Starting phenix.real_space_refine
on Sat Jul 26 12:01:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbm_61319/07_2025/9jbm_61319.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbm_61319/07_2025/9jbm_61319.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbm_61319/07_2025/9jbm_61319.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbm_61319/07_2025/9jbm_61319.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbm_61319/07_2025/9jbm_61319.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbm_61319/07_2025/9jbm_61319.cif"
  }
  resolution = 3.83
  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=   0.003 sd=   0.042
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      48      5.16       5
     C    5549      2.51       5
     N    1446      2.21       5
     O    1545      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8588
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1089, 8478
          Classifications: {'peptide': 1089}
          Link IDs: {'PTRANS': 59, 'TRANS': 1029}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 110
          Classifications: {'peptide': 22}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'TRANS': 21}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'UNK:plan-1': 22}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 13.51, per 1000 atoms: 1.57
  Number of scatterers: 8588
  At special positions: 0
  Unit cell: (73.216, 95.68, 148.928, 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      48     16.00
     O    1545      8.00
     N    1446      7.00
     C    5549      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: 5.57
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      54.5% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 64
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 73 through 84
    Processing helix  chain 'A' and resid 99 through 121
      removed outlier: 3.532A  pdb=" N   GLY A 118 " --> pdb=" O   THR A 114 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   HIS A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 129
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 212 through 223
    Processing helix  chain 'A' and resid 233 through 243
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 262 through 295
      removed outlier: 3.637A  pdb=" N   VAL A 267 " --> pdb=" O   TRP A 263 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A 268 " --> pdb=" O   TYR A 264 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU A 290 " --> pdb=" O   ARG A 286 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 349 through 354
      removed outlier: 3.522A  pdb=" N   THR A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 3.955A  pdb=" N   ASP A 366 " --> pdb=" O   PRO A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 379
      removed outlier: 3.690A  pdb=" N   SER A 379 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 420
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 441 through 469
      removed outlier: 3.534A  pdb=" N   ASP A 469 " --> pdb=" O   GLU A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.871A  pdb=" N   VAL A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 510
      removed outlier: 4.707A  pdb=" N   ILE A 495 " --> pdb=" O   PRO A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 519
      No H-bonds generated for 'chain 'A' and resid 517 through 519'
    Processing helix  chain 'A' and resid 520 through 527
      removed outlier: 3.633A  pdb=" N   GLY A 525 " --> pdb=" O   ILE A 521 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 563
      removed outlier: 3.687A  pdb=" N   ILE A 563 " --> pdb=" O   VAL A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 656 through 663
      removed outlier: 3.898A  pdb=" N   SER A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 681
    Processing helix  chain 'A' and resid 697 through 708
      removed outlier: 3.748A  pdb=" N   ARG A 702 " --> pdb=" O   HIS A 698 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LYS A 705 " --> pdb=" O   ALA A 701 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   ARG A 706 " --> pdb=" O   ARG A 702 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLU A 707 " --> pdb=" O   GLU A 703 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA A 708 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 739
    Processing helix  chain 'A' and resid 750 through 761
    Processing helix  chain 'A' and resid 799 through 807
      removed outlier: 4.368A  pdb=" N   LEU A 803 " --> pdb=" O   SER A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 823
    Processing helix  chain 'A' and resid 823 through 831
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 841 through 855
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 868 through 875
    Processing helix  chain 'A' and resid 952 through 958
      removed outlier: 3.505A  pdb=" N   ILE A 956 " --> pdb=" O   GLY A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 1009
      removed outlier: 4.084A  pdb=" N   CYS A 971 " --> pdb=" O   ILE A 967 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A1003 " --> pdb=" O   ALA A 999 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU A1005 " --> pdb=" O   SER A1001 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   TYR A1006 " --> pdb=" O   GLN A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1033
      removed outlier: 3.620A  pdb=" N   ARG A1033 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1080
    Processing helix  chain 'A' and resid 1097 through 1119
      removed outlier: 3.549A  pdb=" N   ASN A1118 " --> pdb=" O   THR A1114 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR A1119 " --> pdb=" O   PHE A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1150
    Processing helix  chain 'A' and resid 1153 through 1160
    Processing helix  chain 'A' and resid 1166 through 1196
    Processing helix  chain 'B' and resid 2 through 22
      removed outlier: 3.696A  pdb=" N   UNK B   6 " --> pdb=" O   UNK B   2 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   UNK B   7 " --> pdb=" O   UNK B   3 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   UNK B   8 " --> pdb=" O   UNK B   4 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   UNK B   9 " --> pdb=" O   UNK B   5 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   UNK B  12 " --> pdb=" O   UNK B   8 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   UNK B  17 " --> pdb=" O   UNK B  13 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   UNK B  18 " --> pdb=" O   UNK B  14 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   UNK B  19 " --> pdb=" O   UNK B  15 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   UNK B  22 " --> pdb=" O   UNK B  18 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 132
      removed outlier: 3.525A  pdb=" N   ALA A  52 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TRP A  54 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ALA A 157 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   GLU A 173 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   LEU A 170 " --> pdb=" O   TYR A 181 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 305
    Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 325
      removed outlier: 6.938A  pdb=" N   VAL A 411 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   ASP A 337 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 359 through 361
      removed outlier: 6.293A  pdb=" N   ASP A 348 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   VAL A 390 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 515
      removed outlier: 7.113A  pdb=" N   THR A 859 " --> pdb=" O   VAL A 877 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   VAL A 879 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   MET A 861 " --> pdb=" O   VAL A 879 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   LEU A 881 " --> pdb=" O   MET A 861 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   GLY A 863 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
      removed outlier: 8.694A  pdb=" N   PHE A 837 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   MET A 745 " --> pdb=" O   PHE A 837 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU A 809 " --> pdb=" O   VAL A 836 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ALA A 838 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU A 811 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   THR A 812 " --> pdb=" O   LEU A 772 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 544 through 549
      removed outlier: 5.055A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   LYS A 714 " --> pdb=" O   TYR A 690 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   LEU A 688 " --> pdb=" O   VAL A 716 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   PHE A 718 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   LEU A 686 " --> pdb=" O   PHE A 718 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   VAL A 720 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ARG A 684 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   TYR A 649 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ARG A 632 " --> pdb=" O   PHE A 626 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   PHE A 626 " --> pdb=" O   ARG A 632 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER A 638 " --> pdb=" O   ILE A 620 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   ILE A 620 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   GLU A 640 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   LEU A 618 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 544 through 549
      removed outlier: 5.055A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   PHE A 715 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 578 through 579
      removed outlier: 3.801A  pdb=" N   MET A 578 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 586 " --> pdb=" O   MET A 578 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    482 hydrogen bonds defined for protein.
