Starting phenix.real_space_refine
on Mon Jul 28 13:50:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dd4_27334/07_2025/8dd4_27334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dd4_27334/07_2025/8dd4_27334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dd4_27334/07_2025/8dd4_27334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dd4_27334/07_2025/8dd4_27334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dd4_27334/07_2025/8dd4_27334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dd4_27334/07_2025/8dd4_27334.cif"
  }
  resolution = 3.1
  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=   1.000
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      73      5.16       5
     C    6624      2.51       5
     N    1807      2.21       5
     O    1922      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10426
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8076
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 981, 8043
          Classifications: {'peptide': 981}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 981, 8043
          Classifications: {'peptide': 981}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 8187
    Chain: "B"
      Number of atoms: 2329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2329
          Classifications: {'peptide': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 269}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG A 617 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 617 " occ=0.50
    residue:
      pdb=" N  AARG A 651 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 651 " occ=0.50
    residue:
      pdb=" N  AARG A 704 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 704 " occ=0.50
  Time building chain proxies: 9.72, per 1000 atoms: 0.93
  Number of scatterers: 10426
  At special positions: 0
  Unit cell: (106.029, 132.804, 112.455, 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      73     16.00
     O    1922      8.00
     N    1807      7.00
     C    6624      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: 2.29
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2410

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 10 sheets defined
      51.7% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.509A  pdb=" N   GLU A  52 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ARG A  54 " --> pdb=" O   PHE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 62
    Processing helix  chain 'A' and resid 64 through 68
    Processing helix  chain 'A' and resid 108 through 122
    Processing helix  chain 'A' and resid 124 through 130
      removed outlier: 4.024A  pdb=" N   PHE A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 155
      removed outlier: 3.515A  pdb=" N   GLN A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP A 155 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
      removed outlier: 3.571A  pdb=" N   ALA A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 3.540A  pdb=" N   TYR A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASN A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 178 through 183'
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 3.589A  pdb=" N   THR A 229 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 297
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.733A  pdb=" N   ARG A 309 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 3.739A  pdb=" N   VAL A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 330 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 326 through 330'
    Processing helix  chain 'A' and resid 488 through 496
      removed outlier: 3.569A  pdb=" N   ILE A 492 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 537
      removed outlier: 3.569A  pdb=" N   ARG A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 557 through 563
      removed outlier: 3.886A  pdb=" N   THR A 560 " --> pdb=" O   TYR A 557 " (cutoff:3.500A)
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 572
      removed outlier: 3.521A  pdb=" N   VAL A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 3.632A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 600
      removed outlier: 3.918A  pdb=" N   GLU A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 603
      No H-bonds generated for 'chain 'A' and resid 601 through 603'
    Processing helix  chain 'A' and resid 608 through 623
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 647 through 658
    Processing helix  chain 'A' and resid 660 through 674
      removed outlier: 3.523A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 696
