Starting phenix.real_space_refine
on Fri Feb 14 16:23:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dd4_27334/02_2025/8dd4_27334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dd4_27334/02_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_27334/02_2025/8dd4_27334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dd4_27334/02_2025/8dd4_27334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dd4_27334/02_2025/8dd4_27334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dd4_27334/02_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-5592/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: 9.76, per 1000 atoms: 0.94
  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: 2.55
  Conformation dependent library (CDL) restraints added in 2.4 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: 3.30

  Time building geometry restraints manager: 2.97 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:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     30.700
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.030
-------------------------------------------------------------------------------
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= 0.187
  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 

*********************** 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  : 1.177 
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: 0.2460
  time to fit residues: 83.4024
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  : 1.224 
-------------------------------------------------------------------------------
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 = 0.131441 restraints weight = 47359.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 5.57
r_work: 0.3425 rms_B_bonded: 5.16 restraints_weight: 2.0000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    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 = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
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= 0.254
  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 

*********************** 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  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: A  250 TYR cc_start: 0.7083 (m-80) cc_final: 0.6866 (m-80)
REVERT: A  689 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7810 (tm-30)
REVERT: B  330 ASP cc_start: 0.8358 (p0) cc_final: 0.7759 (p0)
REVERT: B  521 ILE cc_start: 0.6456 (mm) cc_final: 0.5871 (mm)
REVERT: B  560 ASP cc_start: 0.8083 (t0) cc_final: 0.7851 (t0)
REVERT: B  569 ASP cc_start: 0.8742 (p0) cc_final: 0.8447 (p0)
REVERT: B  578 ASP cc_start: 0.8175 (m-30) cc_final: 0.7704 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 217
  average time/residue: 0.2481
  time to fit residues: 74.6598
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  : 1.194 
-------------------------------------------------------------------------------
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:    0.3980
   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:    0.0970
   chunk 124 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 ** 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 = 0.4366 r_free = 0.4366 target = 0.184302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133227 restraints weight = 54065.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 6.32
r_work: 0.3406 rms_B_bonded: 5.68 restraints_weight: 2.0000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3410
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    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 = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3410
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10627  Z= 0.184
  Angle     :  0.598  12.694  14328  Z= 0.305
  Chirality :  0.043   0.158   1542
  Planarity :  0.004   0.055   1841
  Dihedral  :  3.979  16.953   1385
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.58 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.71 %
    Favored  : 86.00 %
  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:  0.30 (0.24), residues: 1250
  helix:  1.01 (0.21), residues: 589
  sheet: -0.81 (0.42), residues: 141
  loop : -0.33 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   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 577 

*********************** 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: 15
    poor density    : 200
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7896 (mm-30)
REVERT: A  172 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6050 (tm-30)
REVERT: A  250 TYR cc_start: 0.7046 (m-80) cc_final: 0.6723 (m-80)
REVERT: A  689 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: B  341 GLU cc_start: 0.7915 (tt0) cc_final: 0.7674 (pt0)
REVERT: B  476 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6990 (mp0)
REVERT: B  521 ILE cc_start: 0.6570 (mm) cc_final: 0.6097 (mm)
REVERT: B  560 ASP cc_start: 0.8149 (t0) cc_final: 0.7939 (t0)
REVERT: B  569 ASP cc_start: 0.8793 (p0) cc_final: 0.8540 (p0)
REVERT: B  578 ASP cc_start: 0.7994 (m-30) cc_final: 0.7561 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 207
  average time/residue: 0.2424
  time to fit residues: 71.4671
Evaluate side-chains
  192 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 182
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  856 THR
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:    1.9990
   chunk 121 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   chunk 110 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0770
   chunk 40 optimal weight:    0.2980
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.6744

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.181252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.128039 restraints weight = 41991.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 5.05
r_work: 0.3411 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    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 = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10627  Z= 0.265
  Angle     :  0.633  11.606  14328  Z= 0.326
  Chirality :  0.044   0.151   1542
  Planarity :  0.004   0.053   1841
  Dihedral  :  4.095  17.796   1385
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.90 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.17 %
    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:  0.07 (0.24), residues: 1250
  helix:  0.84 (0.21), residues: 595
  sheet: -1.13 (0.41), residues: 146
  loop : -0.40 (0.28), residues: 509

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   0.017   0.002   PHE A 980 
 TYR   0.032   0.001   TYR A 904 
 ARG   0.004   0.000   ARG A 281 