    1398 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: 4.16

  Time building geometry restraints manager: 6.17 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2182
        1.33 -     1.45: 1551
        1.45 -     1.57: 4973
        1.57 -     1.69: 1
        1.69 -     1.81: 70
  Bond restraints: 8777
  Sorted by residual:
  bond pdb=" CG  PRO A 800 "
       pdb=" CD  PRO A 800 "
    ideal  model  delta    sigma   weight residual
    1.503  1.301  0.202 3.40e-02 8.65e+02 3.55e+01
  bond pdb=" N   ARG A 310 "
       pdb=" CA  ARG A 310 "
    ideal  model  delta    sigma   weight residual
    1.453  1.495 -0.042 1.50e-02 4.44e+03 7.83e+00
  bond pdb=" CB  PRO A 800 "
       pdb=" CG  PRO A 800 "
    ideal  model  delta    sigma   weight residual
    1.492  1.604 -0.112 5.00e-02 4.00e+02 5.06e+00
  bond pdb=" CA  TYR A1091 "
       pdb=" CB  TYR A1091 "
    ideal  model  delta    sigma   weight residual
    1.526  1.559 -0.033 1.51e-02 4.39e+03 4.78e+00
  bond pdb=" CA  ILE A 521 "
       pdb=" CB  ILE A 521 "
    ideal  model  delta    sigma   weight residual
    1.534  1.547 -0.013 6.80e-03 2.16e+04 3.40e+00
  ... (remaining 8772 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 11455
        2.73 -     5.46: 396
        5.46 -     8.19: 55
        8.19 -    10.92: 14
       10.92 -    13.66: 5
  Bond angle restraints: 11925
  Sorted by residual:
  angle pdb=" CA  PRO A 800 "
        pdb=" N   PRO A 800 "
        pdb=" CD  PRO A 800 "
      ideal   model   delta    sigma   weight residual
     112.00   99.65   12.35 1.40e+00 5.10e-01 7.78e+01
  angle pdb=" N   PRO A 800 "
        pdb=" CD  PRO A 800 "
        pdb=" CG  PRO A 800 "
      ideal   model   delta    sigma   weight residual
     103.20   91.49   11.71 1.50e+00 4.44e-01 6.09e+01
  angle pdb=" CA  ARG A 702 "
        pdb=" CB  ARG A 702 "
        pdb=" CG  ARG A 702 "
      ideal   model   delta    sigma   weight residual
     114.10  127.76  -13.66 2.00e+00 2.50e-01 4.66e+01
  angle pdb=" C   TYR A 264 "
        pdb=" N   TYR A 265 "
        pdb=" CA  TYR A 265 "
      ideal   model   delta    sigma   weight residual
     120.28  129.10   -8.82 1.34e+00 5.57e-01 4.34e+01
  angle pdb=" N   GLN A1002 "
        pdb=" CA  GLN A1002 "
        pdb=" C   GLN A1002 "
      ideal   model   delta    sigma   weight residual
     111.28  117.91   -6.63 1.09e+00 8.42e-01 3.70e+01
  ... (remaining 11920 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4990
       17.85 -    35.69: 245
       35.69 -    53.54: 40
       53.54 -    71.38: 9
       71.38 -    89.23: 8
  Dihedral angle restraints: 5292
    sinusoidal: 2055
      harmonic: 3237
  Sorted by residual:
  dihedral pdb=" CA  LEU A  36 "
           pdb=" C   LEU A  36 "
           pdb=" N   ALA A  37 "
           pdb=" CA  ALA A  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.10   37.90     0      5.00e+00 4.00e-02 5.75e+01
  dihedral pdb=" CA  PHE A 532 "
           pdb=" C   PHE A 532 "
           pdb=" N   ASP A 533 "
           pdb=" CA  ASP A 533 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" N   ARG A 702 "
           pdb=" C   ARG A 702 "
           pdb=" CA  ARG A 702 "
           pdb=" CB  ARG A 702 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.95   -9.15     0      2.50e+00 1.60e-01 1.34e+01
  ... (remaining 5289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1124
       0.067 -    0.134: 229
       0.134 -    0.200: 33
       0.200 -    0.267: 8
       0.267 -    0.334: 4
  Chirality restraints: 1398
  Sorted by residual:
  chirality pdb=" CB  VAL A 347 "
            pdb=" CA  VAL A 347 "
            pdb=" CG1 VAL A 347 "
            pdb=" CG2 VAL A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CA  ARG A 702 "
            pdb=" N   ARG A 702 "
            pdb=" C   ARG A 702 "
            pdb=" CB  ARG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CB  VAL A 338 "
            pdb=" CA  VAL A 338 "
            pdb=" CG1 VAL A 338 "
            pdb=" CG2 VAL A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.19e+00
  ... (remaining 1395 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 799 "    0.092 5.00e-02 4.00e+02   1.30e-01 2.70e+01
        pdb=" N   PRO A 800 "   -0.224 5.00e-02 4.00e+02
        pdb=" CA  PRO A 800 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO A 800 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1053 "   -0.002 2.00e-02 2.50e+03   3.58e-02 2.57e+01
        pdb=" CG  TYR A1053 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1053 "    0.051 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1053 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1053 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1053 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1053 "   -0.051 2.00e-02 2.50e+03
        pdb=" OH  TYR A1053 "    0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 988 "   -0.024 2.00e-02 2.50e+03   4.73e-02 2.24e+01
        pdb=" C   PHE A 988 "    0.082 2.00e-02 2.50e+03
        pdb=" O   PHE A 988 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   LYS A 989 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 482
        2.73 -     3.27: 9025
        3.27 -     3.81: 13628
        3.81 -     4.36: 16096
        4.36 -     4.90: 26709
  Nonbonded interactions: 65940
  Sorted by model distance:
  nonbonded pdb=" O   GLN A1111 "
            pdb=" OG1 THR A1114 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ASP A 533 "
            pdb=" OG1 THR A 537 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   GLY A1196 "
            pdb=" OG1 THR A1197 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" NZ  LYS A 691 "
            pdb=" O   SER A 712 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OD1 ASP A 337 "
            pdb=" OG1 THR A 421 "
     model   vdw
     2.257 3.040
  ... (remaining 65935 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             180.040
  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:             0.020
  Extract box with map and model:          8.790
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     42.330
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.090
  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:             0.010
  Load rotamer database and sin/cos tables:3.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  235.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
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      :  0.005   0.202   8777  Z= 0.255
  Angle     :  1.197  13.655  11925  Z= 0.708
  Chirality :  0.058   0.334   1398
  Planarity :  0.011   0.142   1511
  Dihedral  : 11.969  89.226   3192
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.32 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.24), residues: 1083
  helix:  0.87 (0.21), residues: 505
  sheet:  0.35 (0.40), residues: 151
  loop : -0.34 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP A 257 
 HIS   0.017   0.002   HIS A 568 
 PHE   0.033   0.003   PHE A 200 
 TYR   0.051   0.005   TYR A1053 
 ARG   0.035   0.004   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16213 (  479)
  hydrogen bonds       : angle       6.92341 ( 1398)
  covalent geometry    : bond        0.00544 ( 8777)
  covalent geometry    : angle       1.19696 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 3.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TRP cc_start: 0.6788 (t60) cc_final: 0.6423 (t60)
REVERT: A  135 ASP cc_start: 0.6864 (t70) cc_final: 0.6382 (t70)
REVERT: A  181 TYR cc_start: 0.7410 (t80) cc_final: 0.7033 (t80)
REVERT: A  214 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6904 (mt-10)
REVERT: A  215 ILE cc_start: 0.8516 (mm) cc_final: 0.8280 (mm)
REVERT: A  253 CYS cc_start: 0.7103 (m) cc_final: 0.6812 (m)
REVERT: A  282 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8258 (mm-40)
REVERT: A  285 MET cc_start: 0.7874 (ttm) cc_final: 0.7575 (ttm)