      removed outlier: 3.782A  pdb=" N   LEU A 687 " --> pdb=" O   ARG A 683 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   GLY A 696 " --> pdb=" O   CYS A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 721
      removed outlier: 4.072A  pdb=" N   LEU A 719 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN A 721 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 739
      removed outlier: 3.521A  pdb=" N   GLN A 731 " --> pdb=" O   THR A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 3.992A  pdb=" N   MET A 745 " --> pdb=" O   ARG A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 857 through 865
    Processing helix  chain 'A' and resid 875 through 885
      removed outlier: 3.859A  pdb=" N   ASN A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 912
    Processing helix  chain 'A' and resid 940 through 944
      removed outlier: 4.237A  pdb=" N   LYS A 944 " --> pdb=" O   LYS A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.674A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 994
      removed outlier: 4.529A  pdb=" N   GLU A 978 " --> pdb=" O   THR A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1005
      removed outlier: 4.143A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1009
      removed outlier: 4.165A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1006 through 1009'
    Processing helix  chain 'A' and resid 1015 through 1026
      removed outlier: 4.047A  pdb=" N   ILE A1019 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR A1021 " --> pdb=" O   ASP A1017 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A1022 " --> pdb=" O   ASP A1018 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A1026 " --> pdb=" O   ILE A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1046
      removed outlier: 3.989A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 347
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 3.884A  pdb=" N   GLY B 388 " --> pdb=" O   HIS B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 410
      removed outlier: 3.837A  pdb=" N   LEU B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 437
      removed outlier: 3.545A  pdb=" N   VAL B 437 " --> pdb=" O   GLN B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 504
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.615A  pdb=" N   PHE B 512 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 588
      removed outlier: 3.525A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
    Processing helix  chain 'B' and resid 591 through 596
      removed outlier: 4.011A  pdb=" N   GLU B 596 " --> pdb=" O   LYS B 592 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36
      removed outlier: 3.719A  pdb=" N   VAL A  32 " --> pdb=" O   CYS A  24 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A  34 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A  20 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU A  99 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   VAL A 101 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 102 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 212
      removed outlier: 3.584A  pdb=" N   TYR A 207 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 340
      removed outlier: 4.647A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 385 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.523A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.523A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 418 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 444
      removed outlier: 3.767A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET A 441 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752
      removed outlier: 3.733A  pdb=" N   PHE A 751 " --> pdb=" O   LEU A 761 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 779 through 784
    Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AB1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 4.106A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN B 377 " --> pdb=" O   LYS B 374 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.18

  Time building geometry restraints manager: 2.76 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: 3414
        1.34 -     1.46: 2343
        1.46 -     1.58: 4756
        1.58 -     1.70: 0
        1.70 -     1.82: 114
  Bond restraints: 10627
  Sorted by residual:
  bond pdb=" CG1 ILE A 819 "
       pdb=" CD1 ILE A 819 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.66e+00
  bond pdb=" C   SER A 199 "
       pdb=" N   PRO A 200 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.57e+00
  bond pdb=" CA  ASP B 337 "
       pdb=" CB  ASP B 337 "