*********************** 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
  218 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7776 (pt0)
REVERT: A  263 GLU cc_start: 0.7774 (tp30) cc_final: 0.7540 (tm-30)
REVERT: A  265 TYR cc_start: 0.7136 (m-80) cc_final: 0.6679 (m-10)
REVERT: A  689 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7824 (tm-30)
REVERT: A  739 MET cc_start: 0.6723 (mmm) cc_final: 0.6434 (mmm)
REVERT: A  978 GLU cc_start: 0.8435 (mp0) cc_final: 0.8234 (pt0)
REVERT: B  419 LYS cc_start: 0.8016 (mppt) cc_final: 0.7121 (mtmt)
REVERT: B  476 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6762 (mt-10)
REVERT: B  564 ASN cc_start: 0.7984 (m-40) cc_final: 0.7762 (m110)
REVERT: B  578 ASP cc_start: 0.8016 (m-30) cc_final: 0.7606 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 209
  average time/residue: 0.2347
  time to fit residues: 69.4168
Evaluate side-chains
  199 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
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  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  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
Chi-restraints excluded: chain B residue  576 THR
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:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 120 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 102 optimal weight:    4.9990
   chunk 107 optimal weight:    0.0970
   chunk 124 optimal weight:    8.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4337 r_free = 0.4337 target = 0.181848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.132197 restraints weight = 47393.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 5.58
r_work: 0.3419 rms_B_bonded: 5.09 restraints_weight: 2.0000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3422
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3422 r_free = 0.3422    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 = 0.3422 r_free = 0.3422    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3422
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2466

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= 0.194
  Angle     :  0.594   8.237  14328  Z= 0.305
  Chirality :  0.042   0.163   1542
  Planarity :  0.004   0.053   1841
  Dihedral  :  4.025  17.802   1385
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.66 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.38 %
    Favored  : 82.63 %
  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:  0.98 (0.21), residues: 596
  sheet: -1.09 (0.41), residues: 146
  loop : -0.36 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 669 
 HIS   0.019   0.001   HIS A 213 
 PHE   0.017   0.001   PHE A 744 
 TYR   0.026   0.001   TYR A 904 
 ARG   0.003   0.000   ARG A 281 

*********************** 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
  220 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.7973 (mp0) cc_final: 0.7769 (mm-30)
REVERT: A  110 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7153 (pm20)
REVERT: A  218 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7756 (pt0)
REVERT: A  263 GLU cc_start: 0.7860 (tp30) cc_final: 0.7575 (tm-30)
REVERT: A  265 TYR cc_start: 0.7246 (m-80) cc_final: 0.6808 (m-10)
REVERT: A  689 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: A  729 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8428 (mmmt)
REVERT: A  739 MET cc_start: 0.7025 (mmm) cc_final: 0.6679 (mmm)
REVERT: A  978 GLU cc_start: 0.8472 (mp0) cc_final: 0.8270 (pt0)
REVERT: B  419 LYS cc_start: 0.8023 (mppt) cc_final: 0.7234 (mmtp)
REVERT: B  476 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6856 (mt-10)
REVERT: B  564 ASN cc_start: 0.8013 (m-40) cc_final: 0.7781 (m110)
REVERT: B  578 ASP cc_start: 0.8012 (m-30) cc_final: 0.7642 (m-30)
  outliers start: 23
  outliers final: 16
  residues processed: 209
  average time/residue: 0.2342
  time to fit residues: 69.1052
Evaluate side-chains
  206 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
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  675 MET
Chi-restraints excluded: chain A residue  738 GLN
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  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:    0.9980
   chunk 110 optimal weight:   20.0000
   chunk 49 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4340 r_free = 0.4340 target = 0.182006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129015 restraints weight = 47028.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 5.36
r_work: 0.3423 rms_B_bonded: 5.09 restraints_weight: 2.0000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    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 = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3424
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10627  Z= 0.191
  Angle     :  0.618  14.235  14328  Z= 0.312
  Chirality :  0.043   0.187   1542
  Planarity :  0.004   0.054   1841
  Dihedral  :  3.999  18.532   1385
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.13 %
    Favored  : 82.63 %
  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:  0.98 (0.21), residues: 596
  sheet: -1.03 (0.41), residues: 146
  loop : -0.36 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 479 
 HIS   0.018   0.001   HIS A 213 
 PHE   0.016   0.001   PHE A 744 
 TYR   0.025   0.001   TYR A 904 
 ARG   0.004   0.000   ARG A 281 