REVERT: A  301 ILE cc_start: 0.8864 (tt) cc_final: 0.8619 (tp)
REVERT: A  312 ILE cc_start: 0.8277 (mt) cc_final: 0.8014 (mp)
REVERT: A  332 ASN cc_start: 0.7298 (m-40) cc_final: 0.7086 (m-40)
REVERT: A  362 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6314 (mt-10)
REVERT: A  364 ILE cc_start: 0.8314 (tp) cc_final: 0.7919 (tt)
REVERT: A  371 ARG cc_start: 0.8096 (ppt170) cc_final: 0.7861 (ppt170)
REVERT: A  389 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7470 (ttmt)
REVERT: A  392 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7371 (tm-30)
REVERT: A  423 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7692 (tm-30)
REVERT: A  465 GLU cc_start: 0.7250 (tp30) cc_final: 0.6929 (tp30)
REVERT: A  480 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7251 (mt-10)
REVERT: A  568 HIS cc_start: 0.7246 (m-70) cc_final: 0.6997 (m90)
REVERT: A  592 LYS cc_start: 0.8357 (tppt) cc_final: 0.8050 (tptt)
REVERT: A  599 ASP cc_start: 0.8092 (m-30) cc_final: 0.7874 (m-30)
REVERT: A  623 ARG cc_start: 0.6138 (mtp85) cc_final: 0.5808 (mtp85)
REVERT: A  633 MET cc_start: 0.6568 (tmm) cc_final: 0.6086 (tmm)
REVERT: A  658 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7670 (mm-30)
REVERT: A  663 MET cc_start: 0.7815 (mtm) cc_final: 0.7192 (mtm)
REVERT: A  702 ARG cc_start: 0.7141 (pmt170) cc_final: 0.6934 (pmt170)
REVERT: A  729 SER cc_start: 0.8351 (m) cc_final: 0.7956 (p)
REVERT: A  733 ILE cc_start: 0.8268 (tp) cc_final: 0.7996 (tp)
REVERT: A  734 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7483 (ttm110)
REVERT: A  736 ILE cc_start: 0.8349 (mm) cc_final: 0.7932 (mp)
REVERT: A  745 MET cc_start: 0.6600 (ttt) cc_final: 0.6319 (ttt)
REVERT: A  846 GLU cc_start: 0.7162 (tt0) cc_final: 0.6872 (tt0)
REVERT: A  861 MET cc_start: 0.7754 (tpt) cc_final: 0.7549 (tpt)
REVERT: A 1022 LEU cc_start: 0.7954 (tp) cc_final: 0.7742 (mm)
REVERT: A 1050 PHE cc_start: 0.7341 (m-80) cc_final: 0.7122 (m-80)
REVERT: A 1074 ARG cc_start: 0.7733 (mpt-90) cc_final: 0.7325 (mpt-90)
REVERT: A 1092 LYS cc_start: 0.7752 (tttm) cc_final: 0.7453 (tttm)
REVERT: A 1126 GLU cc_start: 0.7559 (pt0) cc_final: 0.7200 (pt0)
REVERT: A 1149 LEU cc_start: 0.7231 (tp) cc_final: 0.6969 (tp)
REVERT: A 1192 GLN cc_start: 0.7934 (tp40) cc_final: 0.7317 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.5485
  time to fit residues: 210.3441
Evaluate side-chains
  245 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 83 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 56 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0470
   chunk 86 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.8880

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
A 175 GLN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 HIS
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.145073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123547 restraints weight = 15903.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.127761 restraints weight = 8522.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.130577 restraints weight = 5338.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8777  Z= 0.161
  Angle     :  0.717  12.600  11925  Z= 0.366
  Chirality :  0.046   0.231   1398
  Planarity :  0.005   0.069   1511
  Dihedral  :  4.540  16.142   1185
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.85 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.25), residues: 1083
  helix:  1.40 (0.22), residues: 515
  sheet:  0.68 (0.40), residues: 161
  loop : -0.07 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 257 
 HIS   0.014   0.001   HIS A 568 
 PHE   0.029   0.002   PHE A  70 
 TYR   0.025   0.002   TYR A  75 
 ARG   0.006   0.001   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05123 (  479)
  hydrogen bonds       : angle       5.34526 ( 1398)
  covalent geometry    : bond        0.00349 ( 8777)
  covalent geometry    : angle       0.71687 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 270
  time to evaluate  : 0.835 
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: 0.7552 (mt-10) cc_final: 0.7244 (mt-10)
REVERT: A   78 TRP cc_start: 0.6757 (t60) cc_final: 0.6384 (t60)
REVERT: A  143 LYS cc_start: 0.8087 (pptt) cc_final: 0.7553 (pptt)
REVERT: A  181 TYR cc_start: 0.7499 (t80) cc_final: 0.7127 (t80)
REVERT: A  214 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6850 (mt-10)
REVERT: A  215 ILE cc_start: 0.8717 (mm) cc_final: 0.8452 (mm)
REVERT: A  253 CYS cc_start: 0.7194 (m) cc_final: 0.6905 (m)
REVERT: A  316 GLU cc_start: 0.7542 (mp0) cc_final: 0.7065 (mp0)
REVERT: A  337 ASP cc_start: 0.7116 (m-30) cc_final: 0.6840 (m-30)
REVERT: A  362 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7084 (mt-10)
REVERT: A  364 ILE cc_start: 0.8503 (tp) cc_final: 0.8086 (tt)
REVERT: A  389 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7801 (ttmt)
REVERT: A  392 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: A  423 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7668 (tm-30)
REVERT: A  465 GLU cc_start: 0.7350 (tp30) cc_final: 0.6986 (tp30)
REVERT: A  480 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7320 (mt-10)
REVERT: A  568 HIS cc_start: 0.7401 (m-70) cc_final: 0.6966 (m90)
REVERT: A  633 MET cc_start: 0.6728 (tmm) cc_final: 0.5955 (tmm)
REVERT: A  663 MET cc_start: 0.7799 (mtm) cc_final: 0.7270 (mtm)
REVERT: A  690 TYR cc_start: 0.8170 (t80) cc_final: 0.7575 (t80)
REVERT: A  728 ASP cc_start: 0.7372 (p0) cc_final: 0.7112 (p0)
REVERT: A  734 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7701 (ttm110)
REVERT: A  736 ILE cc_start: 0.8407 (mm) cc_final: 0.7976 (mp)
REVERT: A  846 GLU cc_start: 0.7155 (tt0) cc_final: 0.6919 (tt0)
REVERT: A  861 MET cc_start: 0.7752 (tpt) cc_final: 0.7284 (tpt)
REVERT: A  962 SER cc_start: 0.8511 (t) cc_final: 0.8154 (p)
REVERT: A 1050 PHE cc_start: 0.7518 (m-80) cc_final: 0.7295 (m-10)
REVERT: A 1092 LYS cc_start: 0.7725 (tttm) cc_final: 0.7500 (tttm)
REVERT: A 1106 MET cc_start: 0.8021 (tmm) cc_final: 0.7760 (tmm)
REVERT: A 1126 GLU cc_start: 0.7605 (pt0) cc_final: 0.7272 (pt0)
REVERT: A 1170 LYS cc_start: 0.8743 (tttt) cc_final: 0.8141 (mtmm)
  outliers start: 14
  outliers final: 10
  residues processed: 274
  average time/residue: 0.2512
  time to fit residues: 90.7639
Evaluate side-chains
  265 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 255
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  963 LYS
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1183 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 HIS
A 393 HIS
A 568 HIS
A 625 HIS
A 698 HIS
A 737 GLN
A 867 ASN
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.135934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113748 restraints weight = 15839.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.117840 restraints weight = 8441.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.120591 restraints weight = 5268.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   8777  Z= 0.338
  Angle     :  0.827  15.814  11925  Z= 0.436
  Chirality :  0.050   0.216   1398
  Planarity :  0.006   0.059   1511
  Dihedral  :  5.227  20.841   1185
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.68 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 13.36 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.24), residues: 1083
  helix:  0.59 (0.21), residues: 516
  sheet:  0.71 (0.42), residues: 143
  loop : -0.47 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 257 
 HIS   0.009   0.002   HIS A 568 
 PHE   0.033   0.003   PHE A1115 
 TYR   0.024   0.003   TYR A 807 
 ARG   0.009   0.001   ARG A1042 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06391 (  479)
  hydrogen bonds       : angle       5.56709 ( 1398)
  covalent geometry    : bond        0.00674 ( 8777)
  covalent geometry    : angle       0.82666 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 295
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.8611 (t) cc_final: 0.8299 (t)