    ideal  model  delta    sigma   weight residual
    1.524  1.541 -0.016 1.53e-02 4.27e+03 1.14e+00
  bond pdb=" CG  LEU A 688 "
       pdb=" CD1 LEU A 688 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  bond pdb=" CB  LYS A 179 "
       pdb=" CG  LYS A 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.29e-01
  ... (remaining 10622 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 14047
        1.99 -     3.98: 235
        3.98 -     5.97: 31
        5.97 -     7.96: 10
        7.96 -     9.95: 5
  Bond angle restraints: 14328
  Sorted by residual:
  angle pdb=" C   THR A1052 "
        pdb=" N   THR A1053 "
        pdb=" CA  THR A1053 "
      ideal   model   delta    sigma   weight residual
     121.54  128.42   -6.88 1.91e+00 2.74e-01 1.30e+01
  angle pdb=" CB  MET A 732 "
        pdb=" CG  MET A 732 "
        pdb=" SD  MET A 732 "
      ideal   model   delta    sigma   weight residual
     112.70  122.65   -9.95 3.00e+00 1.11e-01 1.10e+01
  angle pdb=" N   MET B 525 "
        pdb=" CA  MET B 525 "
        pdb=" CB  MET B 525 "
      ideal   model   delta    sigma   weight residual
     110.12  114.72   -4.60 1.47e+00 4.63e-01 9.78e+00
  angle pdb=" CB  MET A1040 "
        pdb=" CG  MET A1040 "
        pdb=" SD  MET A1040 "
      ideal   model   delta    sigma   weight residual
     112.70  121.87   -9.17 3.00e+00 1.11e-01 9.33e+00
  angle pdb=" CB  LYS B 480 "
        pdb=" CG  LYS B 480 "
        pdb=" CD  LYS B 480 "
      ideal   model   delta    sigma   weight residual
     111.30  118.10   -6.80 2.30e+00 1.89e-01 8.75e+00
  ... (remaining 14323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5770
       17.98 -    35.97: 594
       35.97 -    53.95: 113
       53.95 -    71.93: 17
       71.93 -    89.91: 12
  Dihedral angle restraints: 6506
    sinusoidal: 2790
      harmonic: 3716
  Sorted by residual:
  dihedral pdb=" CA  LYS A 573 "
           pdb=" C   LYS A 573 "
           pdb=" N   TRP A 574 "
           pdb=" CA  TRP A 574 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.67  -18.33     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  MET B 326 "
           pdb=" C   MET B 326 "
           pdb=" N   SER B 327 "
           pdb=" CA  SER B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.65  -17.35     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP A 646 "
           pdb=" CB  ASP A 646 "
           pdb=" CG  ASP A 646 "
           pdb=" OD1 ASP A 646 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.23   58.23     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 6503 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 967
       0.033 -    0.067: 404
       0.067 -    0.100: 113
       0.100 -    0.134: 51
       0.134 -    0.167: 7
  Chirality restraints: 1542
  Sorted by residual:
  chirality pdb=" CA  LYS B 480 "
            pdb=" N   LYS B 480 "
            pdb=" C   LYS B 480 "
            pdb=" CB  LYS B 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CA  GLN A 738 "
            pdb=" N   GLN A 738 "
            pdb=" C   GLN A 738 "
            pdb=" CB  GLN A 738 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CA  THR A1053 "
            pdb=" N   THR A1053 "
            pdb=" C   THR A1053 "
            pdb=" CB  THR A1053 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 1539 not shown)

  Planarity restraints: 1841
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 216 "   -0.040 5.00e-02 4.00e+02   6.09e-02 5.94e+00
        pdb=" N   PRO A 217 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 177 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.77e+00
        pdb=" N   PRO A 178 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 178 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 178 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  56 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO A  57 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  57 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  57 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1838 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1416
        2.76 -     3.29: 10300
        3.29 -     3.83: 17329
        3.83 -     4.36: 20116
        4.36 -     4.90: 34360
  Nonbonded interactions: 83521
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 540 "
            pdb=" NH2 ARG B 340 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OE2 GLU A 469 "
            pdb=" NH1 ARG B 481 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OH  TYR A 584 "
            pdb=" OD1 ASP A 608 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP B 540 "