*********************** 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
  227 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 201
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.8004 (mp0) cc_final: 0.7799 (mm-30)
REVERT: A  110 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7255 (pm20)
REVERT: A  218 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7745 (pt0)
REVERT: A  263 GLU cc_start: 0.7898 (tp30) cc_final: 0.7655 (mt-10)
REVERT: A  282 MET cc_start: 0.7048 (tpp) cc_final: 0.6764 (tpt)
REVERT: A  689 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7500 (tm-30)
REVERT: A  745 MET cc_start: 0.7816 (mtm) cc_final: 0.7412 (mmp)
REVERT: A  978 GLU cc_start: 0.8504 (mp0) cc_final: 0.8300 (pt0)
REVERT: B  419 LYS cc_start: 0.8053 (mppt) cc_final: 0.7318 (mmtp)
REVERT: B  476 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6800 (mt-10)
REVERT: B  564 ASN cc_start: 0.7996 (m-40) cc_final: 0.7753 (m110)
REVERT: B  578 ASP cc_start: 0.8010 (m-30) cc_final: 0.7539 (m-30)
  outliers start: 26
  outliers final: 18
  residues processed: 215
  average time/residue: 0.2362
  time to fit residues: 71.3758
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  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  196 VAL
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  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  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
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:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0980
   chunk 68 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4346 r_free = 0.4346 target = 0.182690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.132058 restraints weight = 54739.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 6.49
r_work: 0.3392 rms_B_bonded: 5.58 restraints_weight: 2.0000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    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 = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10627  Z= 0.177
  Angle     :  0.613  11.089  14328  Z= 0.309
  Chirality :  0.042   0.188   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  3.939  16.422   1385
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.90 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.90 %
    Favored  : 82.20 %
  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:  1.03 (0.21), residues: 597
  sheet: -0.95 (0.41), residues: 146
  loop : -0.31 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.019   0.001   PHE A 744 
 TYR   0.022   0.001   TYR A 904 
 ARG   0.004   0.000   ARG A 281 

*********************** 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
  217 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7250 (pm20)
REVERT: A  218 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7766 (pt0)
REVERT: A  263 GLU cc_start: 0.7829 (tp30) cc_final: 0.7591 (tm-30)
REVERT: A  265 TYR cc_start: 0.7192 (m-80) cc_final: 0.6829 (m-10)
REVERT: A  689 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7572 (tm-30)
REVERT: A  745 MET cc_start: 0.7862 (mtm) cc_final: 0.7464 (mmp)
REVERT: A  794 PHE cc_start: 0.8013 (p90) cc_final: 0.7500 (p90)
REVERT: A  978 GLU cc_start: 0.8560 (mp0) cc_final: 0.8257 (pt0)
REVERT: B  348 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8441 (ttm170)
REVERT: B  419 LYS cc_start: 0.8132 (mppt) cc_final: 0.7429 (mmtp)
REVERT: B  476 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6755 (mt-10)
REVERT: B  564 ASN cc_start: 0.7994 (m-40) cc_final: 0.7720 (m110)
REVERT: B  578 ASP cc_start: 0.8148 (m-30) cc_final: 0.7772 (m-30)
REVERT: B  582 MET cc_start: 0.8331 (ttp) cc_final: 0.8013 (ptt)
  outliers start: 22
  outliers final: 18
  residues processed: 209
  average time/residue: 0.2300
  time to fit residues: 67.5360
Evaluate side-chains
  209 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 188
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  196 VAL
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  675 MET
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  394 ASP
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
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:    0.0370
   chunk 18 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.4064

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

Flipped N/Q/H residues before XYZ refinement:
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.180574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.126616 restraints weight = 52018.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 5.67
r_work: 0.3388 rms_B_bonded: 5.18 restraints_weight: 2.0000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    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 = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10627  Z= 0.242
  Angle     :  0.656  10.326  14328  Z= 0.331
  Chirality :  0.044   0.199   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  4.049  17.648   1385
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.06 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.68 %
    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:  0.16 (0.24), residues: 1250
  helix:  0.86 (0.21), residues: 602
  sheet: -1.03 (0.42), residues: 138
  loop : -0.33 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.018   0.002   PHE A 744 
 TYR   0.027   0.001   TYR A 904 
 ARG   0.012   0.000   ARG A 741 

*********************** 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
  214 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 188
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7240 (pm20)
REVERT: A  282 MET cc_start: 0.7088 (tpp) cc_final: 0.6806 (tpt)
REVERT: A  689 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: A  710 GLU cc_start: 0.8112 (pp20) cc_final: 0.7900 (pt0)
REVERT: A  729 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8474 (mmmt)
REVERT: A  739 MET cc_start: 0.7009 (mmm) cc_final: 0.6662 (mmm)
REVERT: A  741 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7041 (mtp180)
REVERT: A  978 GLU cc_start: 0.8431 (mp0) cc_final: 0.8117 (pt0)
REVERT: B  348 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8480 (ttm170)
REVERT: B  419 LYS cc_start: 0.8171 (mppt) cc_final: 0.7487 (mmtp)
REVERT: B  476 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7002 (mp0)
REVERT: B  564 ASN cc_start: 0.8013 (m-40) cc_final: 0.7775 (m110)
REVERT: B  578 ASP cc_start: 0.8100 (m-30) cc_final: 0.7672 (m-30)
  outliers start: 26
  outliers final: 20
  residues processed: 200
  average time/residue: 0.2234
  time to fit residues: 63.0926
Evaluate side-chains
  207 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  193 VAL
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  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 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  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
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:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 114 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 180 HIS
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 = 0.4378 r_free = 0.4378 target = 0.183290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.139507 restraints weight = 41206.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 4.78
r_work: 0.3545 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.43   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 = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3134