REVERT: A   78 TRP cc_start: 0.6896 (t60) cc_final: 0.6517 (t60)
REVERT: A  104 LEU cc_start: 0.7901 (mt) cc_final: 0.7605 (mp)
REVERT: A  138 LYS cc_start: 0.8681 (mmpt) cc_final: 0.8465 (mmpt)
REVERT: A  143 LYS cc_start: 0.8261 (pptt) cc_final: 0.7726 (pptt)
REVERT: A  144 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.8033 (m)
REVERT: A  154 GLU cc_start: 0.7556 (tt0) cc_final: 0.7340 (tt0)
REVERT: A  200 PHE cc_start: 0.6608 (t80) cc_final: 0.6024 (t80)
REVERT: A  214 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6854 (mt-10)
REVERT: A  215 ILE cc_start: 0.8646 (mm) cc_final: 0.8313 (mm)
REVERT: A  229 MET cc_start: 0.5722 (tpt) cc_final: 0.4296 (tpt)
REVERT: A  240 GLU cc_start: 0.7650 (tp30) cc_final: 0.7227 (tp30)
REVERT: A  316 GLU cc_start: 0.7738 (mp0) cc_final: 0.7115 (mp0)
REVERT: A  338 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7840 (m)
REVERT: A  364 ILE cc_start: 0.8869 (tp) cc_final: 0.7775 (tt)
REVERT: A  371 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8112 (ttp80)
REVERT: A  374 ASP cc_start: 0.8580 (t0) cc_final: 0.8348 (t0)
REVERT: A  392 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7288 (tm-30)
REVERT: A  423 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7889 (tm-30)
REVERT: A  478 PHE cc_start: 0.7940 (t80) cc_final: 0.7702 (t80)
REVERT: A  480 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7441 (mt-10)
REVERT: A  568 HIS cc_start: 0.7314 (m90) cc_final: 0.6812 (m-70)
REVERT: A  594 MET cc_start: 0.8387 (mmm) cc_final: 0.7996 (mmm)
REVERT: A  633 MET cc_start: 0.7028 (tmm) cc_final: 0.5969 (tmm)
REVERT: A  654 LYS cc_start: 0.7362 (ptmm) cc_final: 0.6872 (ptmm)
REVERT: A  663 MET cc_start: 0.7985 (mtm) cc_final: 0.7542 (mtm)
REVERT: A  676 THR cc_start: 0.8336 (m) cc_final: 0.7918 (t)
REVERT: A  686 LEU cc_start: 0.8012 (mt) cc_final: 0.7771 (mt)
REVERT: A  690 TYR cc_start: 0.8474 (t80) cc_final: 0.7904 (t80)
REVERT: A  691 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8094 (mmtp)
REVERT: A  716 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.7795 (m)
REVERT: A  734 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7767 (ttm110)
REVERT: A  801 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8045 (mmmt)
REVERT: A  846 GLU cc_start: 0.7454 (tt0) cc_final: 0.7242 (tt0)
REVERT: A  861 MET cc_start: 0.7351 (tpt) cc_final: 0.7119 (tpt)
REVERT: A  869 VAL cc_start: 0.7222 (OUTLIER) cc_final: 0.6876 (m)
REVERT: A  950 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7870 (ttpp)
REVERT: A  956 ILE cc_start: 0.8417 (mm) cc_final: 0.8070 (mm)
REVERT: A  962 SER cc_start: 0.8544 (t) cc_final: 0.8167 (p)
REVERT: A 1035 LYS cc_start: 0.8291 (mttt) cc_final: 0.7783 (mmmm)
REVERT: A 1042 ARG cc_start: 0.7561 (ttp80) cc_final: 0.7255 (ttp80)
REVERT: A 1050 PHE cc_start: 0.7826 (m-80) cc_final: 0.7530 (m-80)
REVERT: A 1060 LEU cc_start: 0.7497 (tp) cc_final: 0.7171 (tp)
REVERT: A 1065 HIS cc_start: 0.7213 (m-70) cc_final: 0.7008 (m-70)
REVERT: A 1090 LEU cc_start: 0.8384 (mm) cc_final: 0.7920 (mp)
REVERT: A 1106 MET cc_start: 0.8390 (tmm) cc_final: 0.7907 (tmm)
REVERT: A 1111 GLN cc_start: 0.7913 (tm-30) cc_final: 0.6983 (tm-30)
REVERT: A 1125 MET cc_start: 0.7544 (mtt) cc_final: 0.7157 (mtt)
REVERT: A 1126 GLU cc_start: 0.7644 (pt0) cc_final: 0.7171 (pt0)
REVERT: A 1192 GLN cc_start: 0.8187 (tp40) cc_final: 0.7617 (tp40)
  outliers start: 39
  outliers final: 20
  residues processed: 309
  average time/residue: 0.2302
  time to fit residues: 95.6081
Evaluate side-chains
  305 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 280
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  441 ASN
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  625 HIS
Chi-restraints excluded: chain A residue  670 ASP
Chi-restraints excluded: chain A residue  691 LYS
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  814 ASP
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   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 119 HIS
A 625 HIS
A 759 GLN
A1061 GLN
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.140447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.118467 restraints weight = 15626.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.122580 restraints weight = 8260.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.125288 restraints weight = 5151.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8777  Z= 0.144
  Angle     :  0.666  13.167  11925  Z= 0.336
  Chirality :  0.044   0.193   1398
  Planarity :  0.005   0.067   1511
  Dihedral  :  4.695  18.827   1185
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.57 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.92 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1083
  helix:  1.09 (0.22), residues: 518
  sheet:  0.29 (0.39), residues: 157
  loop : -0.41 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  78 
 HIS   0.011   0.001   HIS A 625 
 PHE   0.021   0.002   PHE A 252 
 TYR   0.028   0.002   TYR A  75 
 ARG   0.007   0.001   ARG A 839 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04625 (  479)
  hydrogen bonds       : angle       5.00345 ( 1398)
  covalent geometry    : bond        0.00305 ( 8777)
  covalent geometry    : angle       0.66586 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 270
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TRP cc_start: 0.6865 (t60) cc_final: 0.6413 (t60)
REVERT: A  104 LEU cc_start: 0.7766 (mt) cc_final: 0.7388 (mp)
REVERT: A  133 GLU cc_start: 0.6252 (mp0) cc_final: 0.5959 (mp0)
REVERT: A  143 LYS cc_start: 0.8213 (pptt) cc_final: 0.7742 (pptt)
REVERT: A  154 GLU cc_start: 0.7564 (tt0) cc_final: 0.7345 (tt0)
REVERT: A  178 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7970 (ttmm)
REVERT: A  186 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7591 (mtmm)
REVERT: A  200 PHE cc_start: 0.6400 (t80) cc_final: 0.6100 (t80)
REVERT: A  214 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6711 (mt-10)
REVERT: A  215 ILE cc_start: 0.8683 (mm) cc_final: 0.8344 (mm)
REVERT: A  229 MET cc_start: 0.5697 (tpt) cc_final: 0.4378 (tpt)
REVERT: A  277 GLU cc_start: 0.8026 (mm-30) cc_final: 0.6854 (mm-30)
REVERT: A  316 GLU cc_start: 0.7753 (mp0) cc_final: 0.7201 (mp0)
REVERT: A  338 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7728 (m)
REVERT: A  349 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7744 (tt0)
REVERT: A  364 ILE cc_start: 0.8878 (tp) cc_final: 0.7875 (tt)
REVERT: A  371 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8011 (ttp80)
REVERT: A  374 ASP cc_start: 0.8634 (t0) cc_final: 0.8410 (t0)
REVERT: A  392 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7616 (tm-30)
REVERT: A  423 GLN cc_start: 0.8481 (tm-30) cc_final: 0.7592 (tm-30)
REVERT: A  480 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: A  568 HIS cc_start: 0.7382 (m90) cc_final: 0.6904 (m90)
REVERT: A  592 LYS cc_start: 0.8534 (tppt) cc_final: 0.8200 (tptm)
REVERT: A  594 MET cc_start: 0.8094 (mmm) cc_final: 0.7828 (mmm)
REVERT: A  633 MET cc_start: 0.7090 (tmm) cc_final: 0.6164 (tmm)
REVERT: A  654 LYS cc_start: 0.7129 (ptmm) cc_final: 0.6655 (ptmm)
REVERT: A  658 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7844 (mm-30)
REVERT: A  663 MET cc_start: 0.7955 (mtm) cc_final: 0.7529 (mtm)
REVERT: A  690 TYR cc_start: 0.8370 (t80) cc_final: 0.7936 (t80)
REVERT: A  716 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.7726 (m)
REVERT: A  734 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7731 (ttm110)
REVERT: A  760 GLU cc_start: 0.8176 (tp30) cc_final: 0.7867 (tp30)
REVERT: A  801 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7827 (mmmt)
REVERT: A  854 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7770 (tt0)
REVERT: A  861 MET cc_start: 0.7504 (tpt) cc_final: 0.7272 (tpt)
REVERT: A  950 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7792 (ttpp)
REVERT: A  962 SER cc_start: 0.8392 (t) cc_final: 0.8016 (p)