            pdb=" NH2 ARG B 543 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NZ  LYS A 440 "
            pdb=" OE1 GLU A 474 "
     model   vdw
     2.272 3.120
  ... (remaining 83516 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     30.000
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.060
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10627  Z= 0.133
  Angle     :  0.647   9.949  14328  Z= 0.321
  Chirality :  0.043   0.167   1542
  Planarity :  0.004   0.061   1841
  Dihedral  : 14.944  89.912   4096
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.82 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.24), residues: 1250
  helix:  0.84 (0.22), residues: 579
  sheet: -0.23 (0.44), residues: 143
  loop : -0.42 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1051 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.024   0.001   PHE B 456 
 TYR   0.013   0.001   TYR B 556 
 ARG   0.005   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14668 (  485)
  hydrogen bonds       : angle       5.72227 ( 1416)
  covalent geometry    : bond        0.00297 (10627)
  covalent geometry    : angle       0.64654 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 GLU cc_start: 0.6322 (tm-30) cc_final: 0.5979 (tm-30)
REVERT: A  212 ASN cc_start: 0.8424 (p0) cc_final: 0.8185 (p0)
REVERT: A  267 LEU cc_start: 0.8422 (tt) cc_final: 0.8161 (tt)
REVERT: A  689 GLU cc_start: 0.6586 (tm-30) cc_final: 0.6259 (tm-30)
REVERT: A 1032 GLU cc_start: 0.6891 (mp0) cc_final: 0.6510 (mp0)
REVERT: A 1055 MET cc_start: 0.4148 (tmm) cc_final: 0.3831 (tmm)
REVERT: B  521 ILE cc_start: 0.6292 (mm) cc_final: 0.5200 (mm)
REVERT: B  578 ASP cc_start: 0.7625 (m-30) cc_final: 0.7368 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.2409
  time to fit residues: 82.4760
Evaluate side-chains
  201 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 370 ASN
A 444 ASN
A 457 ASN
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.183549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.131440 restraints weight = 47359.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 5.57
r_work: 0.3424 rms_B_bonded: 5.14 restraints_weight: 2.0000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10627  Z= 0.174
  Angle     :  0.642   8.606  14328  Z= 0.331
  Chirality :  0.044   0.149   1542
  Planarity :  0.004   0.054   1841
  Dihedral  :  4.061  17.902   1385
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.90 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  9.59 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.24), residues: 1250
  helix:  0.88 (0.21), residues: 589
  sheet: -0.74 (0.43), residues: 141
  loop : -0.38 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 479 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.014   0.002   PHE A 909 
 TYR   0.028   0.001   TYR A 904 
 ARG   0.006   0.000   ARG B 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 (  485)
  hydrogen bonds       : angle       4.32083 ( 1416)
  covalent geometry    : bond        0.00399 (10627)
  covalent geometry    : angle       0.64202 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 208
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7862 (mm-30)
REVERT: A  250 TYR cc_start: 0.7112 (m-80) cc_final: 0.6887 (m-80)
REVERT: A  689 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: B  330 ASP cc_start: 0.8373 (p0) cc_final: 0.7767 (p0)
REVERT: B  521 ILE cc_start: 0.6458 (mm) cc_final: 0.5878 (mm)
REVERT: B  560 ASP cc_start: 0.8085 (t0) cc_final: 0.7851 (t0)
REVERT: B  569 ASP cc_start: 0.8738 (p0) cc_final: 0.8443 (p0)
REVERT: B  578 ASP cc_start: 0.8165 (m-30) cc_final: 0.7694 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 217
  average time/residue: 0.2725
  time to fit residues: 82.9738
Evaluate side-chains
  191 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0170
   chunk 121 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 124 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.9822

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 738 GLN
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.184042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.132644 restraints weight = 54072.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 6.20
r_work: 0.3405 rms_B_bonded: 5.69 restraints_weight: 2.0000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3407
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3407
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10627  Z= 0.133
  Angle     :  0.601  12.836  14328  Z= 0.307
  Chirality :  0.043   0.158   1542
  Planarity :  0.004   0.056   1841