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= 0.303
  Angle     :  0.685   9.812  14328  Z= 0.348
  Chirality :  0.045   0.202   1542
  Planarity :  0.005   0.057   1841
  Dihedral  :  4.248  19.575   1385
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.55 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.29 %
    Favored  : 80.73 %
  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: -0.02 (0.24), residues: 1250
  helix:  0.69 (0.21), residues: 601
  sheet: -1.09 (0.43), residues: 138
  loop : -0.40 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 479 
 HIS   0.005   0.001   HIS A 450 
 PHE   0.024   0.002   PHE A 744 
 TYR   0.031   0.002   TYR A 904 
 ARG   0.014   0.001   ARG A 741 

*********************** 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
  207 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 184
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7764 (tmtt)
REVERT: A  218 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7664 (pm20)
REVERT: A  252 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: A  263 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7655 (tt0)
REVERT: A  689 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: A  729 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8349 (mmmt)
REVERT: A  741 ARG cc_start: 0.7439 (ttm110) cc_final: 0.6698 (mtp180)
REVERT: B  330 ASP cc_start: 0.8139 (p0) cc_final: 0.7490 (p0)
REVERT: B  348 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8231 (ttm170)
REVERT: B  419 LYS cc_start: 0.8091 (mppt) cc_final: 0.7289 (mtmt)
REVERT: B  578 ASP cc_start: 0.7929 (m-30) cc_final: 0.7524 (m-30)
  outliers start: 23
  outliers final: 19
  residues processed: 196
  average time/residue: 0.2331
  time to fit residues: 64.7707
Evaluate side-chains
  203 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
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  276 CYS
Chi-restraints excluded: chain A residue  327 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 70 optimal weight:    0.1980
   chunk 114 optimal weight:    6.9990
   chunk 34 optimal weight:    0.3980
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.186328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.143081 restraints weight = 49002.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 5.17
r_work: 0.3579 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3575
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3575 r_free = 0.3575    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3575 r_free = 0.3575    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3575
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10627  Z= 0.182
  Angle     :  0.661  13.219  14328  Z= 0.331
  Chirality :  0.043   0.200   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  4.140  27.022   1385
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.15 %
    Favored  : 80.21 %
  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:  0.89 (0.21), residues: 602
  sheet: -0.93 (0.43), residues: 140
  loop : -0.32 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.025   0.001   PHE A 744 
 TYR   0.024   0.001   TYR A 904 
 ARG   0.013   0.000   ARG A 741 

********************** 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
  214 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 195
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7698 (pm20)
REVERT: A  252 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7713 (mm)
REVERT: A  263 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7443 (tt0)
REVERT: A  265 TYR cc_start: 0.7147 (m-80) cc_final: 0.6757 (m-10)
REVERT: A  282 MET cc_start: 0.7004 (tpp) cc_final: 0.6738 (tpt)
REVERT: A  336 ILE cc_start: 0.8349 (mm) cc_final: 0.8118 (mm)
REVERT: A  528 LYS cc_start: 0.8674 (ptpp) cc_final: 0.8461 (mtpp)
REVERT: A  689 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7379 (tm-30)
REVERT: A  729 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8357 (mmmt)
REVERT: A  741 ARG cc_start: 0.7385 (ttm110) cc_final: 0.6638 (mtp180)
REVERT: B  330 ASP cc_start: 0.7801 (p0) cc_final: 0.7479 (p0)
REVERT: B  419 LYS cc_start: 0.8139 (mppt) cc_final: 0.7359 (mtmt)
REVERT: B  476 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7127 (mp0)
REVERT: B  578 ASP cc_start: 0.8013 (m-30) cc_final: 0.7655 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 205
  average time/residue: 0.2310
  time to fit residues: 67.4742
Evaluate side-chains
  204 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
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  276 CYS
Chi-restraints excluded: chain A residue  327 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 114 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.185067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.142180 restraints weight = 43948.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 4.93
r_work: 0.3552 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10627  Z= 0.234
  Angle     :  0.688  14.443  14328  Z= 0.343
  Chirality :  0.044   0.197   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  4.150  25.404   1385
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.98 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.24 %
    Favored  : 79.95 %
  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:  0.11 (0.24), residues: 1250
  helix:  0.86 (0.21), residues: 602
  sheet: -1.08 (0.42), residues: 144
  loop : -0.38 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.022   0.002   PHE A 744 
 TYR   0.016   0.001   TYR A 265 
 ARG   0.013   0.000   ARG A 741 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6385.54 seconds
wall clock time: 113 minutes 50.16 seconds (6830.16 seconds total)