 0.9120 (p)
REVERT: A  466 MET cc_start: 0.9358 (tpt) cc_final: 0.8967 (tpt)
REVERT: A  609 MET cc_start: 0.9214 (mmp) cc_final: 0.8664 (mmp)
REVERT: A  646 MET cc_start: 0.9557 (mmp) cc_final: 0.9217 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1651
  time to fit residues: 46.6981
Evaluate side-chains
  138 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 114 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 115 optimal weight:    9.9990
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.061797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.049569 restraints weight = 59111.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.050955 restraints weight = 39344.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.051903 restraints weight = 28833.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9467  Z= 0.238
  Angle     :  0.881  10.867  12861  Z= 0.440
  Chirality :  0.048   0.196   1519
  Planarity :  0.005   0.050   1573
  Dihedral  :  6.130  31.327   1260
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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: -0.52 (0.25), residues: 1177
  helix:  1.02 (0.19), residues: 770
  sheet: -2.21 (1.00), residues: 24
  loop : -3.20 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP A 469 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.051   0.002   PHE B 488 
 TYR   0.044   0.002   TYR B 589 
 ARG   0.002   0.000   ARG B 654 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2873.90 seconds
wall clock time: 52 minutes 29.79 seconds (3149.79 seconds total)