  Dihedral  :  3.988  16.989   1385
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.50 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.62 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.24), residues: 1250
  helix:  1.00 (0.21), residues: 589
  sheet: -0.82 (0.42), residues: 141
  loop : -0.33 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 669 
 HIS   0.012   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 744 
 TYR   0.027   0.001   TYR A 904 
 ARG   0.005   0.000   ARG B 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  485)
  hydrogen bonds       : angle       4.14018 ( 1416)
  covalent geometry    : bond        0.00302 (10627)
  covalent geometry    : angle       0.60139 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7910 (mm-30)
REVERT: A  172 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6049 (tm-30)
REVERT: A  250 TYR cc_start: 0.7038 (m-80) cc_final: 0.6704 (m-80)
REVERT: A  689 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: B  341 GLU cc_start: 0.7926 (tt0) cc_final: 0.7681 (pt0)
REVERT: B  476 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6882 (mt-10)
REVERT: B  489 GLU cc_start: 0.8821 (tp30) cc_final: 0.8588 (tp30)
REVERT: B  521 ILE cc_start: 0.6584 (mm) cc_final: 0.6077 (mm)
REVERT: B  560 ASP cc_start: 0.8148 (t0) cc_final: 0.7936 (t0)
REVERT: B  569 ASP cc_start: 0.8789 (p0) cc_final: 0.8538 (p0)
REVERT: B  578 ASP cc_start: 0.7995 (m-30) cc_final: 0.7561 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 207
  average time/residue: 0.2838
  time to fit residues: 83.8102
Evaluate side-chains
  190 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 18 optimal weight:    0.0020
   chunk 121 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 110 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 89 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0270
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.9250

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.183711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.133077 restraints weight = 42126.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 5.04
r_work: 0.3457 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10627  Z= 0.128
  Angle     :  0.596  11.004  14328  Z= 0.304
  Chirality :  0.042   0.147   1542
  Planarity :  0.004   0.054   1841
  Dihedral  :  3.931  16.532   1385
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.58 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.35 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.24), residues: 1250
  helix:  0.99 (0.21), residues: 595
  sheet: -0.93 (0.41), residues: 146
  loop : -0.35 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 669 
 HIS   0.011   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 744 
 TYR   0.025   0.001   TYR A 904 
 ARG   0.004   0.000   ARG B 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  485)
  hydrogen bonds       : angle       4.06055 ( 1416)
  covalent geometry    : bond        0.00292 (10627)
  covalent geometry    : angle       0.59598 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 193
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7709 (pt0)
REVERT: A  265 TYR cc_start: 0.7076 (m-80) cc_final: 0.6654 (m-10)
REVERT: A  689 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7575 (tm-30)
REVERT: A  739 MET cc_start: 0.6833 (mmm) cc_final: 0.6557 (mmm)
REVERT: A  978 GLU cc_start: 0.8370 (mp0) cc_final: 0.7878 (pm20)
REVERT: B  419 LYS cc_start: 0.7920 (mppt) cc_final: 0.7028 (mtmt)
REVERT: B  476 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6842 (mt-10)
REVERT: B  564 ASN cc_start: 0.7952 (m-40) cc_final: 0.7721 (m110)
REVERT: B  578 ASP cc_start: 0.8010 (m-30) cc_final: 0.7612 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 203
  average time/residue: 0.2391
  time to fit residues: 69.3572
Evaluate side-chains
  199 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 79 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 102 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   chunk 124 optimal weight:    8.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.183036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131315 restraints weight = 47431.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 5.78
r_work: 0.3427 rms_B_bonded: 5.14 restraints_weight: 2.0000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10627  Z= 0.130
  Angle     :  0.587   8.109  14328  Z= 0.301
  Chirality :  0.042   0.160   1542
  Planarity :  0.004   0.055   1841
  Dihedral  :  3.941  18.057   1385