REVERT: A  993 LEU cc_start: 0.8169 (tp) cc_final: 0.7808 (tt)
REVERT: A 1035 LYS cc_start: 0.8227 (mttt) cc_final: 0.7770 (mmmm)
REVERT: A 1042 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7219 (ttp80)
REVERT: A 1050 PHE cc_start: 0.7686 (m-80) cc_final: 0.7332 (m-10)
REVERT: A 1090 LEU cc_start: 0.8314 (mm) cc_final: 0.7870 (mp)
REVERT: A 1106 MET cc_start: 0.8308 (tmm) cc_final: 0.7803 (tmm)
REVERT: A 1111 GLN cc_start: 0.7982 (tm-30) cc_final: 0.6996 (tm-30)
REVERT: A 1112 MET cc_start: 0.7043 (tpp) cc_final: 0.6756 (tpp)
REVERT: A 1126 GLU cc_start: 0.7599 (pt0) cc_final: 0.7222 (pt0)
REVERT: A 1170 LYS cc_start: 0.8677 (tttt) cc_final: 0.8443 (tttt)
REVERT: A 1192 GLN cc_start: 0.8073 (tp40) cc_final: 0.7556 (tp40)
  outliers start: 33
  outliers final: 18
  residues processed: 280
  average time/residue: 0.2561
  time to fit residues: 97.7175
Evaluate side-chains
  284 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 263
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  670 ASP
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0470
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.0482

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1061 GLN
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.135286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.113792 restraints weight = 15692.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.117745 restraints weight = 8430.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.120408 restraints weight = 5312.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8777  Z= 0.145
  Angle     :  0.650  15.949  11925  Z= 0.325
  Chirality :  0.043   0.181   1398
  Planarity :  0.005   0.069   1511
  Dihedral  :  4.527  18.115   1185
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.12 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.00 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.25), residues: 1083
  helix:  1.25 (0.22), residues: 517
  sheet:  0.21 (0.39), residues: 161
  loop : -0.31 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 756 
 PHE   0.023   0.001   PHE A 252 
 TYR   0.020   0.002   TYR A1071 
 ARG   0.008   0.001   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  479)
  hydrogen bonds       : angle       4.85427 ( 1398)
  covalent geometry    : bond        0.00304 ( 8777)
  covalent geometry    : angle       0.65005 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 280
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TRP cc_start: 0.6869 (t60) cc_final: 0.6412 (t60)
REVERT: A  104 LEU cc_start: 0.7662 (mt) cc_final: 0.7405 (mp)
REVERT: A  143 LYS cc_start: 0.8166 (pptt) cc_final: 0.7712 (pptt)
REVERT: A  176 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8066 (mttm)
REVERT: A  186 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7624 (mtmm)
REVERT: A  200 PHE cc_start: 0.6305 (t80) cc_final: 0.5862 (t80)
REVERT: A  214 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6728 (mt-10)
REVERT: A  215 ILE cc_start: 0.8713 (mm) cc_final: 0.8394 (mm)
REVERT: A  229 MET cc_start: 0.5768 (tpt) cc_final: 0.4617 (tpt)
REVERT: A  240 GLU cc_start: 0.7669 (tp30) cc_final: 0.7417 (tp30)
REVERT: A  311 PRO cc_start: 0.8101 (Cg_exo) cc_final: 0.7885 (Cg_endo)
REVERT: A  316 GLU cc_start: 0.7767 (mp0) cc_final: 0.7279 (mp0)
REVERT: A  349 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7630 (tt0)
REVERT: A  361 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8107 (mmmt)
REVERT: A  364 ILE cc_start: 0.8875 (tp) cc_final: 0.7668 (tt)
REVERT: A  371 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7477 (ptt90)
REVERT: A  392 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: A  423 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: A  478 PHE cc_start: 0.7980 (t80) cc_final: 0.7777 (t80)
REVERT: A  480 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7305 (mt-10)
REVERT: A  485 LEU cc_start: 0.8568 (tp) cc_final: 0.8086 (tt)
REVERT: A  526 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7831 (ttpt)
REVERT: A  568 HIS cc_start: 0.7419 (m90) cc_final: 0.6911 (m90)
REVERT: A  592 LYS cc_start: 0.8558 (tppt) cc_final: 0.8128 (tptt)
REVERT: A  594 MET cc_start: 0.8071 (mmm) cc_final: 0.7815 (mmm)
REVERT: A  633 MET cc_start: 0.7109 (tmm) cc_final: 0.6222 (tmm)
REVERT: A  654 LYS cc_start: 0.7118 (ptmm) cc_final: 0.6692 (ptmm)
REVERT: A  658 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7867 (mm-30)
REVERT: A  663 MET cc_start: 0.7997 (mtm) cc_final: 0.7581 (mtm)
REVERT: A  734 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7770 (ttm110)
REVERT: A  760 GLU cc_start: 0.8170 (tp30) cc_final: 0.7840 (tp30)
REVERT: A  801 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7796 (mmmt)
REVERT: A  853 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8249 (ttpt)
REVERT: A  854 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7786 (tt0)
REVERT: A  861 MET cc_start: 0.7528 (tpt) cc_final: 0.7293 (tpt)
REVERT: A  962 SER cc_start: 0.8329 (t) cc_final: 0.7974 (p)
REVERT: A  993 LEU cc_start: 0.8131 (tp) cc_final: 0.7793 (tt)
REVERT: A 1042 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7329 (ttp80)
REVERT: A 1044 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8204 (tpp80)
REVERT: A 1050 PHE cc_start: 0.7569 (m-80) cc_final: 0.7248 (m-10)
REVERT: A 1060 LEU cc_start: 0.7401 (tp) cc_final: 0.7067 (tp)
REVERT: A 1065 HIS cc_start: 0.7060 (m-70) cc_final: 0.6451 (m-70)
REVERT: A 1090 LEU cc_start: 0.8276 (mm) cc_final: 0.7836 (mp)
REVERT: A 1106 MET cc_start: 0.8315 (tmm) cc_final: 0.7843 (tmm)
REVERT: A 1111 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: A 1126 GLU cc_start: 0.7596 (pt0) cc_final: 0.7258 (pt0)
REVERT: A 1170 LYS cc_start: 0.8696 (tttt) cc_final: 0.8478 (tttt)
  outliers start: 33
  outliers final: 26
  residues processed: 294
  average time/residue: 0.2290
  time to fit residues: 89.1817
Evaluate side-chains
  286 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 259
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  670 ASP
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
A 149 ASN
A 625 HIS
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 874 HIS
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.112353 restraints weight = 15528.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.116293 restraints weight = 8360.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.118897 restraints weight = 5250.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8777  Z= 0.179
  Angle     :  0.661  14.703  11925  Z= 0.333
  Chirality :  0.044   0.185   1398
  Planarity :  0.005   0.069   1511
  Dihedral  :  4.504  17.090   1185
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 18.97 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1083
  helix:  1.23 (0.23), residues: 513
  sheet:  0.15 (0.39), residues: 162
  loop : -0.37 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 756 
 PHE   0.024   0.001   PHE A 252 
 TYR   0.026   0.002   TYR A 690 
 ARG   0.007   0.001   ARG A 839 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  479)
  hydrogen bonds       : angle       4.91940 ( 1398)
  covalent geometry    : bond        0.00374 ( 8777)
  covalent geometry    : angle       0.66051 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 263
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TRP cc_start: 0.6841 (t60) cc_final: 0.6597 (t60)
REVERT: A  115 VAL cc_start: 0.8234 (t) cc_final: 0.7966 (p)
REVERT: A  133 GLU cc_start: 0.6248 (mp0) cc_final: 0.6019 (mp0)
REVERT: A  143 LYS cc_start: 0.8185 (pptt) cc_final: 0.7765 (pptt)
REVERT: A  178 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7898 (ttmm)
REVERT: A  186 LYS cc_start: 0.7945 (mtmm) cc_final: 0.7642 (mtmm)
REVERT: A  200 PHE cc_start: 0.6419 (t80) cc_final: 0.5895 (t80)
REVERT: A  214 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6744 (mt-10)
REVERT: A  215 ILE cc_start: 0.8734 (mm) cc_final: 0.8403 (mm)
REVERT: A  229 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.4743 (tpt)
REVERT: A  240 GLU cc_start: 0.7721 (tp30) cc_final: 0.7396 (tp30)
REVERT: A  252 PHE cc_start: 0.7893 (t80) cc_final: 0.7445 (t80)
REVERT: A  310 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7204 (mmm-85)
REVERT: A  311 PRO cc_start: 0.8279 (Cg_exo) cc_final: 0.8058 (Cg_endo)
REVERT: A  316 GLU cc_start: 0.7824 (mp0) cc_final: 0.7210 (mp0)
REVERT: A  349 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (tt0)
REVERT: A  364 ILE cc_start: 0.8857 (tp) cc_final: 0.7704 (tt)
REVERT: A  392 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7421 (tm-30)
REVERT: A  423 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8103 (tm-30)
REVERT: A  480 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7353 (mt-10)
REVERT: A  485 LEU cc_start: 0.8620 (tp) cc_final: 0.8145 (tt)
REVERT: A  568 HIS cc_start: 0.7447 (m90) cc_final: 0.6948 (m90)
REVERT: A  594 MET cc_start: 0.8075 (mmm) cc_final: 0.7786 (mmm)
REVERT: A  623 ARG cc_start: 0.7013 (mtp85) cc_final: 0.6746 (mtp85)
REVERT: A  633 MET cc_start: 0.7113 (tmm) cc_final: 0.6201 (tmm)
REVERT: A  654 LYS cc_start: 0.7194 (ptmm) cc_final: 0.6687 (ptmm)
REVERT: A  658 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7935 (mm-30)
REVERT: A  663 MET cc_start: 0.7959 (mtm) cc_final: 0.7561 (mtm)
REVERT: A  671 TYR cc_start: 0.7259 (t80) cc_final: 0.7034 (t80)
REVERT: A  690 TYR cc_start: 0.8109 (t80) cc_final: 0.7859 (t80)
REVERT: A  733 ILE cc_start: 0.8375 (tp) cc_final: 0.8141 (tp)
REVERT: A  734 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7823 (ttm110)
REVERT: A  760 GLU cc_start: 0.8202 (tp30) cc_final: 0.7885 (tp30)
REVERT: A  801 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7816 (mmmt)
REVERT: A  823 ASP cc_start: 0.8121 (t0) cc_final: 0.7443 (t0)
REVERT: A  854 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7780 (tt0)
REVERT: A  861 MET cc_start: 0.7506 (tpt) cc_final: 0.7273 (tpt)
REVERT: A  962 SER cc_start: 0.8347 (t) cc_final: 0.7953 (p)
REVERT: A  970 ILE cc_start: 0.8511 (tp) cc_final: 0.8222 (tp)
REVERT: A  993 LEU cc_start: 0.8179 (tp) cc_final: 0.7851 (tt)
REVERT: A 1005 LEU cc_start: 0.7943 (mt) cc_final: 0.7675 (mt)
REVERT: A 1035 LYS cc_start: 0.8246 (mttt) cc_final: 0.7465 (mmmm)
REVERT: A 1042 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7123 (ttp80)
REVERT: A 1044 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8041 (ttm-80)
REVERT: A 1050 PHE cc_start: 0.7592 (m-80) cc_final: 0.7267 (m-10)
REVERT: A 1060 LEU cc_start: 0.7421 (tp) cc_final: 0.7076 (tp)
REVERT: A 1106 MET cc_start: 0.8304 (tmm) cc_final: 0.7810 (tmm)
REVERT: A 1111 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7376 (tm-30)
REVERT: A 1126 GLU cc_start: 0.7617 (pt0) cc_final: 0.7068 (pt0)
REVERT: A 1170 LYS cc_start: 0.8710 (tttt) cc_final: 0.8506 (tttt)
REVERT: A 1192 GLN cc_start: 0.8131 (tp40) cc_final: 0.7596 (tp40)
  outliers start: 42
  outliers final: 32
  residues processed: 278
  average time/residue: 0.2214
  time to fit residues: 83.0644
Evaluate side-chains
  303 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 269
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  702 ARG
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1110 MET
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 46 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0470
   chunk 86 optimal weight:    1.9990
   chunk 8 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0070
   chunk 67 optimal weight:    0.0770
   overall best weight:    0.1654

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.141467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120258 restraints weight = 15538.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.124209 restraints weight = 8492.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.126849 restraints weight = 5362.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8777  Z= 0.112
  Angle     :  0.626  16.111  11925  Z= 0.306
  Chirality :  0.042   0.166   1398
  Planarity :  0.005   0.065   1511
  Dihedral  :  4.234  16.613   1185
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 20.26 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1083
  helix:  1.48 (0.22), residues: 508
  sheet:  0.17 (0.39), residues: 162
  loop : -0.28 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  78 
 HIS   0.007   0.001   HIS A 661 
 PHE   0.022   0.001   PHE A 252 
 TYR   0.022   0.002   TYR A 690 
 ARG   0.007   0.001   ARG A 839 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (  479)
  hydrogen bonds       : angle       4.63878 ( 1398)
  covalent geometry    : bond        0.00238 ( 8777)
  covalent geometry    : angle       0.62569 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 270
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8378 (tp) cc_final: 0.8116 (tp)
REVERT: A   78 TRP cc_start: 0.6677 (t60) cc_final: 0.6238 (t60)
REVERT: A  104 LEU cc_start: 0.7513 (mt) cc_final: 0.7293 (mp)
REVERT: A  143 LYS cc_start: 0.8093 (pptt) cc_final: 0.7723 (pptt)
REVERT: A  215 ILE cc_start: 0.8701 (mm) cc_final: 0.8266 (mm)
REVERT: A  229 MET cc_start: 0.5607 (tpt) cc_final: 0.4557 (tpt)
REVERT: A  277 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7518 (mm-30)
REVERT: A  288 MET cc_start: 0.7200 (tpt) cc_final: 0.6679 (tpt)
REVERT: A  316 GLU cc_start: 0.7750 (mp0) cc_final: 0.7287 (mp0)
REVERT: A  349 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7455 (tt0)
REVERT: A  361 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8031 (mmmt)
REVERT: A  371 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7976 (ttp80)
REVERT: A  374 ASP cc_start: 0.8614 (t0) cc_final: 0.8354 (t70)
REVERT: A  392 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: A  420 ASN cc_start: 0.7082 (m110) cc_final: 0.6837 (m110)
REVERT: A  423 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: A  461 TYR cc_start: 0.8098 (t80) cc_final: 0.7817 (t80)
REVERT: A  465 GLU cc_start: 0.7763 (tp30) cc_final: 0.7254 (tp30)
REVERT: A  478 PHE cc_start: 0.7922 (t80) cc_final: 0.7720 (t80)
REVERT: A  480 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7326 (mt-10)
REVERT: A  526 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7571 (ttmt)
REVERT: A  568 HIS cc_start: 0.7483 (m90) cc_final: 0.7036 (m90)
REVERT: A  592 LYS cc_start: 0.8481 (tptt) cc_final: 0.8241 (tppt)
REVERT: A  633 MET cc_start: 0.7104 (tmm) cc_final: 0.6294 (tmm)
REVERT: A  654 LYS cc_start: 0.7031 (ptmm) cc_final: 0.6658 (ptmm)
REVERT: A  658 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7960 (mm-30)
REVERT: A  671 TYR cc_start: 0.7231 (t80) cc_final: 0.7002 (t80)
REVERT: A  690 TYR cc_start: 0.8164 (t80) cc_final: 0.7930 (t80)
REVERT: A  733 ILE cc_start: 0.8322 (tp) cc_final: 0.8053 (tp)
REVERT: A  734 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7770 (ttm110)
REVERT: A  760 GLU cc_start: 0.8175 (tp30) cc_final: 0.7754 (tp30)
REVERT: A  823 ASP cc_start: 0.7913 (t0) cc_final: 0.7464 (t70)
REVERT: A  853 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8285 (ttmt)
REVERT: A  962 SER cc_start: 0.8259 (t) cc_final: 0.7887 (p)
REVERT: A  993 LEU cc_start: 0.8048 (tp) cc_final: 0.7790 (tt)
REVERT: A 1042 ARG cc_start: 0.7476 (ttp80) cc_final: 0.7103 (ttp80)
REVERT: A 1044 ARG cc_start: 0.8407 (mtp85) cc_final: 0.8171 (tpp80)
REVERT: A 1106 MET cc_start: 0.8268 (tmm) cc_final: 0.7749 (tmm)
REVERT: A 1111 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7566 (tp40)
REVERT: A 1125 MET cc_start: 0.7384 (mtt) cc_final: 0.7149 (mtt)
REVERT: A 1126 GLU cc_start: 0.7533 (pt0) cc_final: 0.7188 (pt0)
  outliers start: 43
  outliers final: 33
  residues processed: 286
  average time/residue: 0.2313
  time to fit residues: 87.6609
Evaluate side-chains
  298 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 264
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  702 ARG
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0980
   chunk 72 optimal weight:    0.3980
   chunk 58 optimal weight:    0.6980
   chunk 55 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.137219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.114518 restraints weight = 15976.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.118728 restraints weight = 8548.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.121522 restraints weight = 5346.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8777  Z= 0.186
  Angle     :  0.675  15.482  11925  Z= 0.336
  Chirality :  0.045   0.185   1398
  Planarity :  0.005   0.043   1511
  Dihedral  :  4.342  17.461   1185
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 22.20 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.25), residues: 1083
  helix:  1.38 (0.23), residues: 509
  sheet:  0.25 (0.40), residues: 160
  loop : -0.40 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 382 
 PHE   0.026   0.002   PHE A 252 
 TYR   0.019   0.002   TYR A 304 
 ARG   0.009   0.001   ARG A1033 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  479)
  hydrogen bonds       : angle       4.74902 ( 1398)
  covalent geometry    : bond        0.00387 ( 8777)
  covalent geometry    : angle       0.67484 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 264
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8441 (tp) cc_final: 0.8151 (tp)
REVERT: A   78 TRP cc_start: 0.6759 (t60) cc_final: 0.6316 (t60)
REVERT: A  104 LEU cc_start: 0.7540 (mt) cc_final: 0.7265 (mp)
REVERT: A  143 LYS cc_start: 0.8214 (pptt) cc_final: 0.7776 (pptt)
REVERT: A  176 LYS cc_start: 0.8642 (mtmm) cc_final: 0.8257 (mttm)
REVERT: A  186 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7701 (mtmm)
REVERT: A  215 ILE cc_start: 0.8626 (mm) cc_final: 0.8312 (mm)
REVERT: A  229 MET cc_start: 0.5991 (tpt) cc_final: 0.4900 (tpt)
REVERT: A  240 GLU cc_start: 0.7763 (tp30) cc_final: 0.7463 (tp30)
REVERT: A  288 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6951 (tpt)
REVERT: A  316 GLU cc_start: 0.7887 (mp0) cc_final: 0.7338 (mp0)
REVERT: A  338 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7750 (m)
REVERT: A  349 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7578 (tt0)
REVERT: A  361 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8032 (mmmt)
REVERT: A  364 ILE cc_start: 0.8887 (tp) cc_final: 0.8571 (tp)
REVERT: A  371 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8095 (ttp80)
REVERT: A  392 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7432 (tm-30)
REVERT: A  423 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: A  465 GLU cc_start: 0.7866 (tp30) cc_final: 0.7353 (tp30)
REVERT: A  478 PHE cc_start: 0.8032 (t80) cc_final: 0.7832 (t80)
REVERT: A  480 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7433 (mt-10)
REVERT: A  526 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7905 (ttpt)
REVERT: A  568 HIS cc_start: 0.7538 (m90) cc_final: 0.7030 (m-70)
REVERT: A  592 LYS cc_start: 0.8607 (tptt) cc_final: 0.8183 (tptt)
REVERT: A  623 ARG cc_start: 0.6946 (mtp85) cc_final: 0.6667 (mtp85)
REVERT: A  633 MET cc_start: 0.6989 (tmm) cc_final: 0.6061 (tmm)
REVERT: A  654 LYS cc_start: 0.7094 (ptmm) cc_final: 0.6677 (ptmm)
REVERT: A  658 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8095 (mm-30)
REVERT: A  671 TYR cc_start: 0.7386 (t80) cc_final: 0.7071 (t80)
REVERT: A  690 TYR cc_start: 0.8285 (t80) cc_final: 0.7869 (t80)
REVERT: A  733 ILE cc_start: 0.8368 (tp) cc_final: 0.8102 (tp)
REVERT: A  734 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7853 (ttm110)
REVERT: A  760 GLU cc_start: 0.8239 (tp30) cc_final: 0.7803 (tp30)
REVERT: A  801 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7767 (mmmt)
REVERT: A  823 ASP cc_start: 0.8127 (t0) cc_final: 0.7634 (t0)
REVERT: A  853 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8394 (ttmt)
REVERT: A  854 GLU cc_start: 0.8125 (tt0) cc_final: 0.7629 (tt0)
REVERT: A  962 SER cc_start: 0.8309 (t) cc_final: 0.7913 (p)
REVERT: A  970 ILE cc_start: 0.8489 (tp) cc_final: 0.8166 (tp)
REVERT: A  993 LEU cc_start: 0.8161 (tp) cc_final: 0.7887 (tt)
REVERT: A 1005 LEU cc_start: 0.8000 (mt) cc_final: 0.7756 (mt)
REVERT: A 1042 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7022 (ttp80)
REVERT: A 1044 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8200 (tpp80)
REVERT: A 1106 MET cc_start: 0.8331 (tmm) cc_final: 0.7606 (tmm)
REVERT: A 1111 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7572 (tp40)
REVERT: A 1126 GLU cc_start: 0.7610 (pt0) cc_final: 0.7299 (pt0)
REVERT: A 1192 GLN cc_start: 0.8133 (tp40) cc_final: 0.7606 (tp40)
  outliers start: 42
  outliers final: 34
  residues processed: 283
  average time/residue: 0.2299
  time to fit residues: 86.5168
Evaluate side-chains
  296 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 259
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  702 ARG
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1128 LEU
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0670
   chunk 88 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0970
   chunk 103 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    1.0320

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.139069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.116265 restraints weight = 15776.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120545 restraints weight = 8421.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.123385 restraints weight = 5263.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8777  Z= 0.143
  Angle     :  0.677  15.733  11925  Z= 0.330
  Chirality :  0.044   0.175   1398
  Planarity :  0.005   0.050   1511
  Dihedral  :  4.350  17.358   1185
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.84 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1083
  helix:  1.29 (0.23), residues: 517
  sheet:  0.36 (0.41), residues: 150
  loop : -0.46 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 382 
 PHE   0.025   0.001   PHE A 252 
 TYR   0.019   0.001   TYR A1071 
 ARG   0.017   0.001   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  479)
  hydrogen bonds       : angle       4.71199 ( 1398)
  covalent geometry    : bond        0.00310 ( 8777)
  covalent geometry    : angle       0.67744 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 272
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8490 (tp) cc_final: 0.8165 (tp)
REVERT: A  143 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7726 (pptt)
REVERT: A  200 PHE cc_start: 0.6294 (t80) cc_final: 0.6086 (t80)
REVERT: A  215 ILE cc_start: 0.8561 (mm) cc_final: 0.8225 (mm)
REVERT: A  229 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5026 (tpt)
REVERT: A  240 GLU cc_start: 0.7746 (tp30) cc_final: 0.7504 (tp30)
REVERT: A  288 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6909 (tpt)
REVERT: A  316 GLU cc_start: 0.7849 (mp0) cc_final: 0.7301 (mp0)
REVERT: A  338 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7645 (m)
REVERT: A  349 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7595 (tt0)
REVERT: A  361 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8001 (mmmt)
REVERT: A  364 ILE cc_start: 0.8900 (tp) cc_final: 0.8577 (tp)
REVERT: A  392 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7423 (tm-30)
REVERT: A  420 ASN cc_start: 0.7196 (m110) cc_final: 0.6964 (m110)
REVERT: A  423 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8104 (tm-30)
REVERT: A  461 TYR cc_start: 0.8262 (t80) cc_final: 0.8060 (t80)
REVERT: A  465 GLU cc_start: 0.7845 (tp30) cc_final: 0.7300 (tp30)
REVERT: A  480 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7428 (mt-10)
REVERT: A  526 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7839 (ttmt)
REVERT: A  568 HIS cc_start: 0.7523 (m90) cc_final: 0.7100 (m-70)
REVERT: A  592 LYS cc_start: 0.8482 (tptt) cc_final: 0.8002 (tptt)
REVERT: A  623 ARG cc_start: 0.6954 (mtp85) cc_final: 0.6641 (mtp85)
REVERT: A  633 MET cc_start: 0.6963 (tmm) cc_final: 0.6098 (tmm)
REVERT: A  658 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: A  671 TYR cc_start: 0.7375 (t80) cc_final: 0.7033 (t80)
REVERT: A  690 TYR cc_start: 0.8256 (t80) cc_final: 0.7816 (t80)
REVERT: A  733 ILE cc_start: 0.8355 (tp) cc_final: 0.8096 (tp)
REVERT: A  734 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7848 (ttm110)
REVERT: A  760 GLU cc_start: 0.8235 (tp30) cc_final: 0.7802 (tp30)
REVERT: A  801 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7737 (mmmt)
REVERT: A  823 ASP cc_start: 0.8054 (t0) cc_final: 0.7573 (t0)
REVERT: A  853 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8240 (ttpt)
REVERT: A  854 GLU cc_start: 0.8116 (tt0) cc_final: 0.7639 (tt0)
REVERT: A  962 SER cc_start: 0.8296 (t) cc_final: 0.7892 (p)
REVERT: A  993 LEU cc_start: 0.8105 (tp) cc_final: 0.7846 (tt)
REVERT: A 1005 LEU cc_start: 0.7957 (mt) cc_final: 0.7640 (mt)
REVERT: A 1042 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6997 (ttp80)
REVERT: A 1044 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8213 (tpp80)
REVERT: A 1106 MET cc_start: 0.8303 (tmm) cc_final: 0.7607 (tmm)
REVERT: A 1111 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7283 (tp40)
REVERT: A 1126 GLU cc_start: 0.7568 (pt0) cc_final: 0.7194 (pt0)
REVERT: A 1170 LYS cc_start: 0.8706 (tttt) cc_final: 0.8379 (tttt)
  outliers start: 40
  outliers final: 34
  residues processed: 287
  average time/residue: 0.2237
  time to fit residues: 85.9589
Evaluate side-chains
  307 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 268
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  143 LYS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  702 ARG
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  846 GLU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 71 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 119 HIS
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.136499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.114697 restraints weight = 15748.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.118783 restraints weight = 8416.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.121457 restraints weight = 5255.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8777  Z= 0.190
  Angle     :  0.710  15.787  11925  Z= 0.355
  Chirality :  0.046   0.192   1398
  Planarity :  0.005   0.053   1511
  Dihedral  :  4.492  18.911   1185
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.59 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 23.81 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.25), residues: 1083
  helix:  1.06 (0.23), residues: 518
  sheet:  0.25 (0.41), residues: 150
  loop : -0.57 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  78 
 HIS   0.004   0.001   HIS A 382 
 PHE   0.026   0.001   PHE A 252 
 TYR   0.022   0.002   TYR A 304 
 ARG   0.012   0.001   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04506 (  479)
  hydrogen bonds       : angle       4.87897 ( 1398)
  covalent geometry    : bond        0.00399 ( 8777)
  covalent geometry    : angle       0.71025 (11925)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 272
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8475 (tp) cc_final: 0.8159 (tp)
REVERT: A   58 ARG cc_start: 0.7199 (tpp80) cc_final: 0.6673 (tpp80)
REVERT: A  138 LYS cc_start: 0.8696 (mmpt) cc_final: 0.8294 (mmpt)
REVERT: A  143 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7753 (pptt)
REVERT: A  200 PHE cc_start: 0.6260 (t80) cc_final: 0.6025 (t80)
REVERT: A  215 ILE cc_start: 0.8555 (mm) cc_final: 0.8221 (mm)
REVERT: A  229 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5220 (tpt)
REVERT: A  240 GLU cc_start: 0.7802 (tp30) cc_final: 0.7492 (tp30)
REVERT: A  316 GLU cc_start: 0.7873 (mp0) cc_final: 0.7338 (mp0)
REVERT: A  338 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7764 (m)
REVERT: A  364 ILE cc_start: 0.8927 (tp) cc_final: 0.8566 (tp)
REVERT: A  392 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: A  423 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: A  480 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7382 (mt-10)
REVERT: A  511 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7954 (tp)
REVERT: A  526 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7978 (ttmt)
REVERT: A  568 HIS cc_start: 0.7508 (m90) cc_final: 0.7112 (m-70)
REVERT: A  592 LYS cc_start: 0.8571 (tptt) cc_final: 0.8158 (tptt)
REVERT: A  623 ARG cc_start: 0.6918 (mtp85) cc_final: 0.6696 (mtp85)
REVERT: A  633 MET cc_start: 0.7046 (tmm) cc_final: 0.6115 (tmm)
REVERT: A  654 LYS cc_start: 0.7139 (ptmm) cc_final: 0.6710 (ptmm)
REVERT: A  658 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: A  671 TYR cc_start: 0.7347 (t80) cc_final: 0.7047 (t80)
REVERT: A  733 ILE cc_start: 0.8402 (tp) cc_final: 0.8138 (tp)
REVERT: A  734 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7834 (ttm110)
REVERT: A  760 GLU cc_start: 0.8234 (tp30) cc_final: 0.7822 (tp30)
REVERT: A  801 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7710 (mmmt)
REVERT: A  853 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8201 (ttpt)
REVERT: A  854 GLU cc_start: 0.8105 (tt0) cc_final: 0.7642 (tt0)
REVERT: A  950 LYS cc_start: 0.8236 (ttmt) cc_final: 0.8033 (tmtt)
REVERT: A  993 LEU cc_start: 0.8196 (tp) cc_final: 0.7950 (tt)
REVERT: A 1005 LEU cc_start: 0.7971 (mt) cc_final: 0.7654 (mt)
REVERT: A 1042 ARG cc_start: 0.7387 (ttp80) cc_final: 0.6983 (ttp80)
REVERT: A 1044 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8226 (tpp80)
REVERT: A 1106 MET cc_start: 0.8250 (tmm) cc_final: 0.7960 (tmm)
REVERT: A 1111 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7293 (tp40)
REVERT: A 1126 GLU cc_start: 0.7610 (pt0) cc_final: 0.7216 (pt0)
REVERT: A 1170 LYS cc_start: 0.8718 (tttt) cc_final: 0.8387 (tttt)
  outliers start: 43
  outliers final: 35
  residues processed: 288
  average time/residue: 0.2387
  time to fit residues: 91.1637
Evaluate side-chains
  306 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 267
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  143 LYS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  702 ARG
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  846 GLU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1028 PHE
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1039 THR
Chi-restraints excluded: chain A residue 1063 PHE
Chi-restraints excluded: chain A residue 1168 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 972 HIS
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.138832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.117215 restraints weight = 15881.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.121295 restraints weight = 8559.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.124000 restraints weight = 5367.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8777  Z= 0.130
  Angle     :  0.678  16.261  11925  Z= 0.334
  Chirality :  0.044   0.184   1398
  Planarity :  0.005   0.053   1511
  Dihedral  :  4.369  18.344   1185
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.31 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 24.25 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.25), residues: 1083
  helix:  1.16 (0.23), residues: 512
  sheet:  0.20 (0.41), residues: 152
  loop : -0.55 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A  78 
 HIS   0.003   0.001   HIS A 382 
 PHE   0.027   0.001   PHE A 252 
 TYR   0.019   0.001   TYR A1071 
 ARG   0.011   0.001   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04028 (  479)
  hydrogen bonds       : angle       4.78042 ( 1398)
  covalent geometry    : bond        0.00285 ( 8777)
  covalent geometry    : angle       0.67814 (11925)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4112.04 seconds
wall clock time: 74 minutes 18.71 seconds (4458.71 seconds total)