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.90 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.78 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1250
  helix:  1.06 (0.21), residues: 596
  sheet: -0.97 (0.41), residues: 146
  loop : -0.33 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 669 
 HIS   0.016   0.001   HIS A 213 
 PHE   0.015   0.001   PHE A 744 
 TYR   0.025   0.001   TYR A 904 
 ARG   0.004   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  485)
  hydrogen bonds       : angle       3.96662 ( 1416)
  covalent geometry    : bond        0.00297 (10627)
  covalent geometry    : angle       0.58737 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7766 (pt0)
REVERT: A  454 ASP cc_start: 0.7568 (t0) cc_final: 0.7255 (t0)
REVERT: A  689 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: A  739 MET cc_start: 0.6812 (mmm) cc_final: 0.6482 (mmm)
REVERT: A  978 GLU cc_start: 0.8491 (mp0) cc_final: 0.8214 (pt0)
REVERT: B  419 LYS cc_start: 0.8043 (mppt) cc_final: 0.7164 (mtmt)
REVERT: B  476 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6768 (mt-10)
REVERT: B  489 GLU cc_start: 0.8898 (tp30) cc_final: 0.8680 (tp30)
REVERT: B  564 ASN cc_start: 0.7994 (m-40) cc_final: 0.7731 (m110)
REVERT: B  578 ASP cc_start: 0.8107 (m-30) cc_final: 0.7729 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 204
  average time/residue: 0.2413
  time to fit residues: 70.7868
Evaluate side-chains
  200 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 110 optimal weight:   20.0000
   chunk 49 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.179735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.128319 restraints weight = 46979.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 5.62
r_work: 0.3367 rms_B_bonded: 5.25 restraints_weight: 2.0000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10627  Z= 0.203
  Angle     :  0.658  15.225  14328  Z= 0.335
  Chirality :  0.045   0.185   1542
  Planarity :  0.004   0.055   1841
  Dihedral  :  4.171  21.071   1385
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.30 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.13 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1250
  helix:  0.82 (0.21), residues: 596
  sheet: -1.20 (0.41), residues: 144
  loop : -0.38 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 669 
 HIS   0.017   0.001   HIS A 213 
 PHE   0.017   0.002   PHE A 909 
 TYR   0.031   0.002   TYR A 904 
 ARG   0.004   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04095 (  485)
  hydrogen bonds       : angle       4.08110 ( 1416)
  covalent geometry    : bond        0.00471 (10627)
  covalent geometry    : angle       0.65770 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7832 (pt0)
REVERT: A  454 ASP cc_start: 0.7683 (t0) cc_final: 0.7459 (t0)
REVERT: A  689 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: A  729 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8482 (mmmt)
REVERT: A  739 MET cc_start: 0.6961 (mmm) cc_final: 0.6744 (mmm)
REVERT: A  794 PHE cc_start: 0.7903 (p90) cc_final: 0.7615 (p90)
REVERT: A  978 GLU cc_start: 0.8519 (mp0) cc_final: 0.8291 (pt0)
REVERT: B  419 LYS cc_start: 0.8058 (mppt) cc_final: 0.7712 (mtmm)
REVERT: B  564 ASN cc_start: 0.8008 (m-40) cc_final: 0.7794 (m110)
REVERT: B  578 ASP cc_start: 0.8075 (m-30) cc_final: 0.7615 (m-30)
  outliers start: 25
  outliers final: 19
  residues processed: 207
  average time/residue: 0.2291
  time to fit residues: 66.9251
Evaluate side-chains
  197 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 177
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  394 ASP
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 110 optimal weight:   20.0000
   chunk 94 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.180782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.128786 restraints weight = 54146.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 5.92
r_work: 0.3391 rms_B_bonded: 5.27 restraints_weight: 2.0000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10627  Z= 0.138
  Angle     :  0.632  11.668  14328  Z= 0.318
  Chirality :  0.043   0.192   1542
  Planarity :  0.004   0.056   1841
  Dihedral  :  4.076  17.463   1385
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.73 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.24), residues: 1250
  helix:  0.93 (0.21), residues: 596
  sheet: -1.13 (0.41), residues: 144
  loop : -0.33 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 479 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.019   0.001   PHE A 744 
 TYR   0.026   0.001   TYR A 904 
 ARG   0.009   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  485)
  hydrogen bonds       : angle       3.98590 ( 1416)
  covalent geometry    : bond        0.00319 (10627)
  covalent geometry    : angle       0.63155 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7787 (pt0)
REVERT: A  250 TYR cc_start: 0.7108 (m-80) cc_final: 0.6899 (m-80)
REVERT: A  252 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7817 (mm)
REVERT: A  282 MET cc_start: 0.7120 (tpp) cc_final: 0.6832 (tpt)
REVERT: A  454 ASP cc_start: 0.7521 (t0) cc_final: 0.7140 (t0)
REVERT: A  689 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: A  978 GLU cc_start: 0.8507 (mp0) cc_final: 0.8189 (pt0)
REVERT: B  419 LYS cc_start: 0.8155 (mppt) cc_final: 0.7457 (mmtp)
REVERT: B  489 GLU cc_start: 0.8866 (tp30) cc_final: 0.8605 (tp30)
REVERT: B  564 ASN cc_start: 0.7992 (m-40) cc_final: 0.7751 (m110)
REVERT: B  578 ASP cc_start: 0.8097 (m-30) cc_final: 0.7722 (m-30)
REVERT: B  582 MET cc_start: 0.8281 (ttp) cc_final: 0.7978 (ptt)
  outliers start: 21
  outliers final: 17
  residues processed: 202
  average time/residue: 0.2360
  time to fit residues: 67.2413
Evaluate side-chains
  202 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 91 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.181695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.128982 restraints weight = 51734.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 5.66
r_work: 0.3412 rms_B_bonded: 5.17 restraints_weight: 2.0000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10627  Z= 0.126
  Angle     :  0.628  11.076  14328  Z= 0.315
  Chirality :  0.043   0.198   1542
  Planarity :  0.004   0.056   1841
  Dihedral  :  4.014  16.499   1385
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.25 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.24), residues: 1250
  helix:  0.97 (0.21), residues: 598
  sheet: -0.98 (0.43), residues: 138
  loop : -0.20 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 669 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.023   0.001   PHE A 744 
 TYR   0.024   0.001   TYR A 904 
 ARG   0.012   0.000   ARG A 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  485)
  hydrogen bonds       : angle       3.91861 ( 1416)
  covalent geometry    : bond        0.00288 (10627)
  covalent geometry    : angle       0.62849 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7747 (pt0)
REVERT: A  252 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7752 (mm)
REVERT: A  454 ASP cc_start: 0.7465 (t0) cc_final: 0.7261 (t0)
REVERT: A  689 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: A  710 GLU cc_start: 0.8074 (pp20) cc_final: 0.7801 (pt0)
REVERT: A  741 ARG cc_start: 0.7759 (ttm110) cc_final: 0.6972 (mtp180)
REVERT: A  794 PHE cc_start: 0.7873 (p90) cc_final: 0.7438 (p90)
REVERT: A  978 GLU cc_start: 0.8435 (mp0) cc_final: 0.8149 (pt0)
REVERT: B  330 ASP cc_start: 0.8363 (p0) cc_final: 0.7750 (p0)
REVERT: B  419 LYS cc_start: 0.8159 (mppt) cc_final: 0.7364 (mtmt)
REVERT: B  489 GLU cc_start: 0.8869 (tp30) cc_final: 0.8470 (tp30)
REVERT: B  492 LYS cc_start: 0.8115 (mttt) cc_final: 0.7737 (mttt)
REVERT: B  564 ASN cc_start: 0.7966 (m-40) cc_final: 0.7716 (m110)
REVERT: B  578 ASP cc_start: 0.8114 (m-30) cc_final: 0.7677 (m-30)
  outliers start: 23
  outliers final: 19
  residues processed: 207
  average time/residue: 0.2430
  time to fit residues: 71.4776
Evaluate side-chains
  211 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 114 optimal weight:    8.9990
   chunk 107 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 180 HIS
A 213 HIS
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.183536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.140140 restraints weight = 41169.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 4.92
r_work: 0.3556 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10627  Z= 0.210
  Angle     :  0.691  10.935  14328  Z= 0.352
  Chirality :  0.045   0.204   1542
  Planarity :  0.005   0.055   1841
  Dihedral  :  4.280  25.122   1385
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.71 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.85 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1250
  helix:  0.68 (0.21), residues: 601
  sheet: -1.14 (0.43), residues: 138
  loop : -0.35 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 479 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.019   0.002   PHE A 744 
 TYR   0.034   0.002   TYR A 904 
 ARG   0.014   0.001   ARG A 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  485)
  hydrogen bonds       : angle       4.04004 ( 1416)
  covalent geometry    : bond        0.00485 (10627)
  covalent geometry    : angle       0.69127 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7614 (pm20)
REVERT: A  252 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7792 (mm)
REVERT: A  263 GLU cc_start: 0.6832 (tp30) cc_final: 0.6590 (tp30)
REVERT: A  454 ASP cc_start: 0.7382 (t0) cc_final: 0.6992 (t0)
REVERT: A  689 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: A  741 ARG cc_start: 0.7368 (ttm110) cc_final: 0.6725 (mtp180)
REVERT: A  794 PHE cc_start: 0.7726 (p90) cc_final: 0.7449 (p90)
REVERT: A 1055 MET cc_start: 0.3456 (OUTLIER) cc_final: 0.2819 (ttm)
REVERT: B  330 ASP cc_start: 0.7796 (p0) cc_final: 0.7474 (p0)
REVERT: B  419 LYS cc_start: 0.8035 (mppt) cc_final: 0.7239 (mtmt)
REVERT: B  578 ASP cc_start: 0.7798 (m-30) cc_final: 0.7391 (m-30)
  outliers start: 24
  outliers final: 20
  residues processed: 198
  average time/residue: 0.2295
  time to fit residues: 64.5353
Evaluate side-chains
  205 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1055 MET
Chi-restraints excluded: chain B residue  394 ASP
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 114 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.185943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.140871 restraints weight = 49125.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 5.39
r_work: 0.3542 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10627  Z= 0.139
  Angle     :  0.659  10.648  14328  Z= 0.332
  Chirality :  0.043   0.200   1542
  Planarity :  0.004   0.055   1841
  Dihedral  :  4.206  24.306   1385
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.98 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.63 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.24), residues: 1250
  helix:  0.81 (0.21), residues: 601
  sheet: -1.05 (0.44), residues: 138
  loop : -0.32 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 669 
 HIS   0.010   0.001   HIS A 213 
 PHE   0.025   0.001   PHE A 744 
 TYR   0.028   0.001   TYR A 904 
 ARG   0.013   0.000   ARG A 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (  485)
  hydrogen bonds       : angle       3.98996 ( 1416)
  covalent geometry    : bond        0.00321 (10627)
  covalent geometry    : angle       0.65872 (14328)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7690 (pm20)
REVERT: A  252 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7733 (mm)
REVERT: A  263 GLU cc_start: 0.6745 (tp30) cc_final: 0.6467 (tp30)
REVERT: A  282 MET cc_start: 0.7123 (tpp) cc_final: 0.6862 (tpt)
REVERT: A  689 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7442 (tm-30)
REVERT: A  729 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8373 (mmmt)
REVERT: A  741 ARG cc_start: 0.7469 (ttm110) cc_final: 0.6757 (mtp180)
REVERT: A  794 PHE cc_start: 0.7839 (p90) cc_final: 0.7492 (p90)
REVERT: B  329 GLN cc_start: 0.8024 (mp10) cc_final: 0.7246 (tm-30)
REVERT: B  419 LYS cc_start: 0.8144 (mppt) cc_final: 0.7351 (mtmt)
REVERT: B  489 GLU cc_start: 0.8797 (tp30) cc_final: 0.8491 (tp30)
REVERT: B  578 ASP cc_start: 0.8050 (m-30) cc_final: 0.7690 (m-30)
  outliers start: 21
  outliers final: 16
  residues processed: 195
  average time/residue: 0.2407
  time to fit residues: 66.8759
Evaluate side-chains
  202 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0870
   chunk 107 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 114 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 370 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.186280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.143210 restraints weight = 44073.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 5.02
r_work: 0.3577 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10627  Z= 0.128
  Angle     :  0.653   9.950  14328  Z= 0.327
  Chirality :  0.043   0.235   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  4.101  24.377   1385
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.06 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.89 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.24), residues: 1250
  helix:  0.93 (0.21), residues: 602
  sheet: -0.98 (0.43), residues: 144
  loop : -0.31 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 669 
 HIS   0.011   0.001   HIS A 213 
 PHE   0.026   0.001   PHE A 744 
 TYR   0.024   0.001   TYR A 904 
 ARG   0.013   0.000   ARG A 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03594 (  485)
  hydrogen bonds       : angle       3.96558 ( 1416)
  covalent geometry    : bond        0.00292 (10627)
  covalent geometry    : angle       0.65334 (14328)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7019.80 seconds
wall clock time: 122 minutes 55.14 seconds (7375.14 seconds